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addde852ed Chri*     Notes on tags used in MITgcmUV
                     ==============================
5dda98cf07 Jean* 
e6feef680a Ivan* o pkg/mnc:
                   - update grid-variable names in pkg/mnc NetCDF files (mostly matching GRID.h)
                     and provide backwards compatibility in MATLab "load_grid.m" and for Python
                     MITgcmutils (restore_MNC_keys).
204068be6a R. S* o pkg/seaice:
                   - new parameter "SEAICE_evpAreaReg" for regularizations of denomU/V in EVP
                     solver ; tested in exp. seaice_obcs new secondary test "regDenom".
                 
58fb4fd147 Jean* checkpoint69i (2025/11/14)
c9c019d2e0 Jean* o pkg/cost:
                   - fix multi-proc initialization of Tapenade adjoint cost-function.
b7411f1a84 Jean* o pkg & model:
                   - remove pkg/timeave ; remove all ALLOW_TIMEAVE code ; remove all timeave
                     related parameters from common blocks (in header files) and from src code
                     and disable/retire these params.
                   - also updates model_ad.flow, TAP_support/flow_tap, OAD_support and most
                     */code_oad/cb2mFiles from verification.
626c6ac944 Jean* o tools (Tapenade):
                   - implement "-ncad" genmake2 option for Tapenade Makefile (similar to TAF),
                     to append each forward src file to corresponding Tapenade-generated AD file,
                     using new short script "append_fwd_src"; otherwise (default), put all
                     adjoint (or Tang.Lin.) tapenade  fortran files "_b.f" (or "_d.f") into a
                     single "adj/tlm/_tap_all.f" file, to be compiled to get an object file.
                   - simply add symbolic-links within pkg/tapenade/ to the few files from
                     "tools/TAP_support/ADFirstAidKit/" that are needed.
                   - fix for case-insensitive file systems (e.g., on Mac-OS) and update optfile
                     "darwin_arm64_gfortran" to use Tapenade on Mac-OS using with "docker".
78dc053d11 Jean* o pkg/diagnostics:
                   - add diagnostic "VSHEARSQ" for the square of vertical shear.
                 
66720c264e Jean* checkpoint69h (2025/10/23)
4b300c49e1 Jean* o pkg/ctrl:
                   - account for shift in record number between original xx_gentim2d_file full
f9b5d1eb8f Jean*     time-series and "effective" sub-set version ; this was previously missing.
4b300c49e1 Jean*     Also enable some debug print from ctrl_get_gen_rec.F (if debugLevel >= 3).
0fa8d50cfc Jean* o pkg/seaice:
                   - fix compilation of seaice_growth_adx.F (left from PR #750).
c3be04357d Jean* o model, pkgs:
                   - remove code within "#ifndef EXACT_CONSERV / #endif" bracket and remove
                     completely CPP option EXACT_CONSERV.
e9828181c3 Yixi* o pkg/bling:
                   - allows to specify a 2D field of light attenuation coefficient (k0_2d) from
                     file "bling_k0_2dFile".
                 
bbbca756c9 Jean* checkpoint69g (2025/09/12)
d4a066fa68 Jean* o verification/short_surf_wave:
                   - fix Non-Hydrostatic pressure initialization issue with implicSurfPress=1/2
                     by re-starting (nIter0=1) from pickup generated with implicSurfPress=1.
bb357ea692 Jean* o tools/mpack-1.6:
                   - fix compilation for recent version of gcc, to pass the compiler test in
                     "configure" and md5 compilation with v15 (comply with C23 standard).
a5926ff804 dngo* o pkg/streamice:
                   - for OpenAD, adjust streamice_write_pickup.F to only write the forward
                     components of state arrays to the binary pickups for later use.
5e44d2ea81 Jean* o verification:
                   - remove all pkg/timeave params from all exp. and no longer compile this
                     pkg in any exp. ; also skip pkg/mnc compilation in 4 fwd test exp ;
                   - switch few remaining exp. to #define EXACT_CONSERV so that no exp is
                     compiled with this option undefined anymore.
13ce79fe94 Ivan* o pkg/profiles:
                   - fix "profilesDoNcOutput" feature (writing NetCDF model equivalents) so
                     that it can be use with pkg/grdchk. Switch profilesDoNcOutput" to True in
                     adjoint test exp.  global_oce_biogeo_bling (both in TAF & Tapenade test).
                   - improve code readability, rename cost_profiles.F to profiles_cost.F
                     and fix obvious multi-threading issues.
                 
214bfe91bf Jean* checkpoint69f (2025/07/10)
00c7090dc0 Mart* o model/src, pkg/kpp:
                   - store shortwave penetration fraction in 3D field SWFrac3D and add run-time
                     params "selectPenetratingSW" to chose between different short-wave heating
                     options (only =1 currently implemented);
                   - remove local (buggy) solution in pkg/seaice ;
                   - add runtime-flag "KPPuseSWfrac3D", set to F by default, because this code
                     can only approximately replace the original pkg/kpp-code ;
                   - update TAF directives in pkg/kpp (mostly related to the code changes);
                   - fix "global_ocean.cs32x15" exp bug in "in_p" and "seaice" tests, update FWD,
                     ADM & TLM ref. output ; set KPPuseSWfrac3D to True in "1D_ocean_ice_column"
                     (both FWD & ADM) test exp. with updated ref. output.
b74a470d07 Jean* o pkg/streamice:
                   - fix "new_partial" initialisation in streamice_adv_front.f (helps Tapenade)
b26a461de7 Mart* o pkg/bling, pkg/dic:
                   - additional store directives to avoid hidden recomputations.
6a6c83f9ac Hajo* o pkg/longstep:
                   - add remaining GM-Redi matrix coefficients (extra-diagonal & diagonal terms)
                     and Bolus transport stream function for time-averaging in longstep pkg and
                     use saved values in longstep time-stepping.
871ac80009 Jean* o pkg/seaice:
                   - fix 3 output formats to allow to run with gfortran v.15
                   - also add "deep_anelastic.vecinv" to multi-threaded tests.
31fb0e0e6d Jean* o pkg/mom_{common,fluxform,vecinv}:
                   - mom_fluxform, new option, selectCoriScheme=4: use hFac averaged transport in
                     Coriolis term so that column integral of tendency match Coriolis time
                     column integral U,V.
                   - mom_vecinv, new option, selectVortScheme=4: by-pass division by hFacZ and
                     instead apply recip_hFacW/S on final tendency. Note: this fixes Angular-Mom
                     (AM) conservation but breaks vorticity tendency matching advection of vort.
                   - new 3-d Coriolis option, select3dCoriScheme=2,3: Alternative discretization
                     using averaged transport; =3 (vs 2), an other alternative discretization of
                     vertical momentum tendency gW.
                   - deep-model, put gU,gV NH-metric terms inside vertical advection, to exactly
                     conserves AM (+ simplify & speed up by skipping NH metric-terms gU,gV
                     calculation). Add CPP option "MOM_USE_OLD_DEEP_VERT_ADV" (in
                     MOM_COMMON_OPTIONS.h) to recover the explicit NH metric-term calculation.
                   - mom_fluxform, new spherical Metric-terms option, selectMetricTerms=2,3: More
                     accurate discretization similar to manual eq. 2.102 & 2.103 but centered at
                     grid-cell corner; Also option (selectMetricTerms=3) to skip the gU spherical
                     metric term by advecting uVel*dxC (simpler, faster and exactly conserve AM).
                   - add diagnostics for Metric-Terms.
                   - verification exp. "deep_anelastic", new secondary "vecinv" test + also
                     update primary test ref output.
                 
69c3e78b15 Jean* checkpoint69e (2025/05/01)
86f389907b Jean* o pkg/atm_ocn_coupler:
                   - update local copy of setdir.c and CPP_EEOPTIONS.h (were left behind);
                   - improve "run_cpl_test" step 1 (pass options to genmake2) and step 2.
c296d11a59 Jean* o tools/genmake2:
                   - use specific "ad_config.template{0,1,2}" in different stages of TAF
                     AD/TL built to avoid race condition issue with "make -jN".
79b5d5775c Jean* o model/src:
                   - no "addMass" contribution to initial (iter=0) vertical velocity ;
                   - with selectAddFluid=1, fix missing implDiv2DFlow factor in "addMass"
                     contribution to solver RHS ;
                   - add a STOP if implDiv2DFlow < 1 with exactConserv=F, (was not right with
                     useRealFreshWaterFlux=T or selectAddFluid=1) and remove untested pieces
                     of code dealing with this case ;
                   - when using cg2d/cg3dTargetResWunit, add missing implDiv2DFlow factor to
                     solver tolerance setting (cg2d/cg3dTolerance) ;
                   - upgrade "global_ocean.cs32x15.viscA4" exp. to test selectAddFluid=1
                     with implDiv2DFlow=1/2 ; also update "short_surf_wave" exp. output.
8908c6917c Jean* o tools/genmake2:
                   - with Tapenade, remove list NON_AD_F77_SRC_FILES from Makefile (not used),
                     remove processing of "dontCompile", "keepOriginal" and "cb2mFiles" lists ;
                   - otherwise, in Makefile, move NON_AD_F77_SRC_FILES and NON_AD_F90_SRC_FILES
                     lists after AD_FILES and AD_F90FILES ;
                   - simplify (remove intermediate targets) and improve the "-ncad" Makefile
                     to ends cleanly when "staf" command fails.
f460f9a57e Ivan* o utils:
                   - improve gluemnc description (usage, dependencies, and example).
fbb692b4e1 Jean* o tools:
                   - replace (obsolete) "egrep" with "grep -E" (or without "-E" if not needed).
7fe51dd492 Jean* o verification:
                   - After merging (5 fwd tests + 2 AD) few exp. into new host-exp. (PR #830),
                     move input dir and ref. output from merged exp. to replace sym-link in new
                     host exp. and remove remaining files/dir (code, build, run) in merged-exp;
                   - Add or update README.md in new host-exp and update list of exp. in the docs.
c8ce5f710c Jean* o pkg/rbcs:
                   - fix error/warning cases and messages.
29b81f1d21 Jean* o pkg/autodiff:
                   - alternative way (printResidualFreq >=0) to get CG2D output from cg2d_mad.F
                   - remove 2 unused CPP options.
b7b61e618a Mart* o tools, autodiff and others:
                   - remove TAMC features, untested, unused and probably broken.
                 
b2c8bc6cea Jean* checkpoint69d (2025/03/01)
5b53130725 Ivan* o tools:
                   - changes to genmake2 to allow TAF to process F90 files with modules, for now
                     only with "-ncad" option;
                   - re-order list of src files sent to TAF (needed with current version of TAF);
                   - add new scrip "f90mkdepend_taf" to add dependencies form TAF generated src
                     code (Adjoint and Tang.Lin) in a file included into Makefile.
                   - more logical and consistent ordering in Makefile target, *.F90 first then
                     *.F77, *.c and *.h
                   - add 2 new variables TAF_F77_FLAGS and TAF_F90_FLAGS (set from genmake_local
                     or adjoint-optfile) to go into the TAF command.
701e10a905 Mart* o model/src and forcing:
                   - for TEOS10, add new S/R to convert model surface Conservative Temperature
                     to in-situ Temperature (SST) and compute and store model SST in new model
                     field (in FFIELDS.h) "gcmSST", just a copy of model Pot.Temp with other EOS.
                   - use model SST to compute surface forcing over open ocean in pkg/exf and
                     pkg/bulk_force ; for now, leave ice/seaice freezing/melting unchanged.
                   - switch test exp. global_ocean.cs32x15.in_p to use TEOS10 + update lab_sea
                     Tapenade ref. output (affected @ machine truncation level).
f955de4ba2 Jean* o tools:
                   - remove old backward compatibility feature, so that env.var ROOTDIR is no
                     longer recognized by genamke2 ;
                   - re-write "suggest_optfile_names" to use parts from "genmake2".
83a53713c2 Oliv* o utils/python:
                   - make MITgcmutils compatible with numpy 2.0.0 again.
c908a600ca Jean* o testreport:
                  - improve way of sending results tar file with "scp", now allowing to combine
                    "ssh" then "scp".
                 
efc7ba3160 Jean* checkpoint69c (2024/12/06)
7bb5a8a109 Jean* o pkg/mom_common,fluxform,vecinv:
                   - remove ISOTROPIC_COS_SCALING code from pkg/mom_vecinv/mom_vi_hdissip.F (was
                     not right); add warning (or stop if side-drag) if used with pkg/mom_vecinv.
                   - move 2 Cos-Scaling CPP options from CPP_OPTIONS.h to MOM_COMMON_OPTIONS.h
                     to be used in horizontal viscosity formulation; more consistent use of
                     GAD_OPTIONS.h where these 2 CPP options are used for horizontal diffusion.
                   - update all verification exp. customized version of CPP_OPTIONS.h,
                     GAD_OPTIONS.h and MOM_COMMON_OPTIONS.h.
4287557481 Jean* o verification/atm_gray:
                   - gray atmosphere test exp moved from "verification_other".
80fd556159 Ou W* o model/src:
                   - add few missing option header files (RBCS, SALT_PLUME, SHELFICE) in few
                     src files ; also illustrate how to catch these (see SALT_PLUME.h and
                     shelfice_ad_check_lev{1,2,3,4}_dir.h).
27ce1202c5 Jean* o eesupp + model:
                   - remove FAST_BYTESWAP code and option
                   - remove empty file AUTODIFF_MYFIELDS.h
cb406db96c Ou W* o pkg/ctrl:
                   - add a STOP when ALLOW_CTRL_OBCSN/S/W/E is defined but corresponding
                     ALLOW_OBCS_NORTH/SOUTH/EAST/WEST is undef ; and fix the code so that, in
                     that case, it will compile and reach the stop before running 1rst time-step
0e6a4460e5 Ivan* o model,pkg:
                   - minor spell checking and formatting updates.
9edc0e3a85 aver* o pkg/bling:
                   - size-dependent phytoplankton growth code cleaned up and related parameters
                     can now be specified in data.bling;
                   - clean up OPTIONS in pkg/bling code ( SIZE_NUT_LIM merged with SIZE_DEP_LIM,
                     MULT_NUT_LIM merged with MIN_NUT_LIM ) and switch USE_QSW to #undef ; this
                     fixes FWD exp. global_oce_biogeo_bling which a) use default BLING_OPTIONS.h
                     and b) since no short-wave is provided, light was zero with USE_QSW defined.
d3172737dc aver* o pkg/profiles:
                   - add option to write model-equivalent profiles in a netcdf file, thus
                     removing the need for post-processing tiled output files.
9f85ea262e Mart* o pkg/grdchk:
                   - write either "grd_ratio_ad" or "grd_ratio_ftl" depending on type of run
                     and remove limitation to "useSingleCpuIO=F" when writing 2D files ;
                   - write "costfunction0000" only once, from pkg/ecco.
                 
7a6b0d88e9 Jean* checkpoint69b (2024/10/31)
8b7be8db08 Mart* o pkg/autodiff:
                   - TAF-store directives for saltFlux (needed for #define EXCLUDE_FFIELDS_LOAD)
                   - little cleaning of ctrl_map_forcing.F (remove duplicated EXCH calls, ...).
71b7a3e5ac Mart* o tools/genmake2:
                   - remove step that generates *.flowdir
c9bf163375 Ivan* o pkg/profiles:
                   - fix missing pieces in this pkg for Tang-Lin model and get this tested in
                     verification exp. global_oce_biogeo_bling.
ee480e7782 amc2* o pkg/seaice:
                   - if SEAICEaddSnowMass=T, include HSNOW in diagnostics "SIenph  ".
58679b5a83 Esta* o utils/python/MITgcmutils/:
                   - augment (llc, examples, ...) and update python utils
c7a06a2c29 Mart* o tools/build_options:
                   - update darwin_arm64_gfortran to be able to compile free-format F90 files.
                 o pkg/seaice:
5bb179ddc2 Mart*   - add new lateral drag parameterisation for landfast ice (Liu etal 2022, JGR)
3a00e4dea9 Jean* o verification/*/results:
                   - update 5 adm + 3 tlm ref. output affected by TAF new version 6.4.5 & 6.5.0
4c91ca28d5 Ou W* o pkg/ecco:
                   - implement sea-ice freeboard cost "m_freeboard".
f79ba37af1 Mart* o tools/xmakedepend:
                   - fix xmakedepend to accept suffix longer than 1.c and add dependencies to
                     Makefile from included headers in F90 src files.
e6e223b277 Jean* o model/src:
                   - Add new param "cg3dTargetResWunit" to skip the normalization of cg3d RHS
                     by specifying the CG3D target residual in term of vertical-velocity units ;
                   - Remove header files SOLVE_FOR_PRESSURE{3D}.h ; clean-up "post_cg3d.F" ;
                   - switch test exp. global_ocean.cs32x15.viscA4 & short_surf_wave to use new
                     param "cg3dTargetResWunit".
95cd2dedde Ivan* o tools/f90mkdepend:
                   - add arguments to f90mkdepend to specify alternative file suffix (e.g.,
                     for MacOS) + minor improvement in error message.
                 
b537eb461d Jean* checkpoint69a (2024/09/08)
0524b7d1ff Mart* o tools/genmake2:
                   - list of src files to Differentiate: change from simply "*.list" to commonly
                     adopted "*_ad_diff.list" (to avoid accidents).
                   - change Makefile to enable TAF to generate Tangent-Linear code from a mix
                     of fixed-form (.F) and free-form (.F90) src code.
                   - test free format *.F90 code in hs94.1x64x5/code_ad/ exp. for AD and TLM.
ae2be6150b Jona* o pkg/dic:
                   - save 3D pH (for calcite saturation calculation, useCalciteSaturation=T)
                     for next time-step and store it in pickup files (for restart).
5237154b93 Jean* o eesupp/src:
                   - new set of Global-Sum vector routines working with shared buffer
                     (=> no needs for input/output to be in common block) and with
                     GLOBAL_SUM_ORDER_TILES implemented ; and remove older versions.
ea893758ea Patr* o tools/genmake2:
                   - change Makefile to enable TAF to generate adjoint from a mix of fixed-form
                     (.F) and free-form (.F90) src code. Also fix for alternative suffix (e.g.,
                     used on MacOS) to work without -ncad.
6d7b0906cb Ivan* o tools/adjoint_options:
                   - allow to pass -f08 flag to TAF by setting TAF_FORTRAN_VERS to "F08".
a340904e5a Ou W* o pkg/mom_vecinv:
                   - add more 3-D momentum tendency diagnostics (originally from Helen Pillar)
                     for harmonic/bi-harmonic dissipation and for bottom + top friction
                     tendency (under new CPP option: ALLOW_MOM_TEND_EXTRA_DIAGS).
                 
6519d60651 Jean* checkpoint68z (2024/07/27)
acacc28f7f Jean* o pkg/diagnostics:
                   - to allow to use ADJ-diags in DIVA runs, change call sequence regarding
                     TURNOFF_MODEL_IO and DIAGSTATS_INI_IO and simplify (fewer tests for
                     "costfinal") the_model_main.F (+ shorten pkg/openad version) ;
                   - restore the use of "diag_pkgStatus" (switch & check) in AD backward sweep
                     with new small S/R for DIVA runs ;
                   - turn on FWD and ADJ-diags in secondary lab_sea AD test "noseaice".
4dea327916 aver* o pkg/bling:
                   - clean-up "bling_light.F" (fix typo related to PHYTO_SELF_SHADING option,
                     move k-loop outside) ; add CHL to bling_ad_check_lev{2,3,4}_dir.h and
                     fix TAF storage directives ;
                   - change "global_oce_biogeo_bling" AD test exp. (both TAF & Tapenade) to
                     use PHYTO_SELF_SHADING (with #undef USE_QSW) and update ref. output.
                   - also clean-up MDSIO_BUFF_WH.h (avoid common block that mixes r4 & r8 vars).
af61e5eb16 Mart* o pkg/obcs:
                   - Neumann boundary conditions for sea ice variables, activate by setting
                     new runtime parameter useSeaiceNeumann=.TRUE. in data.obcs ;
                   - fewer (hidden) recomputations and no recomputation warnings when
                     both ALLOW_OBCS_BALANCE and ALLOW_OBCS_STEVENS are defined.
                 o pkg/cost:
                   - new runtime flag for pkg/cost "cost_mask_file", which can be used
                     for flexible cost function definition.
                 
976081d885 Jean* checkpoint68y (2024/06/05)
6518e4ecc5 aver* o pkg/bling:
                   - fix bigR setting when option CARBONCHEM_TOTALPHSCALE is defined.
00f81e6785 Ou W* o pkg/steep_icecavity + shelfice:
                   - new package to be used together with pkg/shelfice to also account for
                     melting at the vertical faces of a steep ice-shelf interface ;
                   - allows to use non-zero (but constant) ice-shelf salinity ;
                   - new FWD and (TAF) AD secondary test exp. (in isomip) using new pkg.
82e538d851 aver* o pkg/bling:
                   - fix/improve initialization of biomass for the 3 phytoplankton groups ;
                   - add 2D diagnostics of optically integrated chlorophyll concentration
                     within local-time window to be compared with satellite observation ;
                   - improve TAF store directives (reduce recomputations).
672b822630 Jean* o pkg/obcs (tides):
                   - more efficient implementation of OB barotropic tidal velocity components,
                     with both Cos & Sin of phase times Amplitude stored in common block ;
                   - more flexible specification of OB tidal-components (only read-in components
                     with non-zero tidal period) ;
                   - allows to specify tangential component of barotropic tidal velocity at OB ;
                   - rename all OBC tidal component input parameter (period, amplitude and
                     phase of each OB barotropic tidal velocity component input files) ;
                   - upgrade OB tidal example (in seaice_obcs/input.tides) with fewer tidal
                     components (only 4) but including few tangential components.
0c90ef582a Jean* o verification:
                   - changing domain decomposition (more tiles) in global_with_exf experiment
                     (both FWD & AD) and update ref. output ;
                   - use correct CD-Scheme time-stepping in FWD exp. global_ocean_ebm and update
                     ref. output ;
672b822630 Jean*   - simplify global_ocean.90x40x15/code_ad (undef ALLOW_GENTIM2D_CONTROL,
0c90ef582a Jean*     ALLOW_DIFFKR_CONTROL & ALLOW_3D_DIFFKR); remove kpp from global_oce_latlon
                     (from both TAF & Tapenade code) ;
                   - after adjusting new host experiment code, merge forward test:
                       flt_example            --> exp4.with_flt
                       global_with_exf        --> global_ocean_ebm.w_exf
                       global_with_exf.yearly --> global_ocean_ebm.yearly
                       natl_box               --> lab_sea.natl_box
                       natl_box.longstep      --> lab_sea.longstep
                     and TAF & Tapenade tests:
                       global_with_exf        --> global_oce_latlon.w_exf
                     For now, keep original set-up in place and add symbolic links into new
                     host exp. for input dir and ref. output to run these as secondary test.
9e0fdb4065 Garr* o pkg/obcs:
                   - fix unusual division by zero in all 4 (N,S,E,W) orlanski main S/R.
41c4545f8f Jean* o pkg/diagnostics:
                   - new header file "DIAGNOSTICS_P2SHARE.h" (for now, just for useDiag4AdjOutp),
                     and remove DIAGNOSTICS.h in any src code outside pkg/diagnostics;
                   - new params "diag_dBugLevel" (default = main model "debugLevel");
                   - add new arg "seqFlag" to DIAGNOSTICS_SWITCH_ONOFF and DIAGNOSTICS_SUMMARY
                     and prevent "diagnostics_status" to be overwritten when using ADJ-diags.
                 
5f2d22066e Jean* checkpoint68x (2024/04/30)
8fabf86828 Jean* o model/src:
                   - more precise specific-volume anomaly expression for Ocean in P-coord;
                     update reference output of all 3 Ocean in P test experiments.
598aebfcee Mart* o pkg/generic_advdiff:
                   - adjust 2 SOM (Prather advection) store directives to reduce memory overhead
                   - include OS7MP (advScheme 7) in AD code ; switch AD test experiment
                     isomip.htd to use this advection scheme for Temp and Salt.
720a211d38 Ou W* o pkg/ecco, ctrl:
                   - put active_read calls within #ifdef ALLOW_AUTODIFF (missing in few places)
                     and fall back to non-active read (from pkg/rw) if undef;
                   - change argument order in few obcs related pkg/ecco S/R.
20e951135e Mart* o pkg/seaice:
                   - for seaice-dynamics, add missing mapping of (pkg/thsice) snowHeight to HSNOW
                   - this affects results (unless SEAICEaddSnowMass=F); update seaice parameters
                     in test global_ocean.cs32x15.icedyn and update reference output.
                 
7456fbd729 Jean* checkpoint68w (2024/03/05)
5cf4364659 Mart* o pkg/ctrl, grdchk & optim:
                   - clean and improve list of ctrl-var settings (in common blocks) and update
                     ctrl-pack header files:
                     a) define new character fields "ncvartype" for ctrl-var shape type and
                        save ctrl-var (file) name "ncvarfname" ;
                     b) re-define "ncvarindex" to point directly to genArr index (according to
                        ncvartype) or 1,2,3,4 for N,S,E,W obcs-ctrl ;
                     so that map of index (and grdchkvarindex) to file name, array shape and
                     genArr specification is direct, code is simpler, more robust and efficient.
                   - allow to specify grdchk ctrl-var by name in "data.grdchk" (more robust) ;
                   - write ncvartype list to ctrl-pack header files ;
                   - simplify definition of maxcvars to get much shorter "ncvar"-field lists ;
                   - remove unnecessary common blocks, rename ctrl_init.F -> ctrl_init_fixed.F,
                     call TURNOFF_MODEL_IO only once ;
                   - adjust optimisation utility optim and provide backward compatibility
                     regarding changes to ctrl-pack files ; also improve build process ;
                   - update all "data.grdchk" in verification experiments.
a4576c7cde Juli* o pkg/gmredi:
                   - add GEOMETRIC parameterization (Mak etal, JPO, 2018) for GM coefficient,
                     under GM_GEOM_VARIABLE_K CPP-option, turned on with "GM_useGEOM=T" and
                     tested in exp. ideal_2D_oce, secondary test "geom".
35c4fdc74b Emma* o pkg/ecco:
                   - add option ECCO_VARIABLE_AREAVOLGLOB to use the total time-varying volume
                     to weight contributions to m_boxmean cost functions
                 
285cda8c7b Jean* checkpoint68v (2024/02/03)
427e24e121 Jean* o model/src:
                   - change param "metricTerms" to integer param "selectMetricTerms" and change
                     param "use3dCoriolis" to integer param "select3dCoriScheme" but keep former
                     parameters in namelist (backward compatible).
                   - remove un-used param "writeStatePrec" + also in experiment param file "data"
                   - rotateGrid: fix missing 3-D Coriolis term to gV ; adjust usage restriction.
d4b64b229a Jean* o pkg/ecco:
                   - remove call to ECCO_CHECK from ecco_cost_init_fixed.F (but keep the other
                     call from packages_check.F) and move ECCO_SUMMARY call to ecco_check.F
005af54e38 Jean* o pkg/shelfice:
                   - put the update of kTopC code within "#ifdef ALLOW_SHELFICE_REMESHING/#endif"
                     and add run-time switch "SHI_update_kTopC" to allow to turn it off.
                   - Change the initial setting of "kTopC" to remain unaffected by machine
                     truncation error and if using SHELFICEMassStepping, set it according to
                     shelficeMassInit.
aef96ed361 Jean* o verification/solid-body.cs-32x32x1:
                   - update set up (faster flow, smaller planet ..) and fix initial Ps condition.
9af873c532 Hajo* o pkg/ggl90:
                   - revisit Langmuir Circulation (LC) mixing-length calculation: fix bugs in
                     some "mxlMaxFlag" implementation and ensure it works with P-coordinate.
                     Update vermix.gglLC ref. output and add new secondary AD test (with LC on)
                     in global_oce_latlon experiment.
                 
fca39df4c8 Jean* checkpoint68u (2023/12/10)
143d9ce879 Dami* o pkg/seaice:
                   - new/improved LSR convergence criteria (CPP: SEAICE_ALLOW_LSR_FLEX, run-time:
                     SEAICEuseLSRflex) accounting for both Non-Lin and Linear solver residual;
                     tested in offline_exf_seaice.dyn_lsr; also add 2-D diagnostics for residual.
f0ff6e912a dngo* o pkg/streamice:
                   - rename STREAMICE_PETSC.h to STREAMICE_PETSC_MOD.h and rename
                     STREAMICE_ARG_PETSC_mod code module to STREAMICE_PETSC_mod;
                   - include STREAMICE_PETSC_MOD.h in src files rather than the module directly:
                     this obviates the need for alphabetical order in names or serial compilation
15ec8028f7 aver* o pkg/bling:
                   - fix 2 small bugs in carbonate and aragonite saturation states: a) both Ksp
                     coeff are fct of log of temperature (and not log10); b) add missing unit
                     conversion factor to carbonate variable in OmegaC & OmegaAr calculation.
1052c30783 Jean* o pkg/grdchk:
                   - new S/R to get CTRL var/file name from grdchk-index ; use it to simplify
                     (with new arguments) the 3 routines that handle CTRL var/file perturbations
                   - rename grdchk_init to grdchk_get_mask ; move GRDCHK_SUMMARY call ;
                   - report (in summary & in results section) CTRL var/file name used in grdchk.
51e381e9c9 Jean* o pkg/dic:
                   - fix loading of forcing file for the case DIC_forcingCycle = 0 ;
                   - fix inconsistent timing params for loading initial surface-silica file ;
                   - clean-up initialise-varia level S/R, now all called from dic_init_varia.F
                     and move all forcing field initialisation to dic_ini_forcing.F ;
                   - read and process pickup_dic meta file with error/warning (depending on
                     pickupStrictlyMatch = T/F) if missing file or field.
65754df434 Mart* o pkg/ctrl:
                   - reduce pkg/ctrl/optim.h to just "optimcycle" and rename into OPTIMCYCLE.h ;
                   - keep optim_readparms.F namelist unchanged and define variables locally.
                 
ec9548c9e7 Jean* checkpoint68t (2023/10/28)
a2c35952f2 Jona* o pkg/dic:
                   - improve carbonate dissolution options (new params: selectCalciteDissolution)
                     and fix a minor bug in dissolution rates according to Keir et al (1980);
                   - change exp. so_box_biogeo secondary tests caSat0/3 to test option 2 & 3.
f5509be190 Mart* o pkg/gmredi:
                   - fix setting of GM_ExtraDiag that was not (always) turned on with 3D Kappa
                     read from file, with Bates-K3d or QG-Leith, therefore missing 2 terms in
                     isopycnal diffusion tensor; update ref. output of MLAdjust.QGLthGM test ;
                   - add more check and stop for the case #undef GM_NON_UNITY_DIAGONAL ;
                   - add runtime parameter GM_isoFac_calcK to allow to scale dynamically computed
                     Kappa contribution in the Redi-tensor (default = 1.).
018c28d301 Jean* o pkg/autodiff:
                   - adjust call to S/R DIAGNOSTICS_SWITCH_ONOFF in autodiff_inadmode_set_ad.F
                     so that snap-shot Adjoint diagnostics are filled within the same time-step
                     as they are written to output file.
4d72283393 Mart* o pkg/ctrl:
edcd27be69 Mart*   - rename ctrl_dummy.h to CTRL_DUMMY.h, remove unused variables & common blocks
                   - retire CPP-flag ALLOW_HFACC/HFACC3D_CONTROL and remove related code.
                 o pkg/ctrl:
4d72283393 Mart*   - rename header file "ctrl.h" to "CTRL.h".
4ec37fd829 Jean* o utils/matlab/cs_grid:
                   - update some basic matlab-scripts for CS-grid (split_*_cub.m,
                     rotate_uv2uvEN.m, mk_psiLine_CS.m & use_psiLine.m) to a) also work with
                     compact-format input; and (b) always assume "long-vector" are stored one
                     face after the other (compact-format compatible);
                   - new script to generate broken-lines (for computing meridional transport
                     stream-function), simpler than the previous version in cs_grid/bk_line/;
                   - update RGB-dims in 2 latloncap/ scripts to match pkg/exch2 convention.
172933ad7e Mart* o pkg/ctrl:
                   - simplify file name handling in ctrl_map_ini_gentim2d.F to please TAF (fixes
                     hs94.1x64x5 TL test) without upsetting Tapenade & OpenAD.
85c224e862 Ou W* o pkg/autodiff + ecco:
                   - fix a typo in AD-var output file name (addummy_in_stepping.F);
                   - fix and improve weight output in pkg/ecco/cost_generic.F
96b006450c dngo* o pkg/streamice:
                   - implementation of parameterized depth-dependent ice-shelf melt rate ;
                   - new subroutines added to accumulate misfit cost based on time-dependent
                     surface elevation and velocity observations (+ calls in pkg/cost) ;
                   - fix generic ctrl (ctrl_map_ini_{genarr,gentim2d}.F) for OpenAD and
                     add mapping of STREAMICE arrays to generic controls ;
                   - update exp. halfpipe_streamice OAD & Tap setup (remove customized *.F)
                     and switch on new CPP option ALLOW_COST_STREAMICE (+adjust params files).
910e5c3e29 Mart* o pkg/autodiff:
                   - fix a bug in ALLOW_AUTODIFF_WHTAPEIO code with ALLOW_DIVIDED_ADJOINT ;
                   - refine grad-check + update output for AD test "lab_sea.noseaicedyn".
                 
26e63756eb Jean* checkpoint68s (2023/09/11)
19ced9bf8f Mart* o verification:
5a54dbbd56 Jean*   - change default ALLOW_IB_CORR (in pkg/ecco/ECCO_OPTIONS.h) to "#undef" and
                     test that this code compiles in experiment global_oce_biogeo_bling ;
                   - clean/update AD related CPP header files across all experiments and reduce
                     differences with standard version in pkg autodiff, cost, ctrl and ecco.
                 o verification:
19ced9bf8f Mart*   - change global_oce_latlon TAF set-up to multi-tiles (4 tiles, as in code_oad
                     & code_tap) and add SIZE.h_mpi to enable MPI tests (in all 3 code_* dir).
7448700841 Mart* o model/src & pkgs, TAF storage dir:
                   - rearrange and add storing of variables to reduce number of (unwarned)
                     recomp. in fluxform & vecinv pkgs and in model/src (e.g., calc_phi_hyd.F) ;
                   - add store directives in solve_tri/pentadiagonal.F to avoid recomputation
                     warnings with SOLVE_DIAGONAL_KINNER defined ;
                   - add CPP condition inside GAD SOM advection S/R (-> empty ".f" file if
                     neither GAD_ALLOW_TS_SOM_ADV nor PTRACERS_ALLOW_DYN_STATE is defined ) ;
                   - clean-up/refine many unnecessary store directives -> less TAF warnings ;
                   - remove unnecessary checkpointing code from pkg/smooth_diff2/3d.F
b038e3cc4f Mart* o pkg/ggl90:
                   - move computing the mixingLength to a dedicated routine ggl90_mixinglength.F
                   - adjust/add TAF store directives to avoid hidden recomputations.
45315406aa Mart* o pkg/seaice:
                   - new option SEAICE_BGRID_DYNAMICS allows to remove/replace
                     SEAICE_ALLOW_DYNAMICS by ( SEAICE_CGRID or SEAICE_BGRID_DYNAMICS ) ;
                   - exclude more code if SEAICE_CGRID is undefined and clean up/rearrange
                     SEAICE.h to form more consistent groups and common-blocks ;
                   - update SEAICE_OPTIONS.h in verification experiments.
57622776fd Jean* o pkg/mdsio:
                   - Add 2 new arguments (kLo & kHi) to pkg/mdsio Slice I/O routines that allow
                     to select which levels in Slice-array to read-in or to write-out to file.
                 
2a22bb531b Jean* checkpoint68r (2023/08/02)
5bc996898d Mart* o verification:
                   - adjust amplitude of perturbation (grdchk_eps) to improve Fwd/Adj gradient
                     check comparison in exp. global_ocean.90x40x15, global_with_exf & lab_sea ;
                   - change location of grad-check (away from freezing Temp) in exp. OpenAD
                     and rename experiment "OpenAD" to "global_oce_latlon".
444da61630 Mart* o pkg/ctrl + pkg/grdchk:
                   - define PARAMETER nobcs = 4 in CTRL_OBCS.h instead of SIZE.h ; update SIZE.h
                     of all code_ad/oad/tap verification exp.
                   - in pkg/grdchk, rename grdchk.h to GRDCHK.h and adjust src code to work
                     without "nobcs" when OBCS_ALLOW_CONTROL is undefined.
44c9a33d03 Jean* o verification:
                   - Remove duplicated parameter files from input_tap/ dir and adjust prepare_run
                     accordingly ; remove few untested additional files (in OpenAD/ & lab_sea/).
d73d15cdef antn* o pkg/seaice:
8e32c48b8f Mart*   - rename ZMIN/ZMAX into SEAICE_ZMIN/ZMAX to avoid potential conflicts with kpp
                     variables with the same name ; rename swfracb into SEAICE_SWFrac ;
                   - fix a bug in computing SEAICE_SWFrac in pressure coordinates ; update exp.
                     global_ocean.cs32x15.in_p reference output.
                 o pkg/seaice:
d73d15cdef antn*   - SEAICE_USE_GROWTH_ADX: fix a bug related to flooding and fix budget closure
                     for linear free-surface case.
025a9bb173 antn* o pkg/ecco:
                   - in cost_gencost_sshv4.F, enable to also process monthly data (previously,
                     only daily) for SSH cost.
c61a47f63f Mart* o pkg/ctrl:
                   - remove left-over and unused code within ALLOW_NONDIMENSIONAL_CONTROL_IO
                     (except in OBCS_CONTROL pack/unpack code); as a consequence, switch back
                     ALLOW_PACKUNPACK_METHOD2 to #undef in exp. tutorial_global_oce_optim.
                 o pkgs:
de57a2ec4b Mart*   - for local filenames, replace character*(80) by character*(MAX_LEN_FNAM)
                     declaration, where possible, especially in pkgs: autodiff, ctrl, ecco,
                     profiles, smooth & grdchk.
                 
acbfbd3bbd Jean* checkpoint68q (2023/06/29)
5b0716a6b3 Mart* o pkg/ggl90:
                   - non IDEMIX code: fix bug (missing hFac) in matrix coefficient computation ;
                   - fix RI-Number calculation for IDEMIX ; new flag GGL90_IDEMIX_CVMIX_VERSION
                     (defined by default) to update IDEMIX to CVMix version ;
                   - add new diagnostics ;
                   - update Fwd ref. output of exp. isomip.obcs, global_ocean.90x40x15.idemix
                     and global_ocean.cs32x15.in_p.
b4daa24319 Shre* o pkg/tapenade + other Tapenade addition:
                   - add new capability to use Tapenade to generate Adjoint & Tang-Linear model:
                     new package (pkg/tapenade), new tools (tools/TAP_support), update genmake2
                     and testreport ; add some docs (in progress);
                   - modify src code & packages to work with tapenade ; add new code_tap/ &
                     input_tap/ dirs (+ ref output) in 9 verification experiments to get
                     tested with tapenade.
                 
8c2ab294fc Jean* checkpoint68p (2023/05/07)
8377b8ee87 Mart* o pkg/seaice:
                   - fix compile error related to ALLOW_AUTODIFF_TAMC/ALLOW_AUTODIFF mix-up
                     in seaice_evp.F; also replace many ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF
                     where code is not specific to TAF/TAMC;
                   - call S/R seaice_get_dynforcing every timestep to always have valid TAUX/Y;
                   - move most of routine body of seaice_dynsolver.F inside the
                     SEAICE_ALLOW_DYNAMICS block.
b0b45f2373 Ou W* o pkg/ecco:
                   - fix "sterGloH" output after a restart (issue related to Greatbatch
                     correction) by writing & reading (small) new "pickup_ecco" files.
b938a3c63b antn* o pkg/ctrl:
                   - fix record number (mostly in ctrl_map_ini_gentim2d.F) in case of restart,
                     using corresponding xx_gentim2d_startdate1/2 as specified from data.ctrl;
                     this finalizes (+ fix) changes made in PR #260 and #380;
                   - also add more debug print (+new CPP option ALLOW_CTRL_DEBUG);
                   - improve generic-control documentation in Chap.10 (State Estimation).
ab47de63dc Mart* o pkg/mom_common:
                   - new expression for quadratic drag coefficient, function of cell thickness &
                     roughness length (logarithmic law of the wall); for now, only for z-Coords.
                     Turned on with CPP option ALLOW_BOTTOMDRAG_ROUGHNESS (MOM_COMMON_OPTIONS.h)
                     and run-time setting zRoughBot > 0 in data, PARMS01 namelist.
                     Tested in exp. tutorial_plume_on_slope, new secondary test "roughBot".
cda1c18f72 Jean* o model/src & pkgs:
                   Finish to remove code within retired CPP options:
                   - remove orphan code within (many) removed ALLOW_()_CONTROL (as listed in
                     PR #689 comments); remove seaice_ctrl_map_ini.F;
                   - remove code within retired CPP options, remove call to COST_TRANSPORT,
                     remove ALLOW_ECCO_BARSTORES and the 4 "ecco_ad_check_lev?_dir.h" files;
                   - remove (check & stop) "using_cost_bp" & "using_cost_scat" from "data.ecco";
                   - avoid few unused variables; use default CTRL_OPTIONS.h in exp. hs94.1x64x5.
a4e168e012 antn* o pkg/seaice:
                   - SEAICE_USE_GROWTH_ADX: fix diagnostic SIatmFW and add diagnostic SIeprflx
                     to close seaice mass and heat budgets.
a17ca5331e Jean* o pkg/dic:
                   - remove TAF storage dir for variable "OmegaC" (within wrong CPP option).
                 
628b4a6c85 Jean* checkpoint68o (2023/03/13)
d9efc637ba Mart* o model/src:
                   - salt/temp/ptracer_integrate.F: optimise store directives
                   - add mising "obcs_seaice_sponge.f" to obcs_ad_diff.list
4890e8ebab antn* o pkg/ecco:
                   - smoothing in gencost_bpv4: allow to choose between a) call to smooth_basic2D
                     (using a constant length, with run-time params replacing hard-coded values)
                     or b) call to smooth_hetero2D (using a 2D field to be read in).
e99fa9b078 Mart* o pkg/obcs:
                   -  update OBCS configuration summary.
806785c928 Jean* o eesupp/inc, model/inc & pkgs:
                   Clean CPP header files:
                   - remove ALLOW_GENCOST_CONTRIBUTION from COST_OPTIONS.h (is already set in
                     ECCO_OPTIONS.h);
                   - move ALLOW_PACKUNPACK_METHOD2 from AUTODIFF_OPTIONS.h to CTRL_OPTIONS.h;
                   - set EXCLUDE_WHIO_GLOBUFF_2D in MDSIO_OPTIONS.h (found in some customized
                     AUTODIFF_OPTIONS.h);
                   - list CPP options in pkg CPP header file (as undef) when used in any
                     experiment local set-up;
                   - fix typo in 2 CPP option names ; rename few (unused) pkg/fizhi CPP options;
                   - update pkg dependence rule for pkg/bling ; avoid few unused variables.
28038c27d5 Lois* o pkg/kl10:
                   - get stratification from variable "SigmaR" (passed as argument) instead of
                     recomputing locally in-situ density (less efficient and inaccurate when
                     using Non-Linear EOS); update (kl10) ref output for internal_wave exp.
38d78826c7 Ciar* o pkg/ecco:
                   - add new generic integral cost function "m_boxmean_vol" (e.g. to track
                     volume of isoycnal layer); add it to lab_sea secondary AD test "noseaice"
                     and update ref. AD output file.
c26ad343d2 Jean* o tools/build_options:
                   - fix OpenMP option in ifort optfiles for modern intel compiler.
                 
f6d206d1bd Jean* checkpoint68n (2023/02/08)
2b959ba38e Mart* o pkg/seaice:
                   - make all seaice-cost code independent of pkg/ecco and remove few
                     SEAICE_COST.h from pkg/ecco ;
                   - remove unused code related to ALLOW_SEAICE_COST_SMR_AREA (formerly used
                     with ECCO_CTRL_DEPRECATED, seaice_cost_driver.F and S/R called from there),
                     ALLOW_MEAN_SFLUX_COST_CONTRIBUTION + ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION,
                     and retire associated parameters.
2e3e8c330d Jona* o pkg/dic:
                   - rename CPP: CAR_DISS -> DIC_CALCITE_SAT and AD_SAFE -> DIC_AD_SAFE and put
                     all carbonate-saturation code and 3D arrays inside #ifdef DIC_CALCITE_SAT
                     block and time-ave arrays within #ifdef ALLOW_TIMEAVE ;
                   - add run-time params: useCalciteSaturation, calcOmegaCalciteFreq, nIterCO3,
                     selectCalciteBottomRemin, KierRateK, KierRateExp and WsinkPIC ;
                   - switch order of arguments to "myTime, myIter, myThid" in few remaining
                     pkg/dic S/R + S/R calls in pkg/gchem ;
                   - update exp. so_box_biogeo (define CARBONCHEM_TOTALPHSCALE & DIC_CALCITE_SAT)
                     + add 2 new secondary tests (caSat0 & caSat3) with useCalciteSaturation=T
                     and using 3-D silicate input file.
edb6656069 Mart* o TAF tape keys:
                   - rename many local taf keys to use shorter and more consistent names ;
                   - pkg/thsice: fix bug in key computations.
1d99daeaf6 Oliv* o pkg/diagnostics (+doc):
                   - fix index-loop range in diagnostics_sum_levels.F and document "fileFlags"
                     and associated features (vertical interpolation & integral & hFac scaling).
5a6997640b Mart* o pkg/gmredi:
1d99daeaf6 Oliv*   - in gmredi_slope_limit.F, fix tape keys by using local tapes.
9293d3c672 Hajo* o pkg/ggl90:
1d99daeaf6 Oliv*   - cleaning: remove maskS multiplication in ggl90_calc_visc.F (no equivalent
                     for KappaRU) and update "output_oadm.ggl90.txt" in OpenAD exp.
ea7679383f Jean* o pkg/ggl90:
9293d3c672 Hajo*   - Add code in pkg/ggl90 to parameterize Langmuir Circulation (LC) effects on
                     vertical mixing (useLANGMUIR=T); follows: Tak et al, Ocean Modelling, 2023;
                   - Primary effect is to increase mixing length scale due to LC ; the stokes
                     velocity term is also included in the momentum equation (Coriolis term);
                   - Tested in new secondary test "gglLC" in exp. "vermix".
0a1233e81a Ou W* o pkg/ecco:
                   - fix out-of-bound array index issue in cost_gencost_sshv4.F;
                   - fix a small bug in same S/R (skipping call to smooth_hetero2d(anom_slaobs, )
                     if gencost_outputlevel(igen_lsc)=0.);
                   - in same S/R, skip output of "_smooth" file  when smoothing is not applied.
c69ccc91fb antn* o pkg/ctrl:
                   - enable initial sea ice area/heff controls with correct definition of control
                     indices;
                   - move condition on useSEAICE inside seaice_init_varia.F (always initialize to
                     zero) when compiling pkg/autodiff. Similar changes to shelfice_init_varia.F;
                   - fix out-of-bounds index issue in ctrl_map_ini_genarr.F (igen_shiCDrag=0).
a1d0e455fd Hann* o pkg/dic:
                   - enable to read in prescribed 3d silicate fields for calcite-saturation
                     calculation and 3-D pH calculation (#define CAR_DISS).
                   - add 5 new 3-D diagnostics related to calcite-saturation calculation.
                   - fix 2-D silica input file from tutorial_global_oce_biogeo and add 3-D silica
                     input file to so_box_biogeo exp. (currently unused).
                 
af3e3bca65 Jean* checkpoint68m (2022/12/05)
5b172de0d2 Jean* o pkg/gmredi:
                   - update Redi diffusion and GM (skew-flux or advective form) to also work with
                     P-coordinates and most current tapering schemes ; change sign of sigmaR (for
                     now, only within pkg/gmredi) to always be the same as stratification, i.e.,
                     positive if stratified ; add 2 arguments to GMREDI_SLOPE_LIMIT for 'ldd97'.
                   - with p-coord, keep sign of slope component unchanged (same as dSigmaX,Y)
                     and flip sign (-gravitySign) of Redi-tensor extra-diagonal terms ; also keep
                     stream-function components GM_PsiX & GM_PsiY unchanged and flip sign when
                     computing bolus-transport (left handed coord).
a1d0e455fd Hann*   - add unit conversion factor between p and z coord. at level center, function
                     of vertical profile of ref. density ; used inside slope-limiter and tapering
                     function.
5b172de0d2 Jean*   - stop if trying to use P-coord with not yet updated gmredi pieces of code.
                   - add a simple secondary test in front_relax exp. using GM and p-coord.
20dee61641 Mart* o pkg/autodiff:
                   - cleanup tamc.h: remove unused parameters and nthreads_chkpkt as it is (and
                     should be) always one; update all verification exp. code_ad versions.
                   - simplify tape-key dependence on tile indices (remove thread grouping).
f9d7cbfb72 Ou W* o pkg/ctrl:
                   - add run-time variable ctrlDir to specify a directory different from default
                     current directory for I/O of controls adjustment and adjoint gradient (xx
                     and adxx), and other active files; used (as example) in lab_sea experiment.
                 o pkg/smooth:
                   - add run-time variable smoothDir to specify a directory different from
                     default current directory for I/O of smoothing operators.
                 
1575dc0796 Jean* checkpoint68l (2022/10/26)
cc9097e522 Oliv* o pkg/longstep:
                   - fix initialization of LS_fwFlux ;
                   - move params report & check to new S/R LONGSTEP_CHECK.
dbb54b7d7a Jean* o model/src:
                   - fix ocean r-star pressure gradient in case model top is not uniformly at r=0
                   - update ref output of secondary test "isomip.obcs".
d220271442 Oliv* o tools/genmake2:
                   - Remove unnecessary awk escape sequence ; this avoids a warning with recent
                     GNU awk (5.0.1 and newer).
3924ebfa1b Mart* o tools/adjoint_options:
                   - merge five ad-optfiles into single one with compact list of generic control
                     variables and obcs-control variables ;
                   - to use divided adjoint (DIVA), in genmake_local, set new flag USE_DIVA=1
                     (replacing "adjoint_diva");
                   - select which Fortran version is sent to TAF by setting TAF_FORTRAN_VERS
                     to either F77, F90, or F95 (replacing "adjoint_f95") ;
                   - to replace "adjoint_tamc_compatibility", in genmake_local, set new flag
                     TAMC_COMPATIBILITY_MODE=1 ;
                   - remove "-server fastopt.net" to use the default server (fastopt.de)
                   - use the staf default server (currently "fastopt.de") instead of specific
                     server "fastopt.net" ;
                   - remove more commented lines (remove_comments_sed) in src code sent to TAF ;
                   - remove obsolete "ad_taf_output.f.*" diff-patches in tools/ ;
                   - remove "ad_optfile.local" files from some verification experiments ; keep
                     example how to specify local optfile in verification/bottom_ctrl_5x5 ;
8a34959769 dngo* o pkg/streamice:
                   - changes related to PETc solver interface to be compatible with PETSc
                     version 3.8 and above and also available without MPI;
                   - also make sure PETSc is not used at runtime by default.
                 
4cf519afc7 Jean* checkpoint68k (2022/08/17)
cf705a6c8e Mart* o pkg/ctrl, ecco, ... :
                   Remove untested and obsolete ECCO_CTRL_DEPRECATED code: From now on it is
                   only possible to specify control parameters through generic controls.
                   - retire associated pkg/ctrl and pkg/autodiff flags, such as: ctrlUseGen,
                     xx_hflux_file, xx_hflux_startdate1, ..., ctrlSmoothCorrel2D/3D,
                     useSmoothCorrel2DinAdMode. Most of these did not have any effect with
                     undefined ECCO_CTRL_DEPRECATED, but were still allowed in data.ctrl.
                     Now specifying them is an error and stops the run.
                   - remove code that assumes ctrlUseGen=F
                   - remove empty and unused subroutines:
                     * pkg/ctrl: ctrl_weights.h, ctrl_map_ini_gen.F, ctrl_smooth.F,
                         ctrl_map_ini.F, ctrl_map_ini_ecco.F, ctrl_map_ini.F, ctrl_map_ini_ecco.F
                     * pkg/ecco: cost_forcing.F, cost_hyd.F, cost_internal_params.F, cost_ssh.F
                         ecco_cost_summary.F
                     * pkg/smooth: smooth_correl2dw.F
                     * pkg/seaice: seaice_cost_areasst.F
                   - adjust parameters in verification experiment that still contained retired
                     parameters
                   - switch global_ocean.cs32x15.thsice to using generic control variables
                   Note: some untested code (notably pkg/admtlm, which did not compile before)
                     will be more difficult to resurrect without the ECCO_CTRL_DEPRECATED code.
f18a893d42 Mart* o pkg/ggl90:
                   - adjust code to also work under an ice-shelf (with pkg/shelfice); idemix
                     under ice-shelf not fixed yet.
                   - turn on ggl90 in isomip experiment secondary test "obcs" and update
                     reference output file.
94a8024bbe Jean* o pkg/gmredi:
                   - allow to read-in 3-D background isopycnal (Redi) and thickness (GM)
                     diffusivity without pkg/ctrl: new 3-D arrays, new CPP options:
                     GM_READ_K3D_REDI & GM_READ_K3D_GM and new input files: GM_K3dRediFile &
                     GM_K3dGMFile (replacing retired GM_isopycK3dFile & GM_background_K3dFile).
                   - update code for ALLOW_KAPGM_CONTROL & ALLOW_KAPREDI_CONTROL to use
                     these new 3-D arrays (from GMREDI.h) and move setting of 3-D control arrays
                     from from ini_mixing.F to gmredi_init_varia.F (+ adjust call condition);
                   Note: need to define new option GM_INPUT_K3D_GM and/or GM_INPUT_K3D_REDI
                     to use KAPGM_CONTROL and/or KAPREDI_CONTROL.
                   - remove obsolete code & CPP option ALLOW_KAPGM/KAPREDI_CONTROL_OLD
                 
f03a2f5e21 Jean* checkpoint68j (2022/06/28)
cc60455fbb Mart* o pkg/exf:
                   - implement drag coefficient of Large and Yeager (2009), Climate Dynamics, 33,
                     pages 341-364, within #ifdef ALLOW_DRAG_LARGEYEAGER09
fe1862e69b Mart* o autodiff(TAF):
                   - fix few taf recomputation and conflict warnings in: calc_3d_diffusivity.F
                     (PCELL_MIX_CODE), pkg/bling & dwnslope_apply.F ; update reference AD output
                     of exp. that use pkg/dwnslope (lab_sea).
f6de6620bc Mart* o pkg/thsice:
                   - fix bug in computation of ustar (case velocity=0) in thsice_calc_thickn.F;
                   - introduce & document THSICE_REGULARIZE_CALC_THICKN flag.
20a156cdce Mart* o pkg/generic_advdiff (TAF):
                   - in gad_advection.F, replace global tapes "comlev1_bibj_k_gad" &
                     "comlev1_bibj_k_gad" by local tapes; avoid unnecessary recomputations, but
                     recompute full routine (only) once in ad-routine;
                   - this affects results when useApproxAdvectionInAdMode=T, since now all tapes
                     are computed using approximate Adv-Scheme (inAdMode=T); udate AD ref. output
                     of exp. global_ocean.cs32x15.seaice.
3bafcf6020 Timo* o pkg/shelfice:
                   - Remove ALLOW_SHIFWFLX_CONTROL and all xx_shifwflx related code in favor of
                     already implemented gentim2d;
                   - move update of shelficeLoadAnomaly inside shelfice_step_icemass.F (within
                     IF (SHELFICEMassStepping) ...);
                   - fix storage dir for SHELFICEMassStepping, allowing to realFreshWaterFlux=T
                     with ALLOW_AUTODIFF defined (remove STOP there). Still not working with
                     OpenAD (add a STOP in shelfice_check.F).
                 
9bcb497701 Jean* checkpoint68i (2022/04/27)
6b551785d1 Jean* o eesupp/src:
                   - simplify reading parameter file, using single scratch file (instead of 2).
2e7aec9951 dngo* o verification, OpenAD:
                   - make all OpenAD experiments use generic control variables, so that from now
                     on, the ECCO_CTRL_DEPRECATED code is no longer tested in verification
                     (neither in verification_other, where it never was tested), except for
                     global_ocean.cs32x15.thsice (this is intentioal).
113b21cd45 Mart* o autodiff(TAF):
                   - avoid unnecessary local recomputations and associated warnings by storing to
                     local tapes in: seaice/advect.F, gad_dst3fl_impl_r.F, gmredi_slope_limit.F,
                     shap_filt_uv_s2.F, solve_pentadiagonal.F
a85293d087 Mart* o pkg/thsice:
                   - fix store directives + modify code of thsice_calc_thickn.F, thsice_extend.F
                     and thsice_solve4temp.F to avoid 28 recomputation warnings and recomputing
                     the state unnecessarily;
                   - define new tape and retire two old thsice related tapes (commented out for
                     now) in the_main_loop.F;
                   - change offline_exf_seaice.thsice experiment to be more sensitive to changes;
                   - fixing a bug leads to smaller gradient errors and correct TLM cost function
                     values and requires updating (both ADM and TLM) offline_exf_seaice.thsice
                     and global_ocean.cs32x15.thsice reference output;
07b7562e86 Ou W* o pkg/ctrl:
                   - fix issue in S/R CTRL_MAP_GENARR3D by explicitly set xx_gen to zero where
                     wgenarr3d is zero ; also replacing 10^xx_gen with EXP(log(10)*xx_gen) for
                     log10ctrl produces small differences at machine truncation level.
3d93c0a01e Ou W* o eesupp & pkg/mdsio:
                   - new (CPP) Macro to open read-only files with ACTION='read', added to
                     most pkg/mdsio S/R (+ exf_interp_read.F); disable this in few old compiler
                     optfiles (g77, pgf77) by adding EXCLUDE_OPEN_ACTION to DEFINES list.
51575f66de Mart* o model:
                   - new CPP option to exclude (= default) S/R CONVECTIVE_ADJUSTMENT_INI;
                     to reproduce old results, define new option INCLUDE_CONVECT_INI_CALL in
                     two verification experiments: exp2 and tutorial_tracer_adjsens.
                   - add a check for INCLUDE_CONVECT_CALL if cAdjFreq <> 0.
fefbff5637 Mart* o tools/build_options:
                   - new optfile "darwin_arm64_gfortran" for Mac ARM 64-bit processor.
6514215240 Jean* o pkg/gmredi:
                   - add deep-factor to pkg/gmredi code to work with "deepAtmosphere=T".
a99d705983 Jean* o verification/cpl_aim+ocn:
                   - add secondary test set-up using seaice dynamics (pkg/seaice) as part of
                     ocean component and update script to handle option to run multiple test.
adac922254 dngo* o verification/halfpipe_streamice:
                   - update OpenAD test by removing ECCO_CPPOPTIONS.h (but, for now, keep local
                     version: ctrl_map_gentim2d.F & ctrl_map_ini_genarr.F in code_oad).
64811cb024 Jean* o pkg/mypackage:
                   - improve description (for a coding style example).
7e00d7e8f9 Jean* o model:
                   - add option to apply a correction for net global fresh-water flux imbalance
                     proportional to, fixed in time, 2-D weight field that is read-in from file ;
                   - new integer selector "selectBalanceEmPmR" (=0: off, =1: uniform correction,
                     =2: correction scaled by weight) that replaces logical switch "balanceEmPmR"
                     with backward compatibility setting.
                 
479cbc238b Jean* checkpoint68h (2022/03/22)
aa93ca8e85 Ciar* o pkg/ecco:
0cd0083da8 Ou W*   - new src files: ecco_init_fixed.F & ecco_diagnostics_init.F ;
                   - new SSH diagnostics: SSH,SSHNOIBC (with & w-out Inv.Barometer corr.: SSHIBC)
                     STERICHT (steric height anomaly); and Bottom-Pressure/Mass: OBP & OBPGMAP ;
                   - add arg myTime & myIter to S/R ECCO_PHYS and adjust calls ; change to use
                     model "rhoInSitu" (instead of recomputed rho) for Greatbatch correction ;
                     this affects cost "m_eta".
                 o pkg/ecco:
aa93ca8e85 Ciar*   - add new feature (within gencost) to evaluate cost-function contribution
                     over specified density range (instead of depth range, see issue #483);
                   - add few run-time parameters including logical switch: gencost_useDensityMask
                   - test this new feature in lab_sea/input_ad.noseaice and update ref. output.
ef7fa68a19 Jean* o pkg/ptracer (adjoint):
                   - remove AUTODIFF_PTRACERS_SPLIT_FILES as it has no effect.
                 o pkg/generic_advdiff & seaice (adjoint):
1574069d50 Mart*   - avoid recomputation in Second-Order Moment (SOM) advection S/R by using
                     local tapes ; reduce local tapesize in seaice_solve4temp.F ;
479cbc238b Jean*   - fix key and size of tapes in multi-dimensional advection routines and adjust
1574069d50 Mart*     maxcube value (2 or 3 if using CubedSphereExchange) in few exp. "tamc.h".
30ad0459d6 Jean* o pkg/mdsio:
                   - retire all S/R from mdsio_rw_slice.F after replacing the last 2 calls to
                     MDSWRITEFIELD{X,Y}Z in pkg/ctrl/ctrl_set_globfld_{x,y}z.F with calls to
                     S/R WRITE_REC_{X,Y}Z_RL (from pkg/rw).
                   - remove src file mdsio_rw_field.F & mdsio_rw_slice.F from NOOPTFILES list
                     in few linux_amd64_ifort* optfiles.
                   - move if statement out of "lengthBuff" loop in mdsio_{read,write}_whalos.F
16cc32c739 Mart* o verification AD exp.:
                   - remove ECCO_CPPOPTIONS.h from global_ocean_ebm/ and halfpipe_streamice/
                     code_ad/ dir and replace by appropriate AUTODIFF/CTRL/COST_OPTIONS.h ;
                   - for halfpipe_streamice AD exp., make necessary adjustments in pkg/streamice
30ad0459d6 Jean*     and remove ALLOW_GENTIM2D_CONTROL from store directive header files
16cc32c739 Mart*     streamice_ad_check_lev?_dir.h ;
                   - remove customized version of ctrl_map_gentim2d.F & ctrl_map_ini_genarr.F
                     from halfpipe_streamice/code_ad/ and add corresponding code to pkg/ctrl.
                 
ec9af22855 Jean* checkpoint68g (2022/02/19)
0bad585a21 Navi* o doc:
                   - fix some math notation in docs.
385da9f3ec Jean* o pkg/obcs:
                   - avoid division by zero when useOBCStides=.True. and tidalPeriod=0.
8233d0ceb9 Jean* o pkg/gmredi:
                   - fix basic code to also work with dry grid cells near the top (e.g., under
                     ice-shelf) and in this case, for now, stop if unsafe features are used ;
                   - fix tapering 'ac02' and 'stableGmAdjTap' ;
                   - add a secondary test, "input.top", in verification exp. front_relax to test
                     GM with dry cells at the top (+ also 'ac02' tapering) ;
                   - update few adm & tlm & oad ref. output from exp. global_ocean.90x40x15
                     since adding better masking in gmredi_s{x,y}rtransport.F does affect AD &
                     TLM gradient (@ machine truncation level).
3c775cbf98 Mart* o pkg/autodiff:
                   - new CPP-flags allow to turnoff (default) autodiff_store/restore entirely:
                     * New flags AUTODIFF_USE_STORE_RESTORE, AUTODIFF_USE_STORE_RESTORE_OBCS to
                       turn on autodiff_store/restore, undefined by default ;
                     * AUTODIFF_EXCLUDE_ADEXCH_RS to skip calls to some AD-exch (if missing).
                   - improve comments in AUTODIFF_OPTIONS.h, fix some store directives for new
                     default, which are:
                        #define ALLOW_AUTODIFF_WHTAPEIO
                        c#define AUTODIFF_USE_MDSFINDUNITS
                        #undef AUTODIFF_USE_STORE_STORE_RESTORE
                        #undef AUTODIFF_USE_STORE_STORE_RESTORE_OBCS
                     and update local AUTODIFF_OPTIONS.h files from verification experiments.
                   - experiment specific setting:
                     * define AUTODIFF_EXCLUDE_ADEXCH_RS in exp.: hs94.1x64x5, obcs_ctrl & OpenAD
                     * increase "nWH" value in local MDSIO_BUFF_WH.h for exp.:
                       global_oce_biogeo_bling, offline_exf_seaice & tutorial_dic_adjoffline
                   - add a TAF "INCOMPLETE" directive for TICES and wVel to avoid a TAF bug.
                   - fix a TAF store directive to avoid extra call of "load_fields_driver"
                     with EXF_SEAICE_FRACTION defined.
f2389c73b0 Jean* o pkg/gmredi:
                   - rename S/R, CPP option (GM_BATES_K3D), on/off switch (GM_useBatesK3d),
                     parameters (GM_Bates_*) and 3-D var (GM_BatesK3d) of Bates etal (JPO, 2014)
                     scheme that computes 3-D field GM/Redi diffusivity (analog to Visbeck etal
                     variable/option naming example).
                 
65dd265852 Jean* checkpoint68f (2022/01/14)
f2389c73b0 Jean* o pkg/exf:
56d13a40ed Mart*   - clean-up relative wind implementation so that uwind and vwind are kept
                     unchanged (always vanilla atmospheric winds after interpolation) while
                     relative wind is computed locally; add diagnostics for relative wind.
                   - adjust pkg/seaice relative-wind code (+ clean-up SEAICE_GREASE code).
0c240d16ef Jean* o pkg/kpp:
                   - avoid updating input argument "kmtj" in S/R BLDEPTH (in: kpp_routines.F);
                     this also remove/avoid 3 recomputation warnings for kmtj in adm (TAF) built.
0fbff46b46 dngo* o pkg/streamice:
                   - fix regularised coulomb basal stress impl to avoid issues with adjoint ;
                   - cancel metric terms in stress tensor for cartesian grid ;
                   - allow (time-indep) velocities to be imposed from external file rather than
                     solved for ;
                   - allow for specification of log of controls as well as sqrt ;
                   - allow termination of adjoint fixed point loop based on relative and absolute
                     error ;
                   - terminate adjoint fixed point loop when change between most recent iterates
                     begins to increase (a sign of unstable growth from linear solve errors ?);
                     update OAD output of exp. halfpipe_streamice (affected by this modif).
c704c5a1ef Mart* o pkg/seaice:
                   - replace hard-coded parameters for JNKF line search by new runtime parameters
                     SEAICE_JFNK_lsGamma and SEAICE_JFNK_lsLmax ;
                   - increment line search counter after reporting and fix an if statement, so
                     that zeroth step is not counted for more consistent debugging output.
f397060a05 dfer* o tools/build_options:
3ee2cce2f5 Jean*   - update pleiades optfile "linux_amd64_ifort+mpi_ice_nas"
f397060a05 dfer*   - rename/update optfile for UK HPC Archer2.
9f5240b52a Jean* o pkgs:
                   - remove/avoid unused variables from AD verification exp. built except from
                     halfpipe_streamice (pkg/streamice); also clean-up a bit pkg/smooth.
3b6c79e4de Mart* o pkg/autodiff:
                   - introduce separate tapes for integer arrays: the corresponding routines
                     just convert between integer and double precision arrays and call the
                     original adread/adwrite routines.
934d981c17 Jean* o pkg/atm_compon_interf:
                   - only with Atm-Phys pkg, allow "regional coupling", i.e. coupled only where
                     there is ocean, keeping Atm-Phys basic mixed-layer elsewhere.
                 
d7c15ab3ba Jean* checkpoint68e (2021/12/10)
ae17457769 Andr* o lsopt & optim:
                   - update Makefiles and README.
c7de4e3cb2 antn* o pkg/ctrl:
37e373688b Mart*   - remove unused flag ALLOW_ECCO_OPTIMIZATION and associated code, always save
                     "fcloc" to gradient vector file and save fcloc=0 to initial ctrl vector file
                     (which is never used); also remove it from any code*/CTRL_OPTIONS.h.
                 o pkg/ctrl:
c7de4e3cb2 antn*   - replace few calls to MDS_READ/WRITE_FIELD with corresponding call to
                     pkg/rw READ/WRITE_REC_3D_RL ; also clean-up: ctrl_map_ini_gen.F
7855a13227 Mart* o tape related code (adjoint):
                   - clean-up tape code in the init-phase, mainly in the_main_loop.F and in
                     ctrl_map_ini_gentim2d.F ;
                   - remove unused (ecco) cost_averages_bar_directives.h ;
                   - adjust comments in (autodiff) adread_adwrite.F & in main_do_loop.F
c3d0b098ae Lars* o eesupp:
                   - fix scratch file names when using PDAF.
6e2befed03 Oliv* o pkg/exf:
                   - fix issue in interannual monthly forcing addition (case ${fld}period=0)
bb459eb78c Jean* o model/src:
                   - skip reading kapGM and kapRedi from ini_mixing.F when useGMRedi is .FALSE.
deacece587 Oliv* o pkg/exf:
                   - add option for interannual monthly forcing with pkg/cal by setting
                     ${fld}_period=-1. (like -12. indicates climatological monthly forcing),
                     available with or without useExfYearlyFields ; update exp. global_with_exf
                     SST forcing to test this new option with and without useExfYearlyFields.
d68b36a485 Mart* o model/src:
                   - define local arrays cg2d_q/v/z without overlaps in all 4 cg2d*.F
                     and skip initialisation of cg2d_q in cg2d.F
9d0c386f0c dngo* o tools/genmake2:
                   - new option to call OpenAD compiler in a singularity container (if provided);
                     add option to testreport too and update OpenAD doc (in section 7.5).
                 
4300da6d2c Jean* checkpoint68d (2021/11/05)
71a2d60687 Jean* o verification/*/results:
                   - update few adm and tlm refence output to get closer agreement.
75c5b64bda Jean* o verification/global_ocean.90x40x15:
                   - no longer use old bug (fixed in Oct 2015) in KAPGM_CONTROL & KAPREDI_CONTROL
                     code and update AD & TL ref. output for kapgm & kapredi tests ;
                   - other small cleaning: finish removing OLD_THSICE_CALL_SEQUENCE code ; remove
                     "cost_yftype" from experiments "data.ecco" ; move ALLOW_ECCO_OPTIMIZATION
                     to the right header file.
016b84c482 Mart* o pkgs pp81, my82, opps & ggl90:
                   - remove pkg/timeave and pkg/mnc output from these mixing packages (since
                     this functionality is available with pkg diagnostics); add 1 diagnostics
                     to pkg/opps (to replave TAVE output).
7ea6a3439c Jean* o tools/build_options:
                   - add "-DAUTODIFF_USE_MDSFINDUNITS -DPROFILES_USE_MDSFINDUNITS" to DEFINES
                     in g77 optfile ; this allows to run set-up with AUTODIFF_WHTAPEIO and/or
                     with pkg/profiles using g77 (with S/R MDSFINDUNITS) while other compilers
                     continue to use local version with extended range of I/O units number.
ebcc29af97 Jean* o pkg/ecco:
                   - fix halo initialisation for argument "active_var" in cost_genread.F ;
                   - change "facNum" expression in cost_gencost_transp.F, to be consistent with
                     comment in src code, by adding missing factor "nSx"; also avoid division
                     in PARAMETER statement.
1c2b1fa3bc Mart* o model/inc:
                   - move potentially time dependent grid variable from GRID_RS to new common
                     block GRID_VAR_RS (hFacW/S/W, etc.) and split common block CG2D_I_R into
                     a _RL and a _RS part ; adjust AD common block accordingly.
11c3150c71 Mart* o verification AD experiments:
                   Update TAF AD exp. so that none relies anymore on ECCO_CTRL_DEPRECATED code:
                   - remove #define ECCO_CTRL_DEPRECATED from experiments: 1D_ocean_ice_column,
                     bottom_ctrl_5x5, global_with_exf, lab_sea, OpenAD, tutorial_dic_adjoffline,
                     tutorial_global_oce_biogeo & tutorial_global_oce_optim ; use instead generic
                     control and generic cost.
                   - for now, keep experiment global_ocean.cs32x15 with both ECCO_CTRL_DEPRECATED
                     code and generic control + generic cost.
                   - also remove ECCO_CPPOPTIONS.h (use instead set of pkg specific OPTIONS
                     header files) from these experiments above.
                   - results unchanged except few digits in cost & ad-monitor for lab_sea &
                     obcs_ctrl ; and few minor recomp. warnings count changes for
                     tutorial_global_oce_biogeo (-4) and for tutorial_dic_adjoffline (+2).
                   Update pkgs as needed:
                   - pkg/ecco: fix field declarations for ecco_toolbox routines and cost_readgen,
                     new toolbox routines ecco_offset, ecco_maskmindepth, make argument lists
                     more consistent between ecco_toolbox routines and remove unused subroutines;
                   - pkg/cost: fix ALLOW_COST_DEPTH contribution;
                   - pkg/ctrl: add more "ifdef ECCO_CTRL_DEPRECATED" where necessary;
                   - pkg/exf: add xx_snowprecip as generic control, adjust CPP-flags.
d97a730ee3 Jean* o pkg/gmredi:
                   - remove condition (ifdef GM_NON_UNITY_DIAGONAL) around 3-D arrays Kux & Kvy
                     to simplify how GMREDI is applied (e.g., gmredi_x/ytransport); fill up these
                     2 arrays with constant value (gmredi_calc_tensor.F & offline_get_diffus.F)
                     when GM_NON_UNITY_DIAGONAL is undef (to reproduce old results).
                   - also with GM_NON_UNITY_DIAGONAL undef, fix ALLOW_KAPREDI_CONTROL averaging.
c59dd234b1 Jean* o tangent-linear:
                   - fix few hand-written tangent-linear src code (in autodiff & ctrl pkgs);
                   - add new target "ftlobj" to Makefile (similar to "obj" & "adobj" for forward
                     and AD built) and corresponding switch in testreport ;
                   - fix non-standard sed command (for Mac) in TLM testreport.
                 
2ffc13e2be Jean* checkpoint68c (2021/10/02)
dc26f158aa Mart* o pkg/seaice:
                   - update some dynamics solver default so that now:
                     a) SEAICEuseEVPstar = .TRUE. ; b) SEAICEuseEVPrev = .TRUE. ;
                     c) LSR_ERROR = 1.e-5 (previously was 1.e-4) ;
                   - put back old default in exp. lab_sea (primary test);
                   - modify (simplify?) logic in seaice_readparms.F and seaice_check.F.
cf8a0ac466 Jean* o pkg/grdchk:
                   - allow to use "recglo" to specify a particular control time record for
                     gradient check (was previously inactive).
f4a4b4841b Jean* o pkg/exf:
                   - new parameters to reduce AD-exf monitor output:
                     1) exf_adjMonFreq (def= adjMonitorFreq), = 0. suppresses all output
                     2) exf_adjMonSelect: =1 (def): less output ; =3 as before, =0 : no output
                   - fix some AD-common block name + content to match TAF directives (in
                     common.flow) and TAF generated code.
                   - skip monitor of model forcing AD-variables (unless monitorSelect=4).
44d3986245 Jean* o pkg/ecco + other:
                   - fix few non-standard syntax (+ repeated setting of "gencost_msk_is3d").
7fbec11c25 Jean* o pkg/bling:
                   - fix call to S/R BLING_BIO_NITROGEN when USE_SIBLING is defined.
13d362b8c1 Ou W* o pkg/ecco:
                   - put various dimensions related to gencost out of "ecco.h" into specific
                     (new) header file "ECCO_SIZE.h" and rename "ecco.h" to "ECCO.h" ;
                   - add gencost param "gencost_kLev_select" to select a vertical level (from 3-D
                     array) to form 2-D gencost ; currently only used in drifter velocity cost ;
                   - add a couple of costs based on 1) inverse barometer (IB) corrected model sea
                     level for altimetry data comparison 2) OBP excluding contribution from
                     global mean atmospheric pressure for comparisons with GRACE data.
7f5c807389 Jean* o pkg/autodiff:
                   - fix type (_RS vs_RL) of AD-vars in hand-written AD routine cg2d_mad.F and
                     in adcommon.h, common block adgrid_rs.
042d2503e1 Jean* o model/src:
                   - fix missing initialisation of local working arrays that were previously
                     in common block in CG2D.h (needed when using blank tiles).
6b3f5dbce1 Hann* o pkg/dic:
                   - fix calculation of carbonate saturation state (with CAR_DISS defined) when
                     #define CARBONCHEM_SOLVESAPHE ; no current test run with #define CAR_DISS.
aecc8b0f47 Mart* o pkg/autodiff:
                   - add code for Full-Adjoint of cg2d in renamed (from cg2d_sad.F) routine
                     cg2d_mad.F (cg2d manual adjoint) ;
                   - new runtime params cg2dFullAdjoint (data.autodiff), useNSACGSolver (data,
                     default to "FALSE"), cg2dMinItersNSA (data, defaults to 0) ;
                   - new sub-verification experiment bottom_ctrl_5x5.facg2d to test new
                     Full-Adjoint capability ;
                   - update primary test experiment bottom_ctrl_5x5 to always use a minimum
                     number of 10 CG2D iterations (changes results but improves accuracy) ;
                   - modify AD-experiment global_ocean.90x40x15.bottomdrag to use full nonlinear
                     free surface (nonlinFreeSurf=4) and cg2dFullAdjoint=True.
042d2503e1 Jean*   - move CG2D working arrays out of CG2D.h common blocks (not necessary)
                     to local arrays within each cg2d S/R.
aecc8b0f47 Mart* 
93664352be Jean* checkpoint68b (2021/08/24)
906a61c194 Ou W* o pkg/ecco:
                   - add time-series output of global mean steric height change at each time step
                     (variable: sterGloH, with #define ALLOW_PSBAR_STERIC) ; turned on
                     with run-time switch "ecco_output_sterGloH=T" ; add option to keep file open
                     (+ single meta file writing) with "ecco_keepTSeriesOutp_open=T" switch.
31f96e9372 Jean* o pkg/ggl90:
                   - fix EXCH calls in pkg/ggl90 when IDEMIX is used: no additional EXCH when
                     using zero horizontal diffusion of IDEMIX_E (IDEMIX_tau_h=0) but with
                     IDEMIX_tau_h > 0, EXCH both IDEMIX_E and GGL90TKE ; this affects results
                     of test experiment cs32.in_p and fix restart issue ;
                   - more consistent/simpler idemix code: use model parameter value for PI,
                     reduce number of IDEMIX global array, add TKE tendency from IDEMIX as output
                     of S/R GGL90_IDEMIX ; use double product of IDEMIX_E instead of power of 2
                     which affects results at machine truncation level ;
                   - update some IDEMIX default param values (following Pollmann et al., 2017)
                     but keep old default values in global_ocean.90x40x15.idemix ;
                   - apply also option calcMeanVertShear to uStarSquare calculation (wind-stress
                     magnitude) and switch on calcMeanVertShear in test experiment cs32.in_p.
0320e25227 Mart* o model/src + pkgs ggl90, exf & seaice: ocean in P-coordinate
                   - read geopotential anomaly directly into phi0surf instead of via pLoad (was
                     a hack), specified with new input filename "geoPotAnomFile" in data&PARM05 ;
                   - adjust MXLDEPTH diagnostic for pressure coordinates ; make sure sigmaR is
                     computed the same way in P-coord as it is in Z-coord.
                   - for penetrating Short-wave and geothermal heating as well as for exf forcing
                     and seaice, use the correct P-coord vertical index for bottom and surface ;
                   - add a flag sIceLoadFac (in "data", default=1.) to be able to turn off
                     seaice surface pressure loading, mainly for Z-coord (since not currently
                     supported in P-coord) ;
                   - use diagnostics "phiHydLow" for seaice dynamics with P-coord ocean to get
                     surface tilt term (instead of using ETAN as in Z-coord); fix restart by
                     adding phiHydLow (only if useSEAICE and usingPCoords) to main pickup file ;
                   - in pkg/ggl90, apply simple scaling to get mixing-length in meters (from
                     pressure) so that no parameter changes are necessary ; significant code
                     changes regarding surface & bottom index + direction of vertical k loop ;
                   - add secondary test "in_p" to experiment global_ocean.cs32x15 (similar to
                     Z-coord secondary test "seaice" but using pkg/ggl90 and without pkg/gmredi).
62748458e3 Jeff* o tutorial_reentrant_channel:
                   - add python notebook (for analysis), add python script to generate input
                     files (+ update matlab version) and update this tutorial docs.
9c166ce5bb Jean* o verification/vermix:
                   - change ggl90 secondary test to use (pkg/ggl90) mxlMaxFlag=3 (instead of 2)
                     and update reference output.
a78204c019 Mart* o pkg/ctrl:
                   - move S/R CTRL_MAP_GENARR2D/3D out of file "ctrl_map_ini_genarr.F" into
                     a new file "ctrl_map_genarr.F" ;
                   - clean-up local versions of ctrl_map_gentim2d.F and ctrl_map_ini_genarr.F
                     from code_ad dirs (i.e., minimize diff with standard version from pkg/ctrl).
375581a429 Jean* o model/src:
                   - improve REMOVE_MEAN_RL/RS subroutines (address issues raised in issue #501)
                     including results independent of tile to proc mapping, correction extended
                     to overlap regions, improve accuracy of _RS version when RS is real*4 and
                     and enable the use 2-D mask maskInC/W/S when applied to 3-D array. Change
                     argument list (add myIter, flip order + change mask arg from 3-D to 2-D).
def7daa328 Jean* o verification/global_ocean.90x40x15:
                   - increase "grdchk_eps" from 1e-7 to 10 in AD test kapgm to improve
                     accuracy of FD gradients ; update reference output.
ac8f9c9b75 Jean* o verification/OpenAD:
                   - add ggl90 pkg to code_ad/packages.conf to get it tested in one TAF-AD exp.
39fa6219cc Oliv* o doc:
                   - require sphinxcontrib-bibtex 2.0.0 or higher
                 
073783ff30 Jean* checkpoint68a (2021/07/16)
16b9a002a2 Mart* o pkg/seaice:
bcc88b4b54 Jean*   - clean up and simplify TAF store directives in do_oceanic_phys.F
                     for seaice_model to avoid unnecessary recomputations ;
                   - in testreport, count and report number of times s/r seaice_model is called.
                 o pkg/seaice:
16b9a002a2 Mart*   - fix (untested) multi-threading and recomputations in seaice_solve4temp.F
4e4ad91a39 Jean* o files that include "tamc.h":
                   - add missing declaration of local keys for TAF store-dir in pkg/obcs
                     (ALLOW_OBCS_STEVENS) and pkg/bling (USE_BLING_V1, PHYTO_SELF_SHADING) ;
                   - add missing AUTODIFF_OPTIONS.h in few places (e.g., in pkg/ebm), needed to
                     get ALLOW_AUTODIFF_TAMC defined ;
                   - change few ALLOW_AUTODIFF <-> ALLOW_AUTODIFF_TAMC ;
                   - remove included "tamc.h" in few files from pkgs seaice, streamice, bling, +
                     in exf_radiation, longstep_thermodynamics, obcs_sponge & pp81_ri_number S/R.
                   - define ALLOW_OBCS_STEVENS in AD exp. obcs_ctrl (to check it compiles).
93de14eac5 Jean* o pkg/ecco:
                   - fix incorrect order of array indices for "objf_gencost" and "num_gencost"
                     in 2 gencost v4 S/R (bpv4 & sstv4).
4351f9c554 Jean* o eessup/inc & pkg/thsice:
                   - Remove 2 CPP options for deprecated code and remove corresponding code:
                     a) USE_OLD_MACROS_R4R8toRSRL (added in May 2009) and
                     b) OLD_THSICE_CALL_SEQUENCE  (added in Jan 2013).
dcd3df3e6a Ou W* o pkg/shelfice:
4351f9c554 Jean*   - fix missing local keys declaration in shelfice_thermodynamics.F for TAF
dcd3df3e6a Ou W*     storge dir. with SHI_ALLOW_GAMMAFRICT defined ;
                   - remove included PACKAGES_CONFIG.h in many verification exp. "tamc.h".
11d5e9fc04 Gael* o tools/build_options:
                   - update gfortran optfile for MacBook Pro "darwin_amd64_gfortran" to work with
                     gfortran version 10 (or higher), similar to linux version update.
7c50f07931 Mart* o pkg/ctrl & other:
dcd3df3e6a Ou W*   - cleanup: move declarations of local variables from header files ctrl.h and
7c50f07931 Mart*     AUTODIFF.h to the local variables section in the respective routines ;
dcd3df3e6a Ou W*   - move declaration of local keys and variables from header file tamc.h to
                     subroutines where they are used.
                   ==> IMPORTANT: This requires updating all customised versions of "tamc.h",
                     from each and every TAF-AD setup.
7c50f07931 Mart*   - remove tamc_keys.h + remove tamc (+tamc_keys) from all "cb2mFiles" lists ;
                   - disentangle ALLOW_AUTODIFF/ALLOW_AUTODIFF_TAMC/ALLOW_OPENAD a bit more ;
                   - remove unused variables where this is straightforward ;
                   - remove a few i/jmin/max variables.
                 
b7589390f2 Jean* checkpoint67z (2021/06/12)
49a029e3de Mart* o veritication:
                   - make testreport count and report the number calls of S/R load_fields_driver
                     and do_oceanic_phys in AD-code (similar to TAF error & warning count).
2b4c90c108 Mart* o pkg/kpp:
                   - add CPP-flags to turn off diffusivity matching at bottom of boundary layer ;
                   - add CPP-flag to turn on taper shear mixing in the case of very small shear ;
                   - add FLAG to turn on smooth regularisation of divisions by small numbers:
                       1/(var+eps) instead of 1/MAX(var,eps) ;
                   - fix a small masking error ;
                   - fix some unfortunate loop ordering and spurious recomputations ;
                   - add new diagnostics KPPshsq, KPPdVsq ;
                   - update exp. vermix (which has KPP_ESTIMATE_UREF defined) reference output.
aa6b2555c8 Jean* o model/src:
fb2c52cfd4 aver*   - in the main code, add option and code for sound speed calculation with
                     corresponding diagnostics ; turned on in exp. global_oce_biogeo_bling.
                 o model/src:
aa6b2555c8 Jean*   - fix few loop range to allow to run with OLx,y=1 when momStepping=F ;
                   - add check and stop if momStepping=T and overlap-size is smaller than 2.
                 o pkg/ggl90:
ce9abcce9d Jean*   - add 3 store directives for gg90tke in ggl90_calc.F and break some loops
                     in two to help TAF without extra storage requirements.
2383f7d4e9 Mart* o pkg/seaice:
                   - adjust store directives in seaice_growth_adx.F:
                     *) add store directives to avoid calling seaice_solve4temp in AD-mode
                     *) adjust/remove/reorganise for good balance between storing and recomputing
                     *) fix a small bug (full 4D arrays were stored instead of 2D for each bi,bj)
                     *) local option "SEAICE_GROWTH_ADX_STORE_MORE" (not recommended)
                        reduces the recomputations but increases the memory requirements.
                   - update ref. AD output of experiment offline_exf_seaice (the only one using
                     SEAICE_GROWTH_ADX): no Grad-Check changes but differences in AD-Monitor.
7b8b86ab99 Timo* o pkg/ctrl & pkg/shelfice:
                   - generalize masking procedure for control parameters, fixes procedure for
                     ice-shelf controls ;
                   - add ability to control base 10 logarithm in generic control arrays ;
                   - add shiTransCoeffT, shiTransCoeffS, and shiCDrag as control variables ;
                   - add ability to compute shelfice freshwater and heat fluxes through ecco
                     package.
9c41af81f6 Timo* o store directives (model/src, pkg/exf, ...):
                   - By adding many store directives for variables after they have been computed
                     the corresponding s/r load_fields_driver, oceanic_phys, solve_for_pressure
                     no longer need to be called in the AD-routine forward_step_ad.
                     A as a consequence the forward part of forward_step is not recomputed,
                     and there are far fewer store statements in the AD-code.
                   - Most of the new store directives and many of the old ones are collected in
                     two new files "check_lev1_dir_forcing.h" and "check_lev1_dir_ocephys.h" to
                     avoid clutter in forward_step.F
                   - More store directives in pkg/exf allow it to store the forcing fields
                     instead of the level0/1 (e.g. aqh instead of aqh0 and aqh1), thereby
                     reducing the number of stored exf-forcing variables by about two. This is
                     also necessary to avoid calling load_fields_driver from forward_step_ad.
                   - Additional small tweaks of store directives in forward_step.F have the
                     effect that the recomputations are kept to a minimum in all of the AD
                     verification experiments (and in verification_other/global_oce_[llc/cs32])
                     and calling potentially expensive forward routines are not called (e.g.
                     do_stagger_fields_exchange, which involves unnecessary exchanges).
                   - Remove storage of gchemTendency in all checkpoint levels.
                   - Results unaffected except if using real*4 storage (isbyte=4, e.g., in
                     offline_exf_seaice, small changes in AD-monitor).
                 
2389d48735 Jean* checkpoint67y (2021/05/05)
c96d63ff5a Jean* o pkg/shelfice:
                   - Update kTopC when using SHELFICEMassStepping if ice-shelf retreat completely
                     from one column or advance to cover new grid-cell ; add 4 levels TAF storage
                     of kTopC (to prevent major recomputations).
                   - Also prevent ice-shelf mass to become negative.
70ceddf25f Timo* o pkg/mom_common & gmredi:
                   - Adjust Smag and Leith code for use in Adjoint:
                     a) protect against derivative of SQRT(0) in mom_calc_visc.F and
                        gmredi_calc_qgleith.F ;
                     b) add GM-Redi QG Leith routines to ad_diff lists.
0a637c269e Ou W* o pkg/gmredi:
                   - fix/remove 2 TAF recomputations in GMREDI_WITH_STABLE_ADJOINT code.
6463ae49bb Jean* o pkg/generic_advdiff:
                   - improve "slope" calculation in DST2 Flux-Limiter advection scheme to avoid
                     potential over-flow arithmetic in division by small slope (issue #459),
                     similar to what has been done in gad_dst3fl_*.F routines.
e9b2d4871a Timo* o pkg/diagnostics:
                   - use Integer*8 conversion in diagnostics_out.F to get time-record to write
                     in meta file (avoid integer overflow with large time & small diag-freq).
342b4ea43e Mart* o pkg/mom_common:
                   - initialise again hdiv in mom_calc_hdiv.F (in case it got dropped by TAF in
                     calling S/R).
dd54a44307 Mart* o model/src:
                   - fix a bug in convective_adjustment.F AD code by adjusting store directives
                     for theta and salt ; update experiment isomip reference AD output.
                   - a little bit of cleanup: remove unnecessary store directives and options.
9f55dac2bf Jean* o pkg/shelfice:
                   - change expression of pLoc in shelfice_thermodynamics.F to be simply the
                     weight of the ice-shelf (= shelficeMass * gravity) replacing inaccurate
                     estimate from "R_shelfIce". Add TAF directive storage of  prognostic
                     variable "shelficeMass" in all 4 checkpointing levels. Update all reference
                     output of experiments that use pkg/shelfice (isomip & shelfice_2d_remesh)
d81415648f Jean* o verification/testreport
                   - add ad-monitor of 3-D state variables to testreport summary output
638b7d19dd Jean* o pkg/ggl90:
                   - avoid division by zero in adjoint of S/R GGL90_CALC (sqrt related)
                 
aa29a5fd58 Jean* checkpoint67x (2021/04/12)
c512e371cc drin* o pkg/seaice:
                   - Addition to the sea ice package of 6 sea ice rheologies with different yield
                     curves and flow rules ;
                   - Add 4 new verification tests in offline_exf_seaice using new rheologies ;
                   - Update documentation with description of new rheologies and how to use them.
ba0b047096 Mart* o model, pkg & doc:
                   - replace all occurrences of incorrect "psu" and "PSU" by "g/kg" in units and
                     comments ; update the documentation accordingly.
698b6992ee Jean* o pkg/ctrl:
                   - move to pkg/ctrl the local copy of ctrl_map_ini_genarr.F from verification/
                     global_oce_biogeo_bling/code_ad/ with ptracers generic control. Improve for
                     general number of ptracers control.
                   - add missing diagnostics fill for diagnostics 'Um_ImplD' & 'Vm_ImplD' in
                     impldiff.F (otherwise not filled when pkg/autodiff is compiled).
9c8f6b90ac Jean* o pkg/autodiff:
                   Include TICES of pkg/seaice into StoreSEAICE:
                   - split AUTODIFF.h into two to be able to use nITD in the new AUTODIFF_STORE.h
                   - rearrange and cleanup declarations, add CPP flags ALLOW_SEAICE/OBCS/EXF ;
                   - clean up seaice section of autodiff_store/restore.F to remove unused storage
                     space ;
                   - changes AD results of global_ocean.cs32x15.seaice & seaice_dynmix, lab_sea &
                     lab_sea.noseaicedyn => output_adm updated.
cab62edf37 Ou W* o model/src:
                   - make sure the 3 recip_hFac{C,W,S} are reset after resetting the 3 hFac
                     in ini_nlfs_vars.F when using Non-Lin FreeSurf with pkg/autodiff compiled
                     (#define ALLOW_AUTODIFF): this fix problems in gradient-check if recip_hFac
                     is used, e.g., in one {PKG}_INIT_VARIA S/R.
a10c595eb6 Timo* o pkg/autodiff & diagnostics:
                   - Add interface routines to write to binary file and fill diagnostics of
                     single (or pair) of Adjoint variable.
                   - Rewrite addummy_in_stepping.F using set of new interface S/R to make it
                     more compact and easier to add new control variables.
                   - Add all current adjoint variables in addummy_in_stepping, ptracers_ad_dump,
                     seaice_ad_dump & exf_adjoint_snapshots_ad to work with diagnostics package.
                   - turn on Adjoint-variable diagnostics in adjoint verification experiments:
                     *) global_oce_biogeo_bling (with ptracers AD-var diagnostics) and
                     *) global_ocean.cs32x15.seaice (with seaice and exf AD-var diagnostics).
84cf551a2a Jean* o model/src + pkg/mom_common:
                   Fix AB time-stepping of QuasiHydrostatic with staggerTimeStep.
                   - involves new CPP option "ALLOW_QHYD_STAGGER_TS" for storage of previous
                     time-step Quasi-Hydro tendency to enable AB extrapolation in time when
                     using staggerTimeStep.
                   - field added to pickup file for restart ; allows to restart (but not perfect
                     restart) if field is missing and pickupStrictlyMatch=F.
                   - switch to staggerTimeStep=T in experiment "global_ocean.90x40x15.dwnslp"
                     that uses QuasiHydrostatic to test this code; update corresponding output
                     (as well as primary test output due to machine truncation).
                 o verification:
                   In experiments: global_ocean.cs32x15, isomip, obcs_ctrl and offline_exf_seaice
                     replace CPP flag ECCO_CTRL_DEPRECATED by the much nicer generic control
                     variables GENARR/GENTIM2D variant.
                     Also replace ECCO_CPPOPTIONS.h by CTRL/AUTODIFF/COST/ECCO_OPTIONS.h files.
                   This required a number of changes to the general code to make the generic
                     control variables work in a non-ecco context:
6b47d550f4 Mart*   - pkg/thsice: add AUTODIFF_OPTIONS.h and COST_OPTIONS.h header files to
84cf551a2a Jean*     numerous routines ;
6b47d550f4 Mart*   - pkg/seaice: mask tendencies of HEFF/AREA/HSNOW in seaice_growth_adx.F to
84cf551a2a Jean*     reproduce cost function values ;
                   - pkg/shelfice: enable GENARR/GENTIM2D methods ;
6b47d550f4 Mart*   - pkg/obcs: move reading control variable out of S/R obcs_prescribe_read into
                     S/R obcs_calc to be independent of parameter values unrelated to the
84cf551a2a Jean*     adjoint ;
6b47d550f4 Mart*   - pkg/ctrl: make generic control variable work without pkg/cal (works only for
                     time independent control variables), but issue a warning, bonus: make
84cf551a2a Jean*     ctrlprec a runtime parameter that defaults to 64 ;
6b47d550f4 Mart*   - pkg/ctrl: fix flow directives for S/R ctrl_bound_2d/3d and add tangent
84cf551a2a Jean*     linear versions of these subroutines ;
6b47d550f4 Mart*   - pkg/ecco: reorder CPP flags in ecco_cost_weights.F and remove unused
                     variable 'wbaro', move calling S/R cost_obcs out of ECCO_CTRL_DEPRECATED
                     code block in S/R ecco_cost_driver, reorganise CPP flags in
                     cost_averagesinit.F, include CTRL_OPTIONS.h wherever ECCO_OPTIONS.h is
84cf551a2a Jean*     included, because ECCO_CTRL_DEPRECATED is now set in CTRL_OPTIONS.h ;
6b47d550f4 Mart*   - model/src/the_main_loop.F: fix tape initialisation, bonus: suppress a
84cf551a2a Jean*     benign warning ;
6b47d550f4 Mart*   - for each of the verification experiments remove ECCO_CPPOPTIONS.h and
                     replace by CTRL_OPTIONS.h, CTRL_SIZE.h, sometimes COST/ECCO_OPTIONS.h,
84cf551a2a Jean*     EXF_OPTIONS.h, adjust data.ctrl, data.grdchk, data.ecco ;
6b47d550f4 Mart*   - for global_ocean.cs32x15 compile both variants by keeping
                     ECCO_CTRL_DEPRECATED in CTRL_OPTIONS.h and use runtime parameter ctrlUseGen
                     to switch between methods (in global_ocean.cs32x15.thsice). This involves an
                     extra (benign) recomputation warning in this verification experiment because
                     of an if statement with ctrlUseGen in ctrl_init_variables.F
                 
e856cdc61b Jean* checkpoint67w (2021/03/06)
4b1d371a30 Jean* o verification/global_ocean.cs32x15:
                   - fix Adjoint set-up by turning off CPP option "ALLOW_AUTODIFF_INIT_OLD" (that
                     was intended to put back an old bug) and update all 4 ADM and all 4 TLM
                     reference output files.
1e291a3f4c Jean* o pkg/exf:
                   - replace wrong CPP option EXF_SALTFLX with ALLOW_SALTFLX in exf_monitor.F.
a5ae6d70cb Jean* o model/src:
                   - Output dxF, dyF, dxV, and dyU fields to mdsio grid output files.
dc280143ed Oliv* o tools/build_options:
                   - improve intel optfile for engaging (linux_amd64_ifort+impi_engaging).
0d75a51072 Mart* o pkg/autodiff:
                   - Improve, extend & clean-up switch to a simpler advection-scheme in AD-Mode
                     with new parameter "useApproxAdvectionInAdMode to replace inAdMode:
                     * If useApproxAdvectionInAdMode is True and advection scheme is set to 33
                       use advection scheme 30 in AD-model in seaice_advection, gad_advection
                       and gad_calc_rsh ; model stops when parameters are set inconsistently.
                     * Defaults to False, but is reset to True if inAdExact = False to be
                       backwards compatible.
                   - Important change in the meaning of variable inAdMode: now it is always true
                     after calling S/R AUTODIFF_INADMODE_SET_AD and always false after calling
                     S/R AUTODIFF_INADMODE_UNSET_AD.
                     The non-intuitive flags inAdTrue and inAdFalse, which could be T or F, have
                     been removed from the code.
                   - Remove unnecessary TAF related and inAdMode code from seaice_lsr.F, remove
                     SOLV_MAX_TMP in LSR S/R and adjust SEAICElinearIterMax default accordingly.
                   - Change AD exp. global_ocean.cs32x15.seaice to test this new functionality;
                     gradient checks necessarily are poorer because AD advection is approximated.
1e25bc2551 Jean* o tools/build_options:
                   - update standard optfile "linux_amd64_gfortran" to enable to be used with
                     gfortran version 10 (or higher); update comments and clean-up for missing
                     "nf-config".
2ac762dbee Jean* o model/src & pkg/generic_advdiff:
                   - Implement simple isotropic 3D Smagorinsky diffusivity:
                     Smag diffusivity is assumed to be linearly dependent on 3D Smag viscosity
                     (just scaled by inverse of a constant Prandtl number); setting involves:
                      a) CPP Option: ALLOW_SMAG_3D_DIFFUSIVITY in CPP_OPTIONS.h (def. #undef)
                      b) switching on 3D Smagorinsky by setting "useSmag3D = .TRUE." in first
                         namelist of main parameter file "data" ; and, in the same namelist,
                      c) setting smag coeff. "smag3D_diffCoeff" for diffusivity (similar to
                      smag coeff. "smag3D_coeff" for viscosity), which results in constant
                      Prandtl number = smag3D_coeff/smag3D_diffCoeff.
                     Note: Since Smag3D_diffK is lagging by 1 time-step, needs to be stored
                     in pickup files (for restart) when using synchronous time-stepping.
                   - code is compiled in experiment tutorial_deep_convection and ready to use
                     except smag3D_diffCoeff setting in input.smag3d/data is commented out.
                   - also add few missing initialisations in "ini_dynvars.F" (just for
                     consistency with coding practice but no practical side effect).
fef3c33926 Jean* o pkg/ecco:
                   - fix type of argument in S/R MDS_READVEC_LOC call inside cost_gencost_moc.F
9b38007ffc Jean* o verification/lab_sea:
                   - change lab_sea.hb87 from testing EVP to testing aEVP with some sensible
                     parameters ; update reference output "output.hb87.txt"
df462307fb Timo* o pkg/ecco:
                   - Addition of meridional streamfunction maximum (MOC) as objective function
                      within ecco/gencost code ;
                   - MOC objective function tested in verification_other/global_oce_cs32.sens ;
                   - allows to compute sensitivity to hflux/sflux with prescribed atmospheric
                     state (not fluxes) with new flags CALC_HFLUX_SENS and CALC_SFLUX_SENS.
                 
830e1a2c4c Jean* checkpoint67v (2021/02/03)
66fe84e647 Oliv* o tools/build_options:
                   - add optfile for engaging similar to linux_amd64_ifort+impi but with -xAVX
d5254b4e3d Mart* o pkg/seaice:
                   - move store directives of uice/vice to after calling S/R SEAICE_DYNSOLVER to
                     avoid calling this routine in S/R seaice_model_ad which may trigger
                     potential recomputation problems (e.g., with non-exact AD) ;
                   - move if statement inside S/R SEAICE_BOTTOMDRAG_COEFFS : this enables to
                     remove storage of "CbotC" without triggering recomputations ; compile this
                     code in the AD-experiments of global_ocean.cs32x15 ;
                   - remove unnecessary store directives related to pkg/seaice ;
                   - fix/extend diagnostic "SIenph  " to work with all parameter configurations.
4240547d2d Mart* o pkg/autodiff: fix/improve viscFacAdj
                   - fix treatment of viscFacAdj in mom_vecinv.F by removing storage of 2D
                     viscosities if new flag AUTODIFF_ALLOW_VISCFACADJ is defined ;
                   - add a runtime parameter "viscFacInFw" in autodiff_inadmode_unset_ad.F to
                     replace hard-coded one ;
                   - apply viscFacAdj to both viscAh/4_D and _Z ;
                   - test compiling this code in tutorial_global_oce_optim.
f92f728545 Jean* o model/src:
                   - move if statement out of i/j-loops in solve_tridiagnoal/pentadiagonal.F:
                     *) this reduces TAF recomputation warnings by 4 ;
                     *) potentially easier to optimise/vectorise for some compilers.
                 o tools/build_options:
                   - adjust floating point options in: linux_ia64_ifort_ollie:
32ce3e9e96 Mart* o pkg/ctrl:
f92f728545 Jean*   - fix two bugs related to writing and reading control variables and
                     corresponding gradients:
                    a) replace too large loop range endrec by diffrec in ctrl_map_ini_gentim2d.F;
                    b) skip writing meta-files in REVERSE_SIMULATION mode (active_file_control.F)
32ce3e9e96 Mart* 
82ad7f2b88 Jean* checkpoint67u (2020/12/30)
616d857f4a Mart* o utils/python/MITgcmutils
f92f728545 Jean*   - add code to compute horizontal divergence of a vector field, gradient of a
                     scalar field, and averages to c-points on an llc grid.
4a08d54d3a Mart* o pkg/seaice:
f92f728545 Jean*   - fix bug in seaice_lsr, spotted by Martin Vancoppenolle, that lead to solving
                     stationary momentum equations (du/dt -> 0) for SEAICEnonLinIterMax>2 ;
                   - fix minor bug in seaice_bottomdrag_coeffs.F: replace OLy with correct OLx ;
                   - changing ordering of addition (to FORCEX,FORCEY) in seaice_lsr.F results in
                     output differences at machine truncation level: update referece output of
                     several experiments that use LSR solver.
8fc117ecb7 Mart* o pkg/autodiff: fix flow directives for self-adjoint cg2d
f92f728545 Jean*   - new self-adjoint cg2d routine cg2d_sad.F mimics AD-code, but neglects
                     (purposefully) the proper sensitivity propagation
                   - extra storage of cg2d solver coefficients and preconditioner is required
                   - change 2 AD-verification experments (global_ocean.cs32x15 and
                     global_ocean.cs32x15.seaice) to test this code a little better:
                     use full NLFS and nchklev_1 = 2
8fc117ecb7 Mart* 
8b41e6235c Jean* checkpoint67t (2020/11/30)
a67734cba4 Mart* o pkg/kpp:
                   - with CPP-option KPP_ESTIMATE_UREF, fix compilation errors + fix mixed layer
                     depth determination ;
                   - define KPP_ESTIMATE_UREF in verification/vermix ;
                   - a little bit of cleanup.
                 o pkg/seaice:
4dd39c50d9 Mart*   - small modifications of seaice_growth_adx.F to avoid recomputation warnings
                     and to avoid potentially inefficient code ;
                   - remove duplicate version of seaice_solve4temp ;
                   - exclude code of seaice_growth.F if ALLOW_SEAICE_GROWTH_ADX defined ;
                   - switch on SEAICE_USE_GROWTH_ADX AD in experiment offline_exf_seaice and
                     update "output_adm.txt".
76d0c749c4 Jean* o eesupp/src:
                   - add missing "stdio.h" in src code setdir.c
5dda98cf07 Jean* o tools/do_tst_2+2 & tst_2+2:
08bbaa9f0f Mart*   - bug fix: replace some non-standard sed command with POSIX compatible syntax
5dda98cf07 Jean*   - remove second blank at beginning of 2 new lines in file "data".
dae83699f8 Jeff* o doc:
                   - add new SO channel tutorial
0a8794f5ee Mart*   - update pkg/shelfice documentation
7a4abe9124 Jean* o optim:
                   - fix a small bug by initialising myX/YglobalLo=1 in optim_nummod.F
44af98263c Jean* o tools/do_tst_2+2:
                   - for sending restart test output, add same hack in "send" option as in
                     testreport, allowing to use "scp" (instead of an email).
                 o model/src:
                   - fix 2 missing TAF initialisation directives in file "the_main_loop.F";
                     this allows to use TAF recent version 5.0.9 (that does check for missing
                     initialisation).
6de16ba22c Jean* o pkg/seaice:
                   - fix diagnostics additions (from PR #348) for case _RS is real*4.
                 
ede86f4989 Jean* checkpoint67s (2020/07/30)
b9dadda204 Mart* o eesupp/src:
                   - Improve formatting of output for large grids and many processors:
                     adjust formats to actual length of nPx*nPy or Nx and Ny but
                     keep minimal lengths to avoid changing the format for smaller domains;
                   - also increase number of digits for printing tile & proc number in pkg/exch2
                     log files and report to STDOUT.
a284455135 Matt* o pkg/bling:
                   - cleaning: remove USE_QSW_Z code ;
                   - few more CPP options (NEW_FRAC_EXP & SIZE_DEP_LIM defined, SIZE_NUT_LIM
                     undef) related to phytoplankton size and sinking organic matter ;
                   - fix tiled TAF storage directives (were not right for multi-tile per proc);
                     update ADM reference output of experiment global_oce_biogeo_bling (now
                     gradient check are identical whether run on 1 proc - 4 tiles or 4 procs
                     1 tile each).
5867b94c2f Mart* o pkg/seaice:
                   - Replace hard-coded minimum for DWATN by runtime parameter "SEAICEdWatMin":
                     * allows to have zero drag by setting both SEAICEdWatMin and
                       SEAICE_waterDrag to zero. Non-zero drag had been implemented because
                       previous LSR solver could not handle zero entries on the main diagonal.
                     * this fixes a bug (unexpected behavior) reported at MITgcm-support by
                       Kaley Shrestha, but also allows to modify the somewhat arbitrary
                       default minimum value of SEAICEdWatMin = 0.25 ;
                     * freedrift code still requires non-zero drag coefficients,
                       S/R SEAICE_CHECK catches this case.
3770720c1f Jean* o verification/*/packages.conf
                   - Cleaning verification experiment "packages.conf":
                     1) add a 1 line description at the top
                     2) use pkg group "adjoint" in some experiments
                     3) use similar ordering of pkgs in packages.conf:
                       a) eesupp pkgs (e.g., exch2, coupler-pkgs)
                       b) dyn-core pkgs (e.g., gfd pkgs, mom pkgs, cd_code, gad, obcs ...)
                       c) SGS-scheme (+ atm physics) pkgs (filters, gmredi, vert.mixing ...)
                       d) forcing pkgs (e.g., rbcs, exf, cal, ebm, cheapaml)
                       e) other component pkgs (e.g., ice, land, ptracers, biogeo, flt)
                       f) diagnostics pkgs (e.g., sbo, profiles, layers, diagnostics, timeave)
                       g) I/O pkgs, e.g., mnc (+ mypackage at the end)
                       -- blank line --
                       h) adjoint related pkgs (e.g., autodiff, ctrl, cost ...)
                     4) remove unused pkgs: kpp, sbo, timeave ; this results in reduced number of
                        TAF recomputation warning for AD exp: bottom_ctrl_5x5 & global_ocean_ebm;
                 o tools/build_options:
                   - add a symbolic link for optfile "linux_amd64_ifort" to "linux_amd64_ifort11"
7deacd640c Jeff* o doc:
                   - fix link and plot in doc/examples/baroclinic_gyre
5fe78992ba Mart* o pkg/seaice:
                   - Add new mechanical energy diagnostics ;
                   - Move computation of stress diagnostics to seaice_dynsolver.F ; this change
                     affects diagnostics SIpress, SItensil, SIpress, SIzeta, SIdelta, SIshear,
                     because they are now filled after the current time step update, when they
                     are actually available. Note: previously, for the first time step, these
                     variables (and diagnostics) were not properly defined (or zero).
                 
2bc8ced27d Jean* checkpoint67r (2020/06/04)
cd9df85f4a Jean* o pkg/ecco:
                   - fix character length when checking for m_trHeat, m_trSalt & m_horflux_vol.
04904a066e Timo* o pkg/autodiff:
                   - add active read and write routines for global 1D vectors, to be used for
                     compressed cost function vectors (note: not used yet, example to come soon).
42032b6c9d Jean* o model/src & pkg/exf:
                   - Reference atmospheric pressure for seawater EOS was assumed but was not
                     explicitly set. New constant "eosRefP0" is added to make this more clear ;
                   - Add main model reference surface pressure (surf_pRef) so that pLoad
                     is now defined as the atmospheric pressure anomaly relative to surf_pRef ;
                   - Account for differences in 2 ref pressure in EOS S/R ;
                   - Fix few EOS references (in comments) ; fix and simplify S/R EOS_CHECK ;
                   - Keep exf "apressure" field unchanged (still full atmospheric surface
                     pressure) but now initialised to "surf_pRef" and fill "pLoad" with atmos.
                     pressure anomaly relative to surf_pRef.
07e785229e dngo* o pkg/streamice:
                   - add option to specify "regularised coulomb" sliding law to better reflect
                     dependence on subglacial water pressure close to the grounding line ;
                   - above requires CPP option (due to new arrays) STREAMICE_COULOMB_SLIDING
                     and r/t param streamice_allow_reg_coulomb ;
                   - add diagnostic for streamice melt rate (BDOT_SI )
                   - add parameter STREAMICEAdotFile to specify surface mass balance ;
                   - add parameter streamice_maxnliter_Petsc to specify maximum no. of
                     linear solves using PETSc in a single time step (not incl. in doc
                     since PETSc is not part of standard build) ;
                   - update references to PETSC_DEFAULT_DOUBLE_PRECISION to PETSC_DEFAULT_REAL in
                     streamice_cg_solve_petsc.F; former seems to be deprecated in some versions
                     of PETSc while latter is backward compatible ;
                   - for BJACOBI (block jacobi) PETSc preconditioner, use PCICC (incomplete
                     cholesky) rather than PCILU (incomplete LU) ;
                   - for BJACOBI add parameter streamice_petsc_pcfactorlevels to control level
                     of factor fill-in.
                 
18fff58a99 Jean* checkpoint67q (2020/03/19)
e1e000e69f Jean* o pkg/shelfice, remeshing code:
                   - simplify/clarify merging S/R call sequence: all done/called from main
                     remeshing S/R SHELFICE_REMESHING :
                       - remesh_c_mask : now only update geometry & surface fields at grid-cell
                         center and compute merging remeshing weights for tracers;
                       - remesh_uv_mask : now only update geometry & surface fields at grid-cell
                         edges and prepare merging remeshing weights for velocity;
                         also fix thin-wall setting without reading again thin-wall files ;
                       - calls directly CALC_SURF_DR and UPDATE_SURF_DR
                   - move adjustment of state variables into (new) dedicated
                     S/R SHELFICE_REMESH_STATE and change loop range so that no further EXCH
                     calls are needed ; also add missing code for ALLOW_ADAMSBASHFORTH_3 ;
                   - move update of Rmin_surf (formerly in shelfice_remesh_rminsurf.F)
                     before first call to S/R CALC_SURF_DR (where Rmin_surf is used)
                     and in-line S/R SHELFICE_REMESH_RMINSURF into shelfice_remesh_uv_mask.F
                   - add argument "wFld" and "myIter" to S/R SHELFICE_REMESH_CALC_W
                   - fix so that it compiles and run when _RS is real*4 (#undef REAL4_IS_SLOW).
7d270b85fa Jean* o model/src:
                   - Fix for special value of R_low with pkg/shelfice:
                     When bathymetry field value is just rF(k)+hFacMindrF(k)/2, R_low will
                     deepen (by hFacMindrF(k)/2 ) to satisfy the hFacMin criteria. In this case:
                       o if R_shelfIce value (from file) was exactly equal to initial bathymetry
                         depth, original code would create a very thin grid cell of thickness
                         factor hFacMin. Fix this problem by preventing deepening of R_low when
                         initial R_low >= R_shelfIce.
                       o if R_shelfIce value is deeper than original value, the problem does not
                         show up for hFacC (column remains dry) but because of erroneous resetting
                         of rSurfW/S (to be the MAX of rSurfW/S, rLowW/S) this could trigger the
                         same type of artificial deepening at Western and Southern column edges
                         (for hFacW and hFacS). Remove early resetting of rSurfW/S to fix this
                         second issue (see issue #324).
                   - Simplify correction for miss-match between Sum of level thickness at
                     W & S edges and top minus bottom r-position: only adjust rSurfW/S
                     (and not rLowW/S) as done previously for the case useMin4hFacEdges=T;
                   - Non-lin free-surf in r coordinate: for consistency, use rSurfW & rSurfS
                     (which account for adjustment, if any) instead of MIN of adjacent Ro_surf
                     when calculating new thickness factor: hFac_surfW & hFac_surfS ;
                   - Make thin-wall implementation available for sigma-coordinate ;
                   - Record thin-wall position as kSurfW/S = Nr+2 (instead of = Nr+1 for
                     a dry column).
                 o tools/build_options:
                     rename optfile "linux_amd64_ifort" to "linux_amd64_ifort10-"
9acfcdc58c Jeff* o verification:
                   - new reentrant channel tutorial experiment, doc will follow soon.
                 
260efc476e Jean* checkpoint67p (2020/02/12)
bdf98ce602 Edwa* o model/src:
af65683301 Jean*   - rename array "surfaceForcingTice" to "adjustColdSST_diag" and change the
                     description to better reflect what it is: a diagnostic for SST adjustment.
                   - remove most of the TAF storage directive for "adjustColdSST_diag" that were
                     not necessary once it's properly initialized.
bdf98ce602 Edwa* o pkg/gmredi:
                   - improve error handling
                   - additional QGLeith config checks
                   - standardise variable name capitalizations
af65683301 Jean* o pkg/mom_common, mom_vecinv, mom_fluxform:
bdf98ce602 Edwa*   - protect QGLeith code with ifdefs
af65683301 Jean*   - additional QGLeith config checks (in model/src/config_check.F)
40933c9dd3 Jean* o verification:
                   - rename dir "rotating_tank" to "tutorial_rotating_tank".
7a05b40c01 Jeff* o pkg/flt:
                   - improve pkg/flt doc and CPP brackets
1c8cebb321 Jeff* o doc:
                   - new front-page to tutorial chapter, also listing all verif experiments ;
                   - add new section in ch3 about input file format.
                 
45ac9863cf Jean* checkpoint67o (2019/12/23)
9952f046d7 dngo* o pkg/shelfice:
75f34d1991 Jean*   - implement implicit ice-shelf drag, in the same way as implicit bottom drag,
                     using the same run-time switch "selectImplicitDrag".
                   - change 3-D diagnostics of ice-shelf drag tendency (SHIUDrag & SHIVDrag) to
                     2-D diagnostics of ice-shelf drag stress (SHI_TauX & SHI_TauY).
                   - update 4 forward reference output files of experiment "isomip".
                   - switch on implicit drag in experiment shelfice_2d_remesh (to get it tested).
                 o pkg/shelfice:
9952f046d7 dngo*   - addition of functionality described in Jordan et al (2017), "Ocean-Forced
                     Ice-Shelf Thinning in a Synchronously Coupled Ice-Ocean Model";
                     allows "remeshing" of grid-cells in vertical in response to changing free
                     surface due to ice shelf mass change:
                     At SHELFICEremeshFrequency interval, checks for cells that are too thick or
                     too thin and adjusts R_surf & eta accordingly, and updates state variables ;
                   - new main remeshing S/R SHELFICE_REMESHING calling additional S/R in files
                      shelfice_remesh_c_mask.F, shelfice_remesh_uvmasks.F,
                      shelfice_remesh_rminsurf.F and shelfice_remesh_calc_w.F
                     and called directly from top of FORWARD_STEP ;
                   - all new code and call protected under #define ALLOW_SHELFICE_REMESHING ;
                   - add field "R_shelfice" to pkg/shelfice pickup files for restart ;
                   - verification/shelfice_2d_remesh/*: new verification experiment
                     to test remeshing functionality.
                   - additional options to SHELFICEboundaryLayer:
                     a) SHI_withBL_uStarTopDz, to compute uStar from uVel,vVel avergaged over
                        top Dz thickness first and then average horizontally ;
                     b) SHI_withBL_realFWflux, to use real Fresh-Water flux (and adjust
                        advective surface flux) with SHELFICEboundaryLayer.
f4206cb08a Jean* o pkg/ecco:
                   - change S/R ECCO_READWEI to read in uncertainty file and compute weight
                     as 1/sigma if nosumsq is provided as a preprocessing option, or 1/sigma^2
                     if not. This is the expected behavior based on the "generic cost function"
                     section of the documentation.
fb6db187ae Jean* o verification:
                   - new experiment "global_oce_biogeo_bling" move here from verification_other.
b62dee2337 Jean* o pkg/cheapaml:
                   - rewrite advection-diffusion of BL atmospheric variables to use Flux-Form
                     formulation. Affects results (unless cartesian grid is used).
                   - apply special treatment of diffusive flux at Northern & Southern boundaries
                     only if .NOT.cheapamlYperiodic (previously unconditional, gad_diff_2d_y.F);
                   - Skip calls to AB-2 when using "useFluxLimit=T" option since advection scheme
                     used then is DST3FL which does not need AB at all. Affects results if
                     useFluxLimit=T" is used.
                   - clean-up (rename/remove all "gad_*.F" files) and simplify by using few more
                     pkg/generic_advdiff S/R (instead of local copies).
                   - update output of experiment "cheapAML_box" (and in separated PR, experiment
                     "offline_cheapaml" in verification_other)
c8767af0b6 Timo* o pkg/ctrl:
                   - Tangent Linear mode: allows to initialise g_xx fields with user-provided
                     g_xx file (default unchanged, i.e., initialised to zero).
                 
6bdcb6b877 Jean* checkpoint67n (2019/11/26)
9906b3fb84 Jean* o pkg/ctrl:
                   - add doc & storage dir for initial velocity control option.
788c57c2b5 owan* o pkg/autodiff:
                   - sort out checkpoint_lev1_dir header file for when pkg/ecco is used
                     with #undef NONLIN_FRSURF ; similar update in pkg/cd_code & pkg/ptracers;
                     this fixes issue #68.
                   - clean-up and fix pkg/autodiff checkpoint_lev?_dir to be able to compile
                     with #define EXCLUDE_FFIELDS_LOAD.
540437b870 Jean* o model/src:
                   - allows to specify time-dependent (periodic) geothermal heat-flux
                     with "periodicExternalForcing".
6dfad62739 Jean* o pkg/diagnostics:
                   - add diagnostics for thickness factor hFacC, hFacW & hFacS.
8dfb9d9b4c Jean* o pkg/dic:
                   - Fix carbonate chemistry coefficient issues (#269). This affects results when
                     either CARBONCHEM_TOTALPHSCALE or CARBONCHEM_SOLVESAPHE are defined.
                     Update output of verification experiment "so_box_biogeo".
a435e833b1 Mart* o doc:
                   - fix description of zero-layer thermoydnamics
94f0474fee Jean* o verification/*/results/output.txt:
                   - update reference machine from baudelaire.mit.edu (running fc13)
                     to villon.mit.edu (running Ubuntu 18 LTS) and update few output.txt
                   - change travis Docker settings accordingly + update documentation.
                 
5523dc659e Jean* checkpoint67m (2019/10/16)
d67096e55c Jeff* o doc/examples:
                   - Convert remaining old doc tutorials from latex to rst files and add them
                     to current MITgcm documentation.
18d2df1f7f Jean* o pkg/ptracers:
                   - new diagnostics Tp_gTr01, ... for ptracer total transport tendencies
                     (before gchem_forcing_sep); this includes advection and diffusion terms,
                     but also anything added in gchem_add_tendency.
94151a9b18 Jeff* o doc & verification/tutorial_baroclinic_gyre:
                   - split doc for tutorial experiments into separate files
                   - update configuration for baroclinic gyre tutorial
                   - update documentation for baroclinic gyre tutorial
                   - formatting and font changes in algorithm chapter
5752d89cac Ed D* o doc:
                   - add rtfd config file to control build behaviour and options.
                 
b6c7ea7cf3 Jean* checkpoint67l (2019/08/29)
b90cc7fedb Ed D* o QG-Leith viscosity:
                   - pkg/mom_common: bug fix for QG Leith viscosity
                   - pkg/gmredi: bug fix for QG Leith coefficient
                   - update output of experiments MLAdjust.QGLeith & MLAdjust.QGLthGM
abfe198bce Mart* o pkg/obcs:
                   - new feature to balance surface flux of freshwater or ice shelf mass by
                     outflow through open boundary conditions:
                     * requires splitting S/R obcs_calc to move call to S/R obcs_balance and S/R
                       obcs_add_tides after S/R external_forcing_surf call in do_oceanic_phys.F
                     * add contribution for EmPmR of the current time step and the
                       shelficeMassDynTendency (new S/R shelfice_netmassflux_surf).
                   - add new secondary test exp. "isomip.obcs" to text this new feature.
a004e35329 Ed D* o pkg/mom_common & model/src:
                   - new S/R MOM_U/V_BOTDRAG_COEF used both for explicit and implicit bottom drag
                     computation (thus replacing both MOM_U/V_BOTTOMDRAG in explicit case and
                     MOM_U/V_BOTDRAG_IMPL in implicit case) to return a drag coefficient.
                     This modification affects results at machine truncation level.
                   - change diagnostics 'Um_dPHdx' & 'Vm_dPHdy' to 'Um_dPhiX' & 'Vm_dPhiY'
                     for full pressure gradient tendencies (including surf & NH contribution);
                   - remove bottom drag tendency diags (UBotDrag & VBotDrag); add bottom stress
                     diagnostics and implicit viscous tendency diagnostics, both accurate also
                     if using implicit bottom drag (selectImplicitDrag=2).
d7b89710f7 Oliv* o pkg/exf:
                   - re-arrange EXF interpolation header files: move setting of "MAX_LAT_INC"
                     from EXF_PARAM.h to EXF_INTERP_SIZE.h (more logical place). But to avoid
                     having to include EXF_INTERP_SIZE.h each time EXF_PARAM.h is included,
                     move EXF interpolation parameters outside EXF_PARAM.h in new header file:
                     EXF_INTERP_PARAM.h
                   - add S/R to define input grid setting (stored in EXF_INTERP_PARAM.h) to be
                     used for EXF interpolated fields as default input grid.
ebbe8cf013 Jean* o compon_interf pkgs:
                   - fix bi loop range in few initialisation subroutines (2 in each pkg),
                     fixing issue #270
                 
02b4c39948 Jean* checkpoint67k (2019/07/19)
80f7dda68b Jean* o model/src:
                   - fix format in printing 1 error message from S/R SET_PARMS
9d49c8b5d1 Matt* o pkg/bling:
fbb6fdf8a5 mmaz*   - add missing components of SIBLING
                   - add Manizza et al 2005 light attenuation. Enable with PHYTO_SELF_SHADING
c9238c91a3 Jean*   - Replace hard coding of max mixing depth with runtime parameter MLmix_max
fbb6fdf8a5 mmaz* o pkg/ctrl:
796fd0e220 Jean*   - fix reccord number setting in S/R CTRL_GET_GEN_REC ("startrec" substracted
                     for no reason).
bc74f5a574 Jean* o doc:
                   - add a sub-section about optim_m1qn3
6c44cdc71d Jean* o pkg/ctrl:
                   - fix in rescaling option for control vector ("doscaling/noscaling" option,
                     S/R CTRL_MAP_INI_GENARR & CTRL_MAP_INI_GENTIM2D); proper counting of
                     non-zero control vector when weight-mask is different from ocean-mask.
                     Expect differences only when (a) weight-mask is different from ocean mask
                     and (b) xx_genarr2d_preproc='noscaling' (doscaling=.false.).
899473f061 Jean* o pkg/exf:
                   - new run-time parameter "diags_opOceWeighted" (default=T) to weight some exf
                     surface diagnostics (all net and upward fluxes) with open-ocean fraction.
                     Option is turned off when no sea-ice pkg (seaice or thsice) is used.
                   - new S/R EXF_WEIGHT_SFX_DIAGS to do some exf diags as open-ocean weighted
                     according to input argument ice fraction. Called from the right location
                     in time-stepping to get diagnostics that are consistent with wind-stress
                     and buoyancy fluxes that ocean receive.
                 
d1306ef812 Jean* checkpoint67j (2019/06/18)
e0f9a7ba0b Matt* o pkg/bling:
                   - Cleanly seperate NBLING (default), BLING_V1 (enabled with USE_BLING_V1),
                     and also add Silica option (enabled with USE_SIBLING);
                   - New algorithm for calculating mixed layer depth (old enabled with
                     BLING_USE_THRESHOLD_MLD);
                   - Options for updated carbon chemistry (from J. Lauderdale) enabled with
                     CARBONCHEM_SOLVESAPHE or CARBONCHEM_TOTALPHSCALE ;
                   - And other minor spring cleaning changes;
                   - update calls in pkg/gchem for BLING(V1) or NBLING (with Silica).
352c2064d4 antn* o pkg/salt_plume:
                   - fix calculation index range in salt_plume_apply.F (#ifdef SALT_PLUME_VOLUME)
3a78078268 Aras* o pkg/ecco:
                   - fix/simplify local file names in ecco_cost_init_barfiles.F (within
                     #ifdef ALLOW_GENCOST_CONTRIBUTION ).
7843dde2de jm-c  o pkg/mom_vecinv:
                   - add 2 Coriolis schemes which satisfy: d/dt U = f V ; d/dt V = -f U
                     (with U,V = vertically integrated flow).
                   - add new run-time coriolis-scheme selector "selectCoriScheme" to replace
                     "useJamartWetPoints" and "useEnergyConservingCoriolis"; but keep these 2
                     in namelist (backward compatible) to set "selectCoriScheme" accordingly.
77f894c517 Timo* o pkg/ctrl:
                   - Fix bug in ctrl_map_ini_genarr.F regarding missing initialization of
                     igen_uvel & igen_vvel (just like all the other variables).
6acab690ae Jona* o pkg/dic:
                   - Implement SolveSAPHE (Munhoven, 2013), a robust algorithm to calculate
                     oceanic pH/pCO2 ; compiled when CARBONCHEM_SOLVESAPHE is defined (in
                     DIC_OPTIONS.h) and used when (in data.dic) selectPHsolver > 0 ;
                     Add several options for selecting dissociation coefficients, available
                     when CARBONCHEM_SOLVESAPHE is defined.
                   - Change experiment "so_box_biogeo" to compile with CARBONCHEM_SOLVESAPHE
                     defined and add secondary test "saphe" (dir: input.saphe) to this experiment
                     to test GENERAL pH solver (selectPHsolver=1).
dc54d31829 Ian * o pkg/seaice:
                   - add alternative version of seaice thermodynamics two routines that provide
                     accurate adjoint. Switched by defining CPP option: ALLOW_SEAICE_GROWTH_ADX
66046ae6a1 Brun* o pkg/mdsio:
                   - in meta file, write number of records with longer format (10 digits vs 5
                     previously) to accommodate large number of floats.
                 
aa900cad7e Jean* checkpoint67i (2019/05/08)
f2a88c9ff8 jm-c  o autofdiff:
                   - fix to avoid TAF recomputations in ggl90 & salt_plume pkgs
                     and in model/src PCELL_MIX_CODE.
f59d76b0dd Ed D* o pkg/mom_common & pkg/gmredi:
                   - add quasi-geostrophic variant of Leith dynamic visocity
                   - use the quasi-geostrophic Leith dynamic visocity as GM diffusivity
                   - new verification experiment to test QG-Leith (variant of MLAdjust)
                   - updated documentation about new option
39cd4ae623 Ed D* o pkg/seaice:
                   - add Hlimit to seaice namelist in data.seaice
                   - use verification seaice_itd.thermo to test this feature with default
                     values (experiment does not change)
                   - clean up related output in seaice_init_fixed.F a little
aad71d9e67 Mart* o verification/testreport:
                   - for file run_ADM_DIVA, fix sed search syntax so that it works with BSD-sed
6b48f6d519 Mart* o model/src:
                   - fix small bug (wrong balanceEmPmR report) in config_summary.F, spotted by
                     Christopher Wolfe ; add report of balancePrintMean to summary.
1f2be90d9e Ed D* o verification/verification_parser.py
                   - ensure Travis test suite fails when a build or a run fails.
                 
fba140841d Jean* checkpoint67h (2019/03/21)
db0c10dd53 jm-c  o tools/genmake2:
                   - fix option "-nocat4ad" for latest version of TAF: now needs to add TAF
                     option "-fixed" to process *.flowdir files with newer (after 4.1.1) version
                     of TAF (otherwise assumed now to be in free format).
b98355c8c5 jm-c  o model/src:
dc54d31829 Ian *   - remove argument tFld & sFld from S/R CALC_PHI_HYD and from 2 related S/R
bcbb675387 jm-c  o tools/genmake2:
                   - allow to skip "check_fortran_compiler" part (as, e.g., in opt-file:
                      tools/build_options/linux_ia64_cray_archer).
1c87316fba Jeff* o verification/tutorial_barotropic_gyre:
                   - add 1rst tutorial documentation to new manual and update corresponding setup
8b07a23c92 Jean* o pkg/atm_phys:
                   - add 3-D input file for stratospheric ozone
                   - add code from Matt Kasoar for SW absorption by stratospheric ozone,
                     based on following papers:
                     Lacis and Hansen (JAS, 1974) and Forster and Shine (JGR, 1997).
                   - turned on using 2 local run-time parameter: ozone_in_SW (downward)
                     and two_stream_SW (also in upward); default are off.
                   - clean up S/R "radiation_up": rename "net" to "flux_lw" (better name)
                     and remove un-used local (dyn-allocated) arrays.
                   - also avoid division by zero in Rel-Humid diagnostics (atm_phys_driver.F)
bfae2ee370 jm-c  o pkg/seaice:
                   - fix missing update of sIceLoad in the case usePW79thermodynamics=F.
80d7ca01bb Jona* o pkg/dic:
                   - Adjust unit conversions for dissociation coefficients aks, aksi, and akf
                     (#define CARBONCHEM_TOTALPHSCALE).
516b08a580 jm-c  o tools/genmake2:
                   - improve Fortran Compiler check, section: running MPI executable ; also
                     refine the "conclusion" printed message.
                 
29a542dcab Jean* checkpoint67g (2019/01/03)
                 o doc:
                   - add documentation for pkg/streamice
148dd84005 jm-c  o model/src:
                   - change ordering of pkg calls in initialisation: streamice / shelfice and
                     then seaice / salt_plume / thsice;
                   - fix thin ice-shelf issue with pkg/seaice ; implemented by updating (recently
                     added) seaice masks (requiring new ordering of calls).
c87895a3f5 jm-c  o pkg/shelfice:
                   - allow to include thin ice-shelf (i.e., such that hFacC(k=1) > 0 ) when
                     using pkg/thsice, by preventing seaice to form where there is an ice-shelf.
                   - prevent short-wave heating below an ice-shelf (previously still happening
                     below thin ice-shelf); also fix Qnet there (but only for diagnostics).
ec0d7df165 Mart* o pkg/seaice:
                   - move initialisation of masks and metric coefficients and KGEO from
                     seaice_init_varia.F to seaice_init_fixed.F
                   - remove all reference to global masks maskC/maskW/maskS:
                    * introduce new masks SIMaskU/V
                    * initialise HEFFM/SIMaskU/V as copies of surface maskC/W/S
                    * replace maskC/W/S with HEFFM/SIMaskU/SIMaskV; in some places this requires
                      including SEAICE.h and as a consequence renaming a few local variables to
                      avoid name overlap
                   - remove TAF storage directives for "heffm" (no longer needed) and simplify
                     seaice calls and TAF storage dir in do_oceanic_phys.F
73c0056d2e Oliv* o pkg/monitor:
                   - fix local array declaration in mon_stats_latbnd_rl.F
49fc9b4095 Oliv* o tools/example_scripts:
                   - remove all files in tools/example_scripts/
                     (updated testing scripts are all in MITgcm_contrib/test_scripts)
                 o verification:
                   - remove un-tested experiments: cpl_atm2d+ocn, tidal_basin_2d and
                     tutorial_offline
                 
9636f5994f Jean* checkpoint67f (2018/11/23)
83ddf5a6c6 Mart* o pkg/seaice:
                   - add advection ppm and pqm advection schemes ;
                   - test new scheme in verification/offline_exf_seaice.dyn_lsr
                 o pkg/generic_advection:
                   - regularize ppm and pqm advection schemes:
                   - replace unsafe division in the case of numerical underflows by
                     regularized expression sign(max(abs(uCFL),1.d-20),uCFL) and similar,
                     in anology to other advection routines, e.g. gad_os7mp_adv_x/y/z.F
                   - affects verification/advect_xz at truncation level -> updated
                 o eesupp & model:
                   - add entry points for 2-way nesting pkgs.
95edbf0004 chri* o pkg/dic:
                   - fix out-of-bounds error in S/R CAR_FLUX_OMEGA_TOP (#define CAR_DISS)
68432e7ba3 dngo* o pkg/streamice:
                   - new implementation of grounding line smoothing by smoothing of basal
                      traction in partly grounded cell, in streamice_upd_ffrac_uncoupled.F
                   - rename CPP directives: previous smoothing functionality now enabled with
                     STREAMICE_SMOOTH_FLOATATION2, new functionality enabled via
                     STREAMICE_SMOOTH_FLOATATION
                   - affects verification/halfpipe_streamice, FWD, TAF and OpenAD adjoint.
fcc5c8b844 jm-c  o pkg/atm_phys:
                   - change IR absorption formulation regarding the dependence on Water-Vapor
                     in the case wv_exponent = -1 ; update results of experiment "atm_gray.ape"
                     from verification_other repos.
e0fa1cecbf Mart* o pkg/seaice: clean up advection and SEAICE_ITD
                   - make SEAICEmultiDimAdvection a global variable that is set in
                     seaice_readparams.F
                   - do not allow SEAICE_ITD with old 2nd order advection scheme anymore
                   - re-organize SEAICE_ITD code in seaice_advdiff.F
                   - make it possible to compile pkg/seaice without pkg/generic_advdiff
52dd931a85 Timo* o pkg/autodiff:
                   - created addummy_for_etan.F to correctly print adjoint variable for etaN
                 
901d0c4f7d Jean* checkpoint67e (2018/10/16)
                 o pkg/seaice:
                   - fix possible division by zero if LSR_mixIniGuess > 0
85b328ee93 dngo* o pkg/streamice:
                   - fix bugs relating to ice front advance:
901d0c4f7d Jean*     streamice_advect_thickness.F -- overlap update of array passed to
85b328ee93 dngo*      streamice_adv_front which was leading to spurious ice area values
                     streamice_init_varia.F -- proper initialisation of area_shelf_streamice
                      which is used for ice front advance (only affects diagnostics)
1c882252b0 Ed D* o verification/*/data
                   - set "rhoConst" instead of "rhoNil" (unless using Linear EOS)
                   - for net surface heat flux, set "surfQnetFile" instead of "surfQfile"
                     (unless net surface shortwave is also specified).
                   - fix OpenAD/input_oad.kpp set-up where net surface heat flux was used
                     as net heat-flux minus short-wave and update the output.
                 
2df144911f Jean* checkpoint67d (2018/09/04)
dcaaa42497 Jeff* o doc:
2df144911f Jean*   - update few pieces of documentation including addition (in "getting_started"
dcaaa42497 Jeff*     section) of main CPP OPTIONS description and main code full list of
                     run-time parameters.
a60aeb96a0 Oliv* o pkg/generic_advdiff:
                   - move masking of (explicit) vertical diffusive flux to S/R that compute each
                     contribution (pass maskUp as a new argument): This ensures that diagnostics
                     of explicit vertical diffusive flux are properly masked.
faf4966244 jm-c  o tools/do_tst_2+2
                   - Fix up to use absolute paths for results directories.
b8665dacca Mart* o pkg/seaice: some new and hopefully more sensible defaults:
                   - SEAICEscaleSurfStress = .TRUE.
                   - SEAICEaddSnowMass = .TRUE.
                   - SEAICEadvScheme = 77
                   - SEAICE_useMultDimSnow = .TRUE.
                   - SEAICE_Olx/y = Olx/y - 2
                   - SEAICEetaZmethod = 3
                   - SEAICE_drag = 0.001
                   - CPP-flag SEAICE_ZETA_SMOOTHREG defined by default
                   - change SEAICE_waterDrag default to 5.5e-3 and add reference density
                     rhoConst to scale it. Add a warning if SEAICE_waterDrag > 1.
                     This change also involves a slight re-organization (= simplification)
                     in seaice_oceandrag_coeffs.F
                   - all verification experiments are affected, so that all but four
                     data.seaice are adjusted to restore the old defaults. The four experiments
                     that use the new defaults are
                     + global_ocean.cs32x15.seaice
                     + offline_exf_seaice
                     + offline_exf_seaice.dyn_jfnk
                     + offline_exf_seaice.dyn_lsr
                   - updated documentation
b4d50d3323 Oliv* o pkg/dic:
a60aeb96a0 Oliv*   - Promote constants in S/R CARBON_COEFFS_PRESSURE_DEP and
                     S/R CAR_FLUX_OMEGA_TOP to double precision.
1cf5741c70 Jean* o pkg/seaice:
                   - fix bug in seaice B-grid code (call to seaice_advdiff, see issue #134);
                     Note: B-grid code not tested in any verification exp. (only compiled in one)
                     so no need to update any output.txt
a5ec81ed49 Timo* o pkg/diagnostics:
                   - Print adjoint variables for theta, salt, uvel, vvel, wvel, and etan
                     through diagnostics package.
4f8baf0351 Kait* o pkg/shelfice:
                   - fix ice shelf mask for very-thin ice shelf case, when hFacMin
                     and hFacMinDr criteria leave no room for ice (hFac(k=1)=1).
                     Note: thin ice-shelf that results in 0< hFac(k=1) <1 still need
                     to be fixed when using any seaice pkg.
736e27304c Timo* o pkg/ecco:
                   - Replace "mskTrVol" and "gencost_errfile" with "gencost_mask" in
                     "cost_gencost_transp", mirroring "m_horflux_vol".
                   - Document and warn user (via STDERR) of potential issues with using
                     "cost_gencost_transp" to compute volume, heat, or salt transport.
                 
00ab3a8557 Jean* checkpoint67c (2018/06/26)
63eaf06b6a Jean* o pkg/generic_advdiff:
                   - Add per tracer run-time param to switch on/off Smolarkiewicz-Hack:
                     Run-time switch for Temp & Salt are set from main param file "data"
                     (default value = FALSE); and for pTracers, they are set from parameter
                     file "data.ptracers" (default value = TRUE).
                   - Add a test in verification exp. global_ocean.90x40x15.down_slope for
                     Smolarkiewicz-Hack (switched on for Salt and pTracer(1)) but results
                     remains unchanged since, in this exp., Salt & pTr(1) are well above 0.
f149b16d6e Jean* o pkg/mdsio:
                   - apply same substitution to remaining calls to MDSREADFIELD/MDSWRITEFIELD
                     in pkg/ctrl and in pkg/seaice.
                   - disable the use of obsolete MDSREADFIELD and MDSWRITEFIELD S/R (unless
                     USE_OBSOLETE_MDS_RW_FIELD is defined).
f8e779c983 antn* o pkg/ecco:
                   - replace calls to (obsolete) MDSREADFIELD and MDSWRITEFIELD with calls to
                     pkg/rw S/R: READ_REC_3D_RL and WRITE_REC_3D_RL ; this enable to use pkg/ecco
                     without pkg/autodiff.
a51428376c jm-c  o verification exp:
                   - update few (10) adm & tlm output after latest TAF update, from version 3.9.0
                     to version 3.9.6 on May 16-18.
                 
9ba62b8274 Jean* checkpoint67b (2018/05/05)
502f242cbd Mart* o pkg/exf/exf_wind.F:
9ba62b8274 Jean*   - fix a bug detected by Stanislav Martyanov: replace wStress by SQRT(wStress)
                     in computing ustar ; this bug does not appear to affect the verification
                     experiments but has been around for a while (inherited from the ecco-branch)
210ee8461e jm-c  o pkg/seaice:
                   - new run-time parameter to skip the update of ocean surface stress ; could be
                     useful for testing or when seaice-dynamics is off (add a warning otherwise).
                 
411fbe7664 Jean* checkpoint67a (2018/03/10)
                 o pkg/layers
                   - add Moist Static Energy coordinate in layers package
455d18a2e4 Jean* o pkg/aim_v23:
                   - change parameter "aim_abs_pCO2" default value (used if aim_select_pCO2=1,3)
                     to calibrated value (from David Ferreira).
3ba991b895 chri* o pkg/layers
210ee8461e jm-c    - fixed up units reported in diagnostics for THETA and SALT term induced layer
3ba991b895 chri*     thickness changes.
17bd6b9422 jm-c  o pkg/seaice:
                   - move wind-stress over seaice out of SEAICE.h into local seaice_dynsolver.F
                     common block ; move initialisation of TAUX & TAUY accordingly and add them
                     to argument list of S/R SEAICE_OCEAN_STRESS (like SEAICE_GET_DYNFORCING).
                     This enable to remove CPP option "SEAICE_EXCLUDE_WIND_STRESS" (hack from
                     June 2016) in pkg/dic/dic_fields_update.F
034fdcf01f Jean* o doc:
                   - first addition of reST/sphinx documentation (formerly in
                     https://github.com/altMITgcm/MITgcm/doc/), converted from original MITgcm
                     LaTeX manual in: https://github.com/MITgcm/manual-archive with edits
                     (including new sections) from @jrscott and @edoddridge ;
                   - update section on Ocean State Estimation packages by @gaelforget ;
                   - updated seaice pkg description by @mjlosch.
                 
78abfc2fd0 Oliv* checkpoint67 (2018/02/05)
                 o add Sphinx configuration for documentation on https://mitgcm.readthedocs.io
                 o add Travis configuration for testing pull requests
7c72f3fed9 Oliv* o migrate from CVS to Git (2018/01/31)
                 
e1a9cfe6da Jean* checkpoint66o (2018/01/30)
                   => Final CVS tag ; disable CVS check-in.
                 
9f8d0cd292 Jean* checkpoint66n (2018/01/18)
4dedbda92a Jean* o pkg/seaice & down_slope:
                   - remove few files from ${pkg}_ad_diff.list (when calling S/R is not in
                     any *_ad_diff.list)
                 o pkg/shelfice:
                   - account for "shelficeLoadAnomaly" in computation of initial pressure
                     that is used in EOS (case selectP_inEOS_Zc >= 2).
457ca81085 Jean* o pkg/aim_v23:
                   - merge namelist "AIM_PAR_CO2" into "AIM_PARAMS" and replace Aim_CO2_Flag=2
                     option with aim_select_pCO2=2 (using #define ALLOW_AIM_CO2);
                   - add option to derive LW absorption in CO2 band as function of pCO2,
                     using either prescribed pCO2 (aim_select_pCO2=1), or computed pCO2
                     from well-mixed atm-box (aim_select_pCO2=3).
a88d8cd2fb Jean* o pkg/gchem, changes to enable to use several geo-chemistry pkgs together:
                   - new CPP option GCHEM_ADD2TR_TENDENCY around definition of gchemTendency
                     array (replacing #ifndef GCHEM_SEPARATE_FORCING) ;
                   - in GCHEM_FIELDS.h, change dimension of array "gchemTendency"
                     from PTRACERS_num to GCHEM_tendTr_num ; this later one is set in new header
                     file: GCHEM_SIZE.h, to be included anytime GCHEM_FIELDS.h is included ;
                   - new set of S/R, called from GCHEM_TR_REGISTER, to record rank (in pTracer
                     array) and number of tracers for each geo-chemistry pkg ;
                   - check that GCHEM tracers all fit in pTracer and gchemTendency arrays ;
                   - initialise gchemTendency array in gchem_init_vari.F ;
                   - fix storage directives for gchemTendency ;
                   - add some entry points for new geo-chemistry pkg SPOIL.
b82264afff Jean* o verification/isomip:
                   - update secondary test (input.htd): a) drop cd_scheme, useJamartWetPoints=T
                     and increase viscAh ; b) use ivdc_kappa with implicit Diff & Visc ;
                     c) switch off SHELFICEboundaryLayer, turn on pCellMix_select (=20) and
                     use SHELFICEselectDragQuadr=1 ; add new set of pickup files.
0ce06cdb80 Jean* o pkg/shelfice:
                   - Replace CPP option: SHI_USTAR_WETPOINT with run-time parameter:
                      SHELFICE_oldCalcUStar (default=F <--> #define SHI_USTAR_WETPOINT)
                     but keep only original (old) formula in SHELFICEboundaryLayer code.
                 
e699be221d Jean* checkpoint66m (2017/12/12)
40b8e0222d Mart* o add another hook (S/R PDF_FINALIZE) for the Parallel Data Assimilation
                     Framework PDAF (http://pdaf.awi.de/) in the_main_loop.F
d5d280a154 Jean* o pkg/autodiff:
                   - fix pkg/exf AD variable output (mainly ADJprecip), left from pkg/exf modif
                     on Jan 27, 2017. Try also to fix ADJrunoff and TLM output (but less clear).
                 o pkg/obcs:
                   - add simpler setting (single value) of OB indices for the case where
                     indices are uniform over the full section (Bruno Deremble contribution).
5421b78870 Jean* o pkg/rbcs:
                   - increase size of "relaxMaskFile" to read-in from namelist and save it
                     (+check) into new (renamed) "relaxMaskTrFile" array.
fe8f61a7d2 Jean* o model/src:
                   - option (interViscAr_pCell, interDiffKr_pCell) to account for true vertical
                     distance (including hFac) in vertical viscous flux and diffusive flux ;
                   - add option to increase vertical mixing (for both momentum and tracers)
                     near surface and/or bottom where partial cell is too thin ;
                   - for now, both additions above are within: #ifndef EXCLUDE_PCELL_MIX_CODE ;
                 
1a6d19a1b5 Jean* checkpoint66l (2017/10/24)
408a6af91c Jean* o pkg/kpp, ggl90 & ebm:
                   - read namelist without IOSTAT=errIO to force to stop if there is an error
                     in the parameter file namelist.
11fedddd87 Jean* o pkg/cheapaml: major changes to relaxation coefficient setting:
                   - rename parameters cheapaml_taurelax & cheapaml_taurelaxocean (in days)
                     to cheap_tauRelax & cheap_tauRelaxOce (now in seconds);
                   - if using cheapMaskFile, set relaxation coeff to: cheapMask/tauRelax
                     (instead of 1/cheapMask over ocean and 1/tauRelax over land);
                   - with cheapMaskFile unset: set relaxation coeff according to land/ocean mask
408a6af91c Jean*     (unchanged) but skip increase near domain edges for periodic domain (in X
11fedddd87 Jean*     or Y dir) when cheapamlX/Yperiodic=T ; also fix linear increase (over
                     Cheapaml_mask_width grid points) of coeff towards domain edges (previously
                     was increasing away from edges). Update output of experiment "cheapAML_box".
                 o pkg/cheapaml:
                   - move setting of (fixed in time) relaxation coefficient
                     from cheapaml_init_varia.F to cheapaml_init_fixed.F
dc84b236da Jean* o pkg/exf:
                   - add specific forcing field for tides to feed model new geopotential anomaly
                     forcing, for now within #ifdef EXF_ALLOW_TIDES.
                   - remove from common block unused params: exf_inscal_sst & exf_inscal_sss.
1faed850cb Jean* o model:
                   - add new 2-d forcing field for time-dependent geopotential anomaly (e.g.,
                     tidal forcing), in m^2/s^2 ; add run-time param to allow to turn it off.
                 o eesupp/src:
7727ad69a9 Dimi*   - shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F
                     for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h
                 
3cac0e158e Jean* checkpoint66k (2017/09/20)
                 o model/src:
0442cf0340 Gael*   - add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F
                     and the_model_main.F)
                 o ctrl:
                   - use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F)
3cac0e158e Jean*   - call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated
0442cf0340 Gael*     mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F,
                     ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F )
dd5f25c34f Jean* o eesupp:
                   - add CPP option to activate some pieces of code for coupling to GEOS AGCM;
                   - shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM.
59cd39d469 Matt* o pkg/bling:
dd5f25c34f Jean*   - bling_production: Fix typo in calcium carbonate uptake. Also rearranging
                     and cleaning
8880ed1f7d Jean* o model/src:
                   - move k loop inside correction_step.F (+ update calling S/R)
                   - collect implicit pressure gradient tendencies in local 2-D array;
                     affect results (at machine truncation level) when using 3-D solver; update
                     output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
                                     rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
                                     & tutorial_plume_on_slope.
                 
32f5cbc73c Jean* checkpoint66j (2017/08/15)
ba2a21739f Jean* o pkg/ptracers:
                   - fix surface forcing under ice-shelf (useShelfIce=T).
                 o pkg/atm_phys:
                   - use hFac weighted average when applying A-grid atm-phys momentum tendency
                     to C-grid dynamics; this ensures wind-stress match mom tendency.
03aacdc90f Mart* o eesupp/src:
157398927a Mart*   - change default for opening scratch files to avoid STATUS='SCRATCH'
4a3a90a659 Jean*   - close scratch files with STATUS='DELETE'
03aacdc90f Mart*   - changes affect eeset_parms.F and open_copy_data_file.F and many routines
                     that read namelists (because they close the scratch files)
4a3a90a659 Jean*   - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
                     in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
d39315aba7 Jean* o pkg/atm_phys:
                   - fix unset arguments in (unused) S/R surface_flux_0d.
5261466e31 Jean* o eesupp/src:
                   - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
                     (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
                     called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
234f0840d6 Mart* o pkg/streamice:
                   - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
                     preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
                     streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
7d973b58e2 Jean* o pkg/diagnostics:
                   - new option to allow to cumulate thickness-factor (hFac) weighted field
                     (if field permitted); implemented by changing sign of "jdiag" pointer
                     (> 0: cumlulate field, < 0: cumulate hFac weighted field).
                     a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
                        center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
                     b) for now, activated by setting fileFlags 3rd character to 'h'.
                 
d0fc06a0a4 Jean* checkpoint66i (2017/07/18)
                 o pkg/cheapaml:
                   - add parameter "useRelativeWind", default set to False; this change the
                     previous setting which was always using relative wind.
036ec33ebd Mart* o add hooks for the Parallel Data Assimilation Framework PDAF
d0fc06a0a4 Jean*     (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
                     to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
fc55955988 Jean* o pkg/exf:
                   - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
a435e833b1 Mart*     of South-Pole mean value.
d0fc06a0a4 Jean*   - interpolation near the poles, case where second additional row is at the
04a6d3d2ba Jean*     pole (or beyond the pole and moved to the pole): change first addition row
d0fc06a0a4 Jean*     value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
04a6d3d2ba Jean*     row (instead of just a copy of it).
fc55955988 Jean* o pkg/seaice:
f720d02ca0 Mart*   - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
fc55955988 Jean*   - add the option to compute no-slip du/dy, dv/dx (i.e.
                     the offdiagonal strain rate e12) by a second order approximation
                     on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
                     it is too messy to implement for the implicit LSR matrix.
f720d02ca0 Mart*     SEAICE_2ndOrderBC = .FALSE. by default
50ab531fad Mart* 
6a3f62c6cb Jean* checkpoint66h (2017/06/02)
                 o pkg/seaice:
                   - add new routines to compute stress tensor components and stress tensor
e228c48bba Mart*     divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
                   - change names of diagnostics SIsigI/II (commonly used for invariants)
                     to SIsig1/sig2 (more common for principal components) to avoid confusion
5d66a6a2ec Jean* o pkf/exf:
                   - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
                     similarly, stop if rotateStressOnAgrid with constant wind-stress.
caa3182bae Jean* o pkg/seaice:
                   - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
                     EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
                   - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
                     fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
                 o pkg/diagnostics:
                   - small piece of code to rename (old) diagnostics, when namelist is processed.
e9ff366891 Jean* o model/src:
                   - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
                     originally, set as minimum of adjacent hFacC factor ; now (new default)
                     computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
                     Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
caa3182bae Jean* o pkg/seaice:
e9ff366891 Jean*   - add momemtum advection, off by default, still in test phase
                     most of the momentum advection code is adapted and reused from mom_vecinv
caa3182bae Jean* o pkg/mom_vecinv:
                   - pass these runtime flags:
e9ff366891 Jean*     selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
caa3182bae Jean*     as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
e9ff366891 Jean*     so that these routines can also be used in pkg/seaice.
fc0cb18620 Mart* 
4207dc8bfb Jean* checkpoint66g (2017/04/24)
d9c26da9d2 Jean* o model/src:
                   - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
                     to get same expression (regarding machine truncation) in different places
                     in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
                     Update forward output of experiments: global_ocean.cs32x15 (all 5 except
                     viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
e3622e8a9f Jean* o pkg/shelfice:
                   - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
                     to shelfice_init_fixed.F
                   - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
                     ini_masks_etc.F for now) to update ocean upper boundary position according
                     to ice-shelf topography (instead of directly updating hFacC).
559a8104ea Jean* o model/src:
                   - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
                     packages_init_fixed.F to allow other pkgs to set mask and weight fields.
                 
902eadea41 Jean* checkpoint66f (2017/04/06)
4fcf953981 Jean* o model/src:
                   - add specific run-time param to select level of printed plot-field-maps,
                     set by default to debugLevel. Remove internal param "printDomain".
                 o pkg/seaice:
c854efd521 Mart*   - add flag to add snow mass to seaiceMassC/U/V, the default is
                     SEAICEaddSnowMass=.FALSE., not to change previous results
7d18c8ad21 Matt* o pkg/bling
                   - Bug fix in bling_production regarding unit conversion for diagnostics
                     being put in the wrong place
bc982d58e8 Jean* o model/src:
                   - add back recomputation of rSurfW & S to ensure consistent column thickness
                     (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
                     when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
                     revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
fe1663a66d Jean* o pkg/autodiff:
                   - clean-up "checkpoint.flow"
                 o pkg/rw (Contribution from Jody Klymak):
                     option to set mds file suffix as function of time in simulation:
                     *) new input parameter "rwSuffixType" (read from PARM03 namelist)
                        to select file suffix format; by default (=0), use iteration number;
                     *) add simple routine to return file suffix according to rwSuffixType;
                     *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
                        use new S/R to get file suffix, except for debug output file (diagFreq)
                        and pkgs offline & rbcs input files.
                 o pkg/rw:
                   - uniform processing of "I10" suffix across writing fld routines; used to
                     simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
                     (similar to cg3d.F, cg3d_ex0.F)
a94e0175c9 Jean* o pkg/mom_vecinv:
                   - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
                     vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
1906a8e7f8 Matt* o pkg/bling:
a94e0175c9 Jean*   - Many small changes intended to clean the code.
                     Unnecessary ADJOINT_SAFEs removed ;
                     removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
                     diagnostics added.
1906a8e7f8 Matt* 
a035b63002 Jean* checkpoint66e (2017/03/14)
78a0667e15 Jean* o pkg/exf:
                   - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
                     definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
                     use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
728f4c76b4 Jean*     avoid any dynamic allocation ;
                   - S/R EXF_CHECK: add new check & stop when file-name is defined but not
                     read-in ; add warning when file is read-in but not used within pkg/exf ;
                     + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
                   - update exf_summary.F (print {FLD}RepCycle).
78a0667e15 Jean* o verification/global_with_exf:
                   - switch on exf interpolation in AD test (just like the forward test)
52e8352d39 Gael* o pkg/mom_vecinv:
                   - add storage directives to avoid recomputations within mom_vecinv.F
78a0667e15 Jean*     which were generating seg. fault with gfortran -devel
52e8352d39 Gael* o pkg/ctrl, pkg/smooth:
78a0667e15 Jean*   - initialize array halos which were generating seg. fault with
52e8352d39 Gael*     gfortran -devel in adjoint mode
df8491dd93 Jean* o pkg/exf:
ab74fbfba7 Jean*   - for each input field, enable to specify a field specific repeat-cycle
                     ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
                 o verification/lab_sea:
                   - update AD results of primary test and noseaicedyn test after switching
                     to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
                     check stays about the same.
                 o pkg/exf:
df8491dd93 Jean*   - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
d1272ed847 Dimi*   - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
1a68cdf63d Jean* o pkg/bling, USE_EXFCO2 code:
                   - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
                   - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
38dcf987c9 Jean* o pkg/exf:
                   - rename S/R EXF_INIT to EXF_INIT_VARIA ;
                   - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
                     repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
                     and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
                   - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
                     EXF_INIT_FLD) and update calls in exf_init_varia.F
                   - For now, for backward compatibility, keep a simplified version of S/Rs
                     EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
                   - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
                     to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
                 o tools/genmake2:
                   - replace "bc -l" (only used once) by "expr" (already used).
0e208b4985 Jean* o verification/global_ocean.cs32x15:
                   - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
                     Note: exf setting (data.exf) can be compared to other exf secondary exp
                     "seaice" (kept with useCAL=T) which has same time dependent forcing.
                 
68b2841201 Jean* checkpoint66d (2017/02/13)
                 o pkg/exf:
                   - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
                     early on (in packages_boot.F) to stress this change in pkg setting.
                   - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
e88a30daa9 Jean* o model/src:
39fa77e8d0 Gael*   - move call to ecco_phys to end of time step; this may induce minor
                     cost function changes by shifting time averages by one time step
                     for some variables; this revision resulted in changed adjoint results
                     in MITgcm_contrib/verification_other/global_oce_cs32
e88a30daa9 Jean* o pkg/exf:
                   - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
                     this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
                     e.g. precip, are not available.
                 o pkg/flt:
                   - flt_init_varia.F: use pickupSuff if specified
                   - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
                     intermediate, step towards completing pkg/exch2 support within pkg/flt;
                     ifdef DEVEL_FLT_EXCH2 then:
                     - flt_init_fixed.F: comment out stop
                     - flt_exch2.F: conserve ipart, jpart (grid coordinates)
                     - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
                     - flt_mapping.F: attempt to fix longitude diagnostic near date-line
                     - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
ea11a19a76 Jean* o tools/genmake2 & pkg/pkg_depend:
                   - define new type of pkg dependency rule ("=pkg_x"), less strict than
                     the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
                     (-pkg_x in packages.conf).
                   - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
                   - add "+cal" to dependency list of pkg/ecco (needed to compile).
                   - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
127047c0ca Dimi* o utils/matlab:
                   - adding ocean_basin routines for defining basin masks.
6a96fcda5d Jean* o pkg/exf:
450d2d2f88 Jean*   - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
                     arguments, allowing to check (and stop) if parameter setting of
                      {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
                     useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
                     for backward compatibility.
                   - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
                     exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
                 o pkg/bling (USE_EXFCO2 code):
                   - fix missing setting of apco2StartTime according to apco2startdate1 & date2
                     by adding a call to S/R EXF_GETFFIELD_START.
                 o pkg/exf:
40e5c4acf5 Jean*   - allows to compile without pkg/cal (but disabled by current dependency
                     rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
                     run with useCAL=F ; this involves setting directly {FLD}StartTime instead
                     of {FLD}startdate1 & date2 ; consistency check not yet coded.
                 o verification/global_ocean.cs32x15:
                   - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
                     corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
                 o pkg/exf:
                   - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
                     calculations); change FWD experiment global_ocean.cs32x15
                     (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
                 o pkg/exf:
                   - In preparation for addition to NAMELIST, rename internal (_RL) parameter
053dccd244 Jean*      {FIELD}startdate to {FIELD}StartTime
                     Note: new name also fit better the content, i.e, a start time in second.
40e5c4acf5 Jean* o eesupp/src:
                   - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
053dccd244 Jean* o pkg/exf:
6a96fcda5d Jean*   - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
                     to allow to read-in Sensible & Latent Heat flux ;
                   - simplify pkg/exf main options:
                     1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
                        exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
                        compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
                     2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
                        ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
                     3) improve options documentation in EXF_OPTIONS.h.
c63b11972e Gael* o pkg/ecco:
6a96fcda5d Jean*   - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
                     ecco_summary.F: add passive tracer cost functions to gencost;
c63b11972e Gael*     m_ptracer and m_boxmean_ptracer
                 o pkg/ctrl:
6a96fcda5d Jean*   - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
c63b11972e Gael*     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
                     of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
                     xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
                 o model/src:
6a96fcda5d Jean*   - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
c63b11972e Gael*     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
                 o pkg/exf:
6a96fcda5d Jean*   - exf_getffields.F: add to list of implemented gentim2d contol parameters:
c63b11972e Gael*     xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
                 
6b39d139af Jean* checkpoint66c (2017/01/19)
8611775bfe Jean* o verification:
                   - add new option "-src" to testreport to only produce source code (*.f),
                     including taf output src code (if using '-adm'/'-tlm' option).
66f021d63a Gael* o pkg/exf:
                   - add saltflx :: Net upward salt flux in psu.kg/m^2/s
                 o pkg/diagnostics:
bd9df6a12d Jean*   - add run-time variable diagMdsDir to specify a subdirectory for
66f021d63a Gael*     diagnostic output when mds is being used and mdsioLocalDir is not.
c34b076d9e Gael* o pkg/mnc:
9922871071 Gael*   - mnc_utils.F: edit stop message
c34b076d9e Gael* o pkg/autodiff:
66f021d63a Gael*   - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
                     add HAVE_SYSTEM bracket around system call to mkdir
c34b076d9e Gael* o pkg/profiles:
bd9df6a12d Jean*   - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
c34b076d9e Gael*     profiles_readparms.F: call ALL_PROC_DIE before 'stop'
66f021d63a Gael*   - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
                     add HAVE_SYSTEM bracket around system call to mkdir
c34b076d9e Gael* o pkg/smooth:
                   - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
                   - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
                   - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
7b97f426d4 Jean* o pkg/exf:
                   - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
bd9df6a12d Jean*     issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
                     generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
7b97f426d4 Jean*   - summary: skip detailed field report if not used (empty file-name).
93424431c1 Jean* o tools/xmakedepend:
                   - In case line editor "ed" is missing, switch to "sed" command to clean-up
                     Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
5d59af6b6c Jean* o pkg/exf:
                   - change definition of "hflux" input file to always include Short-Wave;
93424431c1 Jean*     this is now consistent with hflux computation (if using bulk-formulae)
5d59af6b6c Jean*     and hflux diagnostic & documentation (in EXF_FIELDS.h).
                 
cd57923099 Jean* checkpoint66b (2016/12/01)
3706e6143e Jean* o model & momentum pkgs:
                   - implement fully implicit bottom friction combined with implicit surf.
                     pressure, for now, only in hydrostic formulation:
                     + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
                       and run with selectImplicitDrag=2 ;
                     + currently missing diagnostics of bottom drag and vert. viscosity tendency;
                   - partial implicit time-stepping (bot. friction + vert. visc first, then
                     surf. press) corresponding to selectImplicitDrag=1 should be applicable
                     to NH formulation but not available until we solve for surf. pressure
                     increment (instead of full etaN).
499c3c4540 Jean*   - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
                     with implicit vertical viscosity.
ff74c947d1 Mart* o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
                   - this is a first version that includes many regularisations that may
                     not all be necessary, to be sorted out,
                   - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
                   - change one verification experiment in seaice_itd to use and test new code
3706e6143e Jean*   - seaice_growth: catch a case where the argument of log can be zero
ff74c947d1 Mart*     or smaller (important for code stability)
c68e15e2a9 Jean* o model/src:
                   - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
                     & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
                     similar A.X'=Y' system (with same matrix A) in subsequent calls;
                     switch based on errCode (In/Out) argument value; in calling routines,
                     initialise errCode before first call.
                 
4a59b36843 Jean* checkpoint66a (2016/10/18)
2661ed7c00 Matt* o pkg/bling:
4a59b36843 Jean*   - BLING package now loads in atmospheric pCO2 file using exf package routines
                     Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
8372d9421d Jean* o model/src & pkg/ptracers:
                   - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
                     GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
                     implicitDiffusion (respectively) are used (even without momImplVertAdv
                     or temp,salt,PTRACERS_ImplVertAdv).
25215968c0 Jean* o model/src & generic_advdiff:
                   - add parenthesis in main diagonal calculation of implicit vertical
                     diffusion matrix (impldiff.F & gad_implicit_r.F).
                     This affects results at machine truncation level; update output of many
                     verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
caec104026 Jean* o pkg/mom_commom & generic_advdiff:
                   - add deep atmosphere and anelastic scaling factor in implicit vertical
                     advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
                 o model/src:
                   - remove few unnecessary temp array copies in solve_tridiagonal.F
                     & solve_pentadiagonal.F
                 
434f2a808d Jean* checkpoint65z (2016/09/28)
                 o pkg/seaice: fix multithreading for seaice_fgmres.F
4d686fb526 Mart*   - remove unecessary variables from common blocks
434f2a808d Jean*   - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
                     basis, that are stored in commom blocks (including integer variable i1)
                   - clean up code a little by removing commented lines that refer to
4d686fb526 Mart*     original code
434f2a808d Jean*   - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
6c3fcd2d73 Gael* o MITgcm manual:
caec104026 Jean*   - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
                     preliminary documentation for generic controls (8.3; ctrl.tex),
                     a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
                     ecco_costfunction.tex
b3b78d9534 Gael* o pkg/ecco:
caec104026 Jean*   - update and cleanup list of CCP options
                   - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
                     is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
                   - add checks that retired run-time options are not used, and in relation
                     to gencost_mask and gencost_errfile
                   - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
                     gencost_nrecperiod
                   - fix m_eta computation for virtual salt flux case
                   - add m_horflux_vol case (selected via gencost_barfile) that computes
                     transports via cost_gencost_boxmean (gencost_flag=-3)
                   - use gencost_flag more systematically (i.e., avoid using gencost_name)
                     for code switches (aside from physical variable selection)
290bbecc29 Mart* o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
                   attempt appears to be a bit of a hack and my need some repair down the road
423bece461 Jean* o pkg/exf:
                   - interpolation near South Pole: fix criteria on input field latitude.
772c88b829 Jean* o pkg/icefront & pkg/exf:
                   - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
                     from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
6708d8dfd2 Jean* o pkg/exf:
                   - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
                     "exf_output_interp" (in namelist: EXF_NML_04); change output file name
                     (add suffix "_out" instead of a prefix); keep same record number as in
                     input file but always write record 1 first (to avoid a STOP in I/O S/R).
                     Change output file content by writing interpolated field before applying
                     land-sea mask (helpful for debug).
                   - 2 compon. vector interpolation with rotation: apply scaling factor on
                     each compon. (Eastward and Northward) just before rotation.
7e2b7aaecb Matt* o pkg/bling:
6708d8dfd2 Jean*   - Cleaned package. Removed not needed code and comments.
                   - adjoint example now works
7e2b7aaecb Matt*     (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
33d60f0145 Jean* o pkg/ptracers:
                   - add Bruno Deremble's code to complete the linear surface correction
                     for tracer conservation;
0aacb0e819 Oliv*   - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
c16ff5b7c8 Mart* 
94ff1e4393 Jean* checkpoint65y (2016/07/29)
92de52e82f Jean* o pkg/debug (stats):
                   - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
                     proc/thread mapping);
                   - fix Min & Max for case where 1 thread has only empty tiles;
                   - use RL variable to count number of wet grid points (with big domain,
                     can be too large to fit into integer*4).
c21a057aef Jean* o pkg/monitor:
92de52e82f Jean*   - use RL variable to count number of wet grid points (but used only for del2)
c21a057aef Jean*   - add new routine to compute Advective CFL within tracer time-stepping with
                     writing delayed until next monitor output.
880a06ccd8 Jean* o pkg/obcs:
                   - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
33d60f0145 Jean* o pkg/cal:
                   - calandar-dump: treat case myTime < timePhase in the same way as in
                     eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
20bafebaa1 Jean* o pkg/dic & seaice:
                   - fix compilation of ocean component for coupled atm+ocn model with
                     seaice dynamics & dic.
                 
1fc3f67886 Jean* checkpoint65x (2016/06/11)
                 o add a license text file in main MITgcm tree.
dca45a136c Matt* o added pkg/bling:
c721362620 Jean*   - intermediate complexity biogeochemical model
dca45a136c Matt*   - see bling_description.txt for details
c721362620 Jean*   - verification experiment is global_oce_biogeo_bling (for now, in
                     Contrib/verification_other/); tested daily on baudelaire with gfortran.
                   - add entry point in pkg/gchem for new pkg "bling".
dd56bd054f Mart* o pkg/seaice: fix tensile stength computation
                   - replace global field tensileStrength by tensileStrFac
                   - tensileStrFac can be computed once in S/R seaice_init_varia
                   - fortunately that does not affect any verification results
                 
4973639fa7 Jean* checkpoint65w (2016/05/12)
b509abd770 Mart* o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
                      with ECCO_CTRL_DEPRECATED defined
9cecfd71bf Jean* o verification/global_ocean.cs32x15:
                   - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
                     with "selectNHfreeSurf=1".
99dd8840a4 Jean* o model/src (non-hydrostatic free-surface):
                   - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
                     was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
                   - Calculate surface vertical velocity after 2-D solver adjustment (accounts
                     for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
                     and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
                     This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
                   - Update output (changes at machine truncation level) of verification exp:
                     exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
                     short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
ca41d54747 Mart* o pkg/seaice: ITD code
99dd8840a4 Jean*   - fix picking up from a single category model by initialising
ca41d54747 Mart*     heff/area/hsnowITD = 0. in seaice_itd_pickup.F
                   - split a long warning message in seaice_check_pickup.F into two lines,
                     because NEC SX-ACE cannot deal with the long line.
8c8ba31314 Jean* o model/src:
                   - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
4ecb7ca1c7 Mart* o pkg/seaice:
                   - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
8c8ba31314 Jean* o pkg/seaice:
02ecb7194f Mart*   - add basal stress as parameterisation for grounding ice
                     following Lemieux et al. (2015)
8c8ba31314 Jean*   - turn on by setting new parameter SEAICEbasalDragK2 to a value
                     larger than 0. Lemieux et al. (2015) recommend 15.
02ecb7194f Mart*   - The adjoint complains with extra recomputations so there is also a
                     new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
                     order to postpone the problem
                   - compile the new code in lab_sea
026b44969e Jean* o verification/halfpipe_streamice:
                   - update both TAF and OpenAD adm output (machine truncation differences)
                 
8692139b79 Jean* checkpoint65v (2016/04/08)
77f624c4e1 Jean* o verification/advect_xz:
                   - increase overlap size from 3 to 4 and add new secondary test for PQM
                     advection scheme (with mono & wino limiter).
                   - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
ef0910b248 Jean* o model/src:
                   - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
                     added phi0Ref) to set vertical axis origin and phiRef origin;
                     keep Ro_SeaLevel for backward compatibility (with a warning).
                    According to coordinate and fluid type:
                     OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
                     ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
                     OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
                     ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
77f624c4e1 Jean*   - remove Ro_SeaLevel from ATM experiment parameter files;
                   - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
                     complement; update output.txt (changes at machine truncation level).
9af9059269 Mart* o pkg/seaice/seaice_evp.F
                   - simplify computation of deltaZ and zetaZ to simple averaging following
                     Bouillon et al. (2013). This removes a lot of code, but also changes
                     verification experiment lab_sea.hb87 -> updated
                 
1ec3766700 Jean* checkpoint65u (2016/03/14)
2c76214192 Jean* o pkg/generic_advdiff:
                   - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
                     with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
                     Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
                     testing and not for actual use.
fc40089cb1 Jean* o model/src:
                   - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
                     origin r = rF(1);
                   - add options (parameter selectP_inEOS_Zc) to select which pressure to use
                     in EOS for height coordinate: enable to include NH Pressure or to use
                     more accurate pressure vertical profile; options not linked to EOS type
                     (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
                   - start to implement variable gravity (along vertical): for now, only with
                     z-coords (not even z*).
                   - add Ideal Gas equation of state for height coordinate.
2c76214192 Jean*   - update OpenAD output (affected at machine truncation level) of exp:
                     global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
564694d02e Gael* o pkg/exf:
                   - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
fc40089cb1 Jean*     of exf interpolation (before any rescaling, rotation or interpolation
                     to velocity point) for each field that gets loaded from file. This option
                     identically mimics the input file organization (e.g. record numbers in year
                     by year input files) besides the change in horizontal grid.
564694d02e Gael*   - add rotateStressOnAgrid run-time switch so that wind stress fields
fc40089cb1 Jean*     can be provided on the A-grid in zonal/meridional direction and
                     rotated on the fly. This only applies to the case when the exf
                     interpolation is off and rotateStressOnAgrid is false by default.
dc293ceb82 Jean* o model/src:
                   - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
                     it's also used with pkg/atm_phys) and add few more parameters (but still
                     inactive, src code yet to come)
                 
388e260d1d Jean* checkpoint65t (2016/02/10)
6eeba9ca6b Jean* o pkg/atm_phys:
                   - from Ruth Geen: add optical depth dependence on CO2 concentration.
74dbf591da Jean* o model/src:
                   - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
                     for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
                     Update output of exp. deep_anelastic (changes at truncation level).
42d6c3122b Jean* o tools:
                   - add a hack in "remove_comments_sed" (used only with TAF) for recent
                     version of OpenMPI (shipped with FC.23): comment out the new header
                     file "mpif-sizeof.h" which causes problems to TAF.
142f5afeb1 Mart* o pkg/seaice:
c9f636aca9 Mart*   - change the termination criterion so that maxits (SEAICElinearIterMax)
                     has an effect
142f5afeb1 Mart*   - unify iteration parameters for implicit solvers (JFNK and Picard)
                     SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
                     SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
                     SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
                     SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
                     SEAICEnonLinTol     replaces JFNKgamma_nonlin
                   - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
                   - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
                     use with SEAICEuseKrylov
                 o pkg/seaice/seaice_lsr.F
42d6c3122b Jean*     fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
                     relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
                     an effect.
e42d0c73e8 Mart* o pkg/seaice: add two new parameters
42d6c3122b Jean*   - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
e42d0c73e8 Mart*     parameter is not in any namelist)
42d6c3122b Jean*   - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
                     a preconditioner for the non-linear Newton iteration of the JFNK
e42d0c73e8 Mart*     solver
2d057da76f Mart* o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
42d6c3122b Jean*   affects some experiments at truncation level:
                   - global_ocean.cs32x15.icedyn (11 digits),
                   - global_ocean.cs32x15.seaice (11 digits),
2d057da76f Mart*   - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
                   - also update global_ocean.cs32x15 adjoint and tangent-linear results
3d01549ccd Jean* o pkg/salt_plume & pkg/thsice:
                   - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
                     connect salt_plume flux to ATM-OCN coupling pkgs interface:
                    a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
                      export to coupler interface) even without compiling pkg/salt_plume ;
                    b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
                      (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
467753bb05 Jean* o pkg/dic:
                   - use the updated seaice fraction (from seaice pkgs) for DIC forcing
                     instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
                     called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
                   - move also update with values from ATM-OCN Coupler in the same new S/R
                     (previously done in ocn_apply_import.F).
                 o tools/adjoint_options:
                   - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
                     has been changed on Jan 14, 2016.
                 o pkg/ggl90:
                   - add alternative discretisation of vertical shear (off by default), to
                     compute the mean (@ grid-cell center) of vertical shear compon instead of
                     vertical shear of mean flow (@ grid-cell center).
                   - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
                     results on adjacent faces of cubed-sphere grids; this fix the restart.
86104489ad Jean* o pkg/atm_compon_interf:
467753bb05 Jean*   - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
86104489ad Jean*     pass last value, stored directly before export to CPL ;
                     Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
                   - remove atmSLPr from pickup files (no longer needed for restart)
                 
96ead4aa58 Jean* checkpoint65s (2016/01/13)
9d1bad620f Jean* o eesupp & genmake2:
                    - first check for Function ETIME and, if it fails, then check for subroutine
                      ETIME and consistent output; use the appropriate version in timers.F
0e1fe683c9 Jean* o model/src:
                   - to check restart test, add option to apply EXCH to U,V earlier, just before
                     integr_continuity; turned off by default.
                 o pkg/dic:
                   - remove CPP option USE_ATMOSCO2 (not needed)
                 o tools/tst_2+2:
                   - try to ignore difference between +0 and -0 in binary file, causing test
                     to fail for no good reason.
                 o eesupp & genmake2:
                   - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
                     but also check (in genmake2) that test runs and returns meaningful results.
a4406a661e Jean* o coupler pkgs:
                   Finish implementation of optionally-exchanged variable switches (started on
                    Nov 12) with addition of few more exchanged fields, including 2-way exchange
                    of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
                    advection in OCN component; this requires sequential coupling.
                   coupler (pkg/atm_ocn_coupler):
                   - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
                     routines (useful for debug).
                   - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
                      flux, DIC fields) if corresponding switch is ON.
                   - add option to export RunOff to OCN (to use for DIC river input)
                   - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
                   components (pkg/atm_ & ocn_compon_interf):
                   - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
                     optionally exchanged fields; add a check & stop in cpl_readparms.F.
                     ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
                     OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
                   - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
                     + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
                   - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
                   - hold in common block coupler optionally-exchanged variable switch
                     and set default "useImportXXX" accordingly; + check & stop if inconsistent.
                   - add diagnostics for all imported fields from coupler (in both OCN & ATM);
                     this is intended to replace the OCN cplFldtave.* output files (not updated
                     to contain new additional exchanged fields).
826e3022ab Jean* o pkg/dic:
                   - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
                 o pkg/thsice:
                   - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
                     and writing of thsice pickup files.
                 o pkg/atm_compon_interf:
                   - move all field individual export-call out of cpl_export_import_data.F
                     into new S/R ATM_EXPORT_FIELDS
df3ba02ef4 Jean* o pkg/atm_compon_interf:
                   - store state variables (for now, only thSIce fields) just before beeing
                     exported (in cpl_export_import_data.F, like on ocean side) instead of from
                     atm_store_my_data.F like all exported fluxes.
                   - new version of pickup_cpl: write field names into meta file and read meta
                     file to find field postion in pickup. Also only write/read fields meeded for
                     restart (same logic as main pickup file ; also using pickupStrictlyMatch)
cc55ade87f Jean* o pkg/dic:
                   - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
238b281666 Mart* o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
cc55ade87f Jean*     pressure replacement method (=1., default) or original Hibler (1979) (=0.)
                     value can be from domain [0,1] to average between the two methods
8f2cc0ef18 Jean* o pkg/atm_phys:
                   - allow to provide 2-d map of albedo and mixed-layer depth from files (but
                     hold fixed in time).
                 
df5ab41a91 Jean* checkpoint65r (2015/12/21)
                 o pkg/seaice:
                     fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
                     solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
                 o pkg/seaice:
                   - fix a bug in computing areaS in (J-J -> J-1) that affects runs
d5321ae2f9 Mart*     when SEAICEscaleSurfStress=.TRUE.,
                   - apply areaW and areaS in S/R seaice_calc_lhs
0b8d317bbe Jean* o pkg/atm_phys:
                   - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
                     (shortwave & longwave, net & downward) and diagnostics of temp. tendency
                     for individual contribution (convection, LSC cond, radiation)
8c8ba31314 Jean*   - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
0b8d317bbe Jean*     information); activated with: solar_exponent=0. and wv_exponent=-1.
                 o pkg/ggl90:
e4d707b911 Mart*   - within IDEMIX add upper limit for horizontal group velocity to
                     avoid instability problems in the explicit horizontal diffusion term for
                     long time steps or high resolution
0602590031 Jean* o pkg/diagnostics:
                   - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
                     (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
                 o testreport:
                   - remove "-v" (verbose option) in default mpirun command.
c162643754 Mart* o pkg/seaice/seaice_growth:
0602590031 Jean*   - catch potential division by zero in ITD code, does not change
c162643754 Mart*     verification results
b8a0aa824d Gael* o pkg/ecco:
0602590031 Jean*   - retire old codes to the Attic. The calls to retired functions are
                     left in a commented form in case they ever need to be re-activated.
b8a0aa824d Gael*   - ecco_check.F: issue warning if any old CPP option is
                     defined that corresponds to retired codes -- then stop.
4240d2d6ae Jean* o pkg/atm_compon_interf:
                   - change seaice fraction (use for OCN dic surf.flux) stored and sent to
                     coupler: use last time-step value instead of average over cplSendFrq_iter
                     time-step, similar to what is done for seaIceMass.
                     This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
f439370875 Jean* o eesupp & genmake2:
4240d2d6ae Jean*   - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
                     <= remove until a fix is found for some ifort version on ia32 machine.
8e20d992b4 Mart* o pkg/seaice/seaice_evp:
                   - refine residual computation
                 
4d2bb60bd2 Jean* checkpoint65q (2015/11/18)
                 o pkg/seaice/seaice_evp:
acd0bab53d Mart*   - fix residual computations so that they no longer affect the actual
                     simulation code
391b36ba77 Mart*   - fix seaice_readparams to be able to actually set new parameters
                     SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
fbe544c5ad Jean* o model/src:
                   - fix wrong truncation (single prec) from "FLOAT" function in expressions
                     like: deltaT*FLOAT(myIter) when myIter is large:
                      a) replaced by DFLOAT (if not seen by TAF);
                      b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
                 o pkg/aim_v23:
                   - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
                     when pickupSuff is set ; do write rolling pickups + at the end of the run.
a90d2d6d41 Jean* o pkg/atm_ocn_coupler + ocn_compon_interf:
                   - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
                     coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
                     add corresponding call in DO_OCEANIC_PHYS.
728fbdfa55 Jean* o coupler pkgs:
                   Start a new way to set-up optionally-exchanged variables (previously, only
                    there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
                    data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
                    send switch to ATM & OCN compon before reading their own "data.cpl" (so that
                    compononent param default can be set accordingly).
                   Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
                    but rather applies to a group a fields (going both ways like for DIC)
                    and corresponds to an option of coupling config.
                   coupler (pkg/atm_ocn_coupler):
                   - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
                     and read namelist directly (without eessup S/R calls) instead of
                     in the very un-flexible old way, 1 param per line, in fixed order;
                   - add error-counter to track errors (e.g., missing "data.cpl") and to stop
                     cleanly in CPL_CHECK_CPLCONFIG
                   - add new coupling-exchange selectors (some not yet active) including
                     cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
                                                          and ocnCpl_exchange_DIC=T in OCNIDS.h);
                   - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
                     component ; called directly from coupler.F, after comp. registrations;
                   - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
                      atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
                       -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
                   components (pkg/atm_ & ocn_compon_interf):
                   - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
                     CPP header file in all pkg source files.
                   - move checking of comp. configs out of cpl_exch_configs.F into new S/R
                     ATM/OCN_CHECK_CPLCONFIG;
                   - add error-counter to track errors (e.g., in "data.cpl") and to stop
                     cleanly in ATM/OCN_CHECK_CPLCONFIG;
                   - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
                     from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
                     before PACKAGES_READPARMS;
                   verification/cpl_aim+ocn/:
                   - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
                     "data.cpl" for coupler (in input_cpl).
2f968f5f13 Jean* o eesupp/inc:
                   - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
                     #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
                     to always cumulate tile local-sum in the same order (still uses
                     MPI_Allreduce like standard code).
                   - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
                     that are now identical to standard version (in eesupp/inc).
4014d9eb9b Dimi* o pkg/shelfice:
                   - add SHELFICETransCoeffTFile for initializing spatially varying
                     heat and salt transfer coefficients
1f88340446 Jean* o pkg/atm_compon_interf & ocn_compon_interf:
                   - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
                     S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
                   - move bi,bj loops inside S/R OCN_STORE_MY_DATA
                 o pkg/atm_ocn_coupler:
                   - initialise to zero ATMVARS.h & OCNVARS.h arrays.
06e0575ae0 Jean* o pkg/rbcs:
                   - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
                     to compile with maskLEN=1 when all tracers use the same RBCS-mask.
                   - add a short report (to STDOUT) about RBCS-mask settings.
                 
87c2bed99f Jean* checkpoint65p (2015/10/23)
53fe7f7443 Mart* o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
87c2bed99f Jean*     there is no adjoint test for EVP, we don't know what it does to the adjoint
                     solution, but at least there are no more recomputation warnings left
5790bd3152 Mart* o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
87c2bed99f Jean*     a chance of giving the same results as a fully converged VP (JFNK) solver
8187002e7a Jean* o tools/adjoint_options/adjoint_diva:
80f3898c9c Jean*   - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
4323a006ce Dani* o pkg/streamice:
8187002e7a Jean*   - spotted bug in streamice_driving_stress using dyG where should have been dxG
fcf4f25c01 Jean* o pkg/exf:
                   - remove STOP statement that prevented to use wind or (wind-)stress
                     interpolation for constant-in-time forcing fields (wind/stress period = 0).
                 o pkg/seaice:
31d3f56edc Mart*   - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
                     5 additionals 2D fields and 6 new store directives
                   - change logic in seaice_readparms.F: EVP code can now be turned on in
fcf4f25c01 Jean*     various ways, setting SEAICE_deltaTev is no longer required,
                     alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
31d3f56edc Mart*     or SEAICEaEVPcoeff
443b4c77b9 Dimi* o pkg/shelfice/shelfice_thermodynamics.F
                   - redefining uLoc/vLoc to u/v, instead of 2u/v
0a62312758 Mart* o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
                   - this is an intermediate state of a truely converging EVP that has
                     the potential of outperforming implicit VP methods, I do not recommend
                     using it yet.
                   - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
                     and all parameters are hardwired
                   - for convergence it still requires very smooth regularisations, that means,
                     if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
                     different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
                     specific averaging appears to be required, still subject to tuning
                   - still needs cleaning and I need to turn parameter into runtime parameters
                   - add code to compute and print residuals of iteration, compile with
                     defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
912323e508 Mart* o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
                   that entered with r1.54 on Sep04, 2015, -> update results
                 
40fe6f59c8 Jean* checkpoint65o (2015/09/14)
4c3e5a1532 Jean* o pkg/mom_vecinv & mom_common:
                   - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
                     called from there.
                   - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
                     allows to use Vector-Invariant form in deep atmos and anelastic formulation
7d06cac49c Mart* o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
                   and Koenig-Beatty+Holland (2012)
                   - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
                   - global 2D field tensileStrength, computed in seaice_calc_ice_strength
                   - requires an extra input argument for S/R seaice_calc_viscosities
                   - tensileStrength's depth dependence is different from Itkin et al. (2015)
                     (to be changed and played with, for now exponential)
22864ea3d8 Mart* o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
                   - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
                     by AREA according to Connelly et al. (2004), JPO.
                   - For EVP and the LSR solver, the implicit part of the drag term is
4c3e5a1532 Jean*     the only non-zero term in the denominator when there is no ice (which
22864ea3d8 Mart*     prevented running the model with zero ice-ocean drag). If
                     SEAICEscaleSurfStress = .TRUE., this results in a division by zero
                     (or zero main diagonals BU/BV) which need to be caught. A practical
                     consequence is that for open water, the momentum equation reduce
4c3e5a1532 Jean*     to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
22864ea3d8 Mart*     they happen to be zero, often leading to a non-zero solution over
                     open water.
4c3e5a1532 Jean* o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
eac2f17d92 Mart*     efficient EVP method.
4c3e5a1532 Jean*   - introduce area-weighted averages for e12 (analogously to
eac2f17d92 Mart*     seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
                     remain, but also changing the order of terms in the previous average
                     changed the results as much) -> update experiment
                   - add SEAICE_DELTA_SMOOTHREG code
4c3e5a1532 Jean*   - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
eac2f17d92 Mart*     TEM-code
                   - adjust loop bounds so that only required fields are computed
4c3e5a1532 Jean*   - add new averaging code for zetaZ/deltaZ (again similar to
eac2f17d92 Mart*     seaice_calc_viscosities.F), inactive by default for now (will change
                     results again), but will replace old code eventually
4b86bb6ef3 Jean* o eesupp/src:
                   - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
                     to always cumulate tile local-sum in the same order
                     (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
                     Still uses MPI_Allreduce (like standard code) but on array of tiles
                     and should be faster than GLOBAL_SUM_SEND_RECV code.
                   - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
                     (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
40fe6f59c8 Jean*   - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
4b86bb6ef3 Jean*      aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
40fe6f59c8 Jean*      fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
                      natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
                      tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
4b86bb6ef3 Jean* 
1e127b2371 Jean* checkpoint65n (2015/07/29)
                 o pkg/thsice:
                   - add a warning when used with pkg/aim but without updating SST
                     (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
d167cbe4e6 Jean* o pkg/offline:
65bcd0f1ad Jean*   - change where Offline-Fields are loaded, from load_fields_driver.F to
                     directly within FORWARD_STEP, just after updating iter number and time;
                   - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
                     S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
                    These changes allow:
                     a) to recover exactly on-line results using deltaToffline=deltaTClock,
                     tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
                     both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
                     time-step, both with GM & KPP files and with recomputing these fields;
                     b) no needs to switch on staggerTimeStep anymore;
                     c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
56d308cb5a Jean*   - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
65bcd0f1ad Jean* o pkg/offline:
d167cbe4e6 Jean*   - change (rarely used) offset-iteration parameter to an offset time (in s):
                     can easily recover previous offset-iter effect by setting offset-time
                     (offlineTimeOffset) to offset-iter x deltaToffline;
                   - do not turn-off Temp & Salinity surface relaxation when using KPP (used
                     in KPP as part of surface buoyancy forcing) in offline run.
4a2e3073c9 Jean*   - fix ptracers KPP non-local term in the case where KPP is re-computed.
2a36d1b911 Patr* o OpenAD
d167cbe4e6 Jean*   - Adding preliminary ggl90 test to OpenAD verification.
                     Config. with ggl90 currently diverges after 64 time steps
                     so will need more work to become more stable
                   - Adding preliminary kpp test to OpenAD verification.
                     required small tweakes in kpp_routines.F
                   - Merge and update from Krishna Narayanan's contrib area:
                     * Add one variable for preliminary OpenAD DIVA
                     * Add replacement time-stepping for OpenAD DIVA
                     * genmake2 flag -diva (but only for OpenAD; preliminary)
                     * required modifs for OAD_support
                     successful preliminary test for tutorial_global_oce_biogeo/
e81dec19cb Mart* o pkg/seaice:
d167cbe4e6 Jean*   - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
                   - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
                     delta with a smooth function in s/r seaice_calc_viscosity
                     (no effect on EVP)
                   - rename local suffix "sqr" into "sq" for more consistent variable names
                 o pkg/seaice:
                     add new parameter SEAICE_deltaMin that is used ***only***
                     for regularizing Delta (and nothing else, like the parameter
                     which is also used for all sorts of things SEAICE_EPS).
                     Defaults to SEAICE_EPS for backward compatibility only.
c9fe27f0ce Mart* o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
d167cbe4e6 Jean*     the wrong key by inialising it before use -> fixes a recomputation
                     problem but does not fix the gradient
abafc19a3b Jean* o pkg/layers:
a3d5c99c9c Ryan*   - move resetting of flux arrays to outside the iLa loop
                     (this caused layers_diapycnal to not work with more than one layer coord.)
                   - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
                 o pkg/layers:
abafc19a3b Jean*   - remove from common block 3D layers fields (used to diagnose transport
                     in tracer coords) and declare them as local arrays in layers_calc.F
d0a27699e8 Mart* o pkg/seaice:
                   - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
                     in lab_sea forward experiment (changes results -> updated)
229dc91f74 Mart*   - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
d167cbe4e6 Jean* o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
                    computations; for SEAICE_VECTORIZE_LSR
d0a27699e8 Mart*   - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
abafc19a3b Jean*     sweep to the outside,
d0a27699e8 Mart*   - remove store directives and add "CADJ loop sequential" directives
                     in analogy to model/src/solve_tridiagonal.F
                   - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
                     boundaries to yield more readable code. This has also the charming side
abafc19a3b Jean*     effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
                     SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
d0a27699e8 Mart*     seaice_lsr_tridiagu/v now requires either of these flags, vectorization
                     still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
                     an additional option)
abafc19a3b Jean*    The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
                    but the adjoint gradients (which are affected by this change) still explode.
15da1f08b8 Jean* o coupler (atm & ocn _compon_interf):
                   - avoid using Exch2 IO mapping if not suitable.
                 
30863fa6ad Jean* checkpoint65m (2015/06/15)
7139ed4ee5 Ryan* o pkg/layers:
18e9f37a89 Jean*   - clean-up old parameters setting (from Sep 2012):
                     + remove old parameters setting from common block (declared locally);
                     + stop if any old parameter is mixed with new parameters;
                     + check for valid or consistent parameter setting (e.g., layers_name)
                   - check that layers_bounds for Pot.Density are in the right range;
                     this is supposed to catch un-updated setting after recently shifting
                     potential density field "prho" by -1000 (now in "sigma" scale).
                 o pkg/layers:
edd113ba3f Ryan*   - Added missing call to layers_fill for keeping track of tottend in
                     pkg/diagnostics/diagnostics_fill_state.F
                 o pkg/layers:
cdcbace143 Ryan*   - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
                     of diapycnal fluxes
                 o pkg/layers:
f6012f0463 Ryan*   - reverted changes to interpolation to previous treatment; there
                     was never actually a problem
                 o pkg/layers:
7139ed4ee5 Ryan*   - fix interpolation of layers tracers in the presence of partial cells
                   - add lots of new functionality to compute water mass transformation
                     (enabled by CPP flag LAYERS_THERMODYNAMICS)
                   - add new calls from main code (diags_oceanic_surf_flux.F,
                     thermodynamics.F, impldiff.F) and gad to save the necessary fields
                     for layers_thermodynamics calculations
152ce31913 Gael* o pkg/ptracers:
18e9f37a89 Jean*   - add capability of stepping a passive tracer forward without advection
                     by setting PTRACERS_advScheme to 0.
9152c0f425 Jean* o pkg/diagnostics:
                   - add few (threads) _BARRIER around any update of "diag_pkgStatus".
9cf13f2e40 Jean* o pkg/layers:
eee4907c3b Jean*   - shift potential density field "prho" by -1000 for density layer averaging so
                     that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
                     Note that density bin boundaries (layers_bounds in data.layers) have
                     to be set accordingly (i.e., shifted, in sigma scale).
                 o pkg/layers:
9cf13f2e40 Jean*   - fix snap-shot output of layer thickness @ V.pt and output of pot.density
                   - fix calculation of layer non-weighted velocity and layer probability
                   - add diagnostics for pot.density used for layer averaging
                 o pkg/seaice:
f81cc74571 Mart*   - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
9cf13f2e40 Jean*     positiveness, modify a few comments and improve variable names,
                   - the changed computation of deltaC affects most seaice-related
                     experiments at the truncation level.
f81cc74571 Mart*     seaice_itd.thermo is affected by far the most, with
                     only 7 digits of agreement remaining; update experiments.
                 
adc564fd15 Jean* checkpoint65l (2015/05/04)
b357f162e4 Dani* o pkg/shelfice:
adc564fd15 Jean*   - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
                     factor drKp1 to zero where it is negative (ie. do not use
b357f162e4 Dani*     SHELFICEBoundaryLayer if hFacC>1)
                   - the same for factor drLoc in shelfice_forcing.F
307b498a12 Mart* o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
adc564fd15 Jean*     with modules in ptracers, when using testreport option "-small_f"
36a331ccdf Mart* o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
                   - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
43f4321b67 Mart* o verification/testreport
                   - add new option -small_f
                     with this option testreport first makes the target small_f (*.f files)
adc564fd15 Jean*     before running make (all). This is useful for explicit inlining when
43f4321b67 Mart*     all sources need to be full available.
adc564fd15 Jean* o pkg/exf/exf_interp.F:
                     remove previous changes related to reverse (decreasing) input grids latitude
43f4321b67 Mart* 
d4262ce583 Jean* checkpoint65k (2015/04/01)
                 o pkg/ecco:
                     fix missing cosphi initialization; use eccoiter in place of optimcycle;
                     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
                     instead of active read/write
                 o pkg/ctrl:
                     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
                     instead of active read/write.
                 o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
b905f133e5 Gael*     return if .NOT.useAUTODIFF
                 o pkg/seaice: add CPP brackets (cost function related).
d4262ce583 Jean* o model/src:
                     add useAUTODIFF run time switch.
                 o pkg/exf/exf_interp.F:
                     add code to allow input grids with latitude starting in the north (i.e. when
                     j=1 corresponds to northern edge of field); modify global_with_exf to test
                     this feature.
0d0ef3b590 Mart* o verification/testreport:
                   - replace "grep -A3" with POSIX conformal sed command, because there are
                     implementations of grep that cannot do contextual searches
                   - replace "cat -n" by "nl" (two occurrences), because not all implementations
                     of "cat" have the option "-n"
d4262ce583 Jean* o model/src:
                     add new file gsw_teos10.F that contains 3 functions, more or less a copy
                     of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
                     convert from conservative to potential temperature. For now they are not
                     called anywhere.
8686b61ec1 Mart* o pkg/ggl90: make "useIDEMIX" useful
                   - re-organize code in s/r ggl90_calc a little to move computations that
d4262ce583 Jean*     are different for idemix into separate loops (changes verification
8686b61ec1 Mart*     experiment idemix at truncation level, 12 digits remain -> updated)
                   - requires 2 new 2D fields KappaM, verticalShear
                   - make hFacI and recip_hFacI local 3D variables that are passed to
                     s/r ggl90_idemix
                   - fix and improve some comments
                 
fec3c1643a Jean* checkpoint65j (2015/02/25)
71e702ab4f Mart* o pkg/openad
fec3c1643a Jean*   - synchronize seawater.F with version in model/src: replace routine
                     body of sw_temp by calling sw_ptmp and fix/add a few comments.
2808e60b18 Jean* o pkg/mnc:
                   - change default value of pickup_read/write_mnc params to FALSE
                     (since few features are missing in reading MNC pickup files).
                 o model/src:
                   - change default (background) vertical diffusivity for salt to be the
                     temperature (background) vertical diffusivity.
                   - change background vertical diffusivity in vertical mixing pkgs ggl90,
                     kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
                     This makes ptracers default diffusivity (that uses salt diffKr) more
                     consistent with vertical mixing schemes.
0948a11536 Jean* o verification/testreport:
                   - fix typo in "-pcls" option ;
                   - put temp files in /tmp (instead of in local dir)
                   - add option "-ncad" to use genmake2 new option "-nocat4ad"
                   - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
418827f27e Jean* o pkg/ggl90 (idemix code):
                   - apply few fixes ; add some missing "_d 0" ; update output of exp.
                     global_ocean.90x40x15.idemix
c7c1da2019 Patr* o OpenAD
                   - enable active file I/O and begin removal of work-around code
                     for OpenAD for handling control variables (memory vs. active files)
                   - new CPP options file OPENAD_OPTIONS.h
ed1e2fbc34 Patr*   - revert to genarr2d gradient check for hs94.1x64x5
                   - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
                   - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
7da87823d7 Jean* o tools/genmake2:
                   - add option for an alternative Makefile (from Martin) where multiple
                     source files are sent to TAF (instead of all in one file).
689aab8014 Mart* o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
d4a41e9da2 Mart*   - code provided by Carsten Eden as an extension of ggl90
7da87823d7 Jean*   - so far the code is turned on within ggl90 by setting a CPP-flag at
d4a41e9da2 Mart*     compile time; a runtime flag implementation is not yet complete
                   - tested in new verification experiment global_ocean.90x40x15.idemix
c9dca15fbe Jean* o verification:
                   - reduce length of the AD test run by half for experiments
                     global_ocean.cs32x15 (std + thsice) and isomip
c7c1da2019 Patr*   - enable active file I/O for OpenAD, adjust verifications accordingly
                   - halfpipe_streamice: change gradient check from genarr2d to gentim2d
58a2b24c42 Mart* o verification/testreport:
                   - fix two non-POSIX sed statements so that there are no error messages
c9dca15fbe Jean*     on Mac OS X
58a2b24c42 Mart*   - replace hostname -s with hostname | sed 's/\..*$//'
c9e57a3110 Mart* o model/src/seawater.F:
                   - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
                     (following the matlab code), which would have avoided the bug caught
                     by Matt (see below) in the first place
a208a455d6 Jean* o pkg/shelfice:
                   - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
                     and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
                   - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
                     ice-shelf case (i.e., within surface level).
c9e57a3110 Mart*   - add config summary in shelfice_check.F
                   - remove global variable recip_SHELFICElatentHeat and replace by a local
                     variable recip_latentHeat
                   - introduce diagnostics for friction velocity uStar (in case of
c9dca15fbe Jean*     SHELFICEuseGammaFrict)
c9e57a3110 Mart*   - change verification experiment isomip.htd:
                     + start from pickup (as input_ad at nIter0=8640)
                     + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
                     + test SHELFICEuseGammaFrict = .TRUE.
                     + test SHELFICEadvDiffHeatFlux = .TRUE.
93bf9c0d32 Jean* o model/src:
                   - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
                     in-situ Temp) and in routine SW_TEMP (in pkg/openad);
                     update output of experiments global_with_exf.yearly and isomip (all 6).
ad3ad8f6cb Jean* o pkg/shelfice:
                   - change setting of kTopC to also be zero where there is no ice-shelf.
93bf9c0d32 Jean*   - zero out surface forcing arrays (for now, for T & S + EmPmR) where
e2b17d5756 Jean*     ice-shelf is.
                   - first attempt to get RealFreshWaterFlux effects: for now, only without
                     SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
3d23c2b9e0 Mart* o pkg/seaice: add the option to prescribe a fixed thickness PDF
                   for thermodynamic calculations
ad3ad8f6cb Jean*   - because of divisions of the type 7/7 not exactly equal to 1, this change
3d23c2b9e0 Mart*     affects results of some verification experiments by up to 4 digits:
ad3ad8f6cb Jean*     global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
3d23c2b9e0 Mart*     seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
                     adjoint: lab_sea, lab_sea.noseaicedyn
                     -> updated
                 
982dd9a048 Jean* checkpoint65i (2015/01/23)
f01a61ff96 Jean* o model/src:
                   - change units of frictionHeating field from W to W/m^2
                   - fix bug in frictional heating from stratospheric drag in
                     S/R ATM_PHYS_TENDENCY_APPLY_V
982dd9a048 Jean*   - with synchronous time-stepping: move resetting to zero of frictionHeating
01d0a60981 Jean*     field from load_fields_driver.F to thermodynamics.F ;
                   - add diagnostics for frictional heating.
172fd5e8fd Jean* o model/src & gmredi K3D:
                   - add frictionHeating field to pickup-files (for synchronous time-stepping)
                   - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
                   - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
                     and name in pickup file).
                   - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
a55487f421 Jean* o model/src:
                   - move (from ini_forcing.F) initialisation of all arrays in header file
                     FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
                     (since Nov 2012) with option selectAddFluid=1.
376915f8ee Jean* o pkg/shelfice:
                   - change units (+ document) of newly added field "shelfIceMassDynTendency"
                   - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
12e9160284 Mart* o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
376915f8ee Jean* o pkg/seaice: two new runtime parameters:
                   - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
12e9160284 Mart*     long overdue
376915f8ee Jean*   - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
12e9160284 Mart*     parameterization of tensil stress for fast ice (does not do anything yet)
                 o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
376915f8ee Jean*     for LSR: move checking overlaps out of JFNK-if-block
ff2a7562da Jean* o pkg/atm_phys:
                   - move copy of grid and dynamical fields out of atm_phys_driver.F into
                     new S/R ATM_PHYS_DYN2PHYS.
                   - fix level height for Linear Free-Surf case (to be consistent with
                     fixed-in-time pressure levels).
5811c5042c Jean* o pkg/mom_common (bottomdrag):
                   - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
                     to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
                     update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
                 o pkg/shelfice (u/v_drag):
                   - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
                   - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
                     (now similar to shelfice_u_drag.F)
                   - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
                     from mom_vecinv.F (similar to mom_fluxform calls).
                 o pkg/mom_common (bottomdrag):
                   - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
                   - add options for alternative discretisation of velocity norm in quadratic
                     bottom drag: averaging of grid-cell-center KE to U.point and V.point
                     (selectBotDragQuadr=0, original code) can produce noisy patterns; this
                     improves when averaging only the other component (e.g. vVel for U bottom
                     drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
                   - add options (bottomVisc_pCell) to account for partial-cell in bottom
                     friction (no-slip BC) thus getting the true distance from the bottom;
                     off by default since this also reduces model stability (explicit bottom
                     friction). Changes produce different machine truncation with linear-drag
                     + no-slip BC: update output of experiments exp4.stevens (10 digits) and
                     front_relax (bvp & mxl, 10 & 11 digits).
cda18d4551 Jean* o model/src & mom pkgs:
                   - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
                     since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
                   - for now and until vertical mixing scheme are updated to fill up level Nr+1,
                     just copy level Nr value to level Nr+1.
                 o doc:
                   - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
c721362620 Jean* o pkg/shelfice:
07201d0927 Dani*   - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
                     SHELFICE.h: move array shelficemass to init_varia, initialise
                     from array shelficemassinit, which is set in init_fixed and
                     has option to be set from file; introduce array
                     shelficeMassDynTend array, set thru file in init_fixed
                   - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
cda18d4551 Jean*     shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
07201d0927 Dani*     pkg/streamice
cda18d4551 Jean*   - shelfice_thermodynamics.F: call shelfice_step_icemass if
07201d0927 Dani*     SHELFICEMassStepping = .true.
cda18d4551 Jean*   - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
07201d0927 Dani* 
eabebaa9d2 Jean* checkpoint65h (2014/12/17)
83c35e2265 Gael* o verification/global_ocean.90x40x15, global_ocean_ebm:
                   - update to generic controls.
                 o pkg/ctrl:
                   - ctrl_map_ini_genarr.F: test for igen>0
                   - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
eabebaa9d2 Jean*   - move gentim2d part of ctrl_map_ini_genarr.F to
83c35e2265 Gael*     new separate routine : ctrl_map_ini_gentim2d.F
                   - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
eabebaa9d2 Jean*     add time variable weights and cyclic controls (time mean,
83c35e2265 Gael*     seasonal cycle, etc) capabilities to gentim2d
                 o pkg/ecco:
                   - move reading of error, conversion to weights from
                     ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
                 o global_oce_llc90, cs32:
                   - activte sbo.
                   - CTRL_SIZE.h : add maxCtrlProc.
                   - activate the new genctrl capabilities.
a435e833b1 Mart*   - update following reorganization of global_oce_input_fields.tar.gz
83c35e2265 Gael* o pkg/ctrl/ctrl_ad_diff.list:
                   - add missing ctrl_init_rec.f
                 o tools/OAD_support/keepOriginal:
                   - add ctrl_init_rec.F
                 o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
                   - avoid recomputations of xx_gentim2d_dummy.
a3e6888a7e Jean* o momentum diagnostics:
                   - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
                     mom_vecinv.F to timestep.F (to include Smag-3D contribution).
                 o pkg/seaice/seaice_lsr.F:
                   - fix computation of BU/BV, make sure they are non-zero, only necessary
                     for cubed sphere exchanges and SEAICE_OLx/y>0.
                     This makes calling s/r fill_cs_corner_rl obsolete (removed).
07df50d3e2 Mart* o verification/global_ocean.cs32x15/input.seaice
                   - add test for strong implicit coupling and restricted addtive Schwarz
                     methods for LSR
                   - update results/output.seaice.txt
e0b9102457 Jean* o verification/tutorial_global_oce_biogeo:
171611a792 Jean*   - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
                     and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
                     update output_adm,_oadm,_tlm.txt
                 o pkg/dic:
                   - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
                   - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
                     for tracer 1 & 2 is set (to avoid double counting of dilution effect).
                 o verification/tutorial_global_oce_biogeo:
e0b9102457 Jean*   - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
                     dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
                     update output_adm,_oadm,_tlm.txt
171611a792 Jean* o eesupp/src:
                   - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
e0b9102457 Jean*     and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1a814ccfcd Mart* o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
                   LSR (following Hutchings et al. 2004)
                   - introduce zetaZ as a global variable (requires adjustments in
                     seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
e0b9102457 Jean*     in seaice_calc_viscosities.F
1a814ccfcd Mart*   - new flag SEAICEuseStrImpCpl (default off)
                   - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
                     momentum equations
                   - JFNK-solver (preconditioner) adjusted to allow using this method
                     (where it does not have any positive effect)
d6f9f4aeb9 Mart* o pkg/seaice
                   - add overlap for restrictive additive Schwartz method also to LSR, but
                     turn it off by default (because it only seems to work for non-cubed
                     sphere/llc topologies)
c8020f78c8 Mart* o pkg/autodiff
                   - add extra exchanges in addummy_in_steppging also for mnc output
                 o pkg/seaice:
                   - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
                     to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
e87a86147c Jean* o pkg/obcs:
                   - add option to specify domain-connected piece Id along OB though files
                     (for now, only used to diagnose PhiVel; default =1 -> global correction)
                   - modify obcs_diag_balance.F to process each connected-part separately;
                     exclude OB where Id = 0 but keep the full divergence there (-> constant
                     Psi along this portion of OB and all inflow derived from grad(Phi))
                   - add example of OB-conect files in verification/so_box_biogeo/input.
                 o pkg/diagnostics:
88137b1de0 Jean*   - improve treatment of Open-Boundaries in Velocity-Potential calculation:
                   a) use non zero matrix element across OB and solve for Phi 1 grid point
                      outside OB (i.e, where tracer OBCS are applied).
                   b) global imbalance of inFlow/outFlow across OB: instead of modifying
                      velocity across OB, spread it uniformly along the OB in the RHS.
                 
790de314fc Jean* checkpoint65g (2014/11/19)
                 o pkg/diagnostcis:
                   - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
075f468e41 Jean* o pkg/my82,pp81,kl10:
                   - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
                     field diffKr as background diffusivity to set minimum diffusivity value.
                 o pkg/seaice:
                   - add new parameter SEAICEuseEVPrev (for revisited EVP by
d6ef696f9b Mart*     Bouillon et al 2013)
                   - add SEAICE_evpAlpha/Beta to namelist
075f468e41 Jean*   - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
d6ef696f9b Mart*     involve trivial re-ordering of divisions/multiplications that should not
                     have any effects, but ... they do change the results of lab_sea.hb87 so
075f468e41 Jean*     that only 2 digits of agreement remain, in line with the general
d6ef696f9b Mart*     instability/fragility of the evp-code. For now, I do not care and just
                     update the verification experiment
ce66b4105d Gael* o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
075f468e41 Jean*   - remove xx_genarr2d_numsmooth etc
ce66b4105d Gael*   - use xx_genarr2d_preproc etc instead
075f468e41 Jean*   - carry out smooth_correl2D at initialization stage rather than during
                     time stepping.
ce66b4105d Gael*   - get smoothOpNb from xx_gentim2d_preproc
                 o global_oce_cs32 :
                   - add test of generic ecco capabilities.
                 o pkg/exf/exf_getsurfacefluxes.F :
                   - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
                 o pkg/ctrl,ecco :
075f468e41 Jean*   - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
                     is defined.
efb8db572a Mart* o pkg/seaice: add diagnostics for Delta (deformation parameter)
c604292c00 Jean* o model/src:
075f468e41 Jean*   - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
c604292c00 Jean*     diffusivity (background) is specified but ignored.
                 o verification:
                   - in testreport, convert hostname to lower case for default output dir name
bb3b849103 Gael* o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
7c3a77b9ab Jean* o pkg/dic: add modifications from Hajoon:
                   - add iron sedimentation flux function of the flux of PO4 out of bottom layer
                   - light attenuation: add self-shading effect by climatological Chlorophyll
                     (read from file).
                 o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
                     compiles when SEAICE_ALLOW_DYNAMICS is undefined
                 o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
                     AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
                     ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
                     approach where CPP_OPTIONS.h includes an omnipotent
                     ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
                 o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
                     ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
7c5e2c853b Gael* o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
7c3a77b9ab Jean*     to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
                     (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
7c5e2c853b Gael* o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
                   add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
                   - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
                   - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
                   - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
7c3a77b9ab Jean* o pkg/ctrl,ecco,exf :
3ae7845edf Gael*   - remove variables associated with NON-generic costs,
                     unless ECCO_CTRL_DEPRECATED is defined.
7c3a77b9ab Jean*   - remove NON-generic NON-obcs controls,
3ae7845edf Gael*     unless ECCO_CTRL_DEPRECATED is defined.
                 o pkg/ctrl : added ctrl_local_params.h
                 o pkg/ecco : added ecco_local_params.h
7c3a77b9ab Jean* o verification : added ECCO_CTRL_DEPRECATED to most as and oad
                     experiments, which will progressively be removed once the
                     experiments are revised to use only generic controls/costs.
3ae7845edf Gael* 
f9e490a40b Jean* checkpoint65f (2014/10/13)
e9cfc0e399 Gael* o pkg/ctrl, ecco, seaice : minor changes in headers
edcd1bebe3 Gael* o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
7c3a77b9ab Jean*     cost function and control capabilities added since checkpoint65c.
675cbb9806 Gael* o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
f6a9bac81e Gael* o pkg/ecco: increase modularity and improve logic
f0a41ddc00 Gael*   - ecco_toolbox.F (new) : basic operations that are often used,
                     including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
                     ecco_addcost, ecco_add, ecco_div, ecco_readbar.
f6a9bac81e Gael*   - cost_gencal.F (new) : determine filnames and records.
f0a41ddc00 Gael*   - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
f6a9bac81e Gael*   - cost_generic.F : use spzeroloc rather than hard-coded -9999,
                     and exploit the above functions leading to more compact code.
f0a41ddc00 Gael*   - cost_genread.F : rm un-necessary arguments, re-arrange args order.
f6a9bac81e Gael*   - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
                     using_ers, using_gfo, using_mdt is now only defined within gencost)
6a200487bb Gael* o pkg/ecco: extend generic cost capabilities
                   - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
f9e490a40b Jean*     capabilities via gencost_preproc (+ _c,_i,_r related params),
45a442938f Gael*     gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
                     gencost_outputlevel arguments to cost_generic
6a200487bb Gael*   - pkg/ecco/cost_genread.F (new) : interface between cost_generic
                     and active_read, making room for gencost_preproc to take effect.
45a442938f Gael*     Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
6a200487bb Gael*   - pkg/ecco/cost_generic.F :
                     compute and store misfit maks*(model-data) in localdif that is
                     then used in cost and for output, output misfit if outlev.GT.0
                   - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
                     rather gencost_barfile for deciding whether to write barfile
                   - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
                   - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
                     ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
                   - pkg/ecco/ecco_summary.F : report gencost variables
f6a9bac81e Gael*   - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
6a200487bb Gael* o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
a883885bf1 Gael* o pkg/ecco: internal re-organization
f9e490a40b Jean*   - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
a883885bf1 Gael*     (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
f9e490a40b Jean*     mv relevant variables definition from ecco_cost.h to ecco.h,
a883885bf1 Gael*     make sure gencost routines only include ecco.h)
                   - throughout : add missing CCP switches, rm unused variables,
                     and rm un-necessary CPP switches
f9e490a40b Jean*   - throughout gencost routines : replace modelstartdate with
a883885bf1 Gael*     gencost_startdate when needed
                   - cost_bp_read.F : use arguments, instead of common blocs
f9e490a40b Jean*     so that it can be used also by (new) cost_gencost_bpv4.F
a883885bf1 Gael*   - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
                   - ecco_phys.F : compute etanFull
                   - ecco_readparms.F : rename using_topex as using_tpj, add
                     bpv4-grace to gencost list, initialize added parameters
                   - ecco_summary.F : include SIZE.h needed for augmented ecco.h
                 
82fee2871e Jean* checkpoint65e (2014/09/28)
8d1168a02a Dimi* o pkg/obcs:
432b2a4585 Dimi*   - replaced the just-added CPP options with run-time variables
                     (see pkg/obcs/OBCS_PARAMS.h for details)
                 o pkg/obcs:
                   - add additional CPP options for sponge boundary layers
8d1168a02a Dimi*     (see pkg/obcs/OBCS_OPTIONS.h for details)
5de066abfb Jean* o pkg/atm_phys:
                   - implement simple (obliquity only, assuming circular planet orbit)
                     seasonal cycle for incoming insolation ; used when run-time parameter
                     "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
ba60baccdb Gael* o pkg/exf, pkg/ecco, pkg/ctrl:
82fee2871e Jean*   - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
                   - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
                   - implement gentim2d for xx_tauu, xx_tauv
                 o pkg/ctrl, pkg/ecco :
                   - fix and complement the generic controls implementation
f673b530c1 Gael* o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
5de066abfb Jean*     pkg/shelfice/shelfice_thermodynamics.F,
                     verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
                     verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
                   - add weight in CTRL_GET_GEN calls
f673b530c1 Gael* o pkg/ctrl :
5de066abfb Jean*   - ctrl_get_gen.F : add weight as input parameter, and apply
                     it directly rather than using smooth_correl2Dw (to be retired).
                   - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
f673b530c1 Gael* o pkg/ctrl :
5de066abfb Jean*   - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
                     ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
                   - re-activate ctrl_summary (call in ctrl_init.F)
d797bbd6d6 Gael* o pkg/ctrl/ctrl_cost_gen.F :
5de066abfb Jean*   - fix CCP brackets, remove un-necessary myiter, mytime
ba60baccdb Gael* o pkg/ecco, pkg/ctrl :
5de066abfb Jean*   - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
                   - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
                   - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
                   - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
5e10000fa1 Gael* 
2334e86337 Jean* checkpoint65d (2014/09/15)
139514ed64 Gael* o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
2334e86337 Jean*   - add xx_genarr2d_bounds,xx_genarr3d_bounds,
                     xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
139514ed64 Gael* o pkg/ctrl/ctrl_map_ini_genarr.F :
2334e86337 Jean*   - remove compilation failure
                   - replace hard coded example
                   - use ctrl_map_ini_gen2D, 3D
139514ed64 Gael* o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
2334e86337 Jean*   - on/off switch based upon xx_genarr2d_weight,3d
15e98114ad Gael* o src/packages_init_variables.F :
                   - regroup pkg/estimation calls
                   - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
                     (moved to ctrl_init_variables)
                 o cost/cost_init_varia.F :
                   - remove ecco_cost_init_varia
                     (moved to ecco_init_varia)
                 o ctrl/ctrl_init_variables.F :
                   - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
                   - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
                 o ctrl/ctrl_map_ini.F :
                   - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
                     (moved to ctrl_init_variables)
                 o ctrl/ctrl_map_ini_ecco.F :
                   - remove ECCO_PHYS (mv to ecco_init_varia)
                   - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
                 o ecco/ecco_ad_diff.list :
                   - add ecco_init_varia.f
                 o ecco/ecco_init_varia.F
                   - new routine
291ff6be85 Jean* o pkg/streamice:
                   - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
                     to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
                   - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
c4f4094732 Oliv* o pkg/generic_advdiff:
                   - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
291ff6be85 Jean* o pkg/exf:
                   - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
                      xxg_precip capability
f3207a5bb2 Gael*   - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
291ff6be85 Jean* o pkg/ctrl:
f3207a5bb2 Gael*   - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
291ff6be85 Jean* o model/src/load_fields_driver.F :
f3207a5bb2 Gael*   - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
                     so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
43187e68ca Jean* o OpenAD verification experiments:
                   - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
                     in src files (to enable to skip the ECCO_CPPOPTIONS.h);
                     for now, only in pkgs used in OpenAD verification experiments.
                   - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
                     specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
                     instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
                     This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
                 o OpenAD verification tests:
                   - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
                   - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
                     tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
                   - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
                     and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
781c4efe3e Jean* o model/src & generic_advdiff:
                   - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
                     forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
                     dynamics requires valid tracer forcing only over tile interior but, for
                     some diagnostics, may need to extend it over 1 point in tile halo region.
                   - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
                     tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
                     setting in temp/salt/ptracer_integrate.F
8b57565bf5 Jean* o pkg/dic:
                   - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
                     gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
                     in gchem_forcing_sep.F
                 o pkg/autodiff & obcs:
                   - add storage of current OB values for U & V (was already done for T & S).
                 
34ab325b96 Jean* checkpoint65c (2014/08/30)
649425d785 Jean* o pkg/dic:
                   - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
                     and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
                     AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
4084975ddf Jean* o verification:
649425d785 Jean*   - new experiment testing OBCS and DIC pkgs, using params & output from
                     tutorial_global_oce_biogeo but limited to a sub-domain around Drake
                     passage: take OBCS from the last year of a 2 yrs simulation and initial
4084975ddf Jean*     conditions from t=1.yr while keeping the same forcing.
e564aebabb Jean* o model/src:
                   - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
                     (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
a14051dc1f Jean* o pkg/diagnostics (Stats-Diags):
                   - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
                     a) refine region where stats are computed, excluding where arrhFac=0 ;
                     b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
                     c) extend regional stats over the region edges (for U or V pt location).
ec7eae4c86 Jean* o pkg/gchem:
                   - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
                     pkg/dic is currently changing/updating ptracers values beyond the OB).
cd979ff82b Jean* o verification (hs94):
                   - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
                     bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
                     hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
                     apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1097960fb8 Jean* o pkg/ptracers:
                   - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
                     switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
                   - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
                     with AB-2 code (so that it get tested).
                 o model/src:
                   - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
                     with AB-2 code (previously only available with AB-3 code).
                     Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
                     to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
                     there, by calling CYCLE_AB_TRACER).
                 o pkg/generic_advdiff:
                   - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
                     GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
                     + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
                     S/R temp/salt/ptracers_integrate.F
54809f081d Jean* o model/src & pkg/ptracers:
1097960fb8 Jean*   - remove common block variables gT,gS (in DYNVARS.h), except when
                      USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
54809f081d Jean*   - remove common block variable gPtr.
b613689ef8 Jean* o model/src & pkgs:
                   - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
                      ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
                      IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
                      GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
                   + change accordingly all calling S/R.
                   - use local temperature/salinity/ptracer tendency array (without bi,bj)
                     in S/R temp/salt/ptracers_integrate.F
da10b40ad9 Mart* o pkg/seaice:
b613689ef8 Jean*   - move computation of stress contributions to rhsU/V in s/r seaice_lsr
da10b40ad9 Mart*     to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
                   - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
b613689ef8 Jean*     in seaice_lsr
                   - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
                     in s/r seaice_lsr_calc_coeffs
                 o pkg/mdsio:
                   - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
                     (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
                     too long (e.g., > MAX_LEN_FNAM/2 )
da10b40ad9 Mart* 
175cc7f2f5 Jean* checkpoint65b (2014/08/12)
3a54eed890 Jean* o pkg/matrix:
                   - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
                 o model/src:
                   - fix initialisation of geothermalFile; compile geothermal-flux code in
                     natl_box verification experiment.
09c3b72571 Jean* o model/src & pkg/down_slope:
                   - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
                   - in dwnslp_apply.F, update tracer tendency instead of the future tracer
                     field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
                     results at machine truncation level: update output of experiments
                     global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
                 o pkg/diagnostics (Stats-Diags):
                   - do not cumulate the full volume when DIAGNOSTICS_FILL is
                     called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
                     This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
                     times (but Min,Max and StD are still wrong).
66f9b25d49 Jean* o model/src:
597fa58847 Jean*   - add geothermal flux forcing: read in ini_forcing.F as time-constant
                     field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
                 o model/src:
                   - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
                     _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
                     arrays are already updated while adjustments (filters, conv.adjustment) are
                     still applied later, in S/R TRACERS_CORRECTION_STEP.
                 o model/src:
66f9b25d49 Jean*   - store in common bloc array "rhoInSitu" the virtual potential temperature
                     anomaly that is used to compute geopotential: this make the atmos code
                     more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
549401e3a9 Mart* o pkg/seaice/seaice_lsr.F
                   - rename integer variable ilcall to ipass (that's what it is called
                     in the residual diagnostics
                   - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
66f9b25d49 Jean*     default) for improved non-linear convergence of the first few steps
2344d2d5a9 Mart*   - adjust a few comments and add new ones to explain some of the store
66f9b25d49 Jean*     directives
                 o pkg/generic_advdiff (& ptracers):
                   - re-work the code to check for valid advection scheme and for minimum
                     size of overlap (now stored in local common bloc in gad_advscheme.F)
d192729d83 Mart* o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
                   - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
                   - add an auxilliary variable "bet" and fix store directives and keys in
                     seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
                     less exact gradients in my tests); but there are still
                     recomputation warning (although gradients are sort of OK), when
                     SEAICE_LSR_VECTORIZE is not defined, so this flag and
                     SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
66f9b25d49 Jean*   - update verification experiments lab_sea.
d192729d83 Mart*   - change some comments in S/R seaice_calc_viscosities
a25b59d486 Jean* o model/src:
                   - if staggerTimeStep=T, always apply exchange to velocity field in
                     do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
                     (independent of using multi-dim advection or not); no effect on FWD run
                     but affects AD results (at machine truncation level): update output of
                     experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
                     and isomip (oad: 12.d).
                 o pkg/generic_advdiff:
                   - stop if doAB_onGtGs is set to FALSE but ignored
                   - refine warning related to stability of tracer time-stepping
                     regarding internal wave dynamics.
                   - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
                     on staggerTimeStep & implicitIntGravWave (will now get a warning
                     if potentially unstable).
56bf0dc039 Jean* o pkg/kl10:
                   - add new pkg "kl10" for mixing due to internal wave breaking, from
                     http://www.sciencedirect.com/science/article/pii/S1463500310000144
                     (contribution from Jody Klymak), tested in verification experiment
                     verification/internal_wave/input.kl10/
b4dd8aa52b Jean* o isomip experiment:
                   - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
                     (input.htd) and update the output.
                 o cd_code experiments:
                   - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
                     #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
                     global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
                     update the corresponding output.
                 o pkg/seaice:
2a89c844fd Mart*   - reduce the number of include files and store directives in
                     S/R seaice_lsr_tridiagu/v
                   - change the order of loops in one case in S/R seaice_lsr_tridiagv
                     (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
b4dd8aa52b Jean*     get rid off one store directive (a TAF bug?)
2a89c844fd Mart*   - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
                     S/R seaice_lsr_tridiagv to change the loop range for consistency
b4dd8aa52b Jean*   - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
2a89c844fd Mart*   - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
                     S/R seaice_lsr_tridiagu/v (requires update of
b4dd8aa52b Jean*     offline_exf_seaice/input.dyn_jfnk)
2a89c844fd Mart* 
391aedad50 Jean* checkpoint65a (2014/07/27)
262a665438 Jean* o model/src:
90ac475d2f Jean*   - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
                     surrounding hFacC=1 @ edge of a step with different kSurfC on either side
391aedad50 Jean*     (topo in p-coords, ice-shelf in z-coords); update output of experiments
                     tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
90ac475d2f Jean* o model/src:
262a665438 Jean*   - collect momentum forcing tendency into local 2-D array (passed as argument
                     to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
                     parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
                     affects results at machine truncation level (e.g., if using OBCS_SPONGE).
                   - collect T & S forcing tendency into local 2-D array (passed as argument to
                     apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
                     affects results at machine truncation level (e.g., ocean: if using
34ab325b96 Jean*     SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
                     correction due to vertical advection).
262a665438 Jean*   - update output of experiments: fizhi-cs-32x32x40 (13 digits),
                     global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
                     seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
                     obcs_ctrl (ad & fwd grd @ 12 & 7).
a991652077 Jean* o pkg/ptracers & diagnostics:
                   - use ptracers (short) name (instead of long one) to make ptracers diagnostics
                     title (to avoid some unexpected truncation); sort out ptracers diags units.
262a665438 Jean*   - collect ptracer forcing tendency into local 2-D array (passed as argument
                     to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
a991652077 Jean* 
77d0805fa2 Jean* checkpoint65 (2014/07/18)
09aa940b92 Jean* o pkg/fizhi:
                   - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
                     affects results at machine truncation level. Update output of experiments
                     fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
48bef89a30 Mart* o pkg/seaice: more clean up
                   - rename TAF common block tapes to be more consistent and remove
                     unnecessary duplicates
09aa940b92 Jean*   - add store directives to remove more recomputations, but use smaller
                     tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
                     The idea behind this flag is to reduce the memory footprint when the
                     adjoint of the LSR is not required. As of now, defining the flag
15c6e2792a Mart*     SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
09aa940b92 Jean*     a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
                     For experiment offline_exf_seaice, this means on a linux box with gfortran
                     nearly a factor of 10 (but keep in mind there is mostly seaice code in
77d0805fa2 Jean*     this experiment):
15c6e2792a Mart*     > size mitgcmuv_ad
790de314fc Jean*     text    data        bss     dec        hex
                     5100659 1216  220458952  225560827  d71c8fb
48bef89a30 Mart*     5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
09aa940b92 Jean*     but only a moderate increase of 36% for global_ocean.cs32x15:
48bef89a30 Mart*     text    data        bss     dec        hex
                     6695027 1648 1014578664 1021275339 3cdf6ccb
                     6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
                   - note: there are still recomputations in global_ocean.cs32x15 and
15c6e2792a Mart*     offline_exf_seaice and the gradient agreement changes (gets a
                     little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
48bef89a30 Mart*   - in general, the AD gradients still are wrong
53bebe4a64 Patr* o OpenAD
                   - clean up code_oad/ directories somewhat by moving files
                     dontCompile, dontTransform, keepOriginal to OAD_support/
f398288312 Jean* o model/src:
930ff12251 Jean*   - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
                     (not currently tested): add dissipation terms before NLFS rescaling of
                     tendencies (previously done after).
                 o pkg/diagnostics:
                   - write stats-diags in ascii file with more digits (same as in monitor).
                 o pkg/down_slope:
                   - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
                     NLFS (not tested), use new recip_hFac value in order to conserve tracer.
                 o model/src:
f398288312 Jean*   - new file "apply_forcing.F" containing all the code previously in
                     external_forcing.F, but with new argument list: pass, as new argument,
                     the current level tendency array to update (instead of a direct update
                     of the common bloc array). Change the corresponding calls.
                   - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
                     EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
5e1701d480 Mart* o pkg/seaice/seaice_lsr, a little bit of clean up
                   - rearrange some code blocks, so that now all calculations for
f398288312 Jean*     setting up the right-hand-sides done within one single block
5e1701d480 Mart*     (I find that easier to read and understand)
                   - rearrange freedrift-code to reduce the number of ifdefs
                   - adjust some indentations and comments
                 
6544591561 Jean* checkpoint64z (2014/07/10)
c1d95c335c Jean* o model/src and several pkgs:
                   - change argument list of all S/R called from external_forcing.F and
                     called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
                     to pass, as argument, the current level tendency array to update
                     (instead of a direct update of the common bloc array).
                   - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
                   - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
a122714692 Mart* o pkg/seaice/seaice_lsr.F
                   - always initialize local arrays in seaice_lsr_tridiagu/v
                   - add more local tapes to seaice_lsr_tridiagu/v
c1d95c335c Jean*   - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
a122714692 Mart*     keep it in bi/bj loop; this seems to be essential
                   - gradients are still wrong but only by 4-7 orders of magnitude
                     instead of 15 orders of magnitude, lab_sea improves a little
822f9de729 Mart* o pkg/seaice
                   - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
                     generates unnecessary code in seaice_lsr_ad
                   - add more store directives in seaice_lsr to avoid unnecessary code
                     in seaice_lsr_ad
                   - exclude some residual computations in seaice_lsr when
                     ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
c1d95c335c Jean*     in seaice_lsr_ad
822f9de729 Mart*   - add more storing, a new tape (model/src/the_main_loop.F) and
                     another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
c1d95c335c Jean*     and klockey should be checked by a specialist)
822f9de729 Mart*   - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
                     and update lab_sea after previous changes in pkg/seaice below
c1d95c335c Jean* o pkg/autodiff:
                   - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
d572335125 Gael*     viscFacInAd : run time parameters allowing for adjoint switches
                     note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
c1d95c335c Jean* o pkg/ecco:
                   - introduce cost_gencost_boxmean.F that computes a box mean
d572335125 Gael*     temperature (for use in adjoint sensitivity studies).
                 o model/src/set_defaults.F : initialize viscFacAdj to 1.
c1d95c335c Jean* o pkg/mom_common/mom_calc_visc.F:
d572335125 Gael*   - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
c1d95c335c Jean* o pkg/seaice/seaice_summary.F:
d572335125 Gael*   - statement for SEAICEadjMODE now in autodiff_readparms.F
c1d95c335c Jean* o pkg/seaice:
1fa25402a0 Mart*   - remove some store directives and add new ones in an effort to get
                     finally rid off the recomputation warnings. This is successful
1d0e5c687d Mart*     when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
                     defined (i.e. no extensive recomputation warnings left), but there
                     are still too many recomputations on the solver iteration level
0e792109e6 Mart*   - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
e06bd90b00 Mart*   - move definition of MPSEUDOTIMESTEPS into TAMC-block in
                     SEAICE_SIZE.h
                   - add a store directive in S/R seaice_calc_viscosities
fdfdc49113 Jean* o pkg/seaice (ITD code):
                   - fix definition of Hlimit for multi-threaded case
                   - use double precision arithmetic to compute Hlimit: this affects results;
                     update output of experiment seaice_itd.
7f033dc113 Mart* o replace content of verification/seaice_itd
                   - instead of a 1D column use the configuration of offline_exf_seaice
                     to test the ice thickness distribution code with ridging
                   - this is a first shot at this experiment
                   - change of some defaults of ridging parameters SEAICEhStar (from
                     100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
fdfdc49113 Jean*     and lot of new comments.
7f033dc113 Mart* 
4fddc18258 Jean* checkpoint64y (2014/06/20)
                 o pkg/seaice/seaice_reg_ridge.F:
                   - modify the regularization of very small volumes of ice; only check
                     total volume HEFF, and do not apply correction to individual ice
                     classes because that leads to funny patterns in the heat and fw-fluxes
c7c86ceb32 Mart*     into the ocean. Adjust seaice_itd/results/output.txt
                   - replace nITD by SEAICE_multDim in loop-ranges
0a1362090f Jean* o pkg/exf:
                   - add code to process the case field period = -12. with UV interpolation.
                   - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
                     into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
f893122504 Jean* o verification/global_with_exf:
4fddc18258 Jean*   - switch all fields period to -12. (was previously untested) in input/data.exf
f893122504 Jean*     (but keep secondary test ".yearly" unchanged); update the reference output.
                 o pkg/cal:
                   - new calendar type "noLeapYear" for 365 days calendar without any leap year.
                 o pkg/exf:
                   - new integer parameter "exf_debugLev" (default set to main model debugLevel)
                     to replace logical switch "exf_verbose"
4fddc18258 Jean*   - report in STDOUT when loading a new record (if exf_debugLev >= 3)
3d5a62f3cd Jean* o pkg/sbo:
                   - update from Katherine Quinn: evaluate mass directly from density and SSH
                     (budget using Finite Volume method) instead of from bottom pressure.
8471337f5d Jean*   - allow testreport to collect few selected SBO output ; tested in exp.
                     global_ocean.90x40x15 (after updating the results, to include SBO output).
                   - fix some multi-threading issues (in output part).
39a405bbb4 Jean* o model/src & most packages:
                   - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
                   - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
                     PACKAGES_UNUSED_MSG to print a weak warning when parameter file
                     "data.{pkg}" exist ; and leave the S/R (return) just after.
f459cc48d3 Jean*   - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
                     + call LAND_READPARMS from packages_readparms.F
39a405bbb4 Jean* o pkg/seaice:
efc672bc35 Mart*   - remove code that resets useThSice in S/R seaice_readparms and
c7c86ceb32 Mart*     replace it by a warning in S/R seaice_check
efc672bc35 Mart*   - remove parameter MULTDIM, replace with nITD and runtime
                     parameter SEAICE_multDim (still hard-wired to nITD if
                     SEAICE_ITD is defined)
                 
32263cf74c Jean* checkpoint64x (2014/05/24)
bb8f3ffecf Patr* o verification/lab_sea:
32263cf74c Jean*   - update adjoint and TLM output following changes to pkg/salt_plume
                   - un-do the update after putting back local recip_Cp in few places.
bb8f3ffecf Patr* o pkg/salt_plume: modifications by An Nguyen:
32263cf74c Jean*   - add capability to do brine rejection (salt-plume) as function of
bb8f3ffecf Patr*     volume+tracers (instead of only salinity tracer).
32263cf74c Jean*   - conserve volume by exchanging volume from each kLev to above to
bb8f3ffecf Patr*     accommodate in-coming brine volume
                   - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
32263cf74c Jean*   - switch KPP surf buoyancy due to brine forcing to 3-d
bb8f3ffecf Patr*     (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
                   - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
32263cf74c Jean*   - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
bb8f3ffecf Patr*     in East/West Arctic.
751362a27d Jean* o pkg/sbo:
32263cf74c Jean*   - incorporate modifications from Katherine Quinn to enable the use of sbo
751362a27d Jean*     pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
                     output for future testreport verification (unfinished).
60958941f8 Jean* o pkg/atm_phys:
                   - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
                     skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
                     output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
0ad17fdd8c Mart* o pkg/seaice
60958941f8 Jean*   seaice_calc_ice_strength.F: modify expression to avoid divisions
0ad17fdd8c Mart*     (affects truncation)
                   seaice_do_ridging.F: clean up the insectarium
3fba0517c3 Mart*   - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
                   - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
                   - set closing/openingRate to zero where no extra iteration is need (3rd bug)
60958941f8 Jean*   - add some debugging information and error messages (warnings)
b062ea86d0 Jean* o model/src: modifications relatd to atmosphere p*:
                   - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
                   - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
                     of vertical profile tRef in geopotential background and anomaly.
                   - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
                     and pkg/atm_phys.
                   - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
                     fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
419c1f0b27 Mart* o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1c0e70142a Oliv* o pkg/ptracers: compute ptracer source/sink due to linear free surface.
                     not used right now, but can be used in BGC packages to fix conservation.
                 o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
                     other packages too.
b062ea86d0 Jean* o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
                     SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
728a44199c Jean* o model/src:
                   - since we have several heat capacity (even in model/src), define "recip_Cp"
                     as local variable (no longer in common block) to avoid any confusion.
                   - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
7bb11c2f45 Jean* o pkg/exf:
                   - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
                     air density as function of air Temp, Humidity and atm pressure.
                 
80e9662843 Jean* checkpoint64w (2014/05/02)
4faee70d47 Jean* o verification:
                   - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
                     seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
                     code from seaice_growth.F & seaice_advdiff.F to new ridging routines
b062ea86d0 Jean*     seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
419c1f0b27 Mart*     (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
bcc533dbd4 Jean* o model/src: for atmosphere in p* coords:
                   - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
                   - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
                     but not yet activated.
cabb1e150c Mart* o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
                   - move computation of opnWtrFrac = 1-AREA to before computing ice strength
bcc533dbd4 Jean*   - this changes the results (but not for any verification experiment, because
                     none tests this), but avoids having an extra field in the restart files
97d542e805 Mart* o pkg/seaice: remove global variable TICE (not needed)
bcc533dbd4 Jean*   - replace by TICES or local variable where necessary (cost_seaice_test,
97d542e805 Mart*     seaice_diagnostics_state)
                   - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
                   - use specific read/write routines for reading and writing individual leves
                     of a multilevel field
b1bf8777db Jean* o pkg/ctrl & model/inc:
                   - move additional anomaly fields of control vars (related to options:
                      ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
                     from DYNVARS.h into new header file: CTRL_FIELDS.h
cc5e1bc684 Mart* o pkg/seaice: some small modifications to the ridging code
                   - make fw2ObyRidge a global variable and add the freshwater flux to
                     seaice_growth
b1bf8777db Jean*   - pass actual thickness from seaice_prepare_ridging, so that it is
cc5e1bc684 Mart*     computed only in one place and compute it in the same way as in
                     seaice_growth
                   - initialise more fields in seaice_do_ridging that where cause floating
                     point exceptions over land
e990a77247 Mart* o pkg/seaice: preparations for ridging code and first real ridging code
b1bf8777db Jean*   - move most of "PART 1" of S/R seaice_growth into a new and separate
e990a77247 Mart*     S/R seaice_reg_ridge that will both regularize the state variable after
                     advection call the actual ridging routine;
b1bf8777db Jean*   - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
e990a77247 Mart*     d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
                   - remove ridging code from seaice_advdiff
b1bf8777db Jean*   - clean up remaining part 1 of seaice_growth in an attempt to make it
e990a77247 Mart*     more readable (this is probably subjective)
                   - call seaice_itd_redist once in the initialisation phase to have the initial
                     conditions in the correct category
                   - finally: add new ridging routine for ITD code
                 
e36f9ede36 Jean* checkpoint64v (2014/04/11)
9994e4e8cb An T* o pkg/ecco:
                   - add runtime parameters mdt[start,end]date[1,2]
                   - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
e36f9ede36 Jean* o pkg/seaice:
                   - make deltaC a global variable, so that it can be used in ridging code
67f02628d2 Mart*   - first step towards ridging: introduce new routines that compute
                     ice strength based on ridging parameters
79793b3c13 Mart*   - add diagnostic for HSNOWITD
                   - add opnWtrFrac as a global variable (required for ridging scheme)
9994e4e8cb An T* o pkg/salt_plume + pkg/seaice/seaice_growth.F
                   - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
                     AREA exceeds a threshold (code contributed by I.Fenty in 2011)
684ea763ea Jean* o verification/hs94.1x64x5:
                   - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
                   - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
                 o autodiff:
                   - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
                     and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
                     For now, only in pkgs used in verification/hs94.1x64x5.
                   - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
                     which are specific to TAF/TAMC).
                   - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
                     since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
                     is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
                   - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
                     building mitgcmuv_ad (make adAll).
d85e4bb9df An T* o pkg/ecco:
                   - cost_gencost_seaicev4.F:
                      reformulate proxy cost as function of sst and local param SEAICE_freeze
                      change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
                   - add stop statement if old names siv4-[sst,vol] are used
                   - add snapshots + cost reports for atmospheric longwave
                   - remove factor 0.1 in front of wtau[u,v]
                   - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
                      ALLOW_TMI_SST_COST_CONTRIBUTION
684ea763ea Jean* o pkg/atm_phys:
d68eb785a9 Jean*   - add some diagnostics for Short-wave and for convection S/R.
684ea763ea Jean* o pkg/seaice/seaice_growth:
ea66a54ac4 Mart*   - fix a bug in the lateral melt parameterization for SEAICE_ITD
                     in seaice_growth; tempFrz needs to be computed inside the i/j-loop
                   - rearrange loop order for better vector code in the same code block
                   - rewrite the floeDiameter formula to have fewer divisions
                   -  (miraculously) none of this changes the results of seaice_itd
684ea763ea Jean* o pkg/smooth:
                   - move param smooth2Ddiffnbt to pkg/ecco
                 o pkg/salt_plume:
                   - salt_plume_frac.F:
                      clean up local param names
                      reformulate (1-frac) to frac; original 1-frac was based on swfrac code
6d2104f414 Jean* o pkg/rw:
                   - add RS version of S/R READ_MFLDS_LEV.
                 o pkg/streamice:
                   - fix the restart test by writing/reading pickup_streamice files.
                 o pkg/seaice:
0e4bf54f91 Mart*   - refine checks for jfnk-related parameters
                   - comment out if statement with SEAICEuseIMEX parameter as long as there
                     is no IMEX code to avoid confusion and surprises
                 
1b217122f8 Jean* checkpoint64u (2014/03/07)
85157af967 Jean* o verification/MLAdjust:
                   - rename secondary test suffix:
                      1.leith  -> A4FlxF  + switch to flux-form & add side-drag
                      0.leithD -> AhFlxF  + switch to flux-form
                      0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
                      0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
f0b594ffe2 Jean* o pkg/mom_vecinv:
                   - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
                     to be before mom_calc_visc.F)
                   - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
                   - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
                     this is simpler for the adjoint and for diagnostics.
7ab8a42a9d Jean* o model/src + pkg/momentum:
                   - add input files for  2-D additional Western and Southern cell-edge wall
                      (e.g., to add "thin-wall" where it is =1).
                   - fix sideDrag option for thin-walls with Non-Lin Free-Surf
                     using 2nd hFacZ that is computed from initial (fix domain) hFac
                   - known limitations of thin wall implementation: not yet coded for sigma
                     coords; not working with CD-scheme neither.
21cfbf5d41 Jean* o pkg/seaice:
65555308b7 Mart*   - rename recently introduced parameters from (wrong name) AB to
                     BDF (backward difference time discretisation)
                   - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
21cfbf5d41 Jean* o tools/adjoint_options:
                   - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
65555308b7 Mart* 
0819a3aef8 Jean* checkpoint64t (2014/02/01)
d85e4bb9df An T* o pkg/ecco
                   - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
                     runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
                   - replace hard-coded record number and period which only work for monthly
                     with read-in runtime param that works for other periods (month,day,year)
a4e96d71ae Patr* o pkg/thsice
                   - corrected store directive fixes thsice adjoint gradient checks
c610335cdc Jean* o genmake2 & testreport:
                   - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
                     in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
                     Update testreport accordingly. No need to set "export OPENAD=true"
                     in adjoint_options/adjoint_oad anymore (will be removed later).
9a846a36d2 Jean* o pkg/shelfice:
                   - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
                     only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
                     so that surface forcing applies to k=kSurf if using pkg/shelfice.
62997f5aad Patr* o pkg/ctrl, pkg/grdchk, pkg/ecco:
9a846a36d2 Jean*   - Changes to make GENARR more modular (i.e. invisible if not used)
cde67b4ce1 Gael* o model/src/temp_integrate.F and salt_integrate.F
9a846a36d2 Jean*   - re-include store directives that were removed on Dec 27th.
3dbdd94ad6 Gael* o model/src/external_forcing_surf.F
9a846a36d2 Jean*   - add storage directives for EmPmR and PmEpR to avoid recomputation of
                     seaice_model in the adjoint that is problematic when seaice_model is
                     turned off in the adjoint. The resolved issue dated back to July when
                     EXTERNAL_FORCING_SURF call was moved.
                     Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
20bd954105 Mart* o pkg/exf/exf_check.F
9a846a36d2 Jean*   - fix a small bug again (originally found by Wentao Liu, now found again)
                   - streamline error output
20bd954105 Mart* o pkg/streamice and aim_v23:
9a846a36d2 Jean*   - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
                     Apple's /usr/bin/cpp knows what to do:
                     Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
                     Target: x86_64-apple-darwin13.0.0
20bd954105 Mart* 
f23338cc5b Jean* checkpoint64s (2014/01/05)
ce5f09424a Jean* o tools/adjoint_options:
                   - switch to fastopt.net TAF server (instead of default fastopt.de) for
                     AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
                 o model/src:
                   - remove some unnecessary TAF storage directives in forward_step.F and
                     in dynamics.F (note: not always removed by TAF, e.g., double storage
                     of kappaRU,kappaRV in former version of dynamics.F).
f2a2ecef28 Jean* o model/src & pkg/ptracers:
ce5f09424a Jean*   - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
f2a2ecef28 Jean*     salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
                     and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
                   - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
                   - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
                   - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
e71dbcdc66 Jean* o useSingleCpuInput separates single-CPU input from single-CPU output;
                     for now only implemented for in exf_interp_read.F
                 o verification/advect_xy:
                   - fix missing EXCH call in local version of ini_salt.F and update output.
                 o momentum diagnostics:
                   - fix which deltaT is used in Total-Tendency diagnostics.
                   - fix typo in diagnostics for momentum tendency from AB.
                 o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
                     SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
05b3bcee70 Mart* 
49ba07ded8 Jean* checkpoint64r (2013/12/08)
21fae43a0a Jean* o verification/*/results:
                   - Update reference output of experiments that were passing with just 13 digits
                      (make it easier to detect future changes in results)
4175fa5a6c Jean* o model/src & pkg/ptracers:
                   - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
                     inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
                     to inside ptracers_integrate.F ; remove ptracers_advection.F
13e111d31a Jean* o coupling interface pkgs:
                     [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
                   - change the config check to test the agreement of Ocean Depth
                     with ATM land/sea mask (instead of ATM orography);
                   - send to coupler the number of coupler time-steps to do for this run:
                     this allows to check for consistency and don't need anymore to be
                     specified in parameter file "data";
                   in coupler:
                   - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
                   - improve report to log-file of config setting (pass log-file unit to few S/R)
                 o pkg/compon_communic:
                   - add coupling send/receive for non-tiled integer vector;
                   - add S/R to check and stop if any proc has an error (similar to
                     eesupp/src/stop_if_error.F but single thread and across Comm_World).
b7f9d4a417 Jean* o pkg/exch2:
                   - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
                     through list of all tiles my proc owns.
                 o model/src:
                   - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
                     from rTrans) to simplify dependencies (no need to store rTrans anymore in
                     calling S/R); this affects AD results at machine truncation level:
                     update AD-output (TAF) of experiments: 1D_ocean_ice_column,
                     bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
1088379d6a Jean* o tools/build_options:
                   - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
                 o coupling interface pkgs:
                     [compon_communic, atm_compon_interf & ocn_compon_interf]
                   - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
                     to each S/R that needs it; remove un-used variables.
                   - change component tile registration (cpl_register.F in both compon_interf
                     and mitcomponent_tile_register.F) to pass the full list of tiles
                     information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
                   - with pkg/exch2: adopt the same convention used for I/O to define mapping
                     towards coupler global array (unless W2_useE2ioLayOut=F):
                      a) can now use different tiling between atm & ocn comp.
                      b) no needs to modify the run-Off map when changing tiling (was needed
                         even if using the same tiling between atm & ocn).
                      c) will allow to run with blank-tiles in 1 component (e.g., for ocean
                         full land tiles); not yet tested.
                   - check for valid mapping from comp. tile to coupler global array
                   - improve report of tile registration results to log file.
                 o pkg/exch2:
                   - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
                     tile-registration (CPL_REGISTER);
                   - activate (un-comment) definition and setting of "W2_tileIndex" list to
                     store the local bi,bj indices of each tile;
                   - also print bi,bj in local report to log file;
                   - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
                     Jun 2009 modif of pkg/exch2).
                 o testing on baudelaire:
                   - run 2 tests at a time: no significant slow down (since enough cpu) and
                     get the full set of test done earlier
                   - switch the ifort test to "-devel" ; run the OpenAD test everyday.
a9265de95a Jean* o model/src/thermodynamics.F and routines called from it:
                   - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
                     gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
                     velocity (outp) by adding bolus velocity.
                   - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
                     mass transport from velocity + lateral grid cell area
                   - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
                   - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
                  in thermodynamics.F
                   - remove k from thermodynamics.F and move it to temp_integrate.F
                     salt_integrate.F and ptracers_integrate.F (now done inside the tracer
                     loop).
                   - compute locally (in thermodynamics.F) 3-D velocity field that is used to
                     advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
                     PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
                     GAD_IMPLICIT_R and PTRACERS_IMPLICIT
                   - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
                     global_ocean.90x40x15, tutorial_global_oce_biogeo and
                     tutorial_tracer_adjsens (+ TLM output).
1088379d6a Jean* o tools/OAD_support and (verification/*/) code_oad:
8f959368b3 Jean*   - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
                     module conversion ; remove unneeded CPP_EEOPTIONS.h.
                   - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
1088379d6a Jean*     version (closer to model/inc/CPP_OPTIONS.h).
8f959368b3 Jean* o model/src:
                   - remove parameter "useOldFreezing" from PARAMS.h and push it to the
                     retired list of parameters (routine FREEZE has been replace by surface
                     freezing (10.yrs ago) and by pkg/frazil (interior freezing).
                 o pkg/gmredi:
                   - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
                     velocity (same scheme but affects machine truncation) for GM_AdvForm.
                   - update output of FWD experiments: front_relax.bvp,
                     global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
                 
ccabb03de3 Jean* checkpoint64q (2013/11/17)
7669301999 Jean* o verification:
                   - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
                     tutorial_global_oce_biogeo and global_ocean.90x40x15.
                   - generate new output (growth & melt) for seaice_itd experiment after
                     updating the input pickup_seaice files (previously wrong).
d498609aae Jean* o pkg/cost:
                   - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
                     (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
c610335cdc Jean*     o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
d498609aae Jean*       cannot be applied to var in common block).
                     o allows to get results independent of tile-per-proc setting (if using
                       slower GLOBAL_SUM_SEND_RECV option).
                   - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
                     thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
                     forward gradients: update output).
                   - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
                     S/R and, for most exp., also comment out GLOBAL_SUM_R8.
586c949ecf Jean* o pkg/mom_common:
                   - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
                     code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
                     viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
                     ensure that all field value that are used are set.
4eccb07ab1 Jean* o tutorial_deep_convection (smag3d):
                   - add missing scaling in mom_calc_smag_3d.F;
                   - set smag3D_coeff in input.smag3d such that results do not change.
                 o pkg/dic:
                   - change dic_cost.F to compute cost on each tile first and then apply
                     GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
                     tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
35050126c6 Oliv*   - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
a5d44ed107 Jean* o eesupp/src & pkg/mdsio:
                   - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
                     (from pkg/mdsio) since they are no longer used for tape IO.
                   - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
                     (+ keep a copy in pkg/atm_ocn_coupler).
2e81182906 Jean* o verification/isomip:
                   - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
                 o tools/build_options:
                   - optfile linux_amd64_ifort11, fast (no ieee) case:
                     to get a working restart for all experiments, add "-fp-model source"
                     to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
                 
a01940b562 Jean* checkpoint64p (2013/10/20)
5bfbd26026 Jean* o pkg/autodiff:
                   - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
                     criteria, return to simple (default) tape IO format.
645a01b465 Jean* o pkg/mdsio (+ eesupp/src):
                   - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
                     previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
                   - fix globalFile and singleCpuIO options using simpler global mapping.
                   - new pairs of scatter/gather vector S/R (one for each type, generated from
                     template) corresponding to simpler global mapping.
                   - adread_write.F: switch to new S/R (but leave old calls commented) and write
                     to globalFile when parameter globalFiles is set to True.
                   - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
b798a7d810 Jean* o pkg/autodiff:
5bfbd26026 Jean*   - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
                     with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
b798a7d810 Jean*     missing, just add a STOP if array type do not match.
dc136770de Jean* o pkg/exf:
                   - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
                      rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
                      and rename array obsSIce to exf_iceFraction.
94e0cca872 Jean* o tutorial_deep_convection:
                   - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
                     for now all in this exp. code dir.
                   - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
                     testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
                 o eesupp/src:
                   - added SINGLE_DISK_IO option because reading of parameter files on
                     very large number of processors did not work with existing set-up
                 
cc89d07104 Jean* checkpoint64o (2013/09/25)
                 o pkg/atm_phys & atm_compon_interf:
                   - allows for coupling of gray-atmosphere (atm_phys) with ocean.
6bd6f7be12 Jean* o tools/build_options:
                   - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
                     & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
                     remove CPP setting (was identical to genmake2 default).
1115280ea7 Mich* o pkg/gmredi & model/src: Some updating and work done on the residual model.
                   - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
6bd6f7be12 Jean*   - fixed up the calculation of the eddy stress and how it is added to the
1115280ea7 Mich*     external forcing via taueddy_external_forcing.F
                   - at the moment, it is very experimental and only works with the variable eddy
                     diffusivity calculated in gmredi_k3d.F
6bd6f7be12 Jean* o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
                     lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
                 o testreport (& tools/do_tst_2+2):
                   - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
addfa94074 Jean* o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
                   - remove CPP='cpp -traditional -P' (this is genmake2 default)
                   - add switch (for big setups) to use 'medium' memory-model (but leave it
                     commented out for now). Note: needed with FC 19 to compile big setups.
3dca81485c Jean* o pkg/atm_compon_interf:
                   - regroup per field origin (model & pkgs) the coupling storage routines
                      (which accumalate in time each coupling field)
addfa94074 Jean*   - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
3dca81485c Jean*     update accordingly + simplify aim_do_physics.F
                 
8f1243bebb Jean* checkpoint64n (2013/08/26)
5f5cc705f4 Dimi* o pkg/bbl:
                   - update formulation to reduce dispersion of tracer properties in bbl
                   - replaced horizontal and vertical transport parameters with velocities
                   - changes results for verification/global_with_exf.yearly
ffbb57e6f3 Dani* o verification/halfpipe_streamice:
                   - change to matrix construction; update both Fwd & AD output.
c91228a3b5 Jean* o verification/tutorial_tracer_adjsens:
                   - OpenAD test: switch to vector-invariant momentum since fluxform with
                     rStar causes problems with OpenAD; update output.
983705b2af Jean* o tools:
c91228a3b5 Jean*   - genmake2: define a common prefix for all temp-file names ; move them
                     to local /tmp disk (but would be easy to move them back);
                   - xmakedepend: apply the same switch for temp-files.
983705b2af Jean* o pkg/offline:
c91228a3b5 Jean*   - changes for use with rStar (NLFS): assume that we continue to provide
983705b2af Jean*     UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
                     output files) and apply r* scaling at each time-step (function of the time
                     varying Eta field); use normal pickup files (needed for restart with NLFS).
28e8749e94 Oliv* o adjoint with OpenAD:
                   - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
                     package openad.  This package has to be compiled for all runs with OpenAD
                     instead of specifying code_oad_all as a modification directory.
                   - link the fortran templates from tools/OAD_support to the build directory
                     for preprocessing to avoid conflicts between different setups compiled
                     simultaneously and simplify cleanup.
96b2fd29af Jean* o pkg/exf:
                   - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
                     main model or other pkgs are exchanged in EXF_MAPFIELDS).
                 o model/src:
                   - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
                     (similar to do_fields_blocking_exchanges.F).
                 o tools/genmake2:
                   - remove TAF output src code just before calling staf (when not doing a fresh
                     built, will stop if things go wrong with staf).
                   - fix target "adobj" (left from TAF version-2 transition)
2cbfd59e75 Jean* o pkg/diagnostics:
                   - add a parameter to track the status of pkg/diagnostics activation;
                     this replace/extend the use of logical param "settingDiags" (to check
                     when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
                     New S/R to print error message and stop when pkgStatus is not right.
                   - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
                 
45d3f75a8f Jean* checkpoint64m (2013/08/13)
ee9d1fdd8f Jean* o model/inc:
                   - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
                     8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
                 o pkg/kpp & aim_v23:
                   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
19c1d5675e Jean* o pkg/seaice:
                   - restore (last time on 2011/12/24) ability to compile pkg/seaice with
                     undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
ee9d1fdd8f Jean*   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
                 o eesupp/src:
                   - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
                     in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
51fc369eef Jean* o switch to TAF version-2:
                   - add flow directives to "freeze" naming convention for ad-routines that
                     are used in I/O routines of adjoint state and associated common blocks
                     that are used in adcommon.h (backward compatible with version-1)
                   - update all ad-optfiles (in tools/adjoint_options + few local to some
                     verification exp) to switch to latest TAF version (currently 2.5.5);
                     merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
                     out except for diva).
                   - the major change with TAF version-2 is that both the differentiated
                     routines and the forward routines (new) are returned as part of the TAF
                     output source code. Update genmake2 accordingly.
                   - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
                     with version-2 when compared to TLM or FWD gradient); other experiments
                     output show minor changes (machine truncation level); update the few AD &
                     TLM output with 12 matching digits only (some prior to version-2 switch).
                 
5ed109e8ff Jean* checkpoint64l (2013/08/05)
f66939121e Jean* o model/src:
                   - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
ea7e42c5a8 Jean*   - main_do_loop.F: no longer includes additional (AUTODIFF) header files
                     when using TAF but only if using OpenAD.
c7389f7fae Jean* o pkg/mom_common+fluxform+vecinv:
                   - always set horiz. viscosity arrays to background value before calling
                     MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
                     only when using variable horiz. viscosity (useVariableVisc=T);
                   - simplify mom_vecinv.F (only 1 block for momViscosity).
d9f9cc1105 Jean* o pkg/mom_common: variable horiz. viscosity in NH code
                   - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
                     from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
                   - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
                     useBiharmonicVisc & useVariableVisc.
                   - fix old bug (already in 1rst implementation of variable horizontal viscosity
                     in calc_gw.F, version 1.27, 2006/06/20):
                     horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
                     even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
                   - change background horiz viscosity in vertical momentum (gW) to always be
                     viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
                     any type of variable viscosity, e.g., viscAh/4Grid)
                   - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
                     viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
                     horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
                     default viscAh,viscA4 is zero).
e636cf27b8 Jean* o model/src:
                   - extend length of drC & recip_drC from Nr to Nr+1.
e8ed922ed3 Jean* o Divided Adjoint (DIVA) with MPI:
                   - genmake2: do not create local ./mpi_headers dir when no file to copy into.
                   - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
                     and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
                 
8dca956637 Jean* checkpoint64k (2013/07/23)
dee062a69c Jean* o tools/OAD_support:
8dca956637 Jean*   - avoid the need for file "oadtempflile" in insertTemplateDir.bash
                     and remove it from genmake2.
dee062a69c Jean* o tools/build_options:
                   - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
                     MPI_HEADER_FILES list (let genmake2 find the missing headers)
4be02e3b08 Dani* o verification/halfpipe_streamice:
dee062a69c Jean*   - change to driving stress formulation; update both Fwd & AD output.
                 o tools/genmake2 and Divided Adjoint with MPI:
                   - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
                   - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
                   - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
                     Makefile, which is set by genmake2, and check which mpi-headers are needed.
                     Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
                   - update target "CLEAN" (to also remove ./mpi_headers/ dir).
bcf312c024 Jean* o testreport:
                   - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
                     perform additional runs (number of additional runs is "add_DIVA_runs" taken
                     from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
                 o verification/lab_sea (AD test):
                   - change to test Divided Adjoint Run in this set-up (both standard AD test
                     and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
0f31045802 Jean* o pkg atm_ & ocn_compon_interf:
                   - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
                     staggerTimeStep implementation) and disable (retired) corresponding
                     parameter.
d761a6c43f Jean* o pkg/offline:
                   - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
                   - add S/R OFFLINE_CHECK to print offline parameter summary
                     and stop if loading a file that is not used;
                   - enable to calculate GMRedi tensor, KPP mixing and convective index
                     when the corresponding file(s) is/are not specified (but pkg is used).
2bbc535596 Jean*   - comment out resetting of monitorFreq (to endTime) since it still useful
                     for monitoring CFL numbers and checking offline fields.
e44d40886c Jean* o OpenAD:
                   - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
                     smaller standard output) and generate new (smaller) output (on baudelaire
                     using gfortran with -ieee) for exp. tutorial_tracer_adjsens
5c3afaf8cf Jean* o model/src:
                   - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
                     (where external_forcing_adjust was called) and change list of arguments;
                   - merge external_forcing_adjust.F into external_forcing_surf.F
                   - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
                     which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
                     previously in file "balance_relax.F", now removed); remove corresponding
                     arrays in FFIELDS.h.
                   - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
                     a hack for getting back surfaceForcingS (loaded from file) when using
                     ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
                   - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
                     (was getting only 11 digits for AD-grad, due to different truncation
                      error in AD code).
                 
f15d0780a7 Jean* checkpoint64j (2013/07/04)
b9ef6e0869 Jean* o pkg/offline:
                   - to enable the use of other features with pkg offline (e.g., obcs),
                     also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
                   - comment out "allowFreezing" (now active) in 2 offline testing exp.
27ebbc08f6 Dimi* o pkg/exf ALLOW_RUNOFTEMP
                   - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
5c3afaf8cf Jean*   - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
684284fdda Dimi*   - changes verification/global_ocean.cs32x15/results/output.seaice.txt
d2e18b684b Jean* o pkg/atm_phys:
                   - allows to add some damping on uVel,vVel (strength only function of k).
978ac82129 Jean* o verification, ad-tests:
                   - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
                     global_ocean_ebm and offline_exf_seaice.thsice.
b8dffaf82f Dani* o verification/halfpipe_streamice:
                   - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
                     flux input boundary conditions to be ignored; a fix for this bug changed
978ac82129 Jean*     verification results for forward test.
                   - add adjoint test.
7ee27107e3 Jean* o pkg/ptracers:
                   - allow to restart without SOM pickup (resetting SOM to zero).
0d1e4b948d Mich* o pkg/gmredi:
                   - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
                   - It uses mixing length theory and suppression by steering level effects to
                     calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
                     to JPO, for more details).
                   - It also uses the diffusivity to calculate an eddy induced streamfunction
                     based on a PV closure (rather than a buoyancy closure as in GM).
7ee27107e3 Jean*   - New files added to pkg/gmredi:
0d1e4b948d Mich*     gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
                       induced overturning streamfunction (called from gmredi_calc_tensor)
                     gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
                       for use in gmredi_k3d
                     gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
                       the eddy diffusivity
ffc1393533 Mich* 
fe0ec941c0 Jean* checkpoint64i (2013/06/18)
e68ed13a81 Jean* o pkg/cheapaml:
                   - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
                     that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
                     with pkg/cheapaml.
                 o utils/python: add subpackage for cubed sphere function, first example is
                     simple cs.pcol to plot 2D fields on a map
531678d622 Dani* o pkg/streamice:
                   - This is a new package in MITgcm, which solves dynamic equations for ice
                      sheets and ice streams
e68ed13a81 Jean*   - At the moment it is independent of atmosphere/ocean dynamics, or any
531678d622 Dani*     other physical packages in MITgcm, even ShelfIce (although it is anticipat-
                     ed that this will change)
e68ed13a81 Jean*   - There is a new verification exercise that tests it, halfpipe_streamice,
531678d622 Dani*     evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
                     rectangular embayment
                   - halfpipe_streamice is forward-only for now, will have TAF test soon
                   - for questions, email dgoldber@mit.edu
04cb5dc10d Jean* o pkg/thsice:
                   - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
                     of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
                   - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
                      call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
                   - allow precip from pkg/cheapaml to make snow over seaice.
a5f3de150b Jean* o pkg/cfc:
ac5b32ca4b Jean*   - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
                   - remove atmos CFC 2-D arrays from common bloc (now local variables)
                   - change some hard-coded constant to run time parameter for reading and
                     and interpolating atmospheric CFC ; keep same default as previously.
                   - more flexible reading of Atmos CFC (number of records no longer hard-coded)
                   - put arguments in standard order: myTime, myIter, myThid
                   - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
                     atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
                   - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
                   - new routine to print summary of CFC params and check for consistency.
7a8082e765 Mart* o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
                   similar to thsice_advdiff.
                   Note that for the B-grid case the routine parameters uc/vc are overwritten.
ac5b32ca4b Jean* o pkg/cfc:
a5f3de150b Jean*   - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
                     update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
ac5b32ca4b Jean*   - fix interpolation of atmphspheric CFC between Sorthern and Northern
                     hemisphere value.
5dd9cc40ef Jean* o pkg/seaice:
                   - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
a8ebf896c4 Mart* o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
                               so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
                   - requires an additional time level that is stored in the pickup
                   - you can start with AB2 from a pickup without this time level with
                     pickupStrictlyMatch = .false.
                 
2d517edcde Jean* checkpoint64h (2013/05/26)
06294f69b9 Jean* o pkg/cheapaml:
                   - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
                     affect machine truncation (but exp cheapAML_box still pass with 13 digits).
                   - consistent treatment of uWind,vWind location: assume everywhere in
                     pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
                     (Note: was already the case for Tair,Qair advection);
                     add option (INCONSISTENT_WIND_LOCATION) to recover old results.
                   - compute diabatic forcing only in the interior (excluding overlap regions)
                   - fill in array "Qsw" (for short-wave heating);
                   - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
                     before any update (consistent with MITgcm state var diagnostics);
                   - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
                     non periodic ; + adjusted for uWind,vWind (C-grid).
                 o pkg/seaice:
                   - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
                     add explicitly pkg/exf in experiments that currently use pkg/seaice.
                   - allows to compile pkg/seaice without pkg/exf.
142cc892c8 Jean* o tools/OAD_support:
                   - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
                     of array "ourStepOf" in function rvNextAction (revolve.F90).
723a22990a Jean* o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
                   - change pkg name (to be used with other atmospheric physics pkg)
                     but by-pass CVS when making the new pkg so that we keep the CVS history.
a280c86ad5 Jean* o pkg/offline:
                   - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
                     (previously called from pkg/dic_surfforcing_init.F)
                 o model/src:
                   - re-order sequence of calls within packages_init_variables.F, using
                     standard order, except for:
                      DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
                      CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
ac0d2c71f0 Jean* o new pkg: atm_phys
2edfb1b43c Jean*   - add entry point and source code (previously in contrib
                       verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
                     (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
ac0d2c71f0 Jean*   - re-order sequence of calls within packages_readparms.F,
                      packages_init_fixed.F and packages_write_pickup.F
                     (but skip packages_init_variables.F because of TAF issues).
2edfb1b43c Jean*   - update contrib/*/atm_gray/ experiment.
b7399a7436 Jean* o pkg/seaice (ITD code):
76166139ef Jean*   - simplify and fix the writing of pickup-files for ITD case
                 o pkg/seaice (ITD code):
b7399a7436 Jean*   - introduce floe size dependent lateral melt for ITD case;
                   - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
                   - update seaice_itd experiment main output.
ffa44e5be9 Jean* o pkg/thsice:
                   - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
                     declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
                     changed accordingly pkg/atm2d.
                 
134aa64c5b Jean* checkpoint64g (2013/05/01)
8f8fcb55e3 Dimi* o pkg/exf ALLOW_RUNOFTEMP
                   - if defined,  river and glacier runoff temperature can be read-in from
                     runoftempfile; runoftempfile needs to have same format as runofffile
a665b019b3 Jean* o pkg/thsice (& pkg/bulk_force):
                   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
                     for energy content of Precip + RunOff & Evap (like with pkg/exf).
                   - change computation domain to always be the interior (without overlap).
                   - fix bug (wrong overlap) when using EXF and stressReduction > 0.
690aeca19f Oliv* o verification/tutorial_global_oce_biogeo:
                   - add preliminary OpenAD setup (still has problems)
134aa64c5b Jean* o pkg/seaice:
6c4c641ea1 Mart*   - turn some parameters for choosing the convergence criterion of
                     the inexact Newton method (JFNK) into runtime parameters for convenience
134aa64c5b Jean*   - clean up seaice_calc_viscosities.F: remove/retire two options for
6c4c641ea1 Mart*     SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
                     the results of lab_sea/input because a division has been replaced by
                     a multiplication with the reciprocal (sumNorm)
                   - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
134aa64c5b Jean*     convergence of solver (changes results, of course), and to test some
6c4c641ea1 Mart*     new features
14111182a7 Jean* o model/src:
                   - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
                   - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
                   - move forcing adjustment (balancing surface forcing) in specific S/R
                     where might also be applied exchanges (if needed) to forcing arrays.
f63796dcfc Jean* o pkg/shelfice:
                   - allow to specify the Ice-Shelf mass per unit area (instead of
                     shelficeLoadAnomaly) and do the conversion from one to the other
                   - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
                     to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
                     (b) will be loaded in time (before calling INI_PRESSURE) in case it is
                     needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
                   - update isomip experiment forward output (get machine truncation error
                     from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
01fb631dba Jean* o verification/offline_exf_seaice:
                   revise data.seaice in input.thermo and input_ad and update results accordingly
b57d4b5259 Gael*     HO = 0.2, SEAICE_areaLossFormula = 2,
01fb631dba Jean*     SEAICE_growMeltByConv = .TRUE.,
b57d4b5259 Gael*     SEAICE_doOpenWaterMelt = .TRUE.,
01fb631dba Jean*   Improve consistency with input.thsice and fix the spurious 500m ice corners
                 o verification/global_ocean.cs32x15:
                   - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
                     in icedyn (thsice+seaice-dyn) test and update output.
                 o verification/offline_exf_seaice:
                   - adjust list of tested variables (with testreport) and update
                     standard test output with better slection of monitored fields.
8fe5c1e95b Jean* o pkg/cd_code:
                   - swtich off Adams-Bashforth on the 1rst iteration. Update output of
                     experiment lab_sea.hb87
9f4f698356 Jean* o tools/genmake2:
                   - change default makedepend from the system default to tools/xmakedepend:
                     When no makedepend is specified, select tools/xmakedepend it the test pass,
                     otherwise select the system default (if exist and pass the test) or
                     try to build cyrus-makedepend ; stop if none of the 3 works.
329d560e65 Jean* o pkg/exf & pkg/thsice:
                   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
9f4f698356 Jean*     for energy content of Precip + RunOff & Evap. Assumes:
329d560e65 Jean*    1) Rain has same temp as Air.
                    2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
                    3) Run-Off comes at the temp of surface water (with same Cp)
                    4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
                     put directly into Latent Heat flux & should use water-vapor heat capacity.
                    5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
                     with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
f21dfbc609 Mart* o pkg/seaice: simplify the use of CPP flags in JFNK-related files
                     (compile when SEAICE_ALLOW_JFNK is defined)
47259ecf74 Jean* o pkg/thsice:
                   - fix oceanic flux diagnostics & timeave (left from new sequence of calls
                     implementation): move THSICE_AVE call after the advection (called directly
                     from thsice_do_advect.F).
0005dc42e3 Patr* o verification/global_ocean.90x40x15 and OpenAD:
                   New experiment for OpenAD is identical to the one in input_ad except that
                     multiDimAdvection=.FALSE.,
                   There is still an issue with this.
b105fb69b1 Jean* o pkg/thsice:
                   - account for ice velocity (ocean relative velocity) in turbulent heat flux
                     at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
                     and offline_exf_seaice (main test).
                 
490ead03b8 Jean* checkpoint64f (2013/03/31)
                 o verification/OpenAD:
                   - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
                 o verification/isomip, pkg/shelfice and OpenAD:
789efdf83c Patr*   - add OpenAD setup to this exp and make shelfice package work with OpenAD
490ead03b8 Jean* o verification/tutorial_global_oce_biogeo:
                   - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
                 o verification/offline_exf_seaice:
                   - replace adjoint experiment (now similar to fwd input.thermo/ setup).
ee82888721 Oliv* o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
                   - add OpenAD setup to this exp and make ptracers package work with OpenAD
490ead03b8 Jean* o pkg/seaice/seaice_evp.F:
                    mask the asymmetric contribution of the ice-ocean stress (when
                    the turningAngle is non-zero) over open water to avoid stripes
                    in the EVP-solutions after many EVP-substeps. This does not change
                    the verification experiment (because turningAngle=0 in that experiment),
                    but will affect other EVP solutions with turningAngle.ne.0
d38c2a4135 Jean* o verification, AD & TLM output:
                   - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
                     additions and multiplications which affect results at machine truncation
                     level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
                     lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
                     (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
                     digits of matching.
b3668e95f2 Mart* o pkg/seaice:
d38c2a4135 Jean*    modify lsr-algorithm so that it vectorizes AND converges by using a
                    "zebra" method: split vector loop into two with step size 2; this
                    solves a general convergence problem for the JFNK solver on a vector
                    computer. It has the potential to even improve convergence for
                    non-vector machines, but it does change the results so it is turned
                    off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
                    SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
b3668e95f2 Mart* 
06b25f9a40 Jean* checkpoint64e (2013/03/05)
59b6bd98c8 Patr* o pkg/ecco and several verification experiments:
06b25f9a40 Jean*    Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
                    from ecco package, and revert to unified routine in model/src/
                    Adjust verification experiments accordingly, especially gloal_oce_llc90
                    Should conclude long-standing work by Gael to reconsile the_main_loop with
                    ECCO and will enable OpenAD's revolve loop in ECCO setup.
7c6b6a09d0 Jean* o pkg/generic_advdiff:
ccf9e62cda Jean*   - implement compressible flow method for multi-dim advection (similar to
                     gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
                     TAF generates many recomputations) to use it; no yet coded with implicit
                     vertical advection.
                   - change experiment advect_cs (new output) and advect_xy (same output)
                     to test compressible flow multi-dim advection.
                 o pkg/generic_advdiff:
7c6b6a09d0 Jean*   - fix SOM advection for unusual cases (linear Free-Surf in r*, other
                     cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
                 o pkg/seaice:
cfab924fcb Mart*   - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
7c6b6a09d0 Jean*     bug affects two verification experiments (lab_sea and lab_sea.hb87),
                     recover old (wrong) results by setting noSlipFac = 2. in
cfab924fcb Mart*     seaice_calc_strainrates.F;
8c657eb247 Mart*   - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
7c6b6a09d0 Jean*   - add runtime parameter SEAICE_JFNKepsilon for that finite difference
8c657eb247 Mart*     gradient in the Jacobian times vector operation (s/r seaice_jacvec)
                   - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
c59d410006 Mart* o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
                   - new subroutines seaice_lsr_tridiagu/v
                   - introduce loop bounds i/jmin/max to be able to use a restricted
                     additive Schwarz method, but not used for now.
                   - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
                   - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
9743b80f75 Patr* o OpenAD support
06b25f9a40 Jean*    Reorganize S/R call for overall time-stepping loop to facilitate
                    OpenAD revolve loop replacement
                    (new S/R main_do_loop.F)
6dd77b4354 Jean* o model/src:
                   - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
                   - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
                     ADAMS_BASHFORTH2.
7bfbef8b82 Jean* o pkg/cheapaml:
                   - add new parameter (default=F, same as before) to disable full domain
                     (including land) periodicity in X & Y dir.
                   - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
                     prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
                     into single S/R CHEAPAML_TIMESTEP.
                 
544247e9eb Jean* checkpoint64d (2013/02/17)
11fe9ae9a2 Jean* o pkg/monitor (angular momentum):
                   - do not add Eta contribution to the total AM if using rigid-lid;
                   - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
                   - horizontal discretisation: compute Zonal wind contribution separately for
                     each component (instead of from cell centered averaged) and use the 4
                     grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
                   - Check that AM is conserved with linear dynamics (momAdvection=F and linear
                     FreeSurf) if using vectorInvariant momentum.
                 o model/src (horizontal grid):
                   - move initialisation of all horizontal grid arrays to null value
                     from specific horizontal grid S/R to main S/R INI_GRID;
                   - add 2 new arrays to project model C-grid velocity on to zonal direction
                     (similar to AngleCosC & -AngleSinC but at U and V point location) and
                     compute them in S/R CALC_GRID_ANGLES.
48a47574f9 Mart* o pkg/seaice: replace a hard coded parameter by a runtime parameter
11fe9ae9a2 Jean*     SEAICE_JFNK_tolIter
a1321f078e Mart* o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
                     preconditioner for JFNK (run LSR into the overlaps as far as possible,
                     i.e OLx/y-2, but overwrite the solution in the overlaps)
                   - extend loop range in seaice_calc_viscosity
                   - add new parameters SEAICE_OLx/y (default = OLx/y-2)
                   - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
                   - slightly modify loops in tridiagonal solver lsr-preconditioner
                   - by default remove the extra exchange in seaice_preconditioner with a
                     replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
                   - modify offline_exf_seaice so that old results without RAS are reproduced
                     for output.dyn_jfnk.txt
                   in seaice_fgmres.F (unrelated to RAS)
                   - add a cpp-flag option for a re-ordered mapping (potentially more
                     efficient), but because this changes the results, turn it off by
                     default
                   - replace the save statement by local common blocks
4a6b51e826 Jean* o utils/matlab:
                   - fix tile-offset in rdmnc.m when output was produced using EXCH2.
                   - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
                     instead of local script "load_cs.m".
0d86f34c41 Mart* o pkg/seaice:
                   - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
                     to the scalarProductMetric and the unrolling. By chance this does not
4a6b51e826 Jean*     change the verification experiment, because of the particular domain
0d86f34c41 Mart*     decomposition
4956a0134a Jean* o pkg/diagnostics:
                   - change default missing_value from UNSET_RL to -999.
b24144b856 Mart* o pkg/layers: improve vectorization of layers_fluxcalc.F
4a6b51e826 Jean*   - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
b24144b856 Mart*     time spent in this routine by more than a factor of 3 on an NEC-SX8
                   - step 2: replace search algorithm by a bisection algorithm found in
4a6b51e826 Jean*     Press et al. Numerical Recipes in Fortran. This algorithm can be
b24144b856 Mart*     vectorized and finds the correct bin in approx. log2(Nlayers) steps.
                     For now, use this algorithm only for TARGET_NEC_SX defined.
                   - moved the search algorithm into a separate subroutine, that is kept
                     within the same file for automatic inlining.
                   - modified catching potential errors
4956a0134a Jean* o pkg/ecco:
27b515a5c9 Gael*   - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
4956a0134a Jean* o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
27b515a5c9 Gael*   - modifications for ALLOW_GENTIM2D_CONTROL
                   -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
                   -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
                   -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
                   -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
f193ea8b76 Jean* o model/src:
                   - account for moist thermodynamics in (dry) potential temperature equation;
                     update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
                     and cpl_aim+ocn.
25fdd6d933 Jean*   - also switch to standard compiler (gfortran, was using ifort previously)
                     for fizhi-cs experiments reference output.
f193ea8b76 Jean* o pkg/ctrl:
93e42e1e05 Patr*   - 1st step toward generic time-varying control variable (2D) via CPP option
                     ALLOW_GENTIM2D_CONTROL
                   - note new namelist ctrl_nml_genarr in data.ctrl
df3d2037ba Jean* o verification/global_ocean.cs32x15:
                   - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
                     thsice calling sequence and update "output.icedyn.txt" output file.
a618488a45 Jean* o pkg/ptracers:
                   - from Ryan A.: code to allow to restart a tracer at regular time interval
                     specifying a reset frequency and a reset-phase (for each tracers).
8d7c0d8037 Jean* o pkg/thsice:
b8ed299f9d Jean*   - implement new sequence of calls for thsice+seaice:
                       previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
                       new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
                   - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
                     in CPP_OPTIONS.h) to recover old sequence;
                   - update diagnostics for Intermediate State thsice diagnostics: now filled
                     just before advection (instead of just after advection in old sequence);
                   - update output of experiment offline_exf_seaice (standard test);
                   - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
                     by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
                 o pkg/aim_v23:
                   - use tiled array for aim_CO2 and surface wind speed for export to coupler;
                   - use standard pkg/mdsio routines to read & write CO2 pickup file;
                   - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
                   - Implement new sequence of calls for seaice advection (with thsice and
                     seaice diffusion): do ice advection after ice-Thermodynamic (previously
                     was done before); change aim_do_physics.F (split the bi,bj loops block);
                   - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
                 o pkg/thsice:
8d7c0d8037 Jean*   - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
                     where just seaice diffusion is used without seaice-dynamics.
                 
9f6899b968 Jean* checkpoint64c (2013/01/18)
                 o pkg/seaice:
                   - add a parameter JFNKres_tFac that can replace JFNKres_t
9ebe58d4fa Mart*     (= JFNKres_tFac*JFNKresidual before JFNK solver)
                   - add a line search option to the JFNK solver
9f6899b968 Jean*   - move update of u/vIce and computation of initial residual into a separate
c937d257c3 Mart*     routine (same file); makes the code a little easier to read (?)
                   - the line search requires computation of the residual and for some reason
9f6899b968 Jean*     I cannot do the update of u/vIce at the beginning of the Newton loop
c937d257c3 Mart*     without changing the results, so we move computation of the new residual
                     also to the end of the Newton loop, even without the line search
3b4e62adf7 Jean* o pkg/mdsio:
                   - write missing value (corresponding to undefined array value) to meta files;
9f6899b968 Jean*     skip this if missing value is one (UNSET_RL would be a better value for the
3b4e62adf7 Jean*     case of undefined missing value but it's current the default missing-value);
                     Also update mdsio_read_meta.F (reading timeInterval & missing-value).
93ace0b1be Jean* o pkg/exf & thsice:
9f6899b968 Jean*   - for diagnostics purpose, fill-up and update Qsw array (+ fill the
9ebe58d4fa Mart*     diagnostics) even when SHORTWAVE_HEATING is #undef;
93ace0b1be Jean* o verification/cfc_example:
9f6899b968 Jean*   - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
9ebe58d4fa Mart*     illustrate how to use it).
7f496449e0 Jean* o verification/offline_exf_seaice:
                   in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
                     files to only one time-record.
                   in input.thermo: narrow the 2 bands of low initial ice-concentration near
                     N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
9f6899b968 Jean*     snapshot output; same mcPheePiston value as in thsice with
9ebe58d4fa Mart*     surf-current=0.2m/s.
7f496449e0 Jean*   in input.thsice: similar set-up as in input.thermo (channel with same seaice
                     initial conditions).
a504296e19 Jean* o verification/cfc_example:
                   - update file "data" with more standard choice (default rotationPeriod,
                     exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
                     set deltaTFreeSurf to deltaTtracer) and update the output.
                 o pkg/layers:
                   - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
                   - ensure that "layers_bolus" is switched to False when useGMRedi=False.
                 o verification/offline_exf_seaice:
                   - set all {field}period to zero for constant-in-time forcing (not tested
                     anywhere else).
bde2cd981d Jean* o verification/offline_exf_seaice:
                   - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
                   - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
a4ef5db77d Jean* o model/src:
                   - implement Finite-Volume method for (hydrostatic) presure gradient
                     from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
                 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
                   - In order to be compatible with the default EVP code, this requires changing
                     the EVP code around a little; and because any small change immediately
                     breaks the lab_sea.hb87 verification experiment, the reference output is
                     updated two times (each time the remaining aggrement was only 2 digits):
                     - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
                     - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
                     The adjoint test lab_sea.evp also needed to be updated.
                   - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
                     SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
                     a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
                     explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
                     INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
                     kept obscure, because I need to test it a little more.
9902b68429 Jean* o pkg/cheapaml:
                   - fix few incorrect type (_RL/_RS) in subroutine calls.
                 o pkg/seaice:
                   - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
                     to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
8ecbb13ed3 Jean* o model/src:
                   - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
                     change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
                     experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
01e3fdb926 Jean* o pkg/cheapaml:
                   - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
                     update output of experiment cheapAML_box.
d9f9739596 Jean*   - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
                     and set them only in one place (cheapaml_readparms.F).
                   - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
                   - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
                     and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
69e136acfe Gael* o model/src/the_main_loop.F:
                   - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
                 o pkg/seaice:
                   - remove legacy branch code.
                   - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
                 o verification/*/code*/SEAICE_OPTIONS.h:
d9f9739596 Jean*   - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
01e3fdb926 Jean*     SEAICE_CAP_HEFF).
b4639cc807 Jean* o pkg/cheapaml:
                   - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
                     to load new forcing fields.
                   - add missing "_d 0" where it's needed; + some editing (improve indentation).
                   - remove switch to "-r8" compiler option (no longer needed) in verification
                     cheapAML_box, keep same output (small trucation error differences).
692e8490be Jean* o verification/offline_exf_seaice:
54b88f0722 Gael*   - add thermodynamics only test.
692e8490be Jean* o verification/cheapAML_box:
                   - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
                     keep same output (same 14 digits for cg2d).
                   - switch on "-r8" compiler option (some numerical values are missing
                     the "_d 0") and update output (only 6 digits for cg2d were preserved).
54b88f0722 Gael* 
026a4385c5 Jean* checkpoint64b (2012/12/24)
51ad14de13 Jean* o pkg/cheapaml:
                   - remove un-used variables (Qnet,EmPmR) from pickup files.
                   - store tendency of advected variables into cheapaml pickup file
                     and fix the AB-2 restart.
0ef659ed72 Gael* o verification/offline_exf_seaice and lab_sea adjoint:
51ad14de13 Jean*   - switch to new code (#undef SEAICE_GROWTH_LEGACY).
                   - switch to 4 time steps in offline, consistent with lab_sea.
026a4385c5 Jean*   - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
51ad14de13 Jean*   - update results after change of experiment seaice.
026a4385c5 Jean* o pkg/seaice:
                   - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
                     parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
                     still defined since SEAICE_multDim needs to be set to MULTDIM value (from
                     SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
7755429b93 Jean* o model/src:
                   - add run-time parameter to select CG2D solver minimum-residual solution
                     (in case of a poor convergence).
262f1a37c5 Mart* o pkg/seaice/seaice_lsr.F
7755429b93 Jean*   - move calculation of matrix coefficients into new
ed8217d1df Mart*     S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
                     file; the main purpose of this change is to be able to reuse the code
                     in S/R SEAICE_PRECONDITIONER
262f1a37c5 Mart*   - modify the computation of the residual so that the mass of sea-ice
026a4385c5 Jean*     is not used twice; this simplifies the calculations, but since
262f1a37c5 Mart*     the residual is never used except when LSR_mixIniGuess.ge.4---and this is
                     not tested in testreport---this does not affect the testreport results.
adb13907c3 Dimi* o verification/seaice_obcs:
                   - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
                     verification/lab_sea/input.salt_plume; changes results/output.txt*
c178b9393a Jean* o model/src:
                   - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
7e9893ac33 Mart* o pkg/seaice:
                   - improve description of parameters in seaice_fgmres.F and start
                     cleaning up the code
c178b9393a Jean*   - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
7e9893ac33 Mart*     second argument
                   - add a metric based on grid cell area to SEAICE_SCALPROD; update
                     results of offline_exf_seaice.dyn_jfnk
                   - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
e4684a75d6 Jean* o pkg/aim_v23:
                   - fix an other bug in dissipation heating (grid-cell area was missing).
2dc84f624e Jean* o model/src + pkg/seaice:
                   - add global (multi-tile) linear solver for pair of tri-diagonal system
                     along X and Y lines, respectively for U and V component.
                     Note: 1) MPI and cube-exchange not yet coded.
                         2) probably not accurate for poorly conditioned / large size problem.
                   - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
                     default: not compiled and not used.
88a8f1f812 Mart* o pkg/seaice:
                   - first attempt at a multi-threaded fgmres solver for the JFNK solver:
2dc84f624e Jean*     introduce bi/bj loops and use global_sum_tile_rl instead of
88a8f1f812 Mart*     mpi_allreduce in seaice_fgmres.F
                   - improve diagnostics output for fgmres solver (seaice_fgmres.F)
                   - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
                   - add a verification experiment for JFNK in offline_exf_seaice
d5a9a292e9 Jean* o verification:
6531f48833 Jean*   - change (for now, only fwd test) offline_exf_seaice experiment:
026a4385c5 Jean*     use a re-entrant channel with idealized coastline (trapezoidal shape)
6531f48833 Jean*     at southern boundary to explore seaice dynamics and thermodynamics
                     with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
                     secondary test (input.thsice) use thermodynamics only with SST relaxation.
                   - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
                 o pkg/exf:
                   - disable "sstExtrapol" when Nr=1
                 o verification:
d5a9a292e9 Jean*   - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
                     to test pkg/cheapaml.
46af042642 Jean* o pkg/aim_v23 & pkg/shap_filt:
                   - fix dissipation heating (erroneous gravity multiplication factor).
                 o pkg/seaice:
7729ab9475 Mart*   - remove unused field pressPre from jfnk solver
                   - rename two subroutines in seaice_preconditioner.F
e5a4e727cd Jean* o eesupp/src:
                    - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
6ac4f1544e Mart* o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
                    - remove wrong parts of the rhs and the lhs (were in there
                      because I did not understand the concept of this preconditioner)
                    - add an exchange between u- and v-sweep. This increases communication
                      by a factor of two but improves the convergence of jfnk. Ideally,
                      one would like the u- and v-sweep to be independent. So far within
                      undocumented ifdefs
                    - reorganize the extra computations for printing the residuals
24fc5488c9 Jean* o tools/genmake2:
                   - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
                     since it's not necessary (and was preventing to use MNC in some cases).
                 
3b68c5ef24 Jean* checkpoint64a (2012/11/16)
0e1d0943d5 Jean* o pkg/autodiff:
                   - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
                     autodiff_readparms.F no longer depends on calling order (within
                     packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
                     rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
                     and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
ed6db82373 Dimi* o pkg/obcs:
                   - adding tidal velocity forcing capability to obcs
                     for usage example, see verification/seaice_obcs/input.tides
7972e6de33 Mart* o pkg/seaice:
0e1d0943d5 Jean*   - turn the LSR-relaxation parameters WFAU/V into runtime parameters
7972e6de33 Mart*     SEAICE_LSRrelaxU/V
356e5485d1 Mart*   - introduce runtime parameter SEAICEetaZmethod (=0 by default)
be55e6379a Jean* o pkg/aim_v23:
                   - implement heating from friction (bottom friction and stratospheric drag).
                 o pkg/shap_filt:
                   - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
                     dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
0c723af82e Jean* o model/src:
                   - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
                     time-constant addMass field from file (addMassFile);
                   - support for heating due to friction (and Kinetic Energy dissipation):
                     add option, run-time switch and 3-D field array + support code ; each pkg
                     or S/R can add heating contribution (if there is a sink of KE); the sum is
                     accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
93029454d2 Mart* o pkg/seaice:
96c8307cd6 Patr*   - complete merge of ITD code into seaice_growth.F
                     from MITgcm_contrib/torge/itd/code/
                     no verification so far, but Torge Martin tested
                     "1-D test case and Beaufort set up;
                     deliver okay results after 1 model year."
                   - complete merge of SEAICE_SIZE.h into all relevant routines
db6b283965 Mart*   - move computation of eta at Z-points into calc_viscosities
                     + introduce global field etaZ
                     + add different methods for computing etaZ, for now the old
                       method (simple averages of eta to Z-points) is hardwired
0c723af82e Jean*     + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
db6b283965 Mart*       seaice_preconditioner
                   - simplify computations for SEAICE_ZETA_SMOOTHREG
0c723af82e Jean*   - seaice_preconditioner:
773a0cee43 Mart*     + replace one remaining press by pressLoc (mistake)
                     + adjust printing of residuals
54dc59c155 Mart*   - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
0c723af82e Jean*     + add (SEAICE.h) and rename some counters (initiliased in
54dc59c155 Mart*       seaice_init_fixed.F)
                     + add _BEGIN/END_MASTER (myThid)  around print statements
                     + print total number of iterations and failures over SEAICE_monFreq
                       interval to STDOUT
                   - move control over output-messages by fgmres to seaice_jfnk to save
                     some operations
93029454d2 Mart*   - move resetting initial guess for fgmres outside of seaice_fgmres_driver
                     in order to make restarts with sol .ne. zero (fgmres with restarts)
                     (seaice_jfnk.F, seaice_fgmres.F)
                   - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
                     a serious convergence problem when open boundaries are involved
0c723af82e Jean* o pkg/ggl90: fix computation of control volumes for the case of
58e6249dd7 Mart*   ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
                   up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
8e17d76640 Mart* o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
48ffb9e808 Patr* o pkg/autodiff
                   - Add inAdMode switch for SEAICEuseDYNAMICS:
0c723af82e Jean*     SEAICEuseDYNAMICSinAdMode
48ffb9e808 Patr*     (extend logic in ADAUTODIFF_INADMODE_SET)
17353ce854 Patr* o pkg/seaice
                   - Step 1 of merging ice-thickness distribution (ITD) code from
                     MITgcm_contrib/torge/itd/ (author: Torge Martin)
                     The code implements concept laid out in Thorndike et al. (1975);
                     code is enabled via CPP flag SEAICE_ITD
                     nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
                     code is not complete yet!!
48ffb9e808 Patr*   - SEAICE_SIZE.h now included in almost all seaice routines
d28bbf0830 Jean* o verification (using seaice):
                   - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
                     global_ocean.cs32x15.seaice ; update results.
                   - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
                   - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
                     offline_exf_seaice (previously compiling B-grid).
b3a1d973db Jean* o pkg/exf:
                   - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
                     to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
                     forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
c6bd7aced7 Jean* o pkg/layers (adjust changes from Sept 19):
dfcf827164 Jean*   - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
                     this allows to remove "layers_maxNum" dimension from all layers arrays.
                 o pkg/layers (adjust changes from Sept 19):
c6bd7aced7 Jean*   - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
                   - snap-shot extended to all type of layers (not just the 1rst type);
                   - remove layers variables when corresponding CPP option is undef.
                 o pkg/layers:
                   - rename pkg/layers variable and add new output (layer exist & un-weighted
                     velocity in layer)
                 o pkg/seaice:
2c43bfffcf Mart*   - simplify (?) ocean-drag coefficent computations by using
                     the same routine in all three solvers (saves some code lines)
                   - remove global fields DRAGA and DRAGS from C-grid code and
                     declare them locally in lsr.F (the only place where they are
                     still used)
0db5f1068d Jean*   - update AD output of lab_sea.evp (very sensitive anyway).
8c62e844bf Mart* o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
                   (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
                   and SEAICEuseJFNK=.true. A few things to note:
                   - involves a FGMRES, that is parallel but very inefficient,
                     because of many scalar products (global sums) in the Gram-Schmidt
                     orthogonalization method. Needs to be replaced. Original code
                     from J.-F. Lemieux
                   - preconditioner for FGMRES is a stripped down version of LSOR
c6bd7aced7 Jean*   - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
8c62e844bf Mart*     preconditioner. For the preconditioner, the default is set to 10.
                   - Jacobian times vector is computed with finite differences
                   - marginally related to JFNK-solver: add a smooth regularization for
                     zeta with tanh that will improve convergence (Lemieux and Tremblay,
                     2009) for any implicit solver (not implemented for EVP because EVP
                     does not need this regularization in the first place). Define
                     SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
8e5804ab61 Jean* o eesupp/src:
                   - check in genmake2 that intrinsic S/R flush is available.
                   - add S/R to flush IO unit (if intrinsic S/R flush is available)
                   - flush standard & error msg unit before MPI termination
                   - if debugMode, flush IO unit after printing msg
                 o pkg/ctrl:
                   - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
                     to ctrl_set_unpack_xyz.
                 
f9281bf7f3 Jean* checkpoint64 (2012/10/09)
6ae30b06da Patr* o pkg/shelfice
f9281bf7f3 Jean*   - in mom_fluxform.F, mom_vecinv.F:
                     CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
                     Bug fix KappaRU -> KappaRV
                     does not change verification/isomip but may change other setups
                     (presumably constant KappaRU=KappaRV)
9574f2afeb Mart*   - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
5e26aed318 Dimi* o pkg/obcs:
                   - fixed some indexing bugs in obcs_seaice_sponge.F
                   - added obcs relaxation subroutines for HSALT and HSNOW
                   - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
78e0c35225 Mart* o pkg/seaice:
                   - add "multicategory" parameterization for snow in analogy to ice,
                     default is off for now.
fd94cbb100 Jean* o pkg/obcs:
c7c4b57180 Dimi*   - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
                     see verification/seaice_obcs/input.seaiceSponge for example application.
fd94cbb100 Jean*   - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
                     index setting by master-thread. This fix multi-threads Pb in previous modifs.
4d8bc9f16f Gael* o pkg/layers :
fd94cbb100 Jean*   - add diagnostics to pkg/layers
                   - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
                     (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
4d8bc9f16f Gael* o pkg/generic_advdiff/gad_implicit_r.F :
fd94cbb100 Jean*   - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
                 o pkg/seaice/seaice_growth.F:
4d8bc9f16f Gael*   - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
9bb13a83a0 Jean* o pkg/obcs:
f9543ec2af Jean*   - change default setting of OBCS_UVICE_OLD from defined to undef;
                   - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
                     in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
                   - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
                   - change OB null index value (OB_indexNone) to -99 ; this fix the problem
                     with Southern & Western OB at a tile edge (at least in a simple set-up).
                 o pkg/obcs:
9bb13a83a0 Jean*   - change settings of OB index in case OB coincides with tile edge (shared by
                     2 tiles), so that common OB location is registered by both tiles (instead of
                     only 1). However, for Southern and Western OB, index value = 0 is not
                     recognized as valid OB index (=default null value) and needs to be fixed.
                   - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
f9543ec2af Jean*   - new parameter "OB_indexNone" for null index value (for now, still zero)
9bb13a83a0 Jean*     to replace hard-coded null index value of zero.
c783d09169 Jean* o pkg/exch2:
                   - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
                     always check buffer-size (but outside the loop); move checking for valid
                     index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
                     print each tile and point connection only if |W2_printMsg|>= 2 and 3.
307cef9ba4 Jean* o pkg/ctrl (pack & unpack):
                   - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
                     (locally defined) for different variables (+ remove the variable-specific
                     file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
                     (to be extended to other local file names in ctrl.h).
                 o pkg/flt:
                   - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
31ef3766a3 Jean* o pkg/mdsio:
                   - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
4308379183 Jean* o tools/genmake2:
                   - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
                     (added by Alistair in version 1.51 for building without make depend);
                   - remove Header files list (H_SRC_FILES) from the dependence of targets
                      ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
                     place in version 1.23): this save going through staf when unrelated header
                     file has been modified.
                    Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
                     "make depend" step, still need to do "make links" before "make adtaf".
e4daa51e76 Jean* o eesupp/src (+ few pkg src files) & genmake2:
                   - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
                   - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
4308379183 Jean*   - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
e4daa51e76 Jean*      upper/lower case ; account for space between "#" and undef/define)
                 o pkg/flt (with exch2):
                   - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
4308379183 Jean*   - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
e4daa51e76 Jean* 
441c88984f Jean* checkpoint63s (2012/09/05)
8de17d15ea Gael* o pkg/ecco:
f1085458a2 Jean*   - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
                   - add more relevant #ifdef ALLOW_SMOOTH ones.
                   - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
8de17d15ea Gael* o pkg/ctrl:
                   - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
                     ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
f1085458a2 Jean*   - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
                     doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
                     ctrlSmoothCorrel3D (new).
8de17d15ea Gael*     The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
                   - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
f1085458a2 Jean*   - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
8de17d15ea Gael*     controls when useAtmWind, and vice versa.
                   - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
                   - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
f1085458a2 Jean*       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
                   - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
                       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
                   - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
                     replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
8de17d15ea Gael* o pkg/smooth:
f1085458a2 Jean*   - remove un-necessary includes.
                   - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
                     Those CPP options were never defined, and not necessary.
8de17d15ea Gael* o model/src:
                   - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
                   - standard treatment of useSMOOTH.
                 o pkg/autodiff:
f1085458a2 Jean*   - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
                     useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
dace8652ae Jean* o pkg/exch2:
                   - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
8de17d15ea Gael*     + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
dace8652ae Jean*   - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
                     and tiles to process mapping.
                   - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
                     moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
                     rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
                     from w2_eeboot.F to w2_readparms.F.
                 o eesupp/src:
                   - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
                     ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
                     also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
                   - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
                     is defined (remove condition on usingMPI) to match cases where MPI_INIT
                     has been called.
                   - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
                   - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
                     (so that on 1 proc, get same myPid independently of usingMPI)
                   - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
                     useCubedSphereExchange with EXCH-1 (safer).
                   - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
e2a9470322 Jean* o pkg/ggl90:
                   - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
                     used in ALLOW_GGL90_SMOOTH code.
                 o pkg/flt:
                   - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
                     floats at the Southern end of the domain).
                 o eesupp/inc:
                   - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
                     but not used (and not to be used) anywhere, just for documentation.
c7b36da2b3 Jean* o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
                   - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
                     a) can damage previously written records in any other multi-record files.
                     b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
32c6b8e3e2 Jean* o tools/genmake2:
                   - define variable MAKE within Makefile and use it in place of 'make';
                   - update AD_CONFIG.h (if needed) before building any of the executable
                     (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
                     and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
                   - always print usual warning comment 'this file is automatically generated'
                     from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
c7b36da2b3 Jean* o pkg/cheapaml:
                   - updated to correspond to the code used in accepted paper (Nico Wienders).
32c6b8e3e2 Jean* o pkg/exf:
                     added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
                     ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
                     and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
                 o pkg/exf, autodiff, ctrl, ecco and seaice:
                     remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
                 o pkg/ctrl, ecco:
                     allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
                     Depending on useAtmWind, one is inactive, and the other is active (see
                     exf_getffields.F/exf_getsurfacefluxes.F).
4681beea4a Jean* o tools/genmake2:
                   - improve error msg when failing in 2nd test of check_for_broken_Ff
                   - fix option '-makefile' short-name (-mf according to genmake2 -help)
                   - source local config file "genmake_local" just after processing the genmake2
                     command arguments (previously done before processing arg).
07c8ca60a9 Jean* o pkg/grdchk:
                   - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
                     to this routine from cost_final has been dropped in g_cost_final)
                   - improve printed information (more explicit msg, no longer using "print *,"
                      fix fcpertminus printed value).
0c39183c54 Jean* o model/src:
                   - move call to COST_INIT_VARIA out of packages_init_variables.F directly
                     into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
                     this prevents getting cost-funct reset in adinitialise_varia recomputations.
2b983d7243 Jean* o pkg/dic:
                   - move initialisation of "freefe" array from from dic_biotic_forcing.F to
                     fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
                 o pkg/grdchk:
c78fad8e88 Gael*   - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
2b983d7243 Jean*   - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
5be1b702e4 Gael* o pkg/autodiff/ctrl/grdchk :
2b983d7243 Jean*   - attempt to sort out what works and what does not,
5be1b702e4 Gael*     with regard to I/O, and to warn/stop accordingly.
2b983d7243 Jean* o pkg/grdchk:
5be1b702e4 Gael*   - attempt to fix grdchk in the case of useSingleCpuIO.
                   - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
                    statements were moved from grdchk_main.F and into
                    grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
                   - a global sum is applied to record numbers icvrec/layer
                    out of grdchk_loc so that they be passed to I/O routines.
2b983d7243 Jean* o pkg/smooth:
                   - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
5be1b702e4 Gael*     smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
97ed0955b8 Jean* o verification/testreport:
                   - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
                   - can also use compressed (gzip) reference output file;
                   - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
                     to be easier to collect by testreport.
                   - update existing TLM output (half out-of-date by more than 3 yrs).
090e7aded7 Jean*   - report NETCDF & LAPACK settings (from genmake2) in output dir.
                   - report run-time in each individual summary (previously only for AD test);
                     for TLM test, add also TAF version.
                   - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
97ed0955b8 Jean* 
5ea440c02d Jean* checkpoint63r (2012/08/15)
                 o tools/genmake2:
                   - fix Makefile for target ftlall (+ update files to clean after make ftlall)
a7fab58b1c Gael* o pkg/ecco/ecco_cost_final.F :
5ea440c02d Jean*   - fix fc print statements (to stdout and costfunction0000) so
a7fab58b1c Gael*     that the printed value is always after the global sum.
                 o pkg/seaice/seaice_dynsolver.F :
                   - fix ice strength assymptote at SEAICE_area_max<1
                     (no change for the standard case of SEAICE_area_max=1)
f0c312b070 Jean* o some cleaning:
5ea440c02d Jean*   - pkg source files: ensure that all *.F files from each pkg included the
f0c312b070 Jean*     corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
5ea440c02d Jean*     only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
f0c312b070 Jean*     code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
5ea440c02d Jean*     includes;
f0c312b070 Jean*   - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
5ea440c02d Jean*   - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
                     is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
f0c312b070 Jean*     ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
                   - update option-file CPP_OPTIONS.h of all AD experiments:
5ea440c02d Jean*     * no longer include PACKAGES_CONFIG.h ;
                     * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
                     * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
f0c312b070 Jean*       including ECCO_CPPOPTIONS.h).
0185f8e796 Jean* o pkg/cost, pkg/ctrl, pkg/ecco option-file:
                   - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
                     separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
                     not necessary accurate).
                   - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
                     pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
                     deliberately break compilation (a remainder that it needs to be customized)
                   - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
                   - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
                   - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
                 o tools/genamke2:
                   - check for lapack.
53ea01923d Gael* o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
0185f8e796 Jean*   - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
                     jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
                     from both packages.
53ea01923d Gael*   - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
                   - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
0185f8e796 Jean*   - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
                     of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
53ea01923d Gael* o pkg/cost : add comments to explain special and/or untested setups.
6e25847946 Jean* o pkg/exf:
                   - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
                     (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
                 o verification/*/code_ad:
                   mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
                   - reccord when this file is included (define ECCO_CPPOPTIONS_H)
                   - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
                     allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
c67a77c8bb Gael* o pkg/seaice :
6e25847946 Jean*   - added possibility to change ice strength/PRESS0 relationship to
                     HEFF, according to the following run time parameters
                     SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
                     SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
                     SEAICEpresH0   :: HEFF threshold for ice strength            (m)
c67a77c8bb Gael* o pkg/ggl90 :
6e25847946 Jean*   - added run time flag mxlSurfFlag to include the code that ensure
c67a77c8bb Gael*     mixing between first and second level (previously included as a comment)
135650b823 Gael* o verification/1D_ocean_ice_column/input_ad/data.autodiff :
6e25847946 Jean*   - add test of newly added dumpAdByRec=T option where
135650b823 Gael*     we write all records to one file per variable.
                 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
                   - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
                     to check that this code is ok with taf and compiles in adjoint.
                 o pkg/autodiff :
                   - added run time param dumpAdByRec : ad dump format switch.
6e25847946 Jean*     If true then write all records to one file per variable.
                     Else write one file per record (remains the default).
135650b823 Gael*   - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
e9b3a4dec3 Gael* o pkg/seaice:
                  - Added SEAICEuseTILT run time switch : if set to
6e25847946 Jean*    false then omit the tilt term in seaice dynamics.
e9b3a4dec3 Gael*  - Fix free drift calculation.
a8eec7f730 Patr* o pkg/shelfice:
6e25847946 Jean*   When initializing SHELFICEDragQuadratic, set default to be
                   consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
a8eec7f730 Patr*   but retain option to set it independently
                   (inconsistenty spotted by Veronique Dansereau)
fe9611ab7a Jean* o eesupp/inc:
                   - in EEPARAMS.h, add real-type constant for some frequently used simple number
                      (0,1,2,1/2), with name explicitly referring to RS/RL type.
                 o model/src:
                   - move balancing of relaxation terms to new S/R balance_relax.F.
9eb8003f99 Jean* o pkg/autodiff:
                   re-write active I/O high-level (control) S/R:
                   - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
                   - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
                   - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
                     MDS_READ/WRITE_FIELD); change loops to multi-threads.
                   - update and merge active_file_control_slice.flow into active_file_control.flow
                   - update the calls in lower level S/R (active_file.F, active_file_g.F and
                     active_file_ad.F) keeping the argument list and function unchanged.
ee91acaaf9 Jean*   - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
                     =.TRUE.") and remove high-level (control) _loc version (not called anymore).
75bd0a9954 Jean*   - new low-level active I/O routines, one for each type (RL/RS), for active var
                     of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
                     fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
                     right type.
9eb8003f99 Jean* o autodiff and RS=real*4:
                   - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
                     ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
                   - change argument type of 3-D mask argument to _RS to match type in the call
                     (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
4cdea015c1 Jean* o pkg/thsice:
                   - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
                   - option to correct ocean fresh-water flux for imbalance of Atmos+Land
                     fresh-water flux: uniform correction or proportional to local precip.
10741bb907 Patr* o pkg/ctrl:
                   - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
                   - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
                                         ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
                   - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
4cdea015c1 Jean* 
5ba9855446 Jean* checkpoint63q (2012/07/30)
09b7b7656d Jean* o pkg/autodiff:
                   note about monitor and snap-shot of ad-variables:
                   a) need to apply ADEXCH before monitor or output of ad-vars to include
                    overlap contributions (was done for adjDump but missing for monitor).
                   b) since ADEXCH implies adding overlap values to interior array, machine
                    truncation error is expected when adding an ADEXCH call in the middle of
                    the time-stepping (although mathematically identical).
                   modifs:
4d079479ad Jean*   - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
                     declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
09b7b7656d Jean*   - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
                     apply ADEXCH before monitor or snap-shot of ad-variables:
                        =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
                   - implement new method (copy+adexch) for snap-shot and monitor of main model
4d079479ad Jean*     ad-vars (initially not used by default -> output unchanged).
                   - change default (set to 2) to use new method and update few output_adm.txt
                     with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
                     and both tutorial_tracer_adjsens tests).
                   - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
                     and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
01d011442e Patr* o pkg/ctrl:
                   enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
                   generic control variables via
                   #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
                   Only required customization should be S/R ctrl_map_ini_genarr.F
                   (routine in repository contains example)
7f14c670e9 Jean* o pkg/exf:
                   - fix and refine checking of surface-relaxation setting when using EXF
cda8c5ef00 Jean* o verification (adjoint exp):
                   - reduce length of simulation by half for experiment global_ocean.cs32x15
                     (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
a2b6ec31fa Mart* o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
cda8c5ef00 Jean*   - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
a2b6ec31fa Mart*     of KE that can occur with aggressive optimization
cda8c5ef00 Jean*   + put quadratic bottom drag calculation in separated loops (only done if
                     using bottomDragQuadratic)
fb5ebe7993 Jean* o model/src: CG2D_NSA
                   - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
                      and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
                   - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
                      change cg2d residual target to be expressed in Wunits (=> do not normalise
                      RHS ; this fix global_max Pb with TAF); update output.
04c0091821 Jean* o verification/tutorial_tracer_adjsens:
fb5ebe7993 Jean*    improve parameter consistency (and get rid of warnings):
04c0091821 Jean*    - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
                    - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
                    - use staggerTimeStep (for stability) in som81; use default rotation period.
0288336348 Jean* o pkg/exch2:
                   - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
                     reset to 0 = 1 long line in X)
                 o pkg/mdsio:
                   - fix reading of dimensions from meta file for large-size domain
02de2b8dd0 Jean* o model/src:
                   - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
                   - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
                     Cubed-Sphere Exch with CS-corners inside the domain;
                     make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
                     globalArea and to set hasWetCSCorners.
                   - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
                     metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
                   - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
                     useCDscheme and useCubedSphereExchange).
b1b02f4641 Gael* o pkg/seaice/seaice_growth.F :
02de2b8dd0 Jean*   - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
                     for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
                     when the previous code was not correct.
                   - in all cases diagnoze the boundary condition mismatch to SIaaflux
                   - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
                     that term to QNET (essentially to set the melt/freeze water to 0degC).
                     when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
82e953e38c Gael* o verification/global_ocean.cs32x15/input.seaice :
02de2b8dd0 Jean*   - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
                   - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
                   - update results (output.seaice.txt) accordingly.
82e953e38c Gael* o verification/lab_sea/input/data.seaice :
02de2b8dd0 Jean*   - remove SEAICEheatConsFix, which is now be tested
                     in global_ocean.cs32x15. The presently coded fix
                     is only consistent with real fresh water + nlfs.
                   - update results (output.txt) accordingly.
b0139591bd Gael* o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
81055d8424 Jean* o AD_CONFIG.h file:
02de2b8dd0 Jean*   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
                   - remove #include "AD_CONFIG.h" from all included OPTIONS files and
                     add it explicitly in each fortran src file where it is needed.
                     motivation: header file AD_CONFIG.h is generated/modified after "make depend"
                     thus introducing potentially wrong dependency; therefore, better to include
                     it only where it's really needed, and after any other included OPTIONS file
                     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
                     or ALLOW_TANGENTLINEAR_RUN).
81055d8424 Jean* 
361210b820 Jean* checkpoint63p (2012/07/06)
94af53ae23 Jean* o pkg/autodiff:
                   - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
                   - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
                     which are now read from new parameter file "data.autodiff" (inAdExact
                     previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
                   - add file "data.autodiff" in all verification/*/input_ad/ directories.
6101a96b98 Jean*   - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
                     mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
aa94224112 Patr* o verification/tutorial_tracer_adjsens/
                   - add extra sub-verification which uses "SOM" advection scheme
                     (2nd Order-Moment Advection Scheme, Prather Limiter) with
94af53ae23 Jean*       #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
aa94224112 Patr*     and in data:
94af53ae23 Jean*       multiDimAdvection=.TRUE.,
                       tempAdvScheme=81,
                       saltAdvScheme=81,
d3350d435b Gael* o model/src:
                   - introduce ALLOW_BALANCE_RELAX which allow the removal
                    of the global mean of relaxation terms by setting
                    balanceThetaClimRelax and balanceSaltClimRelax
361210b820 Jean*   - disable balanceEmPmR and balanceQnet in the case when useSeaice.
d3350d435b Gael*    This case is now treated appropriately in seaice_growth.F
                 o pkg/seaice:
361210b820 Jean*   - do balanceEmPmR and balanceQnet based on the net fluxes
                     (SItflux) that enter the ocean+ice system rather than QNET
                     and EMPMR. Works best in real fresh water.
                   - SIatmFW, SIatmQnet, and SItflux computations had to be moved
                     out of the diagnotics bloc, and stored in global arrays.
aa94224112 Patr* 
e03d424aa5 Jean* checkpoint63o (2012/06/29)
7ea3641d7d Jean* o vertical mixing schemes:
                   - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
                   - replace computation of density (in Function STATE1, opps_calc.F) by a call
                     to S/R FIND_RHO_SCALAR
                   - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
                     and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
                     affects output (vermix.ggl90) at truncation level.
de24565c3d Jean* o testreport:
                   - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
                     (nSx,nSy) for the number of threads (from eedata.mth)
11491399e8 Jean* o model/src:
                   - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
                     related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
f7139038cb Patr* o verification/tutorial_tracer_adjsens/
                   - compile with ALLOW_CG2D_NSA
                   - run with nonlinFreeSurf=3
                   - update reference output_adm.txt
69c15f0fc5 Jean* o tools/genmake2:
                   - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
                     refine usePROFILES switching off (only when NetCDF is not available).
781a2dcf80 Jean* o verification (atmospheric set-up):
                   - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
89f2ec68ea Gael* o pkg/profiles : refine profiles and files handling.
                 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
c8b7080413 Gael* o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
                   - changes to use model/src/the_main_loop.F rather than the ecco version
                     in ecco type adjoint runs.
18d45ae82f Jean* o model/src:
781a2dcf80 Jean*   - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
                   - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
                   - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
                 o model/src:
                   - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
18d45ae82f Jean*     update output of test experiment bottom_ctrl_5x5.
d8428293bd Jean* o pkg/generic_advdiff:
                   - implement vertical bi-harmonic diffusion (for now, only for T & S and
                     only explicitly).
1beab3301f Patr* o verification/bottom_ctrl_5x5/
                   update reference output (results changed quite some time ago,
                   not sure when; but new reference results look ok in terms of grdchk)
2478d50aeb Patr* o verification/1D_ocean_ice_column/
                   For verification purposes, the exact adjoint rather than an approx.
                   should be used (e.g., to comare against F.D. or TLM).
                   removed autodiff_inadmode*_ad.F routines in code_ad/
                   Update results/ accordingly.
2889362499 Jean* o pkg/cal:
                   - change cal_getdate.F so that output date is function of input time only
                     (less ambiguous, not mixed up with input iteration number).
                   - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3078ffbadd Jean* o pkg/diagnostics:
                   - implement calendarDumps also for stats-diags
                   - implement calendarDumps also for snap-shot output (negative freq)
                   - for now, ignores calendarDumps if non-zero phase-lag.
                 
fb29d0ce0b Jean* checkpoint63n (2012/06/04)
e2c4129169 Jean* o model/src:
                   - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
                     between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
95205589aa Jean*   - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
                     similar to calc_r_star.F); update results of experiment internal_wave and
e2c4129169 Jean*     tutorial_global_oce_in_p (affected @ truncation level).
                 o pkg/shelfice:
                   - add parameterisation of advective-diffusive flux into the ice shelf
c1ef53a9f3 Mart*     according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
                   - simply eps3/3a computation
83625f7fb2 Jean* o eesupp:
                  - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
                    between tiles, just fill-in edges assuming locally periodic subdomain) and
                    add corresponding exchange subroutines (EXCH0);
                  - new CG-solver version (_EX0) for disconnected-tiles special case.
30e5f8e0a0 Jean* o model/src (CG-solvers):
                  - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
                    (similar final residual output and max-Iter number as with standard version);
                  - allows to store and use lowest-residual solution (standard & _SR versions);
                  - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
                  - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
                 o eesup/src:
                  - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
                    ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
0f5e9791d2 Patr* o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
                 
b4f2dc2460 Jean* checkpoint63m (2012/04/27)
fa1b72b057 Jean* o pkg/shelfice:
                  - account for partical cells in surface level below ice-shelf for hydrostatic
                    pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
f74931b354 Jean* o ad test experiments:
                  - update and rename to "ad_optfile.local" local AD-optfile specific to a
                    particular adjoint verification experiment (in verification/*/code_ad/)
fb5f9f12be Patr* o pkg/seaice & pkg/exf:
f74931b354 Jean*  - Part two of ECCO-CLIVAR code merges.
fb5f9f12be Patr*    Completes merge of seaice area relax. code.
                    Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
                    to be set in EXF_OPTIONS.h since this pkg controls its I/O
                    (and avoids second CPP option in SEAICE_OPTIONS.h)
f74931b354 Jean*  - change default value of costIceStart & costIceEnd to a valid date.
f053446eb2 Dimi*  - add snowPrecip to HSNOW in seaice_growth
2db9a89c59 Jean* o pkg/ptracers:
                  - move ptracers summary and setup check into separated S/R ; add a check for
                    valid PTRACERS_Iter0 value (error+stop or just warning).
9afd0876bd Jean* o pkg/cal (+ pkg/ecco):
                  - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
                    as input; and for AD, unless both are not differentiable (e.g., k index)).
546970fc27 Jean* o model/src:
                  - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
                    is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
                    temporary set to usingZCoords value (to be changed to F when using shelfice).
                  - hydrostatic pressure: implement partial cell near the surface also for
                    Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
                    usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
                 o pkg/ctrl/ctrl_init.F:
                  - add a formal parameter to s/r ctrl_init_rec to print
d993cf017d Mart*    xx_$(ctrl_valiable)_file for easier debugging
                  - move call of cal_* routines into the if-block where they are really
546970fc27 Jean*    needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
d993cf017d Mart*    to specify a startdate
5b4194ac9e Jean* o pkg/seaice:
                  - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
                    global_ocean.cs32x15/code versions).
                  - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
                    verification experiment global_ocean.cs32x15.seaice and update results.
0c1f58d8ac Jean* o pkg/exf:
                  - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
                    (according to useExfYearlyFields).
e876af632a Jean* o pkg/cal:
                  - move calendar setting & summary (previously in cal_readparams.F) into new
                    S/R CAL_INIT_FIXED to be called later in the initialisation process, once
                    length of the simulation is set (after SET_PARMS call); This is an attempt
                    to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
                  - For safety: keep a record of pkg/cal parameter settings status
                            to allow to STOP if one pkg/cal S/R is called too early.
0c1f58d8ac Jean*  - add a stop in all basic pkg/cal subroutines if called before setting is done.
                  - modify cal_getdate.F: stop when nothing was returned;
                    if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
                    this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
e876af632a Jean* 
c0d26944d6 Jean* checkpoint63l (2012/04/04)
39e65f8d9e Jean* o pkg/bbl:
                   - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
                     update global_with_exf output.yearly.txt file.
ceea6e3706 Jean* o pkg/cal:
                   - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
                   - remove 2 unsused and very short (1 line only) functions ;
                   - remove unsused subroutines from AD-Diff list.
e8bf169f85 Jean* o model/src:
                   - start to implement clean wait to stop in initialization S/R (config_check.F,
c0d26944d6 Jean*      packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
e8bf169f85 Jean* o folowing PRINT_MESSAGE changes:
                   - remove reminder multiple print to the same file (STDOUT) when multi-threads.
28ed837189 Dimi* o pkg/bbl:
                   - modification so it can work with z*
                   - replace deltaT with dTtracerLev(k) for asynchronous time stepping
                   - global_with_exf/input.yearly verification; changes output.yearly.txt
c064649ac0 Jean* o eesupp/src:
                   - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
                     writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
                   - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
                     # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
                   - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
                   - when using MPI, always set usingMPI=T ; set default accordingly and stop
                     if not consistent.
                   - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
                     argument is zero (in case called within single-thread section).
45e37a1efd Jean* o pkg/fizhi:
                     clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
                     in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
12a35945df Jean* o pkg/exch2:
                   - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
                     activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
                   - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
                     but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
                     with bad ones coming from a not-yet-updated halo.
                     This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
bb86b07795 Dimi* o pkg/frazil:
12a35945df Jean*     move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
                     http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
16e5bb3e87 Mart* o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
709f986fa5 Patr* o verification/lab_sea
                   * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
                   * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
                   * nTimeSteps 3 -> 4
                   * changed reference output accordingly
                 o pkg/ctrl:
                   * fix ctrl_get_gen for xx_sst, xx_sss
0a88b6db42 Jean* o pkg/fizhi:
                   - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
                     update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
6a018349c4 Jean*   - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
                     fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
                     clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
4afb828a3b Jean* o pkg/gmredi:
                   - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
e39d8c1644 Jean* o pkg/fizhi:
                   - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
                     (old)aces open64 tuv test.
fe82383027 Dimi* o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
55118a358d Jean* o pkg/mom_vecinv:
                   - fix 1 loop range in mom_vecinv.F to be like all the other loops which
                     set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
                     with non-lin free-surf).
                 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
                   in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
a826ffe6b9 Mart*   some compilers (gfortran 4.6.0 on MacOS)
71f40693ee Jean* o momentum:
                   - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
                     & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
                     fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
                 
104669e183 Jean* checkpoint63k (2012/03/17)
ecdd0492fa Jean* o model/src:
                    - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
                      flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
                    - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
                      (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
20e7fd8d99 Jean* o model/src: solve_*diagonal.F
                    - replace division with multiplication by inverse (similar to original version)
de7acf9ff6 Jean*      update output of AD exp. global_ocean.90x40x15.
20e7fd8d99 Jean*    - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
                      to enable the use of the vectorized & differentiable solve_tridiagonal.F
de7acf9ff6 Jean*    - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
                      vertical advection (to get solve_tridiagonal tested in AD mode).
20e7fd8d99 Jean* o pkg/seaice: ECCO-CLIVAR merge:
                   1. seaice AREA relaxation
65e93cc4f0 Patr*      * CPP option: SEAICE_ALLOW_AREA_RELAXATION
                      * runtime flag: SEAICE_tauAreaObsRelax
20e7fd8d99 Jean*   2. modified global mean cost imbalance code: CPP option
                       ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
b0f7f403cf Patr* o another iteration on solve_*diagonal.F
20e7fd8d99 Jean*    Make choices independent of AUTODIFF
                    Default will be the adjoinable vectorized version.
                    Alternative choices are:
                    * non-adjoinable original version with low memory footprint:
                      #define SOLVE_DIAGONAL_LOWMEMORY
                    * still adjoinable but does not vectorize (k as inner-most loop):
                      #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
49c840e1d0 Jean* o testreport
                  - add option to use a home made wrapper around "make"
                  - remove MITGCM_IEEE env. variable (no longer active)
fa18eab287 Mart* o pkg/shelfice
                  - improve computation of friction velocity for velocity dependent
                    exchange coefficients: include velocities into SHELFICEBoundaryLayer
                    block to average velocities vertically
                  - add TAF store directives for SHI_ALLOW_GAMMAFRICT
ac52667c1a Patr* o Modify diagonal solvers, now three versions (upon request):
                   #ifndef SOLVE_DIAGONAL_AUTODIFF
                     1. default version (dating back a while ago)
                   #else /* def SOLVE_DIAGONAL_AUTODIFF */
                   # ifdef SOLVE_DIAGONAL_KINNER
                     2. adjoinable version with k-innermost loop (G. Forget)
                   # else
                     3. adjoinable vectorized version of 2.
                   # endif
                   #endif /* SOLVE_DIAGONAL_AUTODIFF */
                   All flags are currently set within routines, but could/should be moved to CPP-options.
                   Array bounds for 1. are as before, for 2.,3. cover the entire domain
                   (could be changed for 1. too).
cc29266a93 Jean* o verification/lab_sea (fwd):
                   - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
                     use 7 categories (except hb87), new solve4temp params (except salt_plume),
                     constant salinity (=4) or variable salinity (salt_plume) done through
                     SItracer.
05513da3da Jean* o pkg/seaice:
                   - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
                   - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
                      SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
                     from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
                     SEAICE_freeze got retired) but already better than previously with
                     SEAICE_freeze=123456.7 deg.C;
                   - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
                     (safer multi-threaded setting); always set SEAICEuseEVP;
                   - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
                     SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
                     stop if multiple specifications for the same coeff; make sure default
                     SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
e6a9f2bf3c Jean* o pkg/obcs:
                   - allow to switch to upwind 1rst order advection scheme for the advective
                     flux computation at the open-boundary; disabled for adjoint built.
e5a3138db8 Jean* o pkg/ptracers:
                   - rename PTRACERS_RESTART.h -> PTRACERS_START.h
                   - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
                   - add parameter to decide when to start a tracer; use internal flag to
                     know which tracer to step-forward; switch this internal flag at the top
                     of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
                     for adjoint built.
3e983913d2 Jean* o pkg/seaice:
                   - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
                   - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
                   - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
ecde946d49 Jean* o pkg/ecco:
                   - fix writing of output file DiagnosCost_ClimSalt/Theta
                     and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3e983913d2 Jean* o pkg/seaice:
e8787c77e2 Jean*   - add missing initialisation of COR_ICE array in dynsolver.F
                   - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
                     compiled either way, and is tested in all exps (multidim was only tested
                     in lab_sea ad before).
                   - cosmetic change to prepare for future addition of ITD. no change to results.
                     no defaults change.
4ed98c0a60 Gael*   - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
e8787c77e2 Jean*   - by lack of adequate verification experiments, I further used custom versions
                     of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
                     should be correct.
4ed98c0a60 Gael*   - avoid recomputations in ad.
7c31770a0d Jean* o array initialisation in adjoint mode:
                   1) pkg/mom_common/mom_calc_ke.F:
                     add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
                     The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
                     part this initialisation is gone, resulting in Floating Point Exception
                     (caught by open64 compiler with debug option).
                   2) model/src/convective_weights.F
                     set output convectCount over the full array range (instead of doing
                     an update): this fix a similar issue when called within recomputation (adjoint)
                     which could by-pass the initialisation (normally done in the caller S/R).
                 o pkg/seaice:
c5b170d8ca Gael*   - final version of turbulent flux params, as agreed at MIT ice meet:
                        SEAICE_mcPheePiston (default is ~ 0.000875)
                        SEAICE_mcPheeTaper (default is 0.)
                        SEAICE_frazilFrac (defualt is 1.)
                        SEAICE_mcPheeStepFunc (default is false)
610e3cd50d Dimi*   - changes results at trunction error level
                   - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
7c31770a0d Jean* o added pkg/frazil:
                   - see frazil_description.tex for details
a7657da9ef Dimi*   - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
bc661abca1 Mart* o pkg/shelfice/shelfice_thermodynamics.F
7c31770a0d Jean*   - fix exponents for velocity dependent exchange coefficients: change
bc661abca1 Mart*     from 2/3(=0) to 0.66666666666666667
7c31770a0d Jean*   - move computation of velocity dependent exchange coefficients into
bc661abca1 Mart*     separate loop, so that it applies to both thermodynamics
                   - move some divisions by constants out of loops
                 
3d1eabb9e3 Jean* checkpoint63j (2012/02/16)
                 o pkg/seaice:
                   - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
                   - SItracer:  added run time params, and allow coupling to ocn salinity.
df0f758af6 Jean* o pkg/seaice: remove (almost) all divisions by constants within loops
                   in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
a54a2ad240 Mart*   results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
df0f758af6 Jean*   those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
                   output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
                 o pkg/seaice :
3d1eabb9e3 Jean*   - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
                     = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
84662a0e96 Gael*   - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
df0f758af6 Jean*   - add permanent SItflux diag that corresponds to TFLUX but includes
3d1eabb9e3 Jean*     ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
df0f758af6 Jean*   - allow activation/testing of a fix for suspected missing term in
3d1eabb9e3 Jean*     ocn-ice heat budget (to be confirmed). To test this, you want to
                     undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
                     SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
84662a0e96 Gael*   - no change in results, fwd or ad.
3d1eabb9e3 Jean* o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
df0f758af6 Jean*   - switch to variable freezing point.
dbf649edf9 Gael*        Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
                   - bug fix : the sublimation term that was missing is now activated.
                        Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
df0f758af6 Jean*   - bug fix : flooding sign term for SIsal0.NE.0.
dbf649edf9 Gael*        Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
                 o pkg/seaice:
                   - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3d1eabb9e3 Jean*     is now the default, and the old default constant freezing point is recovered
                     with SEAICE_tempFrz0    = -1.96,
                          SEAICE_dTempFrz_dS = 0.,
                   - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
dbf649edf9 Gael*   - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
df0f758af6 Jean*   - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
3d1eabb9e3 Jean*     activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
df0f758af6 Jean*   - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
3d1eabb9e3 Jean*     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
df0f758af6 Jean*   - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
3d1eabb9e3 Jean*     seaice_growth r149 for legacy branch (no results change).
                   - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
                     from I. Fenty).
                   - results did not change except for global_ocean.cs32x15, mostly due to the
                     switch to variable freezing point (see above item for detail).
74dd18420e Jean* o pkg/thsice:
                   - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
                     seawater freezing in thsice_calc_thickn (not used).
c2dec35684 Gael* o pkg/seaice: turbulent flux term specification via run time params.
                   - replace CPP switches with run time switches to facilitate testing
3d1eabb9e3 Jean*   - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
                                    GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
c2dec35684 Gael*   - added runtime parameter : SEAICEturbFluxFormula
                   - move Mcphee constants to SEAICE_PARAMS.h
                   - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
3d1eabb9e3 Jean*              SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
                              remove seaice_summary call (moved to seaice_init_fixed)
74dd18420e Jean*   - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
                     SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
3d1eabb9e3 Jean*   - seaice_summary.F : add missing report of read turbulent flux term set up
                                        and SITRACER.
                   - seaice_check.F : check range; inform and stop if retired CPPs are used
                                      (incl. SEAICE_AGE).
74dd18420e Jean*   - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
3d1eabb9e3 Jean*          CPP switch, same computation as before for the different options.
c2dec35684 Gael*   - change results at the truncation level.
1a36f96c43 Jean* o pkg/seaice:
                   - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
                     useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
                     SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
                   - update verification/*/input*/data.seaice:
                     to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
                     code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
                     and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
                     set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
5355c2bbd8 Jean* o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
                   - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
                     algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
                     difference in results only due to machine truncation.
                   - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
                     MaykutPolySatVap; keep MIN_LWDOWN.
                   - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
                   - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
                     + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
f1369fd6d4 Jean* o pkg/salt_plume:
5355c2bbd8 Jean*   - isolate saltPlumeFlux array exch into a specific S/R called from
                     do_oceanic_phys.F
                   - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
f1369fd6d4 Jean* o verification:
5355c2bbd8 Jean*   - move untested set-up to MITgcm_contrib/verification_other.
4a20d767d7 Jean* o pkg/seaice:
ba96883e1a Gael*   - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
                 o pkg/seaice:
4a20d767d7 Jean*   - seaice_solve4temp.F (keeping results unchanged):
                     * add 2 future run-time params to select which saturation vapor pressure
                       formula is used and how post-iteration fluxes are set.
                       Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
                     * New piece of code (not used) to update surf. atmos. heat flux F_ia using
                       the linearized expression to stay consistent with tsurf finding.
                   - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
                     can be < 0.
2953de52a5 Jean* o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
                   - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
                     conductive heat flux F_c , and add it explicitly when updating tsurf as
                     solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
                     so that now F_ia has a consistent meaning through the entire routine.
                     This causes differences at truncation level: update output of fwd exp.
                     global_ocean.cs32x15.seaice.
0c26ee70ab Jean* o pkg/seaice:
c714f5b2dc Jean*   - lots of editing/cleaning in seaice_solve4temp.F + better documentation
                     of arrays, sign/direction of fluxes; no effect on results.
                   - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
                     in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
                     note: this should have been done before changing celsius2K default.
                   - to keep results unchanged, add back old value of celsius2K in verification
                     exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
                   - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
                     SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
                     value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
                     freezing temp is consistent with value in seaice_growth.F ; this causes
                     differences at machine truncation level: update lab_sea AD output (3/4).
                 o pkg/seaice:
0c26ee70ab Jean*   - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
                     and climsst/sss even when using seaice (to prevent calculation that might
                     use SST on land); does not affect any verification exp.
                   - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
                     of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
4091800f77 Mart* o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
                   over land (non-legacy code)
0c26ee70ab Jean* o vectorize salt_plume package:
d797683660 Mart*   - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
                   - this code computes plumebk everywhere (also over land), thus requires
                     code to avoid divisions by zero and catch the case of kLev=Nr.
                   - efficiency of salt_plume_frac is still sub-optimal
a355e8fb2b Jean* o tools (genmake2):
                   - fix makefile NAME specification (option: -makefile NAME) by adding
                     "-f $MAKEFILE" in few places where it was missing including makedepend
                     command (contribution from Paul).
                 
6b11434b7a Jean* checkpoint63i (2012/01/24)
fcc1645548 Jean* o model/src:
6b11434b7a Jean*   - add factorized versions of some EOS code to find_rho.F,
23bdfc896d Mart*     define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
6b11434b7a Jean* o model/src:
fcc1645548 Jean*   - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
                   - change default celsius2K from 273.16 to 273.15
                   - to keep results unchanged, add back old value of celsius2K in verification
6b11434b7a Jean*     exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
                      global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
b730078f53 Mart* o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
                   to make TAF generate vectorizable code
                 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
                    Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
                    have flags that do this more efficiently.
70ade2cedc Mart* o pkg/diagnostics/diagstats_calc.F
                   - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
bd19520b1a Jean* o pkg/obcs (with exch2):
                   - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
                     and remove code (in obcs_readparms.F) which was based on EXCH of indices
                     (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
5759772599 Jean* o pkg/exf and seaice exp:
                   - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
                     so that switching off area & heff advection flags does not affect results.
                   - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
19182668ca Jean*   - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
                     EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
                     results of verification experiments: 1D_ocean_ice_column(fwd),
                     global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
                     and offline_exf_seaice (all 4).
fac86b0a61 Jean* o pkg/seaice:
                   - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
                     remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
                   - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
                     but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
                     not multi-dim advection;
                   - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
                     SHORTWAVE_HEATING #undef.
89b3de8a81 Mart* o optim: make Makefile more robust (?)
7e9d85ac6b Patr* o pkg/obcs:
                   * fix treatment of obcs_read_pickup for TAF
fac86b0a61 Jean* o pkg/shelfice:
7e9d85ac6b Patr*   * add missing initialisation of num_shifwflx
                   * new adjoint verification exp. for isomip
                   * change Prandtl and Schmidt numbers from generic formulations
fac86b0a61 Jean*     (in terms of model diffus. and visc.) to separate runtime
7e9d85ac6b Patr*     parameters, with Holland and Jenkins (1999) default values.
85fbbba158 Jean* o pkg/exf (interpolation):
                   - extended input field (2 rows) near the N & S poles:
                     * fill in with the symetric value (when even Nb of data in longitude)
                     * add average value at the poles only for scalar quantities ; for vector
                       component interpolation, skip the averaging and keep duplicated values,
                       unless the 2 components have same location (uvInterp=T) in which case
                       interpolate the 2 components together using S/R EXF_INTERP_UV.
                   - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
                     together: this allows to account properly for local orientation when
                     averaging at N & S pole.
                   - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
                     exf-interpolation near N & S poles. Undef by default.
                   - add debug check/print on 1rst iter if debugLevel >=2.
45bd772f0f Jean* o pkg/exf:
                   - change masking flags definition (no longer "parameter"), put them in
                     common block and set them in S/R EXF_INIT_FIXED.
                   - change recognized masking flag from s,u,v to c,w,s since the mask
                     to use (maskC,W,S) depends on position on model grid and has little to
                     do with scalar/vector difference; fix masking if using P-coordinates.
                   - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
                     and update results of exp. global_with_exf (x2).
                   - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
dd08a0bdad Mart* o pkg/obcs
                   - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
473f3cfaa4 Jean* o pkg/exf (interpolation):
                   - assume periodicity in X only if input field cover full longitude range.
                   - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
                     and should vectorise).
                   - fix input lat of the 2 added row (in case we provide N.pole data).
                 
afd13745c6 Jean* checkpoint63h (2011/12/30)
d0a750d46b Jean* o pkg/seaice:
                   - change declaration of UVM from _RL to _RS in order to get B-grid
                     uIce,vIce monitor when _RS = real*4
35af42145b Jean* o pkg/offline:
                   - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
                   - compute vertical velocity if not read from file (switch on exactConserv
                     & staggerTimeStep);
                   - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
02149d96ab Jean* o verification:
                   - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
                     with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
                     fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
                   - update output of exp. global_ocean.cs32x15.viscA4 after changing
                     grid-file angles (used here for coriolis-3d);
                   - remove (or gzip) few files not needed to run fizhi-cs experiments.
473f3cfaa4 Jean* o pkg/exf (vector interpolation):
4ee3919357 Jean*   - rotate vector component toward local grid-axis orientation using grid-angles
                     (stored in GRID.h) instead of locally computed rotation angle; keep old code
                     available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
                 o pkg/seaice:
                   - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
                     undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
5803321947 Jean* o pkg/PKG_OPTIONS.h files:
                   - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
                     outside of the #ifdef ALLOW_THISPKG / #endif block.
                   - update verification/*/code/PKG_OPTIONS.h files.
dd0bbd259d Mart* o add a verification experiment (offline_exf_seaice/input.seaice) that test
                   the B-grid LSOR solver
5d7b3caf45 Mart* o pkg/seaice: sort out emissivity and long wave radiation step 2:
5803321947 Jean*   - add emissivity for snow and ice as new run-time parameters
                     (unfortunately) that default to the corresponding exf values; this
5d7b3caf45 Mart*     changes results in most verification experiments so that for backward
                     compatibility these parameter have to be set explicitly to inconsistent
5803321947 Jean*     values (ugly);
5d7b3caf45 Mart*   - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
                     emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
                     until we agree how to handle this bug properly
a2895221f1 Jean* o pkg/exf (interpolation):
                   - add a set of run-time param ({inputfield}_interpMethod), one for
                     each interpolated input field, to select the interpolation method
                     with a value of zero switching off the interpolation;
                   - print interpolation parameters to standard output;
                   - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
                     (to use instead runoff_interpMethod=0 in data.exf).
f156ca0fb7 Jean*   - simplify default setting of interpolation parameters (for all fields,
                     set position to match model grid cell-center position, leading to trivial
                     interpolation in case of regular Lat-Lon grid) and fix for the case of
                     non-uniform delY.
a2895221f1 Jean* o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1ca970e947 Mart*    within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
a2895221f1 Jean*    this factor is absolutely required, because the lw exitance (= out-going
                    long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1ca970e947 Mart*    where the reflectivity rho = 1-emissivity for conservation reasons. Once
                    this is established, we can remove the CPP-Flag (if we want to).
a2895221f1 Jean* o pkg/seaice:
31c8334354 Mart*   - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
                     ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
3fa95d7893 Mart*   - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
                     what the name implies (and not emissivity*BoltzmannConstant), this means
a2895221f1 Jean*     the old default value of 5.5e-8 now means
                     5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
3fa95d7893 Mart*     S/R exf_readparms
                   - FV-discretization of the B-grid LSOR solver, turn on with
1ca970e947 Mart*     SEAICE_LSRBNEW. This new solver also involves a slight re-organization
                     of the calling routine dynsolver, so that B and C-grid code look a
                     little more alike.
31c8334354 Mart*   - fix index bugs in ostres.F (B-grid code)
03e90c79ad Mart* o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
b7727eb6f8 Mart* o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
                   default for SEAICE_emissivity, if useEXF; requires setting a wrong
                   parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
                   backward compatiblity
                 o model/src: use sigmaR in calc_ivdc
                 
b1b3dce3a2 Jean* checkpoint63g (2011/12/16)
abaf70634e Gael* o pkg/seaice/seaice_growth.F:
                   fix heat conservation of the coupled ocean-seaice system.
                   when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
                   solid vs liquid water treatment is resolved via QNET.
                 o pkg/seaice/seaice_growth.F:
                   add missing term for sublimation in saltFlux, which was breaking conservation.
                 o pkg/seaice/seaice_model.F:
                   Remove this patholigical case treatment in evolution branch,
                   where it is un-necessary and breaks conservation.
a2895221f1 Jean*   Update global_ocean.cs32x15/results accordingly for
                   output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
bf53796fe2 Jean* o model/src:
                   useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
                   external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
                 o pkg/obcs:
                   modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
                   tendency for temperature and salinity that is then applied to update
                   theta and salt in S/R obcs_apply_ts; this requires proper masking of all
                   horizontal advection and diffusion contributions on the boundary (in
                   S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
                   removing the mask in S/R timestep_tracer. The advantage of this approach is
                   that the updated tracer values include contributions from the surface
                   forcing and vertical diffusion.
c0f0db71ad Mart*   This modification changes exp4.stevens because of vertical diffusion.
c947c6ddc4 Jean* o model/src:
c79ab16fdf Jean*   change non-curvilinear grid setting to also work with exch2 + blank tiles:
                   - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
                     face dimensions.
                   - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
                     as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
                     and INI_SPHERICAL_POLAR_GRID.
                   change test-experiment global_ocean.90x40x15:
                   - split the domain in many more tiles (9x4 tiles of 10x10 each);
                   - switch to exch2 and remove 1 blank-tile (but only for MPI test).
                   - update results of both test (std & dwnslp).
bf53796fe2 Jean* o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
c0f0db71ad Mart*    tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
c79ab16fdf Jean* o model/src:
f9a1d5f8b7 Jean*   - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
                     and fix initialisation when using sigma-coords.
                 o model/src:
                  - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
                    to their current value at the beginning of forward_step.F": add a new run-time
c947c6ddc4 Jean*    switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
                  - set doResetHFactors=T in the following test exp:
                     global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
                     global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
                     and tutorial_global_oce_in_p (nonLinFS in p)
64ea3e84ce Matt* o pkg/ecco
                   - added IES cost term
be6cb3adad Jean* o verification/advect_xz
                   - scale down the depth by 1/100 (from 200 km to just 2.km)
                   - add secondary test using divergent flow, r-star and implicit vertical advection.
1bf7a90a0b Jean*   - add note (check_conserve_TS.txt) and matlab script to check global
                     conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
be6cb3adad Jean* o pkg/rbcs:
                   - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
212c574d0b Mart* o pkg/obcs (Stevens BCs):
be6cb3adad Jean*   - fix various problems in the phase speed computations of the Stevens
212c574d0b Mart*     boundary conditions:
                     - sign error for western and southern boundaries,
be6cb3adad Jean*     - time tendencies were underestimated by factor of dTracerLev and some just
212c574d0b Mart*       zero (for multidim advection schemes) -> now estimate time tendencies
                       from difference between previous (n) time level and the one before (n-1);
be6cb3adad Jean*       this requires storing a field per tracer per boundary, also in the pickup
212c574d0b Mart*       files.
                     - replace deltaTmom in cflMer/Zon computation with dTracerLev
                     - set default phase velocity to cflMer/Zon
                   - update verification experiment exp4.stevens
2232bea0cd Jean* o pkg/generic_advdiff (implicit_r):
                   - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
                     (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
                   - fix implicit vertical diffusion or advection with NonLin FreeSurf
                     (was using current recip_hFacC instead of future recip_hFacC): set future
                     recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
                     solver S/R ;
                   - fill diagnostics of vertical advective fluxes (computed from tendency)
                     when using implicit vert. advection;
                   - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
                      global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
                      tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
                      and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
                 o pkg/diagnostics:
                   - add diags for T & S tendency which goes through Adams-Bashforth.
                 
3cb41ba0ef Jean* checkpoint63f (2011/11/30)
764028acbf Mart* o pkg/obcs/obcs_calc_stevens.F:
5bef8326ad Mart*   - join some loops to reduce number of if-statements
764028acbf Mart*   - fix a bug in code for northern and southern boundaries.
564b34aefd Mart* o pkg/seaice/seaice_init_varia.F
3cb41ba0ef Jean*   - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
564b34aefd Mart*     caused zero ice-velocities for the B-grid code
2876330f22 Mart* o pkg/seaice/seaice_init_fixed.F
3cb41ba0ef Jean*   - fix a bug in the initialisation of the second metric terms
2876330f22 Mart*     k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
                   - this affects all seaice configurations with useCurviLinearGrid = .true.
                     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
                     = .true. (default)
                   - the only verification experiment affected is global_ocean.cs32x15:
                     icedyn, seaice, and seaice_dynmix (AD)
                 o pkg/thsice/thsice_diagnostics_state.F
                   - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
                     not contain garbage that can lead to surprises in diagstats_calc.F
431cbbbe2d Jean* o model/src:
                   - move bi,bj loops inside INTEGR_CONTINUITY ;
                   - call INTEGR_CONTINUITY directly from forward_step.F
                     (previously called from momentum_correction_step.F)
                   - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
                     forward_step.F and pkg/ecco/the_main_loop.F
fbc9c53f7c Jean* o model/src/do_oceanic_phys.F:
                   - reset addMass to zero only if useICEFRONT ;
                   - separated k-loop for rhoInSitu calculation ;
                   - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
                     and at constant T,S (= WdRHOdP);
                   NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
                     of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
                     transport of locally-referenced potential density);
                     to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
f2d1e2a4fc Mart* o gluemnc:
                   - replace ncrcat with ncks when adding variables to *.glob.nc
                   - change the way variables without record dimensions are handled so that
                     files that have variables with and without record variables can be glued:
                     add a record dimension with a new unique name to be able to differentiate
                     between variable with and without a-prior record dimensions. Remove
                     this record dimension before adding the variable to the *.glob.nc file.
                     This procedure automatically works also for grid.*.nc files that do not
                     have any record dimension.
7f71bb5257 Jean* o verification/cpl_aim+ocn:
                   - generate new reference output on baudelaire (gfortran, mpich2) (previously
                     from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
                 o pkg/obcs/obcs_calc_stevens.F:
b81f64aee3 Mart*   - add code for northern and southern boundaries.
                   - reorder some loops to save some operations and so that drFBar can be scalar
12d8e73fbb Jean* o model/src:
                   - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
                     truncation) and add diagnostics for Adams-Bashforth tendency increment.
                   - update test-exp. AD output:
                     1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
                   and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
                     front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
                     global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
                     matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
                     tutorial_global_oce_in_p, tutorial_global_oce_latlon and
                     tutorial_plume_on_slope.
b06a6ce7ab Mart* o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
                   that vectorises. This code uses 3 extra 2D fields, F90 array assignments
                   and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
                   does not even come with an F77 compiler anymore, this should not be
                   a limitation
                 
34f1dd7af6 Jean* checkpoint63e (2011/11/06)
16b186ab26 Patr* o pkg/seaice adjoint of LSR:
                   - substantially rework STORE dirs.
                   - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
                     this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
                     and only perform SOLV_MAX_FIXED adjoint iters.
37e94e8cfb Patr*     If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
                     always goes to same record, meaning that the last forward field will be
                     the one used in the adjoint - an approximation.
16b186ab26 Patr*   - now produces non-zero LSR-related gradients, and acceptable gradients for
                     An's zonal (x-z) test case (to be checked in)
                   - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
                     (but these are screwed up by the thermodynamics in the first place);
                     reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
                     output_adm.txt also reflects changes to seaice_lsr
34f1dd7af6 Jean*   - global_ocean.cs32x15:
16b186ab26 Patr*     * the "default" input_ad.seaice has been re-defined to always exclude dynamics
                       (output_adm.seaice.txt was updated)
                     * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
                       (output_adm.seaice_dynmix.txt)
ca66b179c0 Jean* o test-exp. exp4+stevens:
                   - switch off pTracers and nonHydrostatic (restart problems with NH); update output
de0cda9935 Jean* o pkg/seaice (lsr solver):
                   - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
                     update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
                   - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
                   - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
                     into initial guess for linearised solver; use weight ~ (1/err)^2,4.
                   - compute (with new S/R) and print initial (+ free-driff sol. if available)
                     and final residual of linearised system.
8a3a83c787 Mart* o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
                   (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
383735f3ce Mart* o pkg/obcs: Stevens BCs (still only for east and west)
                   - fix Stevens BCs by using intermediate velocities of previous
                     time step as "baroclinic" contribution rather velocity of one grid cell
                     inside the boundaries; more consistent but makes the entire treatment
de0cda9935 Jean*     more complicated, requires new pickup files and two new S/Rs:
383735f3ce Mart*     obcs_copy_uv_n and obcs_save_uv_n
de0cda9935 Jean*     keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
383735f3ce Mart*     (undefined by default)
de0cda9935 Jean*   - silently move computation of some grid factors into separate loops to
383735f3ce Mart*     save some recomputations
                   - add a hack for non-linear free surface
                   - add a verification experiment to exp4 that tests this code
14398673cd Mart* o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
                 
77e57aaf77 Jean* checkpoint63d (2011/10/25)
ffb3679b95 Jean* o pkg/obcs + seaice-dynamics:
                   - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
                     solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
                     values (consistent with an implicit method).
                   - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
                     return to older implementation (same results as before); note that none of
                     the "experimental" OBCS_SEAICE options are implemented in the new version.
2d58d55cc0 Jean*   - switch test exp. seaice_obcs to use new version (update output).
6b9597f12c Jean* o pkg/seaice:
ffb3679b95 Jean*   - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
                   - add parenthesis in Water-Ice drag calculations (evp & lsr);
                   - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
6b9597f12c Jean*     and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
                   - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
                     and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
026da5ed8a Davi* o pkg/layers:
                   - Include potential density as new coordinate (Thanks to David Munday)
                 o pkg/dic:
                   - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
                     carbonate computation/output to CALC_PCO2_APPROX
d1527a124d Mart* o pkg/generic_advdiff
77e57aaf77 Jean*   - make TAF generate code that vectorizes:
d1527a124d Mart*     gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
77e57aaf77 Jean* o model/src:
                   - improve vectorization also for adjoint code of
713532b2ce Mart*     solve_tridiagonal and solve_pentadiagonal. As this requires up to
                     5 new 3D-fields, this code is only turned on for the combination of
d1527a124d Mart*     ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
                     for singular matrix check (only for TARGET_NEC_SX).
713532b2ce Mart*   - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
ffb3679b95 Jean*     ALLOW_AUTODIFF. This flag now needs to be set outside of
713532b2ce Mart*     solve_tri/pentadiagonal.F
6857319532 Jean* o pkg/exf:
                   - fix previous modif in exf_readparms.F (revision 1.66: treatment of
                     optional namelist EXF_NML_OBCS).
                   - add many debug-print (to trace down where pkg/cal error msg comes from)
71df2e2fe0 Mart* o pkg/mom_vecinv/mom_vi_hdissip.F
                   - rearrange loops so that vectorization is improved and in particular
6857319532 Jean*     the adjoint routine vectorizes. The code is a little longer now, but I
                     think easier to read.
71df2e2fe0 Mart*     Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
69771f84cc Jean* o pkg/seaice:
                   - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
69238317a2 Jean* o pkg/exch2:
                   - alternative code (without tile x tile matrix) for cumulated (global) sum;
                     used as default; keep using matrix version in adjustment.cs-32x32x1.
5f3dfa25b7 Jean* o tools/build_options:
                   - after merging some MPI and/or multi-threads specific optfiles so that
                     the modified default optfile support both built (using genmake2 -mpi
                     for the MPI built, using genmake2 -omp for OpenMP built),
                     move now obsolete optfiles to tools/build_options/unsupported/
                    (add copy of email sent to support list in doc/optfiles_changes.txt)
                 
348beac9cc Jean* checkpoint63c (2011/09/28)
b0522d7987 Jean* o pkg/ebm:
348beac9cc Jean*   - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
b0522d7987 Jean*     test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
f2b8a2f2ef Patr* o pkg/seaice (SItracer pickup)
                 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
                   To be done:
                   - thorough testing of missing fields in S/R seaice_read_pickup
                   - thorough matching between generic tracers and specific fields used
                     (e.g. volume-weighted age, area-weighted age, salinity, ...)
2475d1c482 Jean* o pkg/grdchk:
                   - all procs calculate and print finite-difference gradient (for testreport)
                   - change description output used by testreport;
                   - AD testing: also compare and report Finite-difference gradient;
                     => update all output_adm*.txt
                 o test exp. global_ocean_ebm:
                   - switch back useRealFreshWaterFlux (no problem anymore with run-off);
                     and turn on exactConserve; update (fwd) output.
22a5e4b7f8 Jean* o pkg/seaice (LSR):
                   - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
                   - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
                     * identical results with non-CS topology (but save up to half of EXCH calls)
                     * no much changes in cs-32 verification tests since no ice at face edges
                      (differences due to convergence criteria, since nb of iterations changed)
                     * expect some differences on lat-lon-cap grid.
                     update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
21773ac32d Jean* o pkg/exch2:
                   - add new CPP option to disable Cumul-Sum matrix (to save storage when using
                     many tiles); until alternative coding is added, just add a stop.
7c74433c3f Jean* o pkg/kpp:
                   - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
                     to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
                 o optfiles:
                   - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
                     into corresponding standard one, which now support different build:
                     (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
                   - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
a9fbe2edc0 Jean* o pkg/obcs (seaice):
                   - add missing EXCH for uIce,vIce after applying OBCS;
                   - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
                     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
                     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
                   - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
                   - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
                     and eedata.mth for MPI and mutlti-threaded testing.
ecd451586c Jean* o pkg/flt:
                   - make FLT EXCH working with multi-threads (and MPI + multi-threads);
                   - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
                   - fix pickup and trajectories + profiles output with multi-threads;
                   - add parameter to select group of fields to write along trajectory and
                     profile (default unchanged);
                   - only call PORT_RAND* function when flt_noise <> 0;
                   - add multi-threaded test for verification exp. flt_example.
                 o eesupp/src:
                   - fix S/R ALL_PROC_DIE for MPI+multi-threads.
                   - USE_OMP_THREADING: check that number of threads (from eedata) matches
                     actual number (from env.var. setting).
2e701c809e Jean* o pkg/ebm:
                   - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
                   - add multi-threaded test for verification exp. global_ocean_ebm
                 
a51afa12b8 Jean* checkpoint63b (2011/08/29)
1554b54595 Jean* o pkg/ebm:
                   - fix sign of runoff;
                   - update directly forcing fields (Qnet,EmPmR) to use standard
                     external_forcing_surf.F (remove ebm_forcing_surf.F);
                   - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
                   - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
                     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
                   - update global_ocean_ebm parameters file data and update output (fwd+ad).
753be3d4e2 Jean* o verification/matrix_example:
fcfc72a991 Jean*   - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
                     MPI and mutlti-threaded testing.
                 o pkg/matrix:
                   - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
                   - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
                   - fix for multi-threaded (remove DATA statement);
                   - use standard DIFFERENT_MULTIPLE function;
                   - add MATRIX_OPTIONS.h
                 o verification/matrix_example:
753be3d4e2 Jean*    To allow to split the domain in several tiles, change the domain size
                     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
                     Western side) of land points.
                 o (*_)write_pickup:
                   - fix few bugs in mypackage_read/write_pickup.F
                   - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
                     array of length 1 (was caught by compiler syntax-check).
6768a51e8b Jean* o pkg/diagnostics (velocity potential solver):
                   - fix initialisation of main diagonal matrix (for overlap values)
02665fe70b Jean* o tools/build_options:
                   - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
                     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
                   - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
                     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
                     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
                     and use "-devel" testreport option for standard testing on baudelaire.
b6649ac208 Jean* o pkg/grdchk:
                   - Assume that all gradient-check position are within the same tile
                     corresponding to global indices (iGloTile,jGloTile) and that
                     positions (i,j indices or nbeg) are local to this tile;
                   - set tile local-indices and proc. number according to tile global-indices;
                   - remove grdchkwhichproc from namelist (retired param);
                   - send adjoint gradient to all procs so that all procs print it to STDOUT;
                   - switch on MPI test for global_ocean.90x40x15 AD test experiment.
15338fa568 Dimi* o adding package bbl (Bottom Boundary Layer)
                   description in MITgcm/pkg/bbl/bbl_description.tex
                   example/test experiment in MITgcm_contrib/bbl
50d533af19 Patr* o adjoint verifications
1c8f7d3c14 Jean*   - changed 5 experiments to multi-tiles
50d533af19 Patr*     * global_ocean.90x40x15
                     * obcs_ctrl
                     * offline_exf_seaice
                     * tutorial_dic_adjoffline
                     * tutorial_tracer_adjsens
                     changed reference output for those that crossed tile boundaries
                     (changed choices of gradient check positions)
1c8f7d3c14 Jean*   - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
50d533af19 Patr*   - temporary bug fix in grdchk_loc.F for obcs
d5826a2b12 Jean* o genmake2 & testreport
                   - add target "obj" (just for OBJFILES files) to Makefile;
                   - add option to specify FEXTRAFLAGS on command line.
ea9625adec Jean* o pkg/mypackage:
                   - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
                 
975e02919b Jean* checkpoint63a (2011/08/02)
ff219d41cf Jean* o pkg/diagnostics (velocity potential):
                   - fix velocity-potential calculation when using OBCS: balance net inflow
                     at each level (new S/R OBCS_DIAG_BALANCE).
                   - fix some of the problems with OBCS in stream-function calculation.
773313b0d2 Mart* o pkg/exf/exf_readparms.F
ff219d41cf Jean*   - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
773313b0d2 Mart*     EXF_NML_OBCS) more consistent, so that you need not have these lists
                     in data.exf when they are not used.
45b245ccf5 Mart* o optim/optim_readdata.F:
                   - add some output about obcs variables that might help debugging
daab778156 Mart*   - add a check about nvarlength
d602d84af0 Mart* o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
4750cf8833 Jean* o pkg/diagnostics (velocity potential):
                   - fix mask for OBCS (still problems in stream-function with OBCS);
                   - add specific parameter (default = main code CG2D params) for solver;
                   - in case of poor convergence, use solution corresponding to lowest residual.
a045c08a46 Mart* o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
                   adjoint code. In general statements like tmpscal=fld(i,j) are problematic
                   and should be avoided where possible.
40639c975a Jean* o model/src (rStar):
                   - include r* effect on reference-state (PhiRef) in totPhiHyd
                     (so that it's really the potential anomaly at the cell center);
                     affect solution only if z* with full pressure in EOS.
                   - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
                     update output (because of z* in totPhiHyd and viscA4 changes);
                   - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
                     @ constant r) until interpolation at constant r is implemented.
                 o pkg/diagnostics
                   - fix RCENTER diagnostics in case cell center is not at interface middle
6a4d8594a7 Mart* o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
                   this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
                   that THETA and SALT are "conservative temperature" and "absolute
                   salinity"
                 o pkg/ctrl
                   - fix computation of endrec in s/r ctrl_init_rec
                   - ctrl_pack/unpack_*: remove unused variables and some obsolete code
aa222beea6 Mart* o pkg/seaice/seaice_growth.F
                   - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
                     remove then obsolete STORE directives
                   - fix STORE directives for tice and tices, so that only the
                     appropriate part of the fields are stored (and not the entire
40639c975a Jean*     field); update global_ocean.cs32x15.seaice AD output.
aa222beea6 Mart*   - cosmetic changes: adjust CPP flags and indentation for better
                     legibilty
                 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
                   Chris Wilson)
5c5b0c67fc Jean* o pkg/gmredi:
                    Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
                    and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
                 
975e02919b Jean* checkpoint63  (2011/07/11)
0efa36856a Jean* o pkg/exch2:
                  - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
                  - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
                    (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
                    increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
9ec7daa021 Jean* o pkg/diagnostics:
                  - deal with pairs of post-processed diags which are computed together; in
                    particular, re-order list of diags within 1 file to save 2nd computation.
                  - add S/R to compute velocity stream-function (called after velocity-potential
                    calculation) from divergence free transport -> new diagnostics "PsiVEL".
32f824cd14 Jean*  - add parameter to select grid-point location where PsiVEL == 0.
9ec7daa021 Jean* o eesupp/src:
                    new S/R to calculate cumulated sum on tiled array, corner grid-cell location
                    (specific S/R needed with exch2 topology - for now, just print an error msg)
f3cfd88687 Patr* o pkg/shelfice
                  - Implement friction velocity-dependent transfer coefficients following
                    Holland and Jenkins, JPO, 1999
                    Original code by M. Losch with small modifs.
                    Enable with CPP option SHI_ALLOW_GAMMAFRICT
                    and runtime flag SHELFICEuseGammaFrict
a8b943f1d9 Jean* o verification lab_sea & global_ocean.cs32x15:
                  - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
                    does not miss some dependencies (but is slower) and also works with many files
                    (default makedepend limitation for AD built).
                  - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
c5e360349a Jean* o pkg/diagnostics:
                  - add run-time parameter "useMissingValue" (def=False) to fill land-point
                     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
                    This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
                  - Extend the use of "missing_value" setting from data.diagnostics for the case
                    of counter-diagnostics (where fraction-weight is zero). This applies both to
                    MNC and MDS output files.
f3bb97e385 Gael* o pkg/seaice/seaice_growth.F:
b7df5ca569 Ian *   - add 'a priori' cap of latent heat flux based on actual mass considerations
                     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
                     non-legacy seaice_solve4temp.
                   - add diagnostic of the residual sublimation freshwater flux (the freshwater
9ec7daa021 Jean*     flux taken from the ocean if the total actual latent heat fluxes exceed
b7df5ca569 Ian *     the maximum)
f3bb97e385 Gael*   - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
                    fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
                   - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
                    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
                   - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
                   - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
12f262973b Ian * o verification 1D_ocean_ice_column:
                    made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
                    update results
43043edca4 Jean* o pkg/diagnostics:
                  - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
                    which are not filled-up but computed from other diags ; In this case, the mate
                    diag points to the primary (filled-up) diag to used for post processing.
                  - Update Velocity-potential computation using post-processed diag framework.
234bdec1fe Jean*  ==> Change the ordering of fields and time-periods in MDS output file
9b34d3ce48 Jean*    when using periodic averaging: now writes one time record with the full set
                    of fields for this time period, then the next time reccord (it used to be
                    one field with the full set of time records then the next field).
234bdec1fe Jean*      Note: this is now similar to NetCDF (MNC) output file. <==
43043edca4 Jean* 
19985267f5 Jean* checkpoint62z (2011/06/21)
fb247706a7 Patr* o adjoint monitor:
                  - Add adjoint monitor output for packages exf, seaice
a18fc746e5 Patr*    and update relevant testreport output
6de796d755 Gael* o pkg/seaice:
                  - re-order diags inits so that they appear in order in available_diagnostics.log
                  - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
                    area/heff/hsnow preceeding thermodynamic growth/melt.
                  - modified diag: SIdA; output actual effect, as the description states.
                  - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
                  - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
3897a97e38 Jean*    (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
6de796d755 Gael*     and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
                  - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
3897a97e38 Jean*  - added diagnostics for seaice generic tracers (SItr*).
6de796d755 Gael*  - added SItrUnit and SItrNameLong run time param (for SItr* diags).
                  - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
d7d0e261c7 Patr*  I. Fenty: 18-Jun-2011:
                  Minor changes to seaice package:
                  1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
                     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
3897a97e38 Jean*    - Differentiated "regularization variables" from "floor variables"
d7d0e261c7 Patr*     * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
                     * hiceMin became SEAICE_hice_reg (old hiceMin)
                       (with _reg meaning regularization variable)
                    - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
                     so as to ensure energy conservation when going between phases
3897a97e38 Jean*   - A22 was not used anywhere
d7d0e261c7 Patr*  2) Changed regularization procedure for heffActual and hsnowActual to ensure
                     well-boundedness and smooth adjoint in seaice_growth.F
                  3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
                     because the old regularization always set heffActual >= 0.05 cm
                  4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
3897a97e38 Jean*     on AREA when HEFF > 0.
                   - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
                     requiring that DISABLE_AREA_FLOOR *not* be defined
d7d0e261c7 Patr*  Affected verifications:
                   - 1D_ocean_ice_column (output.txt output_adm.txt)
                   - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
4c5a4fb4d7 Jean* o pkg/diagnostics:
                   - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
                   - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
                     (was _RL, now integer) with option = 0 to retrieve all levels.
2d3c84b138 Jean*   - add pieces of code to compute velocity potential at each level (new diagnostics
                     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
                     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
3897a97e38 Jean*   - fix few issues with counter diagnostics in diagnostics_setdiag.F &
                     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
                     and in diagnostics_fract_fill.F (do not need a valid pointer for the
                     diagnostics counter-mate); check that definition of counter-diagnostic
                     includes a valid counter-mate (in diagnostics_set_levels.F).
d2ffb46800 Jean* o model/src (rStar):
                   - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
                     affect solution only if z* with full pressure in EOS;
                     update output of test-exp global_ocean.90x40x15.
                 o pkg/seaice:
3b6fc6245d Gael*   - introduce siEps=1e-5 parameter
                   - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
                   - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
d2ffb46800 Jean*   - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
3b6fc6245d Gael*     For now it covers, and was tested for, ice salinity and age (attached to HEFF),
                     as well as ice cover age and ridging index (attached to AREA).
d2ffb46800 Jean*     For now the run time parameters (in data.seaice/SEAICE_PARM03) are
                     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
3b6fc6245d Gael*     Up to SItrMaxNum=3 tracers can be used simultaneously.
                 o pkg/salt_plume:
d2ffb46800 Jean*   -introduce SPsalFRAC run time parameter that sets the fraction of the
                    salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
                    that gets vertically redistributed (fluxed down) by pkg/salt_plume.
43306f4baa Jean* o model debug options:
                   - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
                     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
                   - Refine debug-msg printing selection (3 new levels):
                     debugMode  : controls printing of debug messages (sequence of S/R calls).
                     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
                      debLevZero =  0 ; /* level of disabled aux. msg printing */
                      debLevA =  1 ; /* level of minimum  aux. msg printing */
                      debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
                      debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
                      debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
                      debLevE =  5 ; /* level of extensive debug printing */
                     New debugLevel default: with default debugMode value (=F),
                       = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
                       and if debugMode=T, default debugLevel = 4 (debLevD).
                     Relation with previous settings:
                      debLevB (=2) corresponds to former debLevA (=1)
                      debLevD (=4) corresponds to former debLevB (=2)
                     Note:
                      a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
                      b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
                         to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
                   - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
                     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
8a9e9a473a Jean* o pkg/obcs:
                   - change OBCSfixTopo default from True to False (should not change the results);
                     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
cc3bbdb6bb Jean* o pkg/thsice:
                   - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
                     2nd layer seaice sublimation (unlikely to happen)
                   - use Interior mask for OBCS in thsice_advection.F (similar to what is
                     done in gad_advection & seaice_advection).
bd46b07a96 Patr* o adjoint:
                   bug fix spotted by Gael Forget:
                   seaice_advection and thsice_advection still had
                   legacy CPP options to avoid CS corner updates for adjoint
0c22b81a88 Jean* o pkg/seaice:
                   => Change some of the defaults (2011/05/29):
                      - change SEAICEuseFluxForm default (from False to True)
                      - change DIFF1 default (from 0.004 m/s to 0. m/s)
                      And print warnings if DIFF1 is not set in data.seaice and centered
                       avection scheme is used without any diffusion.
                   also:
                   - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
                   - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
                   - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
                     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
                     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
                   update results of test exp.:
                      lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
                          output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
                          output_adm.noseaicedyn (SEAICEuseFluxForm=T)
                      offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
                      seaice_obcs: output (SEAICEuseFluxForm=T)
                   and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
                       for standard fwd & AD lab_sea tests (to keep the same output).
fc3b49c003 Gael* o pkg/seaice/seaice_growth.F:
0c22b81a88 Jean*   - use Ian Fenty's capping formulas for actual ice
fc3b49c003 Gael*   thickness thoughout EVOLUTION branch.
                   - put treatment pathological case #2) in CPP brackets
                   (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
0c22b81a88 Jean*   - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
fc3b49c003 Gael* o pkg/seaice:
                   - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
0c22b81a88 Jean*   pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
                   also pass fac as a param, which can be 1. (to update the tendency
fc3b49c003 Gael*   field) or the time step (to update the field itself).
0c22b81a88 Jean*   - seaice_advdiff.F: for multidim, call seaice_diffusion with
fc3b49c003 Gael*   e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
                   seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
0c22b81a88 Jean*   - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
fc3b49c003 Gael*   hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
a6e3308c72 Jean* o pkg/seaice:
                   diffusion with centered advection scheme (diffus.F & advect.F):
                   - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
                     to just compute the laplacian of input-field.
                   - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
                   - fix flux-form version in diffus.F to conserve tracer.
                   update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
                    machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
                 
f23903c179 Jean* checkpoint62y (2011/05/26)
b9ea5855ae Gael* o pkg/seaice:
f23903c179 Jean*  - seaice_growth.F : in EVOLUTION branch, always include
b9ea5855ae Gael*    a_QSWbyATM_cover in qnet (as it should be).
                  - verification/global_ocean.cs32x15 : update results accordingly
f23903c179 Jean*    (output.seaice.txt output_adm.seaice.txt).
665e1cc782 Jean* o pkg/seaice + obcs:
                  - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
                    equivalent of assuming no tracer gradient outside the OB region.
                    update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
                  - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
                    after changes above);
                  - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
                    only at OB location (instead of over a band of OLx width).
                 o pkg/seaice:
                  - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
                    (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
ae7ba49648 Jean* o pkg/obcs:
ae802b970e Jean*   - split header file "OBCS.h" into 4 separated files:
                     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
                    Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
435c8dd190 Jean*      (contain no conditional statement which depends on OBCS options).
                   - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
                     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
ae802b970e Jean* o ctrl, cost, grdchk & autodiff pkgs:
                   - make options file more standard (like other {PKG}_OPTIONS.h file but
                     with AD_CONFIG.h); clean-up some of the included header files.
                 o pkg/obcs:
ae7ba49648 Jean*   - do not mask tracer when applying OB (tracer == 0 could generate problems)
                   - apply tracer OB values to tracer field only at OB location (instead of
                     over a band of OLx width)
                   - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
                   - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
                     obcs_apply_tloc.F & obcs_apply_sloc.F
                 o obcs in model/src:
                   - call OBCS_APPLY_W only if NonHydrostatic.
                   - call OBCS_APPLY_ETA only if NonLinFreeSurf.
                   - reset dEtaHdt and wVel to zero outside OB interior region ;
                   - leave tracer unchanged outside OB interior region: This has no effect
                     on the solution but just to prevent unrealistic tracer value outside OB.
                   - zero out velocity outside OB interior region: This has no effect on
                     the solution but just to prevent unrealistic velocity outside OB.
1228ad56fc Jean* o obcs and non-lin free-surf:
                    move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
                    and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
                    + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
                    this fixes missing EXCH + get consistent eta OB value (+ fix restart).
                    update results of test-exp. exp4(nlfs).
b642a711f1 Jean* o exp4 (nlfs) test-exp:
                    use OBC for Eta at Western & Eastern OB (to test prescribing Eta
                    with NonLin-FreeSurf); update output.nlfs.txt
691f44a031 Jean* o obcs and 2d/3d solver norm:
b642a711f1 Jean*    use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
                    and outside OB interior region (will allow to place OB further inside the
                    domain). Depending on the domain, can affects cg2d-Norm (previous
ae7ba49648 Jean*    cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
691f44a031 Jean*    and cg3d-Norm (previous Norm was computed before canceling OB terms),
                    e.g. in tutorial_plume_on_slope.
                   - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
6202f959ce Jean* o pkg rbcs:
                   - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
                   - add capability to apply relaxation to horizontal velocity uVel & vVel.
5f47d9d3a7 Mart* o pkg/grdchk: add gradient check for control variable xx_shifwflx
                 o pkg/shelfice/shelfice_init_fixed.F
                   fix CPP-flag combinations
2706e7ceae Patr* o pkg/seaice: Merge iceage code of Pierre Rampal
                   * update/change/correct ice age calculations
b642a711f1 Jean*   * add age updates for pathological cases
2706e7ceae Patr*   Probably needs more testing...
5f47d9d3a7 Mart* 
fb01456aea Jean* checkpoint62x (2011/05/13)
                 o pkg/mom_vecinv:
6202f959ce Jean*    high-order vorticity scheme: use interior masks (maskInW & S)
fb01456aea Jean*    to zero-out (outside OB) gradient of vorticity.
94a41b18e5 Jean* o verification exp.:
                    turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
                    hs94.128x64x5 and seaice_obcs ; update results.
abb2d742f7 Oliv* o pkg/obcs:
                   fix bug in OBeta for YZ sections in obcs_exf_load.F
94a41b18e5 Jean* o pkg/ctrl, pkg/shelfice, and optim:
                   - add new control variable xx_shifwflx (fresh water flux underneath ice
                     shelves). This is almost as tedious as obcs-ctrl, because the
c39d626e4c Mart*     variables needs its own mask.
94a41b18e5 Jean*   - add a cost function term that penalizes the deviation of xx_shifwflx
c39d626e4c Mart*     from the first guess (zero) in analogy to other control variables
40171df3a2 Patr* o pkg/shelfice:
                   - start basic adjoint
94a41b18e5 Jean* o pkg/ctrl:
a14e708176 Mart*   - remove extra 2D field "for good measure" when initializing in
                     ctrl_set_globfld_[xy/xz/yz].F
00525899b2 Mart*   - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
                   - improve error messages in ctrl_set_unpack_*
cb8d4055f8 Jean* o OBC implementation in momentum:
                    use interior masks (maskInC,W & S) in momentum S/R:
                    - multiply divergence, tension and some del^i.u or del^j.v by maskInC
                    - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
                    - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
                    - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
                    Motivation: fix/clean implementation of OBC with biharmonic-viscosity
                     (and also with Leith/Smagorinsky harmonic-viscosity).
                    Update output of experiment dome and exp4 (+nlfs).
19fda1148c Jean* o exp4 test-exp:
ce8a4681c6 Jean*   - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
                     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
                     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
                     time-varying OB at Western-side for wVel (NonHyd); update output.
19fda1148c Jean*   - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
ce8a4681c6 Jean*     and biharmonic-viscosity ; also use prescribed time varying OB.
19fda1148c Jean* o pkg/obcs:
                   fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
cd0d82611c Jean* o model/src:
                   - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
                   - initialise startTime & nIter0 with unlikely values: allows to set one
                     from the other without ambiguity.
e27288cd7f Jean* o seaice_obcs test-exp.:
                   add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
575d4c6487 Jean* o pkg/obcs:
                   - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
                     no longer needed with maskInC,W,S in pkg/generic_advdiff.
81db1d5414 Ian * o pkg/seaice:
575d4c6487 Jean*   - retired SEAICE_SALINITY and SEAICE_salinity in favor of
81db1d5414 Ian *     SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
575d4c6487 Jean*   - fixed bug in the initialization of sea ice salinity variable HSALT
81db1d5414 Ian *     in seaice_init_varia.F  (removed dependence on ICE2WATR)
3fb96de6bc Jean* o fizhi-cs test exp.:
                    switch reference output convention for these 2 non-standard test-exp,
575d4c6487 Jean*     from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
3fb96de6bc Jean*       to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
                    reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
38710791cb Jean* o model/inc:
                   - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
                     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
c5deacd5a8 Ian * o pkg/seaice:
                   - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
                 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
81db1d5414 Ian *   - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
                     and initial HSALT
c5deacd5a8 Ian * 
1c58c84abe Jean* checkpoint62w (2011/04/26)
0585a400b7 Jean* o pkg/mom_fluxform:
                   - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
                   - use parameter "sideDragFactor" in no-slip BC side-drag part.
                   - update output of exp. global_ocean.90x40x15
f79fbf5b9f Jean* o pkg/mom_vecinv:
                   mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1c58c84abe Jean* o update seaice exp.:
                   use more consistent parameter values (remove "backward compatability only":
                    ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
                   related to thermodynamics seaice. Update output (fwd+AD) of exp.:
                    1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
f79fbf5b9f Jean* o update test-exp global_ocean.90x40x15:
                   o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
                   o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
                   o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
                   o turn on zStar & viscA4 in standard set-up (dir input/)
                     and update output files: output.txt & output.dwnslp.txt
37df334812 Jean* o new AD-test experiment: obcs_ctrl
                   (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
                 o pkg/dic:
                   fix two bugs in handling water vapour pressure in carbonate chemistry
                   and air-sea fluxes. Found by Val Bennington and Galen McKinley
                   (add DIC Option = WATERVAP_BUG to recover old results)
                   update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
7c642b2a2b Dimi* o adding allowInteriorFreezing option to check for water below freezing point
                   at depth and bring the negative heat anomaly to the surface level
37df334812 Jean* o pkgs _fields_load:
                   - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
                   - use new S/R GET_PERIODIC_INTERVAL in pkgs:
62852f670d Jean*     bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
                     rbcs to get interpolation weights and time reccord number.
37df334812 Jean*   - fix multi-threading in aim_fields_load.F
                   - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
83f3340abe Jean* o external_fields_load:
                   new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
                    interpolation weights) to use in a periodic time-series ; do not divide by
                    time-step to convert to integer:
                    - this fixes case where externForcingPeriod is not multiple of time-step
                       (Thanks to Christopher L. Wolfe)
                    - this fixes case where externForcingPeriod is an odd multiple of time-step
                      (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
                   store index of time-record which is currently loaded:
                    - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
                    - needed for the adjoint but not yet used because of extensive recomputations;
                      (to be fixed soon)
                 
aea6723cc0 Jean* checkpoint62v (2011/04/02)
d0b6c8f47c Ian * o verification/1D_ocean_ice_column added to test Ian Fenty's
                   pkg/seaice_growth.F modifications for improving sea ice code differentiability
aea6723cc0 Jean* o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
                   (new velocity statistics after changing maskInW & maskInS definition)
75620d6d39 Jean* o pkg/generic_advdiff with OBCS:
                   use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
                   equivalent to assumption of no tracer gradient outside the OB region.
                   This will affect the results if using obcs+biharmonic diffusion.
                   update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1634337404 Jean* o pkg/obcs:
                   change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
                   (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
                   in Interior region. No impact on solution but affects Velocity monitor stats.
5933dabdc8 Patr* o pkg/ptracers (adjoint)
1634337404 Jean*   New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
5933dabdc8 Patr*   tape file for each tracer
1634337404 Jean* o model/inc/src and pkg/autodiff: add parameters that allow to turn
                   of parts of the adjoint code at run time. For now, there are only
                   useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
                   parameters are set in data.pkg.
                   This is the lazy coward's version of doing this, but still useful for
                   debugging. In order to do it right, everything needs to be moved to
d6ce1e6c67 Mart*   pkg/autodiff.
1634337404 Jean* o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
d6ce1e6c67 Mart*   the end; this fixes the adjoint balancing code for open boundaries.
ae6e7b0b9d Mart* o pkg/ctrl:
                   - change behavior of xx_${varname}period to be analogous to exf-conventions:
                     xx_${varname}period =   0.,  means time-independent control part
1634337404 Jean*     xx_${varname}period = -12., means one-year-periodic monthly control part
ae6e7b0b9d Mart*   - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
                     clean up ctrl_init a little, remove unused variables
e7fdbcdd62 Mart*   - ctrl_init: fixed the handling of the start/endrec for obcs-variables
ae6e7b0b9d Mart*   - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
                 
61d23e1802 Mart* checkpoint62u (2011/03/15)
4866a81958 Jean* o model/src:
                   - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
                     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
                   - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
                     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
                 o pkg/ctrl/obcs/ecco:
633dbf7240 Mart*   - remove obsolete, unused, and partially broken code:
4866a81958 Jean*     ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
633dbf7240 Mart*     ALLOW_CTRL_OBCS_BALANCE
4866a81958 Jean*   - put a stop statement into ecco/cost_obcsvol.F, but also add
633dbf7240 Mart*     cost_obcsvol to ecco_ad_diff.list
d9c90338d2 Mart* o pkg/ecco: fix counting cost function contributions for obcs (code
                   by Matt M.) and diffkr for diagnostics
a5506f4305 Patr* o pkg/ecco, pkg/ctrl, pkg/grdchk:
                   add cost penalty terms for initial uvel, vvel, eta controls
                   and I/O for prior error files
a2fd64e7bb Jean* o pkg/mdsio:
                    move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
                    (new argument) to check for tiled file in mdsioLocalDir : this fix the
                    restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
fbadcb8ae6 Mart* o pkg/ctrl:
                  - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
                    ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
                    unused and superfluous variables
                  - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
8bc4946ad4 Mart* o pkg/ecco
                  - enable adjoint of Stevens OB
a2fd64e7bb Jean* o pkg/ctrl/ecco/grdchk:
ac86e3d04f Mart*   - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
8bc4946ad4 Mart*     Fortunately, we do not have any tests for the numerous cpp-flagged
ac86e3d04f Mart*     option of "obcs as control parameters" so we will never know
                     if this is an improvement (but at least now things compile).
                   - remove an obsolete initialization from ecco_cost_init_barfiles.F
a2fd64e7bb Jean*   - fix some problems within never used ifdefs to make the code compile
7ee9bd2cad Jean* o pkg/obcs:
                  - Refine Interior mask definition to work with more complex OB (e.g.
                    if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
                    read in Interior mask from file. Check if Interior mask is consistent
                    with OB list of indices.
19ebde807c Patr* o pkg/seaice
                  - beginning code for a seaice tracer package,
                    but currently only used for seaice age: SEAICE_AGE
                    SEAICE_num = 4
                    iTracer = 1: area-weighted ice age
                            = 2: volume-weighted ice age
                            = 3, 4: template for one-year vs. multi-year ice
                    data.seaice has new namelist SEAICE_PARM03 for arrays related to
                    SEAICE_num
                 
954840cffd Patr* checkpoint62t (2011/03/05)
686e612f13 Jean* o pkg/obcs:
289f5415be Jean*  - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
                    then normal component. This ensures that the normal component is set
                    correctly even when it conficts with tangential setting from an other OB.
                    Affects results of test-experiment seaice_obcs: update the output.txt
                 o pkg/obcs:
686e612f13 Jean*  - add code to monitor statistics of dynamical fields at OB.
                  - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
                    - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
                    - change default: balance the Net inflow through all OB (instead of balancing
                      each OB separately); keep the old method if setting OBC_balanceFacX < 0.
                  - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
                    to match Nortern OB inflow (OBCS_balanceFacN=0).
7f2854329f Dimi* o pkg/seaice:
                  - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2afe30fba0 Dimi* o pkg/seaice (seaice_growth v 1.113):
                  - reverting seaice_growth to v 1.111 in order to have code with exact bit
                    compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
                    CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
                    runtime flag SEAICEareaFormula is kept but is inactive
fa83c0daea Jean* o model/src:
                  - add new param to scale curvilinear grid distance and area when using
                    a different sphere radius from the grid-files.
                  - test/check multi-threads EXCH applied to local variable (cg2d_x)
878ab8c79d Patr* o adjoint:
                  - enable adjoint of Stevens OB
                  - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
                    (a bit delicate because of potentially modified adj. common block structure;
                    current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
fa83c0daea Jean* 
d6110c5749 Jean* checkpoint62s (2011/02/15)
2afe30fba0 Dimi* o pkg/seaice (seaice_growth v 1.112):
83f1d2d932 Gael*  - introduce SEAICEareaFormula run time parameter, which selects the recipe for
d6110c5749 Jean*    computing the ice cover tendency from effective thickness tendencies. Include
                    Ian Fenty's formula.
                  - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
                    SEAICEareaFormula.
83f1d2d932 Gael*  - simplify notations for the various d_HEFF/d_AREA terms.
6555d1e696 Jean* o pkg/gmredi:
                  - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
                    from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
                    add a verification test-run (front_relax.bvp) to test GM_useBVP.
2afe30fba0 Dimi* o pkg/seaice (seaice_growth v 1.111):
dbc3f8d6b1 Gael*  - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
d6110c5749 Jean*  - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
                    also melt ice.
6555d1e696 Jean* o pkg/seaice:
13127f64f6 Gael*  - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
                  - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
6d3c37bddc Jean* o pkg/cheapaml:
                  - from Nico Wienders: New version of this package.
ffaad0659f Jean* o pkg/flt:
                  - add CPP options to prevent floats to re-enter the opposite side of
                    a periodic domain (default: keep periodicity)
520f9effa6 Jean* o pkg/gmredi:
                  - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
                    (needed for multi-dim advection).
20e9cc15d6 Jean*  - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
520f9effa6 Jean* o model/src:
                  - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
f40e476a49 Patr* o tutorial_tracer_adjsens
                  - extend to NLFS and replace maskC by hFacC
                    (change reference output accordingly)
520f9effa6 Jean* 
24aac58d71 Jean* checkpoint62r (2011/01/24)
b8c827cb68 Jean* o testreport:
                  - add option -deloutp (-do) to remove output file after successful run
                  - add option -mfile (-mf) for MPI machile-file and for each test-exp,
                    extract exact list of procs from this file ; adjust COMMAND by
                    replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
ab3c25e729 Mart* o pkg/ecco: replace old ineffective way of penalizing deviations from
                   first guess (of obcs) with code by Matt Mazloff
b8c827cb68 Jean* o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
aad046c5da Mart*   exf/cal
                   - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
                     and handle case of obcs?period == 0
                     Not affected by these changes: There is still an inconsistency in
b8c827cb68 Jean*     the computation of start/endrec for the obcs variables for ALLOW_CAL
aad046c5da Mart*     defined (see comment by Menemenlis, 7-Mar-2003)
                   - make S/R ctrl_get_gen_rec return something meaningful even if
                     ALLOW_CAL is not defined
b8c827cb68 Jean*   - ctrl_getobcs?: simplify code so that it does not need to use
aad046c5da Mart*                    S/R exf_swapfields
28266d9344 Jean* o testreport:
                    allow to test MPI with different number of processors for each experiment:
                    create file "SIZE.h.mpi" in each build dir.
                    Note: update of "-command" argument not yet implemented.
96bd925d69 Gael* o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
                   alleviate the need for additional 3D tapes when using
                   the non-inear free surface in the adjoint. This is done
b8c827cb68 Jean*   by adding an 'update' of hfacc etc. to their current
                   value at the beginning of forward_step.F.
484f2586c6 Mart* o pkg/seaice
                   seaice_lsr: move stress-divergence computations out of outer pseudo-
3d83c2ccc1 Jean*   timestepping loop
484f2586c6 Mart* o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
                   up, so that the calls of the ctrl_* subroutines are really at the end
                   of the routine.
3d83c2ccc1 Jean* o pkg/gmredi:
                   allow to specify a 2-D horizontal map and a 1-D vertical profil
                   as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
96bd925d69 Gael* o pkg/seaice:
                   move lsr iterations from seaice_dynsolver to seaice_lsr.
                 o pkg/seaice:
                   reduce memory footprint of seaice mutldim advection tapes,
                   by using a 2D tape independent of the generic_advdiff ones,
                   and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
484f2586c6 Mart* 
aaf4b7889a Jean* checkpoint62q (2010/12/29)
56906110dd Jean* o model/src:
                   - check horizontal grid-spacing for unset or zero/negative values.
                   - change AD test hs94.1x64x5 to be truly a 2-D set-up.
9827e6a18a Jean* o pkg/flt:
                   - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
                   - precision of input and output files set according to readBinaryPrec
                     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
                   - initial float position from tiled file was not converted to index space
                     (looks like a bug): fixed to make it similar to initial pos. global file.
7688b175d1 Jean* o global_ocean.cs32x15:
                    change SIZE.h of AD set-up to get same tiling as with MPI.
                    Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
                 o model/src:
                    add flag to control printing of domain fields (bathymetry, hFac ...) in
                    ini_mask_etc (call to plot_fieds_xy*).
                 o pkg/thsice:
                    if useEXF, some forcing fields are not valid in overlap: fixed by computing
                    over the interior only + apply EXCH at the end (like with SEAICE advection).
71e006c2cc Jean* o pkg/mdsio:
                   - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
                     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
                   - change barrier call for safe multi-threads access to 3-D shared buffer.
                   - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
                   - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
                     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1d0c7afaa8 Oliv* o pkg/flt:
                   - add fourth-order Runge-Kutta integration
                   - add basic exch2 support (only 1 facet supported so far!)
824747e6ac Jean* o pkg/mdsio+rw:
                   new S/R to read local (or tile independent) vector (read counterpart of
                    mds_writevec_loc, and front-end write_glvec_rl/rs).
1196ad766d Gael* o global_ocean.cs32x15: additional input_ad.seaice experiment
                     that uses pkg/seaice rather than pkg/thsice.
                     (using multidim advection for seaice)
bba939b996 Jean* o towards more F95 syntax for array specification in namelist:
                   - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
                     of all verification experiments.
                        e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
                       was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
                   - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
a913ac327f Gael* o global_ocean.cs32x15: additional input.seaice experiment
                     that uses pkg/seaice rather than pkg/thsice.
bba939b996 Jean* 
38e5b192c3 Jean* checkpoint62p (2010/12/17)
b8373d841d Gael* o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
                     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
                 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
                     allow for use of multim. advection in seaice adjoint.
a71dccbd8b Mart* o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
                   - first attempt to close budgets by taking into account the freshwater
38e5b192c3 Jean*     flux implied by the sublimation of snow and ice. So far only the
a71dccbd8b Mart*     volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
                     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
0e4cbd8946 Jean* o eesupp/src:
                   new S/R with new option (NML_EXTENDED_F77) to change array specification
                   from F95 standard to commonly accepted extended F77 form.
                   This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
                   and to revert back to the original syntax (with -DNML_EXTENDED_F77)
                   for less tolerant f77 compiler (e.g., pgf77, g77).
8da37cabce Jean* o globalFiles:
                   commented out in parameter file "data" since it's not safe with MPI
                   (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
                   in this case); no longer commented out in restart test (tst_2+2).
                 o add adTapeDir to specify a special directory where adjoint tapes are
                   written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
0e71fc82ff Mart*   and cannot be used together with mdsioLocalDir.
372ecbd193 Jean* o nesting pkgs:
                   - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
                   - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
                   - add parameter files + utils dir + output from short run on beagle.
99f78b5547 Gael* o pkg/seaice:
                     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
372ecbd193 Jean* o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
b3992b16ea Mart*   unnecessary copying in adjoint code, requires new parameter NMAX_ITER
                 
810405d6e0 Jean* checkpoint62o (2010/11/25)
b2aaf537fd Jean* o pkg/exf:
                   - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
810405d6e0 Jean* o pkg/seaice:
                   - seaice_ocean_stress: split a loop for better vectorization of the
                     adjoint code
bb0aaa13c1 Mart*   - seaice_growth.F: fix bug in conservation of freshwater connected to
475a61469a Mart*     capping of heff, put contribution into d_HEFFbyNEG
bb0aaa13c1 Mart*   - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
                     by something more sensible (parameters that are what their name implies)
                   - change some defaults, so that by default exf-parameters are used for
                     things like rhoAir, cpAir,latent/sensible heat parameters, in order
                     to reproduce the old results, many data.seaice now contain funny values
                     for cpAir and latent heat of sublimation
810405d6e0 Jean* o packages_readparms.F: move exf_readparms up in line so that
bb0aaa13c1 Mart*     exf-parameters are visible for other packages (e.g. seaice)
a7e5ab30a6 Jean* o debugMode & debugLevel=2:
                   - differentiate between debugMode & debugLevel=2:
                     debugMode: controls printing of debug messages (sequence of S/R calls).
                     debugLevel: controls printing of algorithm intermediate results and stats.
                   - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
                     => allows to print debug-stats without all sequence of call messages.
                   - switch control of debug print from debugLevel to debugMode in many S/R.
                 o pkg/obcs (obcs-sponge):
                     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
                     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
db3f21a7ea Jean* o pkg/generic_advdiff:
                   - record overlap minimum size for each advection scheme;
                   - refine criteria on overlap minimum size;
                   - check and stop (in gad_check) if overlap size is too small.
                 o pkg/obcs:
                   - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
                     once, in ptracers_implicit.F)
                   - with seaice: remove test on empty file name in obcs_apply_seaice (always
                     apply OB values when tile has OB)
c4900f4204 Jean* o model/src, coriolis setting:
                   - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
                     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
                     files (selectCoriMap=3) with any grid.
                   - add parameter "fPrime" for constant second Coriolis coeff (default=0).
                 o pkg/seaice/seaice_growth.F:
                     a few cosmetic changes that reduce the number of lines of code
36f4ad1be7 Mart* o pkg/obcs: add boundary conditions following Stevens (1990)
                   - the code follows old MOM/NAOSIM code
                   - so far it is only implemented for the eastern and western boundaries
                     and NOT for pTracers
3710b30939 Oliv* o pkg/rbcs:
                   - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
                     beginning of the first rbcs forcing period.
                   - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
                     offline package, i.e., one file per time, labeled by iteration number;
                     deltaTrbcs sets the timestep with which the data was generated;
                     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
                   - rbcsForcingCycle=0 makes forcing non-cyclic.
                   - make arithmetic safe for negative times and odd forcing periods.
                 
19b92f2fb3 Jean* checkpoint62n (2010/11/09)
501625885e Mart* o pkg/seaice:
2a7b0e3fd3 Jean*     fix masking in free-drift S/R ; update results of exp. lab_sea.fd
                 o pkg/obcs:
                    New S/R to copy tracer value from the OB location to narrow band region
                     (width = same as overlap) beyond the OB: preserve OB value (needed for
                     high-order scheme) which were overwritten by EXCH call if in overlap
                     region. Applied to theta, salt, ptracer and advected seaice variables.
                    With seaice: use maskInC in similar way as in gad_advection.F,
                     in seaice_advection.F and advect.F.
                    Update output of experiment seaice_obcs and change exp4 to test OBCS with
                     4th order Adv.Scheme. for pasive salt and ptracer.
                 o tools/genmake2:
                   - when looking for an optfile (not specified), only search for Fortran compiler
                     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
                   - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
                     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
                   - set default for CPP to "cpp -traditional -P" (was the case without specifying
                     an optfile, but otherwise default was just "cpp".
                   - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
                   - when "CC" is not set in the optfile, look for possible C compiler
                     (instead of just setting CC=cc)
                   - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
                     => add a ".F" to ".o" rule for source files with no "#include" (such as
                        port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
                   - move gfortran before g77 in list of possible Fortran compiler (consistent
                     with reference compiler switch from g77 to gfortran)
                 o pkg/seaice:
                   o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
501625885e Mart*     seaice_check that stops the model, when the CPP flag is used.
                   o seaice_growth.F: make capping of ice volume conserving by returning the
                     capped ice as freshwater to EmPmR. This does not change the verification
                     experiments but will change runs where the capping is acutally active
b25aab9f85 Jean* o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
                   (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
                      global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
                      lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
                 o tools/genmake2:
                   - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
                   - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
                   - clean previous genmake log files before anything else.
                   - change Makefile to remove testreport log files (*.tr_log) and genmake log
                     files only with "CLEAN" target (instead of "Clean");
8488313509 Jean* o pkg/generic_advdiff:
                   Change OBCS in multiDim advection (gad_advection.F):
                    Use maskInC to prevent intermediate update of tracer-field in OB regions,
                    thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
                    which were applying future time-step OB values.
                   This way, all explicit calculations use current-time-step OB values
                    (simpler and more consistent).
                   Affects results when set-up uses time-varying OBC and multi-dim advection;
                    update output of experiment seaice_obcs.
7b24ec4b62 Jean* o pkg/seaice:
                   move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
                    this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
                      SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
                   Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
                    but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
                    unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
cc732d4fb4 Davi* o pkg aim (2010/10/26):
                   - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
                     formulation with obliquity, eccentricity, ... as run-time parameters,
                   - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
                     upward shortwave radition at the surface (all-sky and clear-sky).
f84aaa453a Jean* o pkg/obcs:
11aa53a8c7 Dimi*   - writing sections with globalFiles=T does not work: switch to tiled-files
                     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
                   - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
                   - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
f84aaa453a Jean* 
dfe4303922 Jean* checkpoint62m (2010/10/21)
f4c40b0961 Mart* o pkg/seaice: vectorize seaice_solve4temp.F
                   - move iterations loops outside of i/j-loops
                   - requires 2D arrays for TB and effConduct
dfe4303922 Jean*   - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
f4c40b0961 Mart*     modified in this routine
                   - a little bit of clean up, adjusting indentation, etc.
dfe4303922 Jean*   - replaced a few TEN**a by exp(a*log(10.)) in new code for better
                     performance and '**TWO' by '**2' (because TWO is a float),
f4c40b0961 Mart*     replaced ONE, ZERO
2708f6625c Jean* o eesupp/src:
                    fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
473a1d0f79 Gael* o pkg/seaice/seaice_growth.F
2708f6625c Jean*   Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
                   merging process. The merged routine has two branches, and one activates the 'evolution'
473a1d0f79 Gael*   branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
                   In summary, here is what the '10/10 revision' did consist of
2708f6625c Jean*     part 1: seaice_growth.F revisions 1.71 to 1.75
473a1d0f79 Gael*       - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2708f6625c Jean*         The emphasis here was on improving readability (e.g. by trying to use meaningful
473a1d0f79 Gael*         variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2708f6625c Jean*     part 1.5:
                       - revising the lab_sea experiment to make it a more useful (i.e. stable
                         and representative of an actual model run). This was done by generating a
                         (winter) pickup to start from, switching back the main experiment dynamic
473a1d0f79 Gael*         solver from evp to lsr, having one of the experiments use the free drift solution.
2708f6625c Jean*     part 2: seaice_growth.F revisions 1.76 to 1.85
473a1d0f79 Gael*       - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2708f6625c Jean*       - Sorting out the various fields units and sign (set early on and reset at the end)
                         to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
                         fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
                       - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
473a1d0f79 Gael*         and simplifying logical expressions to further improve readibility.
                     part 3: seaice_growth.F revisions 1.86 to 1.89
                       - Re-organize the blocks of code more logically.
                       - Merging the '_if.F' pieces that add something new.
2708f6625c Jean* o pkg/thsice:
                   - vectorize thsice_solve4temp and thsice_get_exf.
65de7ad9cd Mart*     Problem: thsice_solve4temp has an unvectorizable statement that
                     might also be problematic for TAF
2708f6625c Jean*   - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
                     does not change the verifcation experiment, but will change all
65de7ad9cd Mart*     experiments that have this flag undefined (not tested in verification);
                     a little reorganization to save a few 2D fields and recomputations
0d66e9256f Patr*   - 1st step of revisiting thsice adjoint (major recomp. sorted out)
07a36c38a7 Patr*   - 2nd step:  fix some store dirs
                     o seems to work somewhat, i.e. using ifort but not g77
                     o likely cause are incomplete init. or recomputation
                     o start verification/global_ocean.cs32x15/input_ad.thsice
cce7f684db Oliv* o pkg/obcs: add support for exch2
                   - the position of the boundary and prescribed values are specified using
                     a global domain with exch2 facets stacked
                     - in x for N,S boundaries (like W2_mapIO=-1)
                     - in y for E,W boundaries (so E,W boundaries do not overlap)
                 o pkg/mdsio: add support for writing global sections with exch2
                     file layout is as for obcs described above:
                     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
                     - for y-z sections, facets are stacked in y
8f33527490 Jean* o pkg/thsice:
033392cf3f Mart*    - change a few routines for better vectorization: thsice_albedo.F,
                      thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
                      not affected, but in particular the latter routine has changed
                      dramatically (not necessarily easier to read now).
                    - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
8f33527490 Jean*    iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
7117852a81 Gael* o verification/lab_sea:
                   - overhaul of the forward model experiments. The main motivation
2708f6625c Jean*     for this revision is that lab_sea has proven quite fragile (when
7117852a81 Gael*     changing the sea-ice code, and switching platforms) to a point
                     when failures were very hard to attribute to specific code problems.
2708f6625c Jean*   - the suspected reason for this fragility is noise amplification by evp so,
7117852a81 Gael*     to start with, we decided to replace evp with lsr in the main experiment.
                   - the input.lsr experiment thus became obsolete and was removed.
2708f6625c Jean*   - it was replaced with the input.fd experiment that uses an
7117852a81 Gael*     analytical "free drift" solution as the ice velocity field.
                   - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
                     will hopefully allow us to discriminate problems due to dynamic solvers
                     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
                     us to test additional options, along with the salt plume package.
2708f6625c Jean*   - Finally a pickup was generated (at the end of a one year run) to
7117852a81 Gael*     make the tests more representative of an actual model run. Previously
                     the tests starting point was a 1m thickness of ice everywhere.
2708f6625c Jean* o pkg/seaice:
7117852a81 Gael*   - introducing S\R seaice_freedrift.F that compute the
2708f6625c Jean*     analytical solution to an approximate ice momentum
7117852a81 Gael*     equation (i.e. the simple stress/coriolis balance).
                   - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2708f6625c Jean*     of the free drift velocity field, and enable its use.
                     To actually use the free drift solution as the model ice
                     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
9aa451bbe6 Mart* o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
                 
512c5638c7 Jean* checkpoint62l (2010/10/04)
6915e96d9b Jean* o pkg/seaice:
                   -fix the USE_ORIGINAL_SBI version (for variable freezing point);
                   -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
                    version (with USE_ORIGINAL_SBI undef);
ddb00487db Mart* o add hooks for new packages OASIS, the package will follow
                   (hooks exclude the seaice pkg for now)
63712fce08 Gael* o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
6915e96d9b Jean*   Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
63712fce08 Gael*   rather than mdsio_readvector.F/mdsio_writevector.F, within
                   adread_adwrite.F to read/write adjoint-related tapes to disk.
6915e96d9b Jean* o eesupp and pkg/mdsio: ALLOW_WHIO
                   Option to write/read 2D fields to files including tiles halos.
                   The main purpose is for adjoint related "tape I/O".
b7f33b42e8 Gael*   The secondary purpose is for debugging phases.
                   A word on those rather specifically intended purposes.
                   The code was meant to be stripped down to the bare minimum.
6915e96d9b Jean*   Typically, there is a unique and basic mapping to the global
b7f33b42e8 Gael*   buffer (tile by tile, then proc by proc, then level by level), and
                   byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
6915e96d9b Jean*   meant to generate user friendly outputs of various shapes and forms.
b7f33b42e8 Gael*   Rather it is intended, for the knowledgeabale developers,
                   to be largely independent of the many mdsio options, to allow
6915e96d9b Jean*   outputs of tiles+halos in debugging phases and in adjoint runs,
b7f33b42e8 Gael*   and to allow some flexibility in tuning (adoint) I/O depending on each
6915e96d9b Jean*   file system behavior. With regard to tuning, most of the potential knobs
b7f33b42e8 Gael*   (to leave files open, to allocate the I/O indep. of usesinglecpuio,
                   to specify directories, to specify the typical size of I/O calls, etc.)
                   are not yet included, and will be added if they prove useful.
2ec921609d Jean* o pkg/seaice:
65c3c27d2c Jean*    fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
                 o pkg/seaice:
2ec921609d Jean*    new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
                    code (seaice_budget_ice_if.F) which enable to recover old standard
                    code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
                    temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
                 o model/src (rStar):
                    use simple average (not area weighted) of rStarFac at U,V point when using
                    vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
                    update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
813dd65ac9 Jean* 
e356351660 Jean* checkpoint62k (2010/09/17)
05855df642 Patr* o adjoint
                    * changed verification/global_ocean.cs32x15 ; adjoint now tests
                      Adams-Bashforth 3 + NLFS + RSTAR
                    * some more modifs required for ECCO-GODAE v4
54f6436301 Dimi* o pkg/seaice
                    add SEAICE_AGE_VOL option to use volume instead of area for
                    integrating SEAICE_AGE
a89a34c510 Jean* o model/src:
                    first check-in of sigma & hybrid-sigma coordinate code ; also includes
                    non-linear free-surface parts ; but pressure-gradient not yet coded.
96a7eb29e8 Jean* o pkg/ptracers:
                    option for ptracer to convert Salt Relax into additional EmP.
                     tested in exp. global_ocean.90x40x15.dwnslp (update output)
                 
3eaaf3fa4e Jean* checkpoint62j (2010/08/25)
4d3d3c392f Jean* o pkg/ggl90:
                    other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
deff84d11b Mart* o pkg/dic: car_flux.F, phos_flux.F
                   - reduce number of exp-calls in order to improve performance
4d3d3c392f Jean*   - clean up a little (replace fields by their macros, etc., fix
deff84d11b Mart*     typo in CPP-flag)
fa4ac57b5c Gael* o pkg/ggl90: minor changes
                   - GGL90diffKrS was removed --> always use GGL90diffKr
                   - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
4d3d3c392f Jean*   - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
                     (commented out for now)
fa4ac57b5c Gael*   - change in max/min operations to ensure that smoothing is ok
                   - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
                   - always use diffKrNrT as background profile (i.e. never use diffKr field)
3983b1167c Mart* o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
c3c9befee2 Mart* o pkg/dic:
1cfcce3655 Mart*   - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
                     vectorization
33b1baef56 Mart*   - small bug fix in insol for the unlikely case of a cartesian grid
                   - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
                     + now vectorize, which also removes adjoint recomputations;
                     + replace integer maksp1 by _RL maskp1
1cfcce3655 Mart*     + replace a**x by exp(x*log(a)) in phos_flux.F for speed
c3c9befee2 Mart* 
ee1e0f95df Jean* checkpoint62i (2010/07/21)
1e3aeb8ba1 Jean* o pkg/flt:
                   - with OBCS: stop floats which enter the OB region
                 o model/src:
                   - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
                     for implicit vertical advection.
ac416c45e2 Jean* o pkg/seaice:
                  - account for melting in seaice age evolution.
1e3aeb8ba1 Jean*  - remove double counting of seaice ridging effect on seaice age.
ac416c45e2 Jean* 
283e101b7e Jean* checkpoint62h (2010/06/18)
ad5bd052a0 Jean* o pkg/exch2:
                  - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
                 o tools/genmake2
                   - remove "-pdefault" option: redundant with the use of "packages.conf";
                   - remove file pkg/pkg_default : set the default as a pkg group
                     ("default_pkg_list") defined in pkg/pkg_groups;
                   - fix for case pkg/pkg_depend is missing (was hanging before);
                   - add option "-pgroups" to specify a different pkg_groups than the default.
82644c0ee5 Jean* o verification/adjustment.cs-32x32x1:
                    add a "minimal" set-up test (code_min & input_min) which only compiles
                    eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
f30b73b1e2 Jean* o tools/genmake2
                   - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
                   - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
c5f3ee7c60 Mart* o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
                   files are nearly the same anyway.
                   Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
                    - redefinition of tau(i,i) (by a factor of ustar)
                    - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
                    - replace rhonil by rhoConstFresh in computation of evap (bug fix)
                    - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
6f9d992eff Jean*    - replace
c5f3ee7c60 Mart*      rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
                      shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
                      by
                      shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
                      (changes results)
6f9d992eff Jean*    -> exf_bulkformulae v1.22,
c5f3ee7c60 Mart*       update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
                       (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
6f9d992eff Jean*                 output.txt 1.63
c5f3ee7c60 Mart*        offline_exf_seaice: output.seaicetd.txt 1.7
                        seaice_obcs: output.txt 1.10)
                   Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
                    -> exf_bulkformulae v1.23,
                       unfortunately requires updating lab_sea.salt_plume (6 matching digits),
                       and global_ocean.cs32x15.icedyn (only 11 matching digits)
6f9d992eff Jean*   Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
48a7bf5f11 Jean* o adjoint of exch-1:
                  - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
                    (note: was already like this when using EXCH-2) and remove flow dir
                    and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
                  - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
                  - update pkg/exch2 diff list.
                 
1431f62bbf Jean* checkpoint62g (2010/05/19)
0bb3693507 Jean* o eesupp/src (exch-1):
                  - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
                    and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
                    (renamed to exch1_*rx_cube.F).
                  - change accordingly exch_*_rx.template and AD version in pkg/autodiff
                    to call new exch1 S/R ; update Makefile and .cvsignore.
                  - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
                    exch2_xy_rx later)
                   Note: after updating your code, need to run "make clean" in eesupp/src
71519bb137 Jean* o test experiment bottom_ctrl_5x5:
0bb3693507 Jean*    new output_adm.txt with fewer grdchk & less monitor output.
71519bb137 Jean* o model/src:
                   remove the call to ini_cori in initialise_varia.F (just keep the usual one
0bb3693507 Jean*    in initialise_fixed.F). More consistent with coriolis & horizontal grid
71519bb137 Jean*    beeing treated in the same way (ini_grid is not called a 2nd time).
0bb3693507 Jean* o pkg/exf:
1c4c64c172 Mart*   - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
ba8369cbfe Mart*   global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1c4c64c172 Mart*   - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
a435e833b1 Mart*   - cosmetic changes to exf_bulkformulae.F to make it look more like
                     exf_bulk_largeyeager04.F
f286872c74 Jean* o eesupp/src (exch-1):
                   - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
                   - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
                     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
                     (even without using MPI).
                   - Message mode: move RecvAck setting (indicator of buffer being ready)
                     from send_put to recv_get S/R (was useless before, but not sure if
                     it's much more useful now);
71519bb137 Jean*   - Switch the order of sync: MPI-proc 1rst and then threads;
f286872c74 Jean*   - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
71519bb137 Jean*   - fix AD code for communication mode ='get' (but not used).
b74efa0efe Jean* o model/src:
                   initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
                   not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
b42ffdc64e Mart* o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
46e98d66db Mart* o pkg/ctrl: require a specific set of control variables and exf-flags for
                   adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
c3aa58ac7a Gael* o model/src:
4caeefbbc4 Jean*  a) 1rst version of a new driver S/R to turn-off output freq and flags after the
                    1rst forward sweep, to avoid over-writing output files during recomputations
                    recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
                  b) 2nd version:
                   - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
                   - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
                      writePickupAtEnd) + seaice & ptracers output;
                   - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
958aba4d71 Jean* o model/src:
c3aa58ac7a Gael*   - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
7b55f0c147 Jean* o pkg/exch2:
958aba4d71 Jean*   - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
7b55f0c147 Jean*   - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
6f7f051ae5 Jean* o pkg/autodiff & exch2:
                   process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
                   (for now, only if ALLOW_EXCH2 is defined).
72ca7aff83 Jean* o pkg/autodiff:
958aba4d71 Jean*   - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
72ca7aff83 Jean*     (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
                    + clean-up comments (_RS is not always real*4)
                   - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
                   - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
                     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
e4c55a32ae Jean* o testreport (AD-tests):
                   no longer link files from dir "../input" (1rst link files from
                   "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
                 
39ab2f324f Jean* checkpoint62f (2010/04/29)
dd69ba5157 Mart* o model/src/the_main_loop.F:
                   adjust store directives for seaice evp and multicategory according to
                   pkg/ecco/the_main_loop.F
ec74c4ec27 Patr* o adjoint:
e4c55a32ae Jean*   global_sum_ad was incomplete (noted many times by many people ;)
ec74c4ec27 Patr*   nice description by Jean U. as follows:
e4c55a32ae Jean*   * allreduce(var) in global_sum.F can be interpreted as
                     reduce(sum) followed by broadcast of sum.
                   * The adjoint of that is
                     sum(adjoint) followed by broadcast(summed adjoint value)
ec74c4ec27 Patr*     or in other words, allreduce(sum, adjoint vars)
                   We were missing the sum(adjoint)!
                   Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
                   (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
                   The fix should produce 16-digit accuracy between
                   single-CPU multi-tile (e.g. nSx=2, nPx=1) and
                   multi-CPU single-tile (e.g. nSx=1, nPx-2)
                   We'll probably change this yet again shortly
3b017f85c7 Jean* o eesupp/src:
                   - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
94ec5b807d Dimi* o pkg/icefront
                   - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
                     specification of addmass array based on a 2D field, which is added
                     at bottommost wet level at each horizontal location.
c99b00e28d Jean* o model/src:
                  horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
                  layout; (not always compatible with delX,delY setting; commented out for now).
062357823a Jean* o pkg/exch2:
                  change tile to processor setting (case nSy*nPy > 1): allows default model mapping
                  (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
                 
e98d34196c Jean* checkpoint62e (2010/04/15)
a175514333 Jean* o pkg/obcs:
                   - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
6526bf38ab Jean* o pkg/dic:
                   -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
                     (note: not presently tested in any forward verification exp.)
                    update tutorial_global_oce_biogeo AD output file.
                 o pkg/exf:
a294fb3ca0 Gael*   - account for the variation of albedo as a function of zenith angle
6526bf38ab Jean*     by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
e8d83fb93d Jean* o build_options:
                  - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
                 o pkg/dic:
                   change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
                   - use binary pickup file for restart;
                   - initialise atmos-CO2 box from dic_pCO2 parameter;
                   - fix multi-threaded.
186276afbe Jean* o pkg/rbcs:
                  - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
                    change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
                  - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
                    and update output.txt
faaf90f2c5 Jean* o pkg/kpp:
                  - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
                  - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
e8d83fb93d Jean*    (= ratio of KPP non-local (salt) flux relative to surface-flux) when
faaf90f2c5 Jean*    using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
                  - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
                    KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1a6563ae72 Davi* o pkg/offline:
4daea5a88d Jean*   fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
                   (bug was added in version 1.10 on 2007-08-23).
                 o pkg/offline:
1a6563ae72 Davi*   - no need to specify periodicExternalForcing, etc ... to use offline pack
                   - offline input files no longer just single prec --> parameter offlineLoadPrec
3d5d3248cf Patr* o verification/lab_sea:
4daea5a88d Jean*   change AD test to multi-tile setup and update all 4 AD output.
3d5d3248cf Patr*   NOTE: while cost function values remain very similar,
                   gradients are very different, although gradient checks are self-consistent
                   Should try to get to the bottom of this (cost function summation order?)
0978c8a77f Jean* o pkg/dic:
                   in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
                   a weakness of TAF that drops part of double precision in log10 derivative.
d7e064ff4e Jean*   <= changes removed since problem has been fixed in current TAF version 1.9.71
0978c8a77f Jean*   update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
5fd4ec8263 Jean* o pkg/ecco:
                   add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
                   update all 4 lab_sea AD output.
                 
9f4cf29369 Jean* checkpoint62d (2010/03/22)
                 o build_options:
                   remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
b9024a78e5 Jean* o remove unbalanced quote (single or double) in commented line of source code
                   (may cause some warning with some preprocessor/makedepend versions).
                 o pkg/seaice:
87ed893815 Jean*   fix seaice_model.F for adjoint (gael) and update AD results of experiments
                    lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3b0f45b28f Jean* o testreport:
                   add option '-runonly' (short: '-ro') to just do the run part (without make).
2956a926ec Jean* o eesupp: remove JAM communication code (obsolete).
8194302c25 Jean* o add option to genmake2 & testreport to switch "_RS" type to "real*4"
a435e833b1 Mart*   (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
8194302c25 Jean*   to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
                   (update also the output).
                 
f916330b2a Jean* checkpoint62c (2010/03/02)
c805d90c6c Jean* o tools/build_options :
                    move (some) old optfiles from build_options/ to build_options/unsupported/
74230ba5cf Gael* o model/src and pkg/exf
                    surface relaxation -- separating data and data.exf options
                    The point is to ensure that we specify the surface relaxation
a435e833b1 Mart*    either in data or in data.exf (but not half and half) and to
                    avoid an accidental relaxation to 0 (which happened if a time
74230ba5cf Gael*    scale was specified but the file name was left empty)
4b97e458f0 Gael* o model/src model/inc and pkg/mom_common
                    ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
                    => addition to the viscosity field as computed by others schemes
a435e833b1 Mart* o tools/build_options:
076c0d73b3 Jean*   - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
                     but keep the former optfile for few weeks for smooth transition
01d7251472 Gael* o pkg/ecco
                   - allow user defined cost function contributions
cc732d4fb4 Davi*      CPP: ALLOW_USERCOST_CONTRIBUTION
                      USAGE: compute contributions in cost_usercost_all.F
01d7251472 Gael*   - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
                       the two options are complementary.
5939a6479f Gael* o pkg/smooth
                   - migration from contrib to the main repository
076c0d73b3 Jean* 
e7a2735eaf Jean* checkpoint62b (2010/01/26)
075e0d2187 Jean* o pkg/monitor:
a435e833b1 Mart*   - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
075e0d2187 Jean*     (in case someone forgot to update customized pieces of code)
                 o nonHydrostatic:
af06fd5b92 Jean*   - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
                   - add a simple 2-D experiment (short_surf_wave) to test it.
                 o pkg/icefront:
                    adding the shell of, and the hooks to, a new package that
5da8ce63fa Dimi*    will model melting and freezing of vertical glacier ice fronts
af06fd5b92 Jean* o momentum:
451e002b6f Jean*   add diagnostics of momentum tendency from Hydrostatic pressure gradient
                    (without surf.pressure term: would need a 2nd filling since implicit term).
af06fd5b92 Jean* o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
                   two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
                   cannot deal with the former
884840d195 Jean* o cleaning:
451e002b6f Jean*   - remove all (except OpenAD) old TLM output from results_ad dirs.
884840d195 Jean*   - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
                   - comment out maskH definition (replaced by maskInC)
                 o pkg/monitor:
                   - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
075e0d2187 Jean*     & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
884840d195 Jean* 
0be9783367 Jean* checkpoint62a (2010/01/15)
e95eb1d512 Jean* o model/src:
                   - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
987f6e1ae3 Jean* o pkg/diagnostics:
                   - add optional level number diagnostics (i.e., level number to be define
                     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
                   - strictly check for valid parser-code(10) ;
                   - check if adding diag to the list from the right place.
09d7c96a8d Oliv* o pkg/longstep:
                   - change parameters and fix tracer conservation with rstar/nonlinear free surface
f8b182d288 Jean* o diagnostics:
                  - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
                    S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
75ecb6f722 Jean* o pkg/diagnostics:
                  - Add option for writing vertical integral (sum of selected levels) of an output
                     field instead of writing output field levels. Activate this option on a per
                     output-file basis, by setting the 2nd character of fileflag to 'I'.
                  - Add field-specific information relative to level integral in 3rd postion
                     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
                     vertically (x level-thickness x hFac), "r"=same but without hFac.
281db5ef19 Jean* o do_the_model_io:
                   - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
                     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
                     writing pickups and stopping.
                 o pkg/diagnostics (for now, only with mdsio):
                   - write time information to meta file (and modify accordingly rdmds.m) :
                     time-averaged diagnostics output: write starting and ending time of the
                     time-averaging interval ; snap-shot diagnostics output remains unchanged;
e9ac57b72c Jean* o pkg/timeave:
                   - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
                     always Nr), now assumed to be equal to number of levels of averaged field;
                     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
                 o pkg/sbo:
                   - fix ocean bottom pressure global-average & 2-D time-ave output (was
                     neither initialised nor filled).
                   - add starting iteration in suffix of global-average output file
                     (to avoid over-writing the file after a restart)
                   - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
                 o time-average:
                   - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
                     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
                      ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
                     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
                   - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
                   - fix missing accumulation for pkg/opps.
                   - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
                      (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
                   - fix initialisation of time-ave vars and do only full time-step increment
                     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
580b2d0e2d Jean* o pkg/layers:
                   - use standard RW pkg S/R to write the output
                     and remove local write_fld version (which had a problem).
                   - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
                   - fix LAYERS_CALC argument list.
                 o pkg/timeave:
                   - store cumulative-time in a simple tiled array (drop the level index)
                   - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
b59b551857 Jean* o pkg/ocn,aim_compon_interf
                   - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
                 
6a7fcc88c2 Jean* checkpoint62  (2009/12/23)
c32120bcda Jean* o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
                     (was not previously tested in any other exp.)
262f5d9bf0 Jean* o pkg/monitor:
                   - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
6a7fcc88c2 Jean*     mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
262f5d9bf0 Jean*     (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
                   - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
                   - change del2 calculation.
                   - use interior masks (instead of maskH, <- to be remove).
                   - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
                 o mask & obcs:
                   - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
6a7fcc88c2 Jean*   - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
262f5d9bf0 Jean*     (called after packages_init_fixed)
3a86c9b47d Oliv* o pkg/obcs:
                   - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
                     Fixes bug in obcs+exf with nSx*nSy.GT.1
                   - fix multi-tile handling in obcs balance code
c93c5f4bd8 Jean* o nonHydrostatic:
                   - Implement AB-3 for non-hydrostatic vertical momentum ;
                     (change ordering of var. stored in pickup file when using NH)
                   - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
                   - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
                     (in prep. for new NH free surface form).
4d27a257dc Jean* o pkg/obcs:
                   add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
6a7fcc88c2 Jean* o model/src:
4d27a257dc Jean*   fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
                 
0e6056cd20 Jean* checkpoint61z (2009/12/01)
4848a3791a Jean* o nonHydrostatic:
                   Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
                     a spurious source of energy in simple baroclinic adjusment test case.
                   Update all non-hydrostatic exp output.
                 o model/src (3-d solver):
                   Change again 3-D solver free-surface RHS term when exactConserv=T:
                     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
                     (which was not the case with previous formulation).
                   To recover previous version, just reset "oldFreeSurfTerm" to previous value.
                   Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
                 o nonHydrostatic:
                   - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
                     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
                   - change 3-D solver to work with r* (for now, only with linear free-surf.)
                   - add few debug diagnostics (cg3d_x, residual)
85d256894a Jean* o model/src:
                   fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
                     update output of exp. global_ocean.cs32x15.viscA4
f470880b96 Jean* o update output of exp. global_ocean.cs32x15.icedyn after removing
                   #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
                 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
a435e833b1 Mart* o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2a44bd20e3 Mart*   for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
043540edbe Mart* o model: add Christopher Wolfe's implemetation of the single reduction cg2d
f470880b96 Jean*   (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
a435e833b1 Mart*   runtime flag useSRCGSolver. Modify verification experiment global_with_exf
f470880b96 Jean*   to test this code
eb4cdc75fa Jean* o pkg/cd_code:
                   Change defaut D-grid time-stepping to get the same for D-grid momentum as for
                    C-grid momentum. D-grid velocity used to be stepped forward in time with
                    Adams-Bashforth only on surface pressure term. Tests show that using AB on
                    D-grid coriolis term improves stability (as expected from CD-scheme paper).
                   To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
                   Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
                    lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
                    tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
                   Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
4d27a257dc Jean*        global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
4a2ef1ee39 Jean* o pkg/obcs:
eb4cdc75fa Jean*  - fix bug in initialisation (broken since Oct 1rst modification)
4a2ef1ee39 Jean*    for useOBCSprescribe without useEXF.
                 
0e6056cd20 Jean* checkpoint61y (2009/11/15)
10b70e5d9c Mart* o pkg/seaice
                  - change (once again) the discretization for the evp solver: rather than
                    squaring the averages of strain rates, average the squares to give
                    a better approximation to VP behavior (in simple test); this breaks
                    verification experiments that use EVP (lab_sea and lab_sea.hb87)
                     --> update outputs
dde99557d4 Jean* o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
b2a741ef12 Mart*   to improve vectorization of adjoint code on TARGET_NEC_SX
29d62326d0 Davi* o verification/vermix:
a435e833b1 Mart*   - change vermix to a more "classical" 1d column with high vertical
                     resolution, seasonal heat flux forcing and constant wind forcing
10b70e5d9c Mart*     --> update outputs
6636ec7a94 Mart* o pkg/seaice
                  - fix diagnostics of principal stress components for EVP
                  - add optional diagnostics of non-linear convergence for LSOR solver
8eb548676f Mart*  - make maximum zeta a runtime parameter
d7bdbe3409 Jean* o model/src (3-d solver):
                   Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
                    which consisted in removing the Surf. Non-Hydrostatic pressure from the
                    whole column and adding it to Eta (inspired from Casualli, 1999):
                    Only affects 3-D solver initial guess and only if using ExactConserv,
                    but tests did show a degradation of solver convergence. For this reason,
                    decide to disable this piece of code.
                    to recover previous version, just set zeroPsNH = exactConserv (line 78).
                   Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
a435e833b1 Mart* o pkg/ggl90:
8f048929ff Jean*  - fix previous modif (unfortunatly has not been documented here).
ef30cce719 Mart* o pkg/seaice/autodiff:
e69eb16cf6 Mart*  - add CPP flag to include clipping of zeta in EVP code;
                    although clipping of zeta is not necessary for EVP and not recommended
                    it was done by default, now clipping is disabled by default
d68173436e Mart*  - modify computation and store zetaC/Z in seaice_evp for TAF
043891c656 Mart*  - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
6636ec7a94 Mart*  - change seaice_calc_viscosities/strainrates for better
043891c656 Mart*    vectorization after AD by TAF
9fb8a4afa4 Jean*  - rearrange common blocks in SEAICE.h once again for easier dumps of
ef30cce719 Mart*    adjoint output, adjust adcommon.h and g_common.h
                  - change flux form of default advection scheme for better vectorization
                    of adjoint code
a435e833b1 Mart*  - modify lab_sea/input.lsr to test the flux form of default advection
ef30cce719 Mart*    scheme
8c04a08a06 Mart* o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
                   transition in checkpoint61r)
                 
0e6056cd20 Jean* checkpoint61x (2009/10/19)
3ccf557bdf Patr* o adjoint: adding two new verification experiments
a435e833b1 Mart*   * tutorial_global_biogeo: an online dic sensitivity experiment
3ccf557bdf Patr*     (work with G. Forget)
                   * tutorial_dic_adjoffline: an offline dic sensitivity experiment
                     (an update of the Dutkiewicz et al., 2006 paper)
                   Both use the same CO2FLUX cost function, but different controls
                   Gradient checks look good, but some recomp. could still be traightened out
                   Should add xx_dic control variable to test at some point
51b66c683d Jean* o model/src:
                   add run-time parameters to check and/or mask initial Temp & Salt
7744ec9132 Jean* o pkg/ptracers:
                   apply zonal filter (if used) to all passive tracers
                 
0e6056cd20 Jean* checkpoint61w (2009/10/12)
d5930766d9 Patr* o adjoint:
                   * update and finish work on adjoint of dic package (G. Forget)
                   * start adjoint of offline package
                   * bug fix for cube-sphere TLM code (active_file_g.F)
5ff9d8d8a4 Jean* o tutorial_global_oce_optim:
                   now tested with 4 tiles (change data.grdchk and update output_adm.txt)
7784d9f62a Jean*   and add SIZE.h_mpi for MPI testing
442ec6ef47 Mart* o pkg autodiff
                  - fix bug in autodiff_restore
a435e833b1 Mart*  - make genmake2 remove comments and empty lines from ad_input_code.f in
442ec6ef47 Mart*    order to reduce file size (new script file remove_comments_sed)
54e442a4cf Jean* o allows to specify vertical profile of vertical viscosity (viscArNr)
38d9d89a2d Mart* o pkg autodiff
a435e833b1 Mart*   autodiff_ini_model_io: comment out writing of grid information to netcdf
                   files, because at this time the grid fields are a bunch of zeros
                   (this is analogous to ini_mnc_vars.F)
74b7cbac64 Mart* o pkg seaice/autodiff:
a435e833b1 Mart*  left-over from removing the 3-time-level fields:
74b7cbac64 Mart*  - small rearrangement of common blocks (SEAICE.h)
a435e833b1 Mart*  - fix field declaration in order to get meaningful output in
                    adseaice.*.nc (adcommon.h)
7532a9f33f Jean* o pkg obcs:
                  - go through NH code only if nonHydrostatic=T
                  - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
7784d9f62a Jean*  - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
53056a14f9 Jean*    => Update output of experiment seaice_obcs
                  - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
8546425e3d Jean*  - fix NH+Orlanski restart (add wvel OBC value in pickup file)
6463eff00c Jean*  - fix restart for useOBCSprescribe + useEXF
793e0bf23c Mart* o pkg ctrl
                  - make obcs as control parameter work also with useSingleCPUio
                  - replace a few sny and snx by Ny and Nx to be consistent with
                    ctrl_set_globfld_x/yz.F
cffcf702d2 Mart* o pkg seaice
a435e833b1 Mart*  - re-introduce global field frWtrAtm for the case of
cffcf702d2 Mart*    ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
                  - catch the case of an empty filename in seaice_cost_init_fixed.F
                 o pkg ecco:
                  - small bug fixes in the_main_loop
                   . fix order of monitor arguments
                   . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
                   . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
                     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
a435e833b1 Mart*  - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
                    imbalance diagnostics for wmean_h/sflux = 0
cffcf702d2 Mart*  - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
a435e833b1 Mart*  - catch the case of empty filenames in ecco_cost_init_fixed.F
cffcf702d2 Mart*    and ecco_readparms.F
                  - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
793e0bf23c Mart*    to make this statement meaningfull in ecco_cost_weights.F
339ad6c3b5 Jean* o pkg zonal_filt:
                   - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
                   - when using rStar, filter uVel*hFacW instead of uVel
                    (tested without topography: fix a Pb of growing instability with NLFS)
9fba1b3510 Davi* o pkg/aim/thsice:
                  -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
                   (works as SST restoring)
55b32f1302 Davi* o pkg/thsice:
                  -add specific parameter for salt restoring in slab mixed-layer
                    (by default equal to the temperature restoring)
                 
0e6056cd20 Jean* checkpoint61v (2009/09/21)
e5d361f9aa Mart* o pkg/kpp:
a435e833b1 Mart*  -add double diffusive contributions as a hack, turned off by default
                   for now, and the code can be excluded with a CPP-flag
e5d361f9aa Mart*   EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
                  -add a verification experiments to "vermix" to test this code
f81982db08 Davi* o pkg/mom_common:
                   Move computation of length scales to mom_init_fixed.F (avoid recomputation
                   at each time-steps*levels).
0dd6d0e826 Ryan* o pkg/layers:
                   Created a new package for computing volume fluxes in temperature or
                   [not yet implemented] density layers, e.g. for calculating residual
a435e833b1 Mart*   overturning circulations.
                 o pkg/diagnostics:
f4e6557763 Jean*   implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
                 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
f88b29d124 Jean* o pkg/mdsio (& pkg/rw): rework high level S/R interface:
                   To avoid mixing type (RS/RL) of input/output array argument,
                   replace single mixed-type array with a pair from each type (RS/RL).
03e0cc6d31 Jean* o setting pickupSuff force to start from a pickup (even if nIter0=0): this
a435e833b1 Mart*   is now implemented for all pkgs (previously only done for the main pickup)
03e0cc6d31 Jean* 
0e6056cd20 Jean* checkpoint61u (2009/08/25)
7b5bc55348 Mart* o pkg/obcs:
23ff66f209 Mart*   - change OB?eta from _RS to _RL and put them into a separate commen block
                   - add code to read OB?eta from a file via obcs_prescribe_read: the code
                     compiles and does not destroy any other experiments, the data is read
                     properly, but the code is not tested in actual applications
a435e833b1 Mart* o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
                   create a meaningful unit attribute for the time coordinate variable
b6045d9739 Jean* o pkg/ebm: add plenty of missing "_d 0" ;
a435e833b1 Mart*    update results of experiment global_ocean_ebm (fwd + adjoint tests)
b6045d9739 Jean*   Notes: several pieces of code only works for (very) specific set up
a435e833b1 Mart*    (domain size, lat range, etc ...); should be documented & stop if one
b6045d9739 Jean*    of those assumptions is not meet.
6b1574ad60 Jean* o pkg/seaice: add missing "_d 0" in HSNOW initialisation
a435e833b1 Mart*    update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
6b1574ad60 Jean*       and offline_exf_seaice (seaicetd + adjoint).
70d7fbc59b Jean* o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
a435e833b1 Mart*    update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
70d7fbc59b Jean*     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
a435e833b1 Mart* o few changes to pass when compiling with strick checking of arguments
70d7fbc59b Jean*    across S/R (allow to find few bugs in S/R calls).
d5724f98ed Mart* o pkg/seaice:
a435e833b1 Mart*  - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
d5724f98ed Mart*    2d-fields, for slightly better performance
70d7fbc59b Jean* 
0e6056cd20 Jean* checkpoint61t (2009/07/22)
a435e833b1 Mart* o pkg/seaice:
f503466573 Mart*  - remove unused variables in seaice_evp
                  - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
570ee1ae01 Jean* o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
                    named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
5a08ea66a4 Jean*    each processor opens a different file (a fix from Matt).
78e9a5d276 Jean* o cg2d:
                    use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
                    this reduces number of EXCH calls by 2 when using exch2.
a435e833b1 Mart*    For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
78e9a5d276 Jean*    directives and missing simple EXCH (exch_s3d_rx) adjoint code.
a435e833b1 Mart* o pkg/thsice:
78e9a5d276 Jean*    add code for Near Infra-Red albedo (from Jeff)
f3e78cec2b Jean*    (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
78e9a5d276 Jean* o ini_model_io:
                    move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
                    MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
                    to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
f3e78cec2b Jean* 
0e6056cd20 Jean* checkpoint61s (2009/06/30)
2afd155f68 Jean* o pkg/exch2 (exch2_rxN_cube*):
                    remove last BARRIER (no need to synchronise after getting data from shared
                    buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
78c0da63a8 Jean* o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
                   and generate new output (for the 2 tests) using default rotationPeriod.
e33637256c Jean* o pkg/exch2:
                   - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
                     (was already the case with AUTODIFF_EXCH2 defined)
                   - add bj in exch2 arrays and S/R.
78c0da63a8 Jean*   - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
                     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
e8488bfd93 Oliv* o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
                   - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
                     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
                   - verification experiment natl_box.longstep
02bc4aeec0 Jean* o build_options: ifort+mpi_aces optfile (following Constantinos advise):
                   allow different versions of ifort (8 or 9) and different versions
                    of mpi (mpich or mpich2) to be used with the same optfile.
                   requires to load a netcdf module and set MPI_INC_DIR (see comments inside
                    optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
a435e833b1 Mart* o pkg/seaice:
                   fix previous modif (3-level field removed) for old-pickup reading
02bc4aeec0 Jean* 
0e6056cd20 Jean* checkpoint61r (2009/06/25)
a435e833b1 Mart* o pkg/seaice:
88ddcec046 Mart*  - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
64469ab2ce Mart*   1. introduce fields for time step (N-1)
88ddcec046 Mart*   2. do not use levels 2 and 3 anymore (but keep them)
a435e833b1 Mart*   3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
                      includes changes to pkg/thsice/thsice_get_velocity.F,
88ddcec046 Mart*      model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
                      pkg/obcs/obcs_apply_uvice.F.
                  - completely remove code for leap-frog time stepping for second order
                    advection
2e0a6baf06 Patr*  - adjusted adjoint accordingly;
                    gradient checks have improved by an order of magnitude!
a435e833b1 Mart* 
0e6056cd20 Jean* checkpoint61q (2009/06/22)
bfa01eb1b6 Mart* o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
                  - the boundary conditions along open boundaries are unclear, because the
                    associated masks are set to zero and are thus treated as closed when
                    applying the slip-boundary conditions.
                  - move initialisation of grid variables from seaice_init_varia to _fixed
14ff2fe9e4 Dimi* o adding doc/diags_changes.txt
a435e833b1 Mart* o model/src:
                   do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
dddd7d8ee5 Jean*    to avoid "_diags" naming if no relation to pkg/diagnostics.
a435e833b1 Mart*   ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
dddd7d8ee5 Jean*    file and only call PLOT_FIELD_XYZ if debugMode=T.
                   remove few PLOT_FIELD_XY calls outside initialisation.
                   remove few unnecessary BARRIER.
1aca59cbdd Dimi* o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
a435e833b1 Mart*   of salt_plume package in Southern Ocean
                 o pkg/thsice:
                  - fix hOceMxL in overlap (needed for sea-ice advection);
a870da40f8 Jean*    update output of experiment global_ocean.cs32x15.icedyn.
a435e833b1 Mart* o pkg/seaice:
2fe56e7563 Mart*  - make the (placeholder-)tracer IceAge a little more meaningful
0ccf00deac Mart*   by avoiding ridging of age due to convergent ice flow
14ff2fe9e4 Dimi*  - add diagnostics for surface temperature, atmospheric and oceanic
                    heat flux, and atmospheric and oceanic ice growth
0ccf00deac Mart* 
0e6056cd20 Jean* checkpoint61p (2009/06/10)
7b728547f6 Jean* o eesupp (global_max & global_sum):
                  - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
                  - remove starting & endding barrier (no longer needed)
4877fb20d9 Jean* o pkg/mdsio, writelocal:
                    works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
                    (remove the STOP): uses shared buffer IO to store data from all threads
                    and then let master-thread write nThreads tiles.
1f0f779d4b Jean* o pkg/mdsio (read/write field):
                  - tiled IO done in 1 piece (all levels at a time);
4877fb20d9 Jean*  - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1f0f779d4b Jean*  - multi-threaded: allow to read/write local (non-shared) array
                    (was already working with singleCpuIO ; now works also without);
                    => no longer needs barrier call after reading a file (added inside
4877fb20d9 Jean*    mds_read/write field).
1f0f779d4b Jean*  - move barrier calls outside gather/scatter_2d to mds_read/write_field
b54505b067 Mart* o pkg/obcs/exf
a435e833b1 Mart*   - exf_getffieldrec.F: add a few ". _d 0" and
                                         add code to catch the case fldperiod = 0.
                   - obcs_precribe_read.F: change if statements so that they match
b54505b067 Mart*                           the variable type (_RL)
a435e833b1 Mart*   - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
b54505b067 Mart*     exf_iprec) as part of namelist EXF_NML_01
70cbc60ad4 Jean* o pkg/mdsio:
                   - read/write tiled (local) files: read/write 1-level tile chunk at a time
                     (instead of segment of length sNx); expected to speed up tiled IO.
                 o pkg/exch2:
c53c960d6f Jean*   - take buffer copy from/to array out of S/R exch2_send/recv into new
                     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
                     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
                   - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
70cbc60ad4 Jean*   - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
c53c960d6f Jean*     (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
                     including Topology header file (and common blocks).
                   - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
                     remove 2nd exch call in exch2_s3d_rx (no longer needed).
                   - document S/R arg. list (+ update some comments)
1ce2a5cdfd Dimi* o pkg/seaice:
                   - added SEAICE_CLIM_AIR code, which permits modulation of surface air
                     temperature and humidity over sea ice based on climatological values.
3827b3ff39 Mart*   - clean up computation of Hibler+Bryan (1987) stress coupling for the case
a435e833b1 Mart*     of LSR (this change is expected to change the results slightly because now
3827b3ff39 Mart*     it uses slightly difference moduli from the second last LSR solution, but
a435e833b1 Mart*     that is more consistent with the stress computations; this part of the code
3827b3ff39 Mart*     is not tested in the verification experiments)
7beac62984 Mart*   - fix diagnostics for flux of ice in case of B-grid
a435e833b1 Mart*   - turn strain rates eij and press into global fields within global
7beac62984 Mart*     common block in SEAICE.h for more straighforward diagnostics
                   - fix diagnostics for principal stress components, press, zeta, eta
                     to give something meaning full
607aea417f Jean* o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
                   new output (all 4 tests) using default rotationPeriod.
37512d714c Davi* o pkg KPP:
                   - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
                   - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
                     and normal grid from 1 to Nr)
6a8a92ceb1 Davi* o Fix computations of L4rdt in mom_calc_visc.F
4444d50a00 Jean* o eesupp:
                   new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
                   should be called before a "stop" if we know that all process are going
                   to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
                 
0e6056cd20 Jean* checkpoint61o (2009/05/26)
52b3903673 Jean* o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
                 o model/src/ini_curvilinear_grid.F:
680765c772 Mart*    compute angleSin/CosC when they are not read from a file
52b3903673 Jean* o pkg/seaice:
680765c772 Mart*    add pseudo time stepping for LSOR
cfdf8f6dc3 Jean* o pkg/exch2:
                    temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
f834b21bef Dimi* o pkg/seaice:
f81e0cd482 Dimi*    Adding separate sea ice albedo, drag coefficients, and HO in Southern
                    Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
39f815874d Jean* o SingleCpuIO:
                    fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
                 o pkg/seaice:
affccff0e4 Jean*    put exchanged variable in (local) common block for MPI+Multi-Threads
                    to work (necessary with exch1, and for now with exch2 too).
8d614a5ef7 Jean* o verification: to get more experiments tested with mpi, mth and mpi+mth,
                   change tiling of:
                    aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
                    hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
                   update output of exp:
                    exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
                    tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
                   + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
                                    (note: output.txt generated on faulks using only 1 tile)
505fa6b5f0 Jean* o eesupp & mdsio (SingleCpuIO):
                  - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
                    parameter "W2_useE2ioLayOut" (read from file "data.exch2").
                    Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
                  - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
                  - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
                    gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
8dd64871a3 Jean* o pkg/exch2:
                  - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
                    read parameter file "data.exch2" if it exists; otherwise try default regular
                    cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
                  - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
                    with new code (not to be used, just as a backup solution).
a435e833b1 Mart*  - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
505fa6b5f0 Jean*    in utils/exch2/input.
8dd64871a3 Jean* 
0e6056cd20 Jean* checkpoint61n (2009/05/12)
6805d023a2 Jean* o eesupp & mdsio (SingleCpuIO):
                   - move mapping to global io-buffer inside gather_2d/scater_2d: this save
                     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
                     receive real*4 array (instead of real*8) to read/write 32.bit files.
                     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
                      and remove new mapping S/R)
b983b0a9f3 Jean* o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
                   - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
                     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
                     when using exch2. Add S/R to map global io-buffer to global model array.
                   - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
                 
0e6056cd20 Jean* checkpoint61m (2009/04/29)
b983b0a9f3 Jean* o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
                   and add 3 other S/R for other types (R4,R8,RS).
5ae9fbe2f9 Jean*   Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
                 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
                  - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
                  - reduce number of macro definitions (keep only those which are used);
                    can always call directly the corrresponding S/R if needed.
b983b0a9f3 Jean*  - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
5ae9fbe2f9 Jean*    _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
                  Fixed wrong type of arg in:
b983b0a9f3 Jean*    atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
5ae9fbe2f9 Jean*    ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
                  To fix: global_sum of var in common block is wrong (multi-threaded) in:
                    dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
                  To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
b983b0a9f3 Jean* o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
                   "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
52af3a32f7 Jean* o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
                 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
                   edges are closed (zero depth); might happen with "blank tiles";
b983b0a9f3 Jean*   for now, disabled if using OBCS.
52af3a32f7 Jean* o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
855948c4e0 Jean*   link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
52af3a32f7 Jean* o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
6e7414edd7 Jean*   to reduce length of 1.D array print in STDOUT.
71c716cb9b Jean* o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
                   + use 48 tiles (16x8): this will allow to test "blank tiles".
                 o start to test MPI + multi-threaded (change testreport to skip tests
                   where number of tiles do not match).
                 o genmake2: add option "-omp" to turn on Open-MP ;
                   passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
0ab0cf443f Jean* o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
                   and keep the original tile numbering. Note: compatible with old
                   W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
                 
0e6056cd20 Jean* checkpoint61l (2009/04/07)
5a8046a779 Jean* o Overlaps had been forgotten in calculating ijk keys : fixed
                 o fix cyrus makedepend for gcc 4.4
54b0077775 Jean* o experiment fizhi-cs-aqualev20:
                   switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
71c716cb9b Jean*   and generate new output. Note: new output is much closer to the old
                   one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
54b0077775 Jean*   the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
                 o pkg/fizhi:
                  - change to avoid indices going deliberately over array-bounds
                  - remove unnecessary MPI stuff
                  - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
                  - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
                    does not go over array-bounds and therefore returns reliable output.
                  - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
                    this S/R has 4 output arguments, which are used inside "get_alarm";
                    when it is called with the same variable "ndum" in place of several
                    output arguments, this produces weird side effect inside "get_alarm"
                   (e.g., datein=dates(n) is overwritten by timein=times(n) since both
                    datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
                    address) and produces error.
855948c4e0 Jean* o tools/gemake2: (March 27-29 2009)
a435e833b1 Mart*   with option "-mpi": link *_mpi files from "MODS" dir (this is what
855948c4e0 Jean*   testreport does).
405ae5a3ac Jean* o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
54b0077775 Jean* o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
405ae5a3ac Jean*    update lab_sea.lsr & lab_sea.salt_plume results
a435e833b1 Mart* o pkg/seaice:
90652fd079 Mart*   Major overhaul of the LSOR solver: change discretization from original
                   finite differences to finite volume. The old routine is still in the
                   file seaice_lsr.F and can be turned on with the CPP-flag
                   SEAICE_OLD_AND_BAD_DISCRETIZATION
                   Along with this change, the discretization of the strain rates is changed.
                   The same flag turns on the old discretization in seaice_calc_strainrates.F
a435e833b1 Mart*   All verification experiments with seaice are affected (except for
90652fd079 Mart*   seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
                   results by setting the above flag.
                   Further changes involve changes in defaults:
                   - ALLOW_FLOODING is defined and turned on by default
f6450d3114 Patr*   - SEAICEadvSnow = .true. is now the default
                   - SEAICEadvSalt = .true. is now the default
                   - SEAICEadvAge  = .true. is now the default
a435e833b1 Mart*   - SEAICE_clipVelocities  = .false. is now the default
5d15d4162f Mart*                                      (as per J. Zhang's recommendation)
90652fd079 Mart*   - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
                     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
                   - seaice_growth: replace computation of UG by a simple copy from wspeed
                 
0e6056cd20 Jean* checkpoint61k (2009/03/18)
4acbf6fef8 Mart* o pkg/seaice: a few bug fixes mostly concerning the metric terms:
                   seaice_lsr: fixed a few metric terms,
                               affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
                               add more debugging diagnostics
                   seaice_evp: removed superfluous many metric terms of FV discretization
                               of stress divergence
                               affects lab_sea, lab_sea.hb87
                   seaice_ocean_stress: removed superfluous many metric terms of FV discretization
a435e833b1 Mart*               of stress divergence for non-evp solver
4acbf6fef8 Mart*               (this part is not tested anywhere)
                   seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
                               they were effectively only half slip
                               affects lab_sea.hb87
71a18d0f38 Jean*   updated all relevant verification experiments (except lab_sea//output_adm.txt
                     which was left over, but fails at level 7 & 6)
4acbf6fef8 Mart* 
0e6056cd20 Jean* checkpoint61j (2009/03/17)
78416b4f31 Mart* o pkg/seaice: turn a few hard wired parameters into run time parameters
a435e833b1 Mart* o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3393e77079 Mart*   time in seconds as promised by the usints in seaice_monitor and exf_monitor
a32626876a Mart* o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
                   that are not cubed-sphere grids
f577077207 Mart* o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2db8cfe50f Jean* o pkg/ctrl:
                   fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
0ad8ad6f0c Jean* o non-hydrostatic (calc_gw.F):
                   fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
                   update output of exp. global_ocean.cs32x15.viscA4
                 o remove backward compatibility for thetaMin,phiMin
ece53aa93e Jean*   (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
a435e833b1 Mart* o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
                   interpolated wind field not only for curvilineargrid=.true., but also
514437540a Mart*   for a rotated grid (rotateGrid=.true.)
58378fc26e Mart* o pkg/exf: add capability to bypass interpolation for runoff
                   by setting yet another CPP-flag
ece53aa93e Jean* o eesupp/src, B-grid exchange:
                   add simple (6 tiles, non MPI) CS exch + standard interface S/R.
bb9388b6fb Patr* o autodiff
                   new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
                   allows to switch to single-prec common blocks;
                   corresponding switch occurs in tamc.h, integer isbyte
                   TAF store directivs "byte" and "kind" seem equivalent;
                   Most tamc.h have been updated correspondingly.
                 
0e6056cd20 Jean* checkpoint61i (2009/02/13)
05fc4302e4 Patr* o autodiff:
                   fix autodiff_sore/_restore indices for obcs
                   (spotted by I. Hoteit, M. Mazloff)
685514cedc Patr* o pkg/autodiff, pkg/ctrl:
a435e833b1 Mart*   Add flag to reduce all tapelev I/O to single-prec.
685514cedc Patr*   In data.ctrl set
                     doSinglePrecTapelev = .TRUE.
ece53aa93e Jean* o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
                   check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
a435e833b1 Mart* o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
6870c5ed6c Mart*   real fresh water flux (not yet)
a94d876c45 Jean* o pkg/mdsio & rw:
                  - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
                  - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
6be08e3e5c Jean* o pkg/flt:
                  - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
                    init_fixed & ini_varia.
71a5d709a0 Jean*  - clean-up & simplify linear interpolation S/R:
                    move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
                  - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
a94d876c45 Jean*  - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
b57550bbcf Jean*  - add vert. coordinate & horiz. indices to output files.
                  - change vertical position in initial condition, from index to depth [m].
1cae6a1a9f Jean*  - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
                    (easier to get to a curvilinear grid) ; delX,delY no longer used.
97caae06d7 Davi* o pkg/ggl90: a few modifications:
                  - fix bottom boundary condition, and interpolation of KappaE
                    near top and bottom
a435e833b1 Mart*  - use same set of viscosity/diffusivity for TKE/momnetum/tracer
97caae06d7 Davi*  - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
a435e833b1 Mart*  - add a few options for mixing-length upper limit (--> mxlMaxFlag)
d236014eb6 Jean* o rename thetaMin,phiMin -> xgOrigin,ygOrigin
                   (maintain temporary backward compatibility, until next checkpoint)
                 
0e6056cd20 Jean* checkpoint61h (2009/01/27)
021d69ec69 Jean* o pkg/diagnostics with "periodic averaging diagnostics":
a435e833b1 Mart*   fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
794d630b5b Jean* o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
de15b00af7 Mart* o pkg/obcs: fix loop ranges for balancing code
de52daaeea Jean* o pkg/flt:
                  - improve criteria for finding which tile owns a float.
                  - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
d7a6322cee Davi* o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
                   aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
                   with ocean biogeo)
5de0afb7f6 Jean* o pkg/flt:
                  - do some cleaning and fix the restart ;
                  - add output.txt in flt_example/results to get this pkg tested.
                 o genmake2: add an EXTENDED_SRC option and flag.
                    for now, cannot be turned on on command line (only through genmake_local)
b5cd61a537 Jean* o pkg/mdsio: read/write vector:
                  - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
5de0afb7f6 Jean*  - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
b5cd61a537 Jean*    & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
                  - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
                   (drop to 4 digits matching for grad). But this test does not look very
                   reliable (was already failling on eddy, fc5, at 6.digits). Update output.
                 
0e6056cd20 Jean* checkpoint61g (2008/12/29)
ca04df591d Jean* o pkg/flt:
                   - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
                    + make OPTIONS file more standard.
                   - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
                   - fix _BYTESWAPIO CPP-Flag
                   - standard reading of file-parameter "data.flt"
b95b67d7aa Jean*   - fix argument list of S/R FLT_RESTART
ca04df591d Jean*   still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
d67bffc17c Mart* o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
46b3c62480 Mart* o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
                   a still unfixed compiler/optimization bug
                 
0e6056cd20 Jean* checkpoint61f (2008/11/21)
a435e833b1 Mart* o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
45b6388240 Jean*   update results of global_ocean.cs32x15.icedyn test.
aa713d5dbf Jean* o move getcon.F from model/src to pkg/fizhi.
a435e833b1 Mart* o pkg/exf: add parameter for extrapolation of temp up to the surface
df444da92e Jean*    and option to prevent negative evap (in bulk_largeyeager04 only).
a78ca545b5 Jean* o Prather Advection scheme: fix tracer conservation for divergent flow
                   (e.g., when using NonLin Free-Surface).
e18a7f3164 Davi* o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
db624d91db Jean* o gmredi (Visbeck-variable-K):
                  - add more parameters to Visbeck-variable-K.
                  - use a 5 points average for dSigmaR in Visbeck-K calculation
                    (more "homogenous": same stencil and same weights as in dSigmaH)
                  - update output of ideal_2D_oce experiment.
a435e833b1 Mart* o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
8d0c7e204b Mart*   (#undef REAL4_IS_SLOW)
a435e833b1 Mart*  - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
8d0c7e204b Mart*    coordinate variable
a435e833b1 Mart*  - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
8d0c7e204b Mart*    (surface forcing fields), removes some of the functionality
a435e833b1 Mart*  - model/src/write_grid.F: write _RS variables as RS-netcdf variables
                  - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
                    probably not all: copy _RS surface flux fields to RL field before
8d0c7e204b Mart*    calling DIAGNOSTICS_FILL
a435e833b1 Mart*  - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
c983541b6d Mart*    real*4 (CALL EXCH_*_RS) versions.
04c02cca57 Jean*  - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
                    (generate new output).
8d0c7e204b Mart* 
0e6056cd20 Jean* checkpoint61e (2008/10/23)
c01397a2cf Jean* o gmredi (Visbeck-variable-K):
                   - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
a435e833b1 Mart*   - change computation of Visbeck-K where Slope > Smax :
c01397a2cf Jean*     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
                     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
bd21fff799 Jean* o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
                   to be the same as with Z-coord. (i.e., m/s & no-units respectively).
                 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
c3fe1ef4e7 Jean* o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
c01397a2cf Jean*   does not become too large (to avoid precision problems in implicit-diffusion
c3fe1ef4e7 Jean*   solver); update ideal_2D_oce output.
9b7442ecc8 Davi* o pkg ggl90:
                   - in ggl90_cal.F: compute only one set of visc/diff, used to
                     step forward TKE/T/S/momentum
                   - default value of GGL90viscMax/GGL90diffMax larger and equal (to
                     have Prandlt =1)
c01397a2cf Jean* o gmredi (fm07):
284c68fd43 Jean*   - add lower limit on Transition layer thickness + lower limit on 1/lambda
883da68718 Jean*   - allow to set few more params from data.gmredi
5c4169b4ba Davi* o pkg ggl90:
a435e833b1 Mart*       - add missing sqrt(2) factor in computation of mixing length
5c4169b4ba Davi*         scale in ggl90_calc.F
                         (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
                 
0e6056cd20 Jean* checkpoint61d (2008/09/25)
900e7deb27 Patr* o adjoint modifs
                   - adapt to new field rhoInSitu
                   - allow to revert from StoreDynVars2D, StoreDynVars3D
                     to individual fields
                     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
9021e26bd9 Jean* o store 3-D (in-situ) density in commom block (DYNVARS.h)
                  - save 1 rho computation.
                  - no longer modify T & S inland when using down_slope pkg.
a435e833b1 Mart* o gad_som : allow to switch to SOM advection for T & S without corresponding
b3d25f406d Jean*   pickup files (using new S/R: MDS_CHECK4FILE).
                 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
                   (for useSingleCpuIO to work in multi-threaded)
30b946f21e Mart* o pkg/shelfice:
                  - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
                    with SHELFICEtopoFile in data.shelfice
                  - move code for reading ice shelf topography and modifying hFacC into separate
                    subroutines of the shelfice package
                  - separate initialisation of "fixed" and "variable" variables
                  - kTopC is not (yet) replaced by kSurfC, although this is possible
b3d25f406d Jean* o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1c7cf036e1 Jean* o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
                   and rename:
                   ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
                   ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
                 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
                 
0e6056cd20 Jean* checkpoint61c (2008/08/30)
a435e833b1 Mart* o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
                   to add mass source/sink of fluid in the interior (3-D generalisation
f035afc50f Jean*   of oceanic real-fresh water flux).
                 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
aa106dc1b1 Jean* o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4d4605f96d Jean* o new pkg: down_slope
                   density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
                   - presently, modify T & S inland (dwnslp_calc_rho.F).
                     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
                   - implementation for ocean in P-coords not tested.
                   - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
                 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
50f1c7ab80 Jean*   (to facilitate conversion of oceanic pkg to p-coordinate).
a435e833b1 Mart* o change FIND_RHO to FIND_RHO_2D :
f257f8b0f6 Jean*   pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
                 o new pkg: cheapaml
                 
0e6056cd20 Jean* checkpoint61b (2008/08/05)
a435e833b1 Mart* o exch2:
37ee8575fd Jean*   change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
                   - no longer depend on the order sequence (N,S,E,W).
                   - 3rd exchange no longer needed (tested with 24 tiles).
                   - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
                   - exch_UV_A-grid readily available (but not yet tested).
a435e833b1 Mart*   comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
                   (both are no longer needed) in exch_uv: no effect in forward run; but
37ee8575fd Jean*    get truncation error differences with adjoint exch.
a435e833b1 Mart* o exch2:
0e9f2e49ad Jean*  - change index-bounds storage (moved from target to local tile,
                    more intuitive this way) ; rename/remove some variables.
37ee8575fd Jean*  - change utils/exch2/matlab-topology-generator & code_mods accordingly.
0e9f2e49ad Jean* 
0e6056cd20 Jean* checkpoint61a (2008/07/29)
a435e833b1 Mart* o exch2/matlab-topology-generator:
9d45a8c11b Jean*   fix bug in index bounds for N-S internal exchange (hard to tell if this
                   had any effect on the solution).
677d07a6b5 Mart* o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
                   is exceeded
a435e833b1 Mart* o testreport: modify syntax of awk, so that it works also with
0d1768695f Mart*   awk, and not only with nawk and gawk
                 
0e6056cd20 Jean* checkpoint61 (2008/06/24)
0a92c8c20d Patr* o autodiff
                   Change default for TAF usage by removing argument '-nonew_arg'
                   This changes TAF subroutine argument list (ordering of active var.)
                   Omission of this flag leads to incompatibility w.r.t. TAMC
                   To restore TAMC-compatibility, need following modifs:
                   * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
                   * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
                   Tested TAF version is 1.9.22
                   N.B.: exch2 hand-written adjoint code currently not TAMC compatible
                 
0e6056cd20 Jean* checkpoint60 (2008/06/19)
f8c2a15654 Patr* --->>> This is the last checkpoint for which generating the adjoint
                 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
                 --->>> by default.
                 --->>> Future checkpoints will ommit this flag by default.
40cd24c888 Jean* o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
1b63dc87ac Gael* o pkg/grdchk: Add gradient check to etan0 perturbations.
a435e833b1 Mart* o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
                 o pkg/autodiff: more flexibility in zeroadj.
                   model/src: modifying do_oceanic_phys.F accordingly.
fa59c87170 Gael* o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
                 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
a435e833b1 Mart*   special setup of gmredi for which the adjoint is stable
fa59c87170 Gael*   enough for parameter optimization.
e67ddf28f4 Gael* o bridging the gap between eddy stress and GM.
                   -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
                       along with a change in CPP option (now ALLOW_EDDYPSI).
a435e833b1 Mart*   -> when using GM w/ GM_AdvForm:
e67ddf28f4 Gael*       The total eddy streamfunction (Psi = eddyPsi + K x Slope)
                       is applied either in the tracer Eq. or in momentum Eq.
                       depending on data.gmredi (intro. GM_InMomAsStress).
                   -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
                   The key modifications are in model/src/taueddy_external_forcing.F
                   pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
40cd24c888 Jean* 
0e6056cd20 Jean* checkpoint59r (2008/05/29)
0d306f558f Jean* o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
                   from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
                   fix option to read coriolis(@ cell-corner) from files with CS-grid.
aa539d5971 Mart* o pkg/mnc: add some attributes to standard 1D-coordinate variables
79e37afef0 Mart* o pkg/diagnostics: enforce missing_value attribute for scalar variables at
                   mass points, when using mnc for output
a435e833b1 Mart*   - add runtime parameter (missing_value, missing_value_int) to override
79e37afef0 Mart*     default (which is the value of getcon('UNDEF'))
                 o pkg/mnc: prepare mnc for the actual use of missing values with the
                   diagnostics package: small fix in mnc_cw_readwrite.template and more
                   initialisation of never used fields
cebfffcf05 Mart*   - replace mnc_common.h and mnc_id_header.h with corresponding upper case
                   versions
a435e833b1 Mart* o pkg/thsice/thsice_ini_vars.F added default initial values so that
                   thermodynamics sea ice solver does not blow up when some initial fields
cebfffcf05 Mart*   are missing.
87838921ba Jean* o move from external_forcing_surf.F to ini_forcing.F
                   the p-coord. hack consisting in using pLoad to set phi0surf ;
                   update output of tutorial_global_oce_in_p (affected @ truncation level).
a435e833b1 Mart* o Freshen up a bit hs94.1x64x5, notably:
                   remove rotationPeriod and tRef=5*0. (adjoint only), and add
cebfffcf05 Mart*   exactConserv=.TRUE.
34e240c0d3 Jean* o pkg/generic_advdiff:
                   change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
                   applies to files where Temperature & Salinity 2nd Order moments are used.
bc2cda07c1 Oliv* o pkg/ptracers: add second-order moment advection schemes (80 and 81);
                   this uses a dynamically allocated internal state data structure
a435e833b1 Mart*   (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
bc2cda07c1 Oliv*   and requires a fortran 90 compiler
                 
0e6056cd20 Jean* checkpoint59q (2008/05/06)
934822fb62 Jean* o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
                    (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
bb5c940526 Davi* o Refresh tutorial_global_oce_biogeo, notably:
                   - change bathymetry (put back seamounts in ACC, use hFacs)
                   - change EOS (POLY3 --> JMD95Z)
                   - use Bryan-Lewis vertical diffusivity
                   - use multidimensional advection
                   - remove old virtual virtual in dic pkg, now done through ptracer pkg
                   - change a couple of parameters in dic pkg
b488248973 Gael* o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
a435e833b1 Mart* o pkg/obcs: change default to OBCSfixTopo = .true.,
37d6577e8a Mart*   - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
                   - replace "debugMode" with "debugLevel .GE. debLevB"
a435e833b1 Mart* o implementation of TAF directives for gchem,cfc,dic
c668f876bd Jean* o remove "exp5" (replaced by tutorial_deep_convection).
ba199509e7 Mart* o pkg/obcs: add code to fix topography gradients normal to open boundaries;
                   this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
                   the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
68dbdb7bfc Mart*   --> changes results in exp4, seaice_obcs
c668f876bd Jean* o tutorial_deep_convection :
4c59896cb2 Jean*   update the set-up and increase resolution and domain size ; start
                   from pseudo initial conditions = output at t=120mn in order to see
                   something happening when running testreport.
e3f6e77e00 Mart* o pkg/seaice: add os7mp as an advection scheme
                               add check for advection schemes
f414077a87 Mart*               add a flag for restoring T and S underneath sea ice
a435e833b1 Mart* o pkg/my82: add netcdf-support and diagnostics
ea0ee0d61a Davi* o thsice pkg:
ba199509e7 Mart*   - Now hsMax limits snow height by turning it into ice following
ea0ee0d61a Davi*     flooding scheme (and now conserving energy)
                   - Slight rewriting of the formula in thsice_calc_thick.F
                   - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
a435e833b1 Mart*   --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
ea0ee0d61a Davi* 
0e6056cd20 Jean* checkpoint59p (2008/04/10)
2fbf89db82 Jean* o gchem / dic / cfc :
                   - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
                   - add new parameter files: "data.dic" & "data.cfc" ;
                   - various re-arrangement in initialisation & header file ;
                   - fix tutorial_global_oce_biogeo for multi-threaded test.
                 o pkg/dic: test for "pickup_dic" file when restarting ;
                   if no pickup-file, can restart with a re-initialised pH (same as it did
b3b930c218 Jean*   before) providing pickupStrictlyMatch is set to False.
eec9c6a066 Jean* o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
                   + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
9bfbe2231e Jean* o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
                   and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
                 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
                  & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
                    (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2f4da9d91b Jean* o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
                    scheme to use for vorticty-term ;
a435e833b1 Mart*  - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2f4da9d91b Jean*    (with default selectVortScheme, return to original discretisation)
                  - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
0b784ff841 Mart* o pkg/seaice: add a line to the summary to indicate grid type (B/C)
81ea2c715a Jean* o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
                   bottom ; only used with variable horizontal viscosity and non-hydrostatic.
                   also fix diagnostics VISCAHW & VISCA4W.
                 
0e6056cd20 Jean* checkpoint59o (2008/03/07)
92268978d1 Jean* o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
360ad14abb Mart* o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
                   move a few statemens out the main loop into separate loops
a435e833b1 Mart* o pkg/shelfice:
                   - sort out freshwater flux; convert freshwater fluxes to mass fluxes
674cb80ca8 Mart*     (kg/m^2/s), does not break tests, because in verification/isomip,
                     rhoConstFresh=rhoConst (by accident)
e3465203db Mart*   - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
                   - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
                     new file model/src/seawater.F, so that they are available for all pkgs.
                   - convert potential temperature into in-situ temperature. This changes the
                     isomip tests => update tests
a435e833b1 Mart* o add a flag writePickupAtEnd (default=true) to be able to suppress
97a8c939f6 Mart*   writing a pickup at the last timestep
a435e833b1 Mart* o tools/mpack-1.6 :
7739cd8f78 Jean*   - disable automake (not working) and autoconf (not needed).
                   - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
                     also cleaner with much less compilation warnings.
a435e833b1 Mart* o pkg/profiles:
9e1d042ca2 Gael*   rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
                   (for "less than 32 characters name" compiler requirement)
212017a383 Dimi* o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
                   conditions that have a different sampling frequency than S/T/U/V obcs
a435e833b1 Mart* o pkg/diagnostics (stats-diags):
cae4654411 Jean*   - fix global Min/Max in case 1 processor get only empty tiles
e89c0084d6 Mart* o genmake2: replace (4 times)
                      make genmake_tc_1.o >> genmake_warnings 2>&1
                   with
                      COMM="$CC $CFLAGS -c genmake_tc_1.c"
                      echo $COMM >> genmake_warnings
                      $COMM >> genmake_warnings 2>&1
                   to make genmake2 always see the value of CC as specified in the optfile.
2c62398d5b Jean* o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
                   - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
                   - modify verification advect_cs test to test SOM-advection on CS-grid.
239c38208f Gael* o pkg/ctrl:
a435e833b1 Mart*   - Rewrite of ctrl_map_ini_ecco.F,
239c38208f Gael*     introducing a generic routine (ctrl_map_ini_gen.F).
                   - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2c62398d5b Jean* 
0e6056cd20 Jean* checkpoint59n (2008/02/09)
a435e833b1 Mart* o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
ae37e502a3 Jean*   number in dedicate array "hdiag":
                   - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
                     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
                   - many small changes (integer format) for large number of diagnostics
                   - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
                     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
7514c1bd55 Mart* o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
                   usingSphericalGrid, this allows to define the rotated grid coordinates
                   via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
                   geographical coordinates according to the inverse of the rotation defined
a435e833b1 Mart*   by the Euler angles, so that Coriolis parameter and online-interpolation by
7514c1bd55 Mart*   exf works with the geographical coordinates on XC/YC/XG/YG.
a435e833b1 Mart*   Naturally, this feature does not work with all packages, so some
                   combinations are prohibited in config_summary (flt, flt_zonal, ecco,
                   profiles), because there the coordinates are assumed to be regular
                   spherical grid coordinates.
c9e4a2e67d Gael* o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
                   - introduce isopycnal diffusion coefficient control.
a435e833b1 Mart* o tools/adjoint_options:
c9e4a2e67d Gael*   - additional control vector components.
8b4eff4f81 Mart* o pkg/mnc: have mnc create marginally meaning full coordinate variables
a435e833b1 Mart*   (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
                 o pkg/mypackage:
                   - add example of read/write pickup for state-var ;
1c85ab9892 Jean*   - add entry points to the main code for state-vars diags & write-pickup.
659d0ae881 Dimi* o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
                   transitions for useExfYearlyFields
a435e833b1 Mart*   - add new subroutine that determines the file to read from for
510778fc01 Mart*     use*YearlyFields = .TRUE. and .FALSE.
a435e833b1 Mart*   - add a verification experiment to global_with_exf that tests
23f0d70669 Mart*     useExfYearlyFields with USE_EXF_INTERPOLATION defined
a435e833b1 Mart* o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
                   analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
                   subroutines (which could be generated from a template, because they are
7c7f4c7f71 Mart*   almost identical), for now they are included in obcs_prescribe_read.F for
                   simplicity
e189b52423 Mart* o pkg/exf:
a435e833b1 Mart*   - add a little more diagnostic to exf_interp_read (in analogy to
e189b52423 Mart*     mds_read_field, can be turned off with debugLevel < debugLevA=1)
                   - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
a435e833b1 Mart*     ugly but fast by unrolling short inner loops, inserting a unroll=8
4f5a52ae80 Mart*     directive in routine lagran, and splitting a loop and making do while the
                     outermost loop (the latter requires the intoduction of index arrays)
0f64a7d6fb Dimi* o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
02aabb8fe5 Dimi* o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
                   http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3b88786c4e Dimi* o verification/seaice_obcs: updated for restart test and latest options
dadd13178c Mart* o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
                   ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
                   for now this is only available for the C-grid code and also within
                   #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
                 
0e6056cd20 Jean* checkpoint59m (2008/01/14)
b1bf47d3b3 Dimi* o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
                   and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
a435e833b1 Mart* o gad_som : fix flux output (& diagnostics) to have same units as other
                   advection scheme fluxes (was previously multiplied by deltaT).
41fb919ba6 Dimi* o added verification/seaice_obcs both to test seaice open boundaries
                   and to provide an example matlab scrpt for generating them
                 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
5968a91b01 An T* o pkg/salt_plume: clean up salt_plume_frac.F to
                   remove redundancy in PlumeMethod 1 and 4
30c6f5b1cd An T* o pkg/kpp: added saltplume diagnostics
49834856da Dimi* o pkg/obcs and pkg/seaice:
                   - do not set uice and vice to zero when OB*icefile are unspecified
                   - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
                   - moved seaice tracer obcs after call to seaice_growth
824966555a Dimi* o pkg/salt_plume: added various options for salt plume depth
                   criterion and for vertical distribution of the salt
c98c324ec7 Jean* 
0e6056cd20 Jean* checkpoint59l (2007/12/18)
94059a384d Jean* o pkg/ptracers: new version of ptracers pickup:
                   read meta file and write only fields which are needed to restart.
                   ( same logic as main pickup file ; also using pickupStrictlyMatch )
e6b0d1006c Dimi* o pkg/seaice:
f2446b8a43 Mart*   - add timescale for melting due to warm mixed layer as a means of
                     setting SEAICE_availHeatFrac more conveniently
                   - add a CPP-flag/runtime parameter check for flooding algorithm
e6b0d1006c Dimi*   - reformulated availHeat in seaice_growth.F to be independent of AREA
f2446b8a43 Mart* o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
                   unit changes
00127a5872 Dimi* o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
ef5afff8c1 Mart* o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
                   SX vector computer.
6eb23881b9 Dimi* o pkg/seaice:
                   - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
                     seaice forcing fields can now be read only through pkg/exf
                   - removed some unused halos
21234f54a9 Jean* o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
0b49ffce6f Dimi* o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
                   or U/VICE from U/VWIND before computing U/VSTRESS
cd7677e357 Dimi* 
0e6056cd20 Jean* checkpoint59k (2007/11/30)
409b09eb42 Dimi* o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
                   dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
62e148683f Jean* o fix un-initialised variable problem (in mom_vecinv & shap_filt):
94059a384d Jean*   all experiments pass when compile with un-initialised var. checking option.
e4775240e5 Dimi* o added pkg/salt_plume
c28f57ed2e Jean* o script to test restart (for now, in MITgcm_contrib/jmc_script)
a435e833b1 Mart* o pkg/seaice: new read/write pickup version.
c28f57ed2e Jean*   read meta file and write only fields which are needed to restart.
                   ( same logic as main pickup file ; also using pickupStrictlyMatch )
df45546054 Mart* o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
b030fd2059 Jean* o lab_sea.hb87: modify the domain & update output.hb87.txt :
                   lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
                   at j=1 & j=Ny+1 : this case is not treated correctly in the restart
                   process. Fixed here by closing the domain at the Northern boundary.
                 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
                 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
                   a set of consecutive levels in/from a 3-D array.
a435e833b1 Mart* o pkg/ptracers:
b030fd2059 Jean*   use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
74f73e83d7 Jean*   to-do: fix pkg/diagnostics when large number of diagnostics are defined.
                 
0e6056cd20 Jean* checkpoint59j (2007/11/09)
054a6ca04b Jean* o in pkgs: dic, obcs, offline, rbcs:
                   standard way to compute coeff. for time interpolation between 2 time reccords
                   which retains full precision (& make results less dependent on compiler).
                   update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
f82f0d1e3a Mart* o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
                   packages instead of reading ice cover and wind speed separately
dee09995de Jean* o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
                  (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
                   to allow to compile customized code before the update)
a435e833b1 Mart* o cleaning-up:
1330311b36 Jean*   - fix CPP instruction syntax in pkg/obcs
                   - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
                     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
                   - fix some threads issue in IO parts.
7f2d5ae7b4 Davi* o pkg/dic:
                   - add tons of "_d 0" (--> much better testreports !)
                    and then update outputs of tutorial_global_oce_biogeo
7d697fe457 Jean* o pkg/mom_fluxform:
                   add a special version of momentum advection intended to conserve momentum
                   next to a bathymetry step or a coastline edge. (default = off = #undef)
715883b931 Jean* o new read/write pickup version:
                   - for now, only implemented for main (mdsio) pickup file.
                   - write out only what is needed to restart; merge pickup_nh , pickup_ph
                     and main pickup together.
                   - read meta file; read only what is needed to restart; stop if a field
                     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
                     if it make sense (even if the restart is not perfect).
                   - if no meta file, assume that pickup to read corresponds exactly to
                     a pickup that would currently be written.
                   - read pickup written in the old format (until checkpoint59i) if it
                     recognizes an old meta file (no field-list).
                   - add a meta file in exp. which starts from a pickup: 2 cases:
                     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
                      e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
                     b) a meta file describing the content of the associated pickup file
                      e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
                 o pkg/mdsio & pkg/rw:
                   - new routine to read a meta file ; new set of routine to read
                     Multiple-fields file (with meta file).
5459643feb Dimi* o added open boundary conditions capability for seaice
                     HSNOW, HSALT, UICE, and VICE
fa757486b0 Dimi* 
0e6056cd20 Jean* checkpoint59i (2007/10/21)
3420897bc6 Patr* o adjoint:
a435e833b1 Mart*   * fix multiDimAdvection adjoint
3420897bc6 Patr*     (partial recomputation problem by TAF for fVerT(:,:,kDown)
                     and comlev1 size definition (maxpass vs. max. number of tracers)
                   * verification/global_ocean.90x45x15 adjoint now tests
                     NLFS and multiDimAdvection using DST3 (=30)
                   * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
a435e833b1 Mart* o pkg/kpp: add "_d 0" to real constant (if missing);
846ec3a65a Jean*   update output of exp: natl_box (10.digits); vermix (std, 7.digits)
                   and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
97b9193f01 Jean* o prepare for "clever pickup" implementation: add new header file "RESTART.h"
                   for internal parameters related to restart process (formerly from PARAMS.h)
                   and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
                 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
                   as argument. (only atm2d & obcs write_pickup have not yet been updated)
fc36747b80 Jean* o pkg/monitor:
                   - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
                   - fix mon_stats_rs (statistics over the full domain, even where field is zero)
                   - account for deep Atmosphere factor and density factor (anelastic)
b48f786726 Dimi* o added open boundary conditions capability for seaice HEFF and AREA
11b7991b31 Mart* o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
                   thermodynamics
a435e833b1 Mart*   - requires a little reorganization, which affects the testreport results
11b7991b31 Mart*     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
                     so that now the conservative form is tested
                   - add a few comments
fc36747b80 Jean* o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
5cc78a2bb0 Mart* o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
37de51ebf5 Mart* o add new diagnostics to seaice: advective, diffusive fluxes (only for
a435e833b1 Mart*   multidim-advection, for scheme 2 they are not filled) and transports,
37de51ebf5 Mart*   thermodynamic growth rates
5c9e11f575 Jean* o change units of EmPmR (inside the code, + within coupling interface)
                   from m/s to kg/m2/s (mass flux) but leave input file unchanged.
a435e833b1 Mart*   Affects results @ truncation level (cg2d match) and update output of
5c9e11f575 Jean*    experiments: lab_sea(6), global_ocean.90x40x15(10),
8106187dda Jean*   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
                   + adjoint results: global_ocean_ebm(11) and lab_sea (12).
5c9e11f575 Jean*   Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
8106187dda Jean*   Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
                 
0e6056cd20 Jean* checkpoint59h (2007/09/29)
a435e833b1 Mart* o pkg/exf:
97f0a6ab4c Mart*   - improve vectorization by moving if-statement out of loops in
                     exf_mapfields, exf_radiation
                   - exf_bulkformulae.F: introduce 2D fields and vectorize code
63ceaaa79c Dimi* o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
a435e833b1 Mart* o testreport:
                   - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
b60e6e79c3 Jean*     monitor & update offline_exf_seaice exp. output.
                   - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
f09197aee0 Mart* o pkg/seaice:
                   - bug fix in the evp solver: boundary conditions were affected be
                     masking of zMax/zMin (changes results)
a435e833b1 Mart*   - minor bug fix in boundary conditions in seaice_calc_strainrates
f09197aee0 Mart*     (changes results for no_slip)
                   - seaice_lsr.F: make interpolation of eta dependent on boundaries
                   - replace hardcoded lower limit for zeta (zMin) by runtime parameter
                   - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
                     stress formulation and no-slip boundary conditions
453b5521e5 Jean* o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
                   in gad_calc_rhs.F ; add few safety stops in initialisation phase.
e06023d8a7 Dimi* o pkg/seaice: a first HSALT time stepping equation has been checked in
6aebec07e1 Dimi* o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
                   in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
                   without requiring DO-IF statements
acdf6745c2 Jean* o pkg/thsice:
                   use continuous power-law function for partition of energy between lateral
                   melting/freezing and thinning/thickening ; old code using step function
                   still available with #undef THSICE_FRACEN_POWERLAW
                   update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
                 o testreport: change AD testing : check against results/output_adm.txt
                   using same scripts as for forward test.
6aebec07e1 Dimi* 
0e6056cd20 Jean* checkpoint59g (2007/09/17)
6d61a12d79 Jean* o adjoint testing: in preparation for changing testreport:
                   - output format: cost and grad written on separated lines
                   - ad output results in directory "results" (instead of "results_ad")
fdfa8e151f Dimi* o pkg/seaice: adding ice salinity HSALT as a prognostic variable
06687b5615 Dimi* o pkg/seaice: changes for using pkg/seaice with pkg/obcs
a435e833b1 Mart* o pkg/ecco: allow user defined cost function contributions
a3953b5266 Jean* o testreport:
                   Allow to choose (per experiment) the list of tested output variables
                    and the main variable (used to issue a pass/FAIL ) ;
                   - for now, done by adding the specific list in file: [exp]/input/tr_checklist
6d61a12d79 Jean*   - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
a3953b5266 Jean*   Also modify printing of summary:
                    a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
                    b) echo the list of tested variables in the individual summary.txt of
                       each experiment.
768f1a0767 Jean* o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
                   threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
                   (but still depend on the tile decompostion of the domain).
a435e833b1 Mart* o pkg/seaice: change a discretization detail to make the B-grid code
                   "more symmetric". This change is likely to remove all "ridges/leads" that
                   where quasi-aligned with the grid in B-grid solutions. It may also be
9890ce5b02 Mart*   the solution to the stress coupling issues with the B-grid.
746e4b22c8 Jean* o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
                   remove .cvsignore from input dir. (since testreport no longer run here).
00f1a01b56 Jean* o pkg/thsice:
746e4b22c8 Jean*  - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
00f1a01b56 Jean*  - fix reshaping of sea-ice just after advection:
                    melt all the ice only if ice-volume is too small.
                  - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
                    prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
                  and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
be8537d9a0 Jean* o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
                   tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
a435e833b1 Mart* o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
de702e22c7 Jean*   forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
                   (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
                   and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
                   of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
                   -> update output.txt
                 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
                  this affects truncation error: -> update output.txt of exp:
                   global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
                   ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
                 
0e6056cd20 Jean* checkpoint59f (2007/08/21)
a435e833b1 Mart* o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
                 o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
5e4d837505 Gael*   a bounded range (in forward mode)
59227d8f71 Gael* o pkg/ecco, ctrl, autodiff and mom_common:
                  internal parameter controls, completements of implementations
7cb9ec3ac0 Jean* o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
9e6f983930 Jean* o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
                   (not seem any difference in testing results).
a435e833b1 Mart* o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
7cb9ec3ac0 Jean*    at face corners.
a435e833b1 Mart* o pkg/generic_advdiff:
c3947d579e Jean*  - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
                   loop range indices for computing vertical advection tendency
                   and do the calculation in the interior only (no overlap) ;
                   for now, only implemented for SOM advection (to save CPU time).
                  - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
ffa5f4b126 Patr* o exch2 adjoint
                   First set of changes:
                   - add exch2 hand-written adjoint templates
                   - exch2 hand-written no longer use TAF-flag 'nownew_arg'
                     This will require cleanup in pkg/autodiff/*.F
                     (changed routines currently kept separate in verif. code/)
                   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
                     that used to hide exch2 or cubed-sphere specific code
                     (commented via 'cph-exch2')
eb0337bb06 Dimi* o pkg/seaice
                   - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
a435e833b1 Mart* o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
142f944c15 Jean*    output of global_ocean.cs32x15.thsice .
ffa5f4b126 Patr* 
0e6056cd20 Jean* checkpoint59e (2007/07/26)
eed8e492b5 Jean* o exch2: new S/R that only use the cube-tracer (center-position) exchange:
                   for B-grid vector (not yet tested) and C-grid vector (<- only used
                   when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
8c3259a14c Dimi* o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
                   (#ifdef ALLOW_SALT_PLUME)
713e6ff2ab Dimi* o gather_2d/scatter_2d: removed halo regions
ca76150054 Jean* o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
                   scheme and the corresponding test case (under front_relax dir). For now,
                   only available with Skew-flux form and not yet tested in realistic set-up.
a614482486 Patr*   adjoint: store directives updated, but gradient checks deteriorated,
                   so maybe GM/Redi adjoint is now broken.
7dadb0325c Patr* o seaice adjoint
                   * add AREA, HEFF, HSNOW as control variable
                     (should not change lab_sea results)
                   * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
09379e5080 Dimi* o pkg/seaice:
                   * added computation of saltFlux in seaice_growth;
                     For time being, sea ice salinity is assumed constant
                     contribution of snow flooding to freshening of sea ice is neglected.
                     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
                     defaults to 0.0 in order to maintain backward compatibility.
                     Typical values for SEAICE_salinity are 4 to 10 g/kg.
                   * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
                   * added SEAICE_availHeatFrac, which specifies fraction of surface level
                     heat content used to melt or grow ice
c7cb92a732 Dimi*   * commented out cap of HICE: it helps keep ice thinner
                   * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
a6d2313c04 Dimi*   * applied OBCS T/S mask to HEFFM sea ice mask
7dadb0325c Patr* 
0e6056cd20 Jean* checkpoint59d (2007/06/21)
d2b8341951 Jean* o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
                  for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
                  (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
                 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
                  and change default value of parameter "GM_Small_Number";
                  update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
a435e833b1 Mart*    global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
d2b8341951 Jean*    tutorial_global_oce_biogeo, tutorial_global_oce_latlon
f79922cd31 Gael* o pkg/ecco: cost function when applying pkg/smooth to controls
                 o pkg/ctrl: add forcingPrecond run time parameter
6ac96a67e3 Mart* o pkg/seaice:
                  - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
a435e833b1 Mart*  - fix bug in metric terms of u-equation in LSR solver (implicit part),
6ac96a67e3 Mart*    changes verification/lab_sea
                  - rearrange implicit part of u-equation in LSR solver to make it easier to
                    read, understand, and debug. This causes changes at the truncation level.
a435e833b1 Mart*  - fix (serious) bug in the boundary conditions (sign error in the implicit
6ac96a67e3 Mart*    part) of the LSR solver. Changes all LSR results.
de31ea8481 Dimi*  - fixed problem with HSNOW initialization to avoid thick snow when AREA
                    is initilized with small values - does not change lab_sea results.
                  - added HsnowFile initialization capability
a435e833b1 Mart* o pkg/smooth: addition to model/src and pkg/ctrl so allow
bf0c19d334 Gael*  initialization of pkg/smooth and application to control vector
19ab789a27 Mart* o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
249fe8e752 Gael* o dependencies: pkg/profiles requires pkg/cal
8d3088d3d7 Gael* o pkg/profiles:
                  - added option ALLOW_PROFILES_GENERICGRID
                      -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
a435e833b1 Mart*      that interpolation information (grid points and coefficients) is provided
8d3088d3d7 Gael*      within the netcdf input files.
                      -> sample matlab scripts can be found in MITgcm_contrib/gael
                      that allow you to prepare netcdf input files.
a435e833b1 Mart*  - also modified: cleaner include statements, cleaner error print statements,
8d3088d3d7 Gael*    cleaner stops when error, and more tests of the netcdf input files consistency.
a0c93d7fd2 Jean* o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
04b45d6d21 Mart* o pkg/seaice:
583c1cf330 Mart*  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
                    requires a new routine: seaice_diagnostics_fill.F
acaec430f5 Mart*  - make sure that seaice does not move if not forced (pressure replacement
                    method, Hibler and Ip, 1995), changes results
04b45d6d21 Mart*  - and new damping criterion for EVP solver according to Hunke, JCP, 2001
a435e833b1 Mart*  - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
04b45d6d21 Mart*    It is turned off by default (=-1.), because it changes the results.
b1e9686d05 Mart*  - make it possible to read AREA from a file, too.
04b45d6d21 Mart* 
0e6056cd20 Jean* checkpoint59c (2007/06/04)
93133b7df9 Jean* o add S/R and diagnostics for oceanic mixed-layer depth
                 o move GMRedi call after all vertical mixing schemes (including KPP)
a435e833b1 Mart* o pkg/thsice:
93133b7df9 Jean*  - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
                   (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
de3611c1c1 Mart* o pkg/obcs:
                  - bug fix for balance code
2d85697240 Mart* o pkg/seaice:
6bfbbed422 Mart*   - allow values of SEAICE_elasticParm > 1
a435e833b1 Mart*   - add new parameter SEAICE_evpTauRelax as an alternative
b559ca9c5c Mart*     to SEAICE_elasticParm
6bfbbed422 Mart*   - make lsr boundary conditions free slip (by default), changes result
887a79a904 Mart*   - add code for no slip boundary conditions for lsr
2d85697240 Mart*   - set minimum of zeta to zero (and not 4e8) (changes results)
b559ca9c5c Mart*   - add a cap on AREA after advecting AREA if seaice_growth is not called
04010225bf Jean* o change calculation of Visbeck K:
a435e833b1 Mart*   - no longer depend on tapering scheme; instead, compute slope (limited
04010225bf Jean*     by GM_maxSlope). this is equivalent to what was comuted before with
                     clipping or linear tappering.
93133b7df9 Jean*   - fix vertical averaging (wrong by 1/2 level)
04010225bf Jean*   - leave the old version (but will not be maintained) within
                     #ifdef OLD_VISBECK_CALC / #endif
93133b7df9 Jean*   - update output of exp. ideal_2D_oce
ae6dbd4886 Mart* o change error catch in calc_r_star to improve vectorization
fc0ec0c7ea Jean* o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
                   add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
5728d4a98b Patr* o adjoint:
                   Re-organized adjoint checkpointing according to Matt Mazloff
                   (but with modifs/completions/cleanups)
                   Storing is now bundled into large arrays to optimized I/O
                   (and second step in cleanup of the_main_loop)
fc0ec0c7ea Jean* 
0e6056cd20 Jean* checkpoint59b (2007/05/16)
59d7b34837 Jean* o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
                   - export/import (between ocean & coupler) fields needed for ocean DIC.
a435e833b1 Mart* o pkg/seaice:
                   - get rid of three more exchanges seaice_calc_viscosities (required
17cb3b1135 Mart*     different loop boundaries in seaice_lsr and seaice_ocean_stress)
                   - bug fix in seaice_ocean_stress (update of lab_sea required)
                   - reduce loop boundaries to necessary minimum also in seaice_evp
a435e833b1 Mart*   - go back to the old way of computing deltaC/Z as the adjoint likes that
17cb3b1135 Mart*     better
ec0736eb1a Davi* o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
                   passive tracer to an Age Tracer) + update output.txt
93f8102905 Jean* o pkg/exf:
7bb7cdd467 Jean*   - implement A-grid / C-grid selection for wind-stress input files.
                   - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
                   for now, in exf_bulk_largeyeager04.F only :
                   - change implementation for case where windspeed + 2. components wind-stress
                     are read-in. AND use rhoConstFresh to convert evap.
                 o pkg/seaice:
                   - use correct EXCH_UV for wind-forcing (on A-grid).
                   - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
                     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
                 o pkg/exf:
93f8102905 Jean*   - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
a435e833b1 Mart*   EXF_INTERPOLATION:
93f8102905 Jean*   - merge global_with_exf/code version of exf_interp_read.F
a435e833b1 Mart*     to the main code ;
                   - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
                     reading the file ; Important: This options needs to be defined to recover
93f8102905 Jean*     previous code.
                     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
                   - no longer loose real*8 precision along the way when using exf_iprec=64.
2f88b60189 Mart* o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
b3e6145587 Mart*   - change discretisation of evp-solver in order to avoid another exchange
                     (changes lab_sea) and clean up a little
a435e833b1 Mart*   - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
b3e6145587 Mart*     help the adjoint (this also changes the results slightly)
                   - add a few "_d 0" where they had been missing in seaice_evp.F
                   - cleaning up: remove unused seaice_calc_rhs.F
35a74aa2c2 Jean* o pkg/exf: some cleaning-up:
                   - change various "constants" into runtime parameters
                   - cleaned-up Large&Yeager04 routine which should eventually
                     replace exf_bulkformulae.F (changed names of S/R and CPP)
                     and merged various ALLOW_ATM_WIND options
                  only used with thsice pkg (in thsice_get_exf.F):
                   - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
                     which are used when useStabilityFct_overIce=TRUE (= the default)
                   - change default values of ice & snow emissivity and scale downward LW
                     by ice & snow emissivity.
                 o pkg/thsice:
0a9955b282 Jean*  fix few little problems, in thsice_calc_thickn.F:
                   - growth vertically (and not laterally) if iceFrac == iceMaskMax
93133b7df9 Jean*   - melt only laterally if hIce < hThinIce (as the comments say)
0a9955b282 Jean*   and in thsice_extend.F:
                   - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
                   - start to form ice as soon as the minimum ice-volume is reachable.
a435e833b1 Mart*  update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
0a9955b282 Jean*   and cpl_aim+ocn
66b38c4c51 Mart* o pkg/kpp
                  - move computation of surface related input fields to KPP into a new
                    subroutine kpp_forcing_surf.F
0a9955b282 Jean*  - remove wrong (within bi,bj loops) EXCH calls.
                  - little cleaning (add argument myThid in last position, cvs header ...)
a435e833b1 Mart*  - for now, fix conservation problem by exchanging KPPviscAz (may not
0a9955b282 Jean*    be the best fix)
f83c00719e Mart* o pkg/seaice
                  - check for inconsistent evp parameter/cpp-flag combination
                  - remove leftover errIO flat for obsolete name list error handling
4b058176c1 Patr* o OpenAD
                  - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
f83c00719e Mart* 
0e6056cd20 Jean* checkpoint59a (2007/05/01)
09e3b53265 Mart* o pkg/seaice: some parameter clarifications and a little bit of clean up
f8fa27d193 Jean* o pkg/thsice: rename run-time parameters:
                    himin       -> hIceMin
                    himin0      -> hThinIce
                    hihig       -> hThickIce
                    i0          -> i0swFrac
                    transCoef   -> bMeltCoef
                    frac_energy -> fracMelting
                   add new parameters: hNewIceMax, fracFreezing, dhSnowLin
                    with default values (for now) that do not change the results.
                   remove old version of thsice vars advection in pkg/seaice.
a435e833b1 Mart* o in FFIELDS.h:
18ca872a92 Jean*   - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
                   - make pLoad & sIceLoad always available (but still only used if
                      ATMOSPHERIC_LOADING is #define).
fe66051ebd Dimi* o pkg/kpp: replaced _KPP_RL with _RL
059d9fc14f Dimi* o bug fixes for vertical diffusivity computations when both KPP and
a3b5d49db3 Dimi*     3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
                     are no longer updating the vertical diffusivity array
                     (passed as argument) but are (re-) setting those arrays.
2e88c0564a Mart* o pkg/seaice: fix bug in evp solver, while doing that
                   - change (improve?) discretization of stress computations for both
                     cgrid-lsr and evp solver
                   - add a new routine to compute strain rates
ed84a09795 Mart*   - the above changes lab_sea results
                   - add no slip conditions for evp solver (off by default), lsr-version
                     may follow
                   - fix exchange for shear at Z-points (does not change lab_sea)
                   - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
                     (to force the user to pick a time step since there is not "safe" way
                     of choosing it)
4686684434 Mart*   - add principal stress diagnostics
a435e833b1 Mart*   - rearrange fields for evp a little to avoid having to call a: too many
                     exchanges and b: exchanges for stress trensor components which we do
fe367969c0 Mart*     not have.
                   - modify Hibler+Bryan (1987) stress coupling so that it reuses information
                     of evp, complete rewrite for lsr case (latter is does not yet work
                     in all cases)
efab83c021 Mart* o pkg/kpp: add code to have mixing in shelf ice caverns
cb6682d07b Mart*   - add myThid to all kpp routines (long overdue)
efab83c021 Mart* 
0e6056cd20 Jean* checkpoint59 (2007/04/19)
a435e833b1 Mart* o pkg/exf:
62cf11cfe0 Patr*   - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
                     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
a435e833b1 Mart*   - move exf header files from lower_case.h to UPPER_CASE.h ;
62cf11cfe0 Patr*     add missing cvs Header & Name
                   - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
d9a285b784 Patr*   - add namelist param. selectStressGridPosition, exf_monFreq
a435e833b1 Mart*   - retire many _CLIM routines, and remove data.exf_clim
d9a285b784 Patr*     + params moved to data.exf
                     + climsst, climsss now handled by exf_set_gen, i.e.
                       climss?period=0 refers to constant field,
                       climss?period=-12 to monthly forcing
                   - split up namelists in data.exf
e1d22dfae3 Mart* o pkg/seaice:
                   - remove seaice_exch and seaice_exch_uv
                   - remove superfluous exchange of theta
                   - add myThid to seaice_budget_ocean/ice
039e537654 Mart*   - add new interface for atmospheric wind forcing (C-grid only)
                     + new routine
                     + two new field (taux, tauy for stress over ice)
                     + removed one global field (DAIRN) for C-grid case only
62cf11cfe0 Patr* o pkg/thsise
                   - 2nd set of modifs for thsice adjoint in conjunction with exf
d9a285b784 Patr* o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
e1d22dfae3 Mart* 
0e6056cd20 Jean* checkpoint58y_post (2007/04/15)
0aefc24df1 Dimi* o Added capability for latitudinal dependence of Bryan and Lewis, 1979
e40c34e398 Dimi*   vertical diffusivity, similar to that in MOM4; turned on using
                   #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
                   diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
a7c5f770ff Dimi* o Added capability for 3D specification of background vertical diffusion
                   coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
                   in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
                   "data" file that contains the 3D vertical diffusivity coefficients.
a10167ebd7 Jean* o ice dynamics (pkg/seaice) with thsice thermodynamics:
                   - add code within pkg thsice to advect & diffuse sea-ice fields
                   similar to (and will replace) what has been added in  seaice_advdiff.F,
                   but: - conserving Mass, Heat & Salt.
                        - better when using non-linear advection scheme (not yet fully tested)
                        - can also be used in atmospheric set-up (for now, only the diffusion).
bf363e629f Dimi* 
0e6056cd20 Jean* checkpoint58x_post (2007/04/04)
fa535b8213 Jean* o IO option for global-file compact format:
                   - add options when generating topology (utils/exch2/matlab-topology-generator)
                   - add I/O capability (pkg/mdsio).
                   - adapt utils/matlab/rdmds.m to read this format.
                   for now long-line format not yet supported by pkg/mdsio (& exch2).
4c0efb30d8 Mart* o shelfice: add a few diagnostics
                 
0e6056cd20 Jean* checkpoint58w_post (2007/03/13)
db8fa666e0 Jean* o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
                   rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
                   (and replace horiVertRatio in NH code).
a435e833b1 Mart*   Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
db8fa666e0 Jean*                      and tutorial_plume_on_slope (sensitive to truncation)
2496f367f4 Mart* o seaice: if ALLOW_ATM_WIND is undefined use wind stress
                   directly to drive seaice model (C-grid only)
                 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
a435e833b1 Mart*  - reintroduce computation of wind from stress,
                  - compute tau (in exf_bulkformulae.F) from windstress averaged to
2496f367f4 Mart*    mass points to avoid tau = 0
b3d6cfe67b Mart*  - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
2496f367f4 Mart* o rdmnc.m: make it work with "global" files created with gluemnc
fedb0baa62 Jean* o rdmnc.m : some improvements in dealing with singleton dimension
                   (tested on all testreport mnc output files).
                 o genmake2: disable pkg/profiles if netcdf test fails.
108c7eb2d4 Jean* o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
462fd48b6a Mart* o move call to cal_readparms up to make calendar parameters/variable available
                   to all packages
                 
0e6056cd20 Jean* checkpoint58v_post (2007/02/08)
bafc84b6a4 Jean* o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
                   useDynP_inEos_Zc tested.
5d2261ac89 Dimi* o pkg/exf: changes to properly interpolate/mask/scale initial fields
7c705f78f8 Dimi* o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
                   and portions thereof.  See read_cs.txt for description and examples.
c4b9b1e3e9 Jean* o utils/matlab/cs_grid/bk_line: to compute transport through passages,
                   add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
                   following the great-circle arc between those 2 points.
                 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
                   (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
95c3249206 Jean* o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
                  - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
                  - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
                  - still needs work (not working with some options ; efficiency to improve)
                    and serious testing.
                  - use this scheme for temperature & salinity in 2 advection test exp.:
                    advect_xy & advect_xz, respectively.
                 
0e6056cd20 Jean* checkpoint58u_post (2007/01/12)
42a486092f Jean* o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
31fd7701e4 Jean* o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
                 o testreport: add option "-skipdir" to skip some test.
a435e833b1 Mart* o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
31fd7701e4 Jean*   momentum calculation.
                 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
                 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
                   remove checkpoint.F and the_correction_step.F (no longer used);
                   do the k loop inside CYCLE_TRACER (supposed to be more efficient).
a435e833b1 Mart* o add option (linFSConserveTr) to correct for tracer source/sink due to
31fd7701e4 Jean*   Linear Free surface
0e1f0a567f Mart* o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
                 o pkg/thsice: fix reading mnc-pickups
                 
0e6056cd20 Jean* checkpoint58t_post (2006/12/30)
62990a23c1 Jean* o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
                 o pkg/mdsio:
                  - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
                    move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
                    mdsio_write_field.F (S/R MDS_WRITE_FIELD);
                  - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
                  - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
                    either MDS_READ_FIELD or MDS_WRITE_FIELD )
                  - new S/R (to replace MDSWRITEMETA), which allows to write more
                    informations (variable names, time ...) to meta files.
                  - modify rdmds.m to give back the meta file content.
f0676079d6 Jean* o pkg/diagnostics: change vertical interpolation to be safer, and more
                    flexible (define p-levels to interpolate to in data.diagnostics);
a435e833b1 Mart*   add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
f0676079d6 Jean*    diagnostic pointer.
494a260c71 Mart* o pkg/seaice: more cleaning up of seaice_growth, added many comments
0e1f0a567f Mart* o pkg/exf: put runoff0 and runoff1 into the appropriate common block
72f428a311 Mart* o fix multi-category seaice:
a435e833b1 Mart*  - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
72f428a311 Mart*    SEAICE_MULTICATEGORY
                  - fix short wave heat flux
ac10466ef6 Jean* o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
a435e833b1 Mart*    and allow to use EVP solver. Change forward lab_sea: test both EVP
ac10466ef6 Jean*    solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
13ac555e3c Patr* o Initial check-in of lab_sea adjoint
                   (very similar to natl_box_adjoint/code_seaice)
                   * used C-grid and EVP solver
                   * used KPP, GM/Redi
                   * uses inAdExact=.TRUE.
                   * gradient checks fail for both ADM and TLM
                     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
                     f.d. gradients actually seem more problematic than ADM, TLM gradients;
                     issue is related to forward mismatch between g77 an ifort
66cb0aa2f6 Mart* o pkg/seaice: overhaul of thermodynamics
                  - growth.F and groatb.F are replaced by new routine seaice_growth.F
                  - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
                  - move a few global fields out of SEAICE.h into seaice_growth.F and
                    make them 2D (FICE/QNETO/ ...)
                  - remove FO (it is the same as QNETO)
                  - introduce a few local fields to avoid modifying external fields such
                    as atemp, etc.
                 
0e6056cd20 Jean* checkpoint58s_post (2006/12/11)
58d34f56b6 Dimi* o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
                   changed exf_set_gen.F so that
                     genperiod=0 means input file is one time-constant field and
                     genperiod=-12 means input file contains 12 monthly means
475943d866 Jean* o CG2D: use pre-computed solver main-diagonal (stored in common block);
                   this affects truncation error ; generate new output file for exp. which
                   fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
                     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
                     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
                     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
                     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
                     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
c5d33297c7 Jean* o start implementation of deep-atmosphere and anelastic formulation
d83c991b0e Jean* o verification: remove 2nd copy of input files and use script "prepare_run"
                   to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1c10df8cad Mart* o mom_common/vecinv/fluxform: fix a few initialisation isssues
544c96562c Gael* o profiles: fix for multithreaded case
                 
43ae10a9d8 Jean* o diagnostics: rename few diags:
                   s/'PRESSURE'/'RCENTER '/g
                   s/'TICE    '/'oceFreez'/g
                   s/'TAUX    '/'oceTAUX '/g
                   s/'TAUY    '/'oceTAUY '/g
                   s/'SWFLUX  '/'oceQsw  '/g
                   s/DIFx/DFxE/g
                   s/DIFy/DFyE/g
                   and add few ocean-forcing diagnostics:
                   atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
ab48336167 Dimi* o modifications to pkg/seaice/growth.F and budget.F, which change results of
                   lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
                   as actual snow thickness.  It now refers everywhere to effective snow
                   thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
43ae10a9d8 Jean* 
0e6056cd20 Jean* checkpoint58r_post (2006/11/17)
8307959141 Dimi* o modifications to pkg/seaice/growth.F, which change results of
                   lab_sea experiment: fixes pertain to melting snow over open water, to
                   masking EVAP under sea ice, and to using the correct AREA variable for
                   computations of EVAP, PRECIP, HSNOW, and GHEFF
5f4df5533c Ed H* o add ability to read bathy, salt, and theta using MNC (off by def)
eefc792916 Mart* o add flooding algorithm and advection of HSNOW for pkg/seaice;
                   both are turned off by default and do no change any results
a435e833b1 Mart* o seaice advection with pkg/thsice: a step toward the use of non-linear
cc4235ab79 Jean*   advection scheme, but #ifdef or commented out for now (requires more EXCH).
23209571d0 Jean* o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
                   (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
                   in natl_box (affects results @ truncation level: update output.txt)
                 o multi-threading and IO:
ba51931058 Jean*   - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
                   - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
                     (needed to work with SingleCpuIO): tested in all verif. exp.
874c68b9c9 Jean* o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
                   affects the results (but none of the verification test uses this scheme).
9913de8fec Patr* o Adding some pkg/diagnostics capability to pkg/seaice
                   (will certainly be subject to changes)
983e72444d Patr* o ctrl: adding new control variables:
                   lwflux, lwdown, evap, snowprecip, apressure, runoff
9913de8fec Patr* 
0e6056cd20 Jean* checkpoint58q_post (2006/10/20)
f5cbf7b96d Dimi* o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
                   1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
                   high_res_cube configuration by 4% on Columbia.
a615280822 Jean* o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
                   add (in global_with_exf/code) a version of EXF_INTERP_READ without
                   dynamical allocation (seems to work in multi-threaded).
                 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
                   single CPU io) so that TAF does not have to see EESUPPORT.h
725982e0dd Jean* o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
                 
0e6056cd20 Jean* checkpoint58p_post (2006/09/08)
fc187b9c6d Mart* o obcs: stop if obcs is used with useCDscheme = .true.
a435e833b1 Mart* o shelfice:
4fd1c14d86 Mart*  - fix a sign error so that no slip at shelfice interface works
a435e833b1 Mart*  - remove stop for combination non-hydrostatic code and shelfice. That does
4fd1c14d86 Mart*    not mean, that the results are correct, but at least they are numerically
                    stable
bd91f7dab7 Davi* o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
9dd22fcf15 Patr* o added adjoint exch routined for all exch*3d* routines
                   and updated flow directives
bd91f7dab7 Davi* 
0e6056cd20 Jean* checkpoint58o_post (2006/08/28)
acd22c6e91 Jean* o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
                   remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
d0ebb46870 Jean* o change controling S/R for writing pickup file (new S/R do_write_pickup)
                   and clean-up reading/writing of pickup files.
                 o fix local version of read/write pickup (NH part) in rotating_tank/code
49423ca970 Jean* o simplify EXCH interface:
                  - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
                  - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
134f469a8d Ed H* o added the regrid package
a435e833b1 Mart* o shelfice:
29ffe622cd Mart*  - add a simple boundary layer scheme to reduce noise
                  - fix the indexing in shelfice_u/v_drag so that there will be actually drag
49423ca970 Jean* 
0e6056cd20 Jean* checkpoint58n_post (2006/08/14)
a435e833b1 Mart* o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
bbc1d9f1e8 Jean*    local variable (not in common block).
a435e833b1 Mart* o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
                   - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
da8bc3fbe0 Jean*   - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
                     to work with SingleCpuIO.
a435e833b1 Mart* o add "_d 0" to real constant of pkg/cfc subroutines ;
d77b191e54 Jean*    update exp. cfc_exemple & tutorial_cfc_offline output files.
15d8704b4b Jean* o multi-threading and IO:
a435e833b1 Mart*   - all threads call READ_FLD S/R (needed if using SingleCpuIO):
15d8704b4b Jean*     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
                   - barrier before and after reading.
                   - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
                   - avoid using MDS_WRITELOCAL for LAND pkg output.
                   - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
                     common-block variables ; Allows multi-threading with master-thread IO.
a435e833b1 Mart* o change default MAX_NO_THREADS from 32 to 4 ;
                   and stop cleanly when MAX_NO_THREADS is too small.
e20ba03425 Jean* o add S/R BAR_CHECK to check multi-threaded barrier synchronization
                 
0e6056cd20 Jean* checkpoint58m_post (2006/07/17)
ade0862df3 Jean* o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
                    and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4641b6f2a1 Jean* o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
a435e833b1 Mart*    keep global_ocean.90x40x15 (for AD testing) with former secondary test
4641b6f2a1 Jean*    (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
                 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
                     add MITgcm_tutorials (= code + all the tutorials)
61b89af843 Gael* o ecco, option to compute cost for total ssh (mean+anom)
fe8bfd2a85 Gael* o consistent with addition of ptracer and ssh in pkg/profiles
021f06a8d1 Gael* o profiles: adding ptracer and ssh
a435e833b1 Mart* o testreport: change multi-test output-file name
a91df43a18 Jean*   (from output.txt.{name} to output.{name}.txt)
da8bc3fbe0 Jean* o profiles: now ok for mutli-tiles case
a435e833b1 Mart* o seaice: add 4 parameters for different advection schemes for area,
1633c22cfc Mart*   (effective) seaice thickness, enthalphy, and snow height. Their default
                   is the standard parameter SEAICEadvScheme
a435e833b1 Mart* o calc_gw:
78de812e24 Jean*  - add cosFacU in zonal viscous flux (harmonic.visc.).
                  - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
                    of tutorial_plume_on_slope.
                 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1fa758ce8e Jean* o calc_gw: true flux-form, account for horizontal grid spacing.
a435e833b1 Mart*   update rotating_tank results, but not plume_on_slope (affected at
1fa758ce8e Jean*   truncation level, 11 digits).
                 
0e6056cd20 Jean* checkpoint58l_post (2006/07/12)
a435e833b1 Mart* o calc_gw:
1fa758ce8e Jean*  - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
                  - remove side-drag for now (need to fix it); update plume_on_slope results.
                  - fix for partial-cell & non-uniform dz; update plume_on_slope results.
066de0bcd6 Patr* o commit code to make SST/SSS weights spatially variable
                   (based on either variable in-situ or variable initial T/S weights)
9c7011b92a Patr* o pkg/ecco:
                   * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
                     now based on horizontally varying weights wthetaLev, wsaltLev
                   * cost_averagesflags now returns year indices in addition to day, month
a435e833b1 Mart*   * sflux balance is performed on annual basis
9c7011b92a Patr*     (sflxumm, sfluxmm2, bal_sfluxmm)
                   * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
                     including separate counting and multipliers
11d329f17a Patr* o pkg/rbcs
                   * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
926e82ae0e Jean* 
0e6056cd20 Jean* checkpoint58k_post (2006/07/06)
a75fd4a3a0 Jean* o testreport:
a435e833b1 Mart*  - always build in dir. "build" (if not there, mkdir build instead of building
a75fd4a3a0 Jean*    & running in input)
                  - run in dir run (if it exists), in build otherwise.
                  - call prepare_run (if input/prepare_run exists)
                  - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
6519624399 Dimi* o pkg/exf modifications to interpolation and rotation routines for more
                    reasonable treatment of North Pole singularity: for tracers North Pole
                    value is set to northernmost zonal-mean value, for zonal velocity it is
                    set to zero, and for meridional velocity it is set to northernmost value.
35141c3376 Mart* o pkg/exf/exf_check_range.F
a435e833b1 Mart*  - add tile index to diagnostics and move stop statement to the very
                    end of the routine.
05aa25be39 Jean* o pkg/diagnostics: (diagnostics_main_init.F)
                   define title of isomorphic variables according to the current config.
842bb5f1d9 Jean* o pkg/thsice with pkg/seaice dynamics:
6789e1f33d Jean* - fix domain of computation (interior only, required for exf) and do exchanges
                 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
ae35500ca3 Jean* o towards a standard way of dealing with multi-threading in MONITOR
                   and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
a435e833b1 Mart* o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
                    to W momentum equation in nonhydrostatic and quasihydrostatic runs.
6f6b52a4f5 Jean* o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
e03f83af3c Jean* o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
                 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
                    (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
a435e833b1 Mart* o tracer advection:
d8d36aa8bb Jean*  - clean-up and simplify calc_common_factors.F
a435e833b1 Mart*  - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
d8d36aa8bb Jean*    advection subroutine (but still not used within DST advection S/R)
2baa3a4f30 Jean* o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
                 
0e6056cd20 Jean* checkpoint58j_post (2006/06/15)
95f2c2ae3f Patr* o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
                   from file (collects calls previously in FORWARD_STEP)
                 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
a0d26c252a Patr* o adjoint store dir. adjusted accordingly
95f2c2ae3f Patr* o genmake2
                   replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
a0d26c252a Patr* 
0e6056cd20 Jean* checkpoint58i_post (2006/06/14)
a435e833b1 Mart* o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
c9058eda34 Mart*   on wind stress (SEAICEstressFactor defaults to 1.)
4a7f47048d Jean* o Total number of Timers is finite (<=40): comment out 2 non-essential one
                   in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
a435e833b1 Mart* o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
b161d628fb Jean*   on CS-grid: no longer loosing mass.
6be7d7dc38 Jean* o exf & curvilinear-grid: no longer modify longitude xC & xG.
5ea0c8294d Mart* o pkg/ggl90: fix sloppy output and fix a bug
d558d05cf5 Dimi* o pkg/seaice: added SEAICEuseEVPpickup parameter
                   - Set to false in order to start EVP solver with
                     non-EVP pickup files when using SEAICEuseEVP
b53f333527 Mart*   - fix sign error in diffusion in seaice_calc_rhs
5ea0c8294d Mart* 
0e6056cd20 Jean* checkpoint58h_post (2006/06/07)
4a4ac2b6f4 Patr* * Modifications for bottom topography control
                   o replace hFacC by _hFacC at various places
                   o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
                   o add non-self-adjoint cg2d_nsa
                   o update autodiff support routines
                   o re-initialise hfac after ctrl_depth_ini
                   o works for 5x5 box, doesnt work for global_ocean.90x40x15
                 * Adding verification for 5x5 box (4-layer) bottom topography control
                 
0e6056cd20 Jean* checkpoint58g_post (2006/06/07)
6f0ec9a199 Jean* o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
                    used for mean seasonal cycle, mean diurnal cycle); add an example
                    in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
a435e833b1 Mart* o pkg/ggl90:
2539abbd59 Mart*   - add parameter (minimum surface kinetic energy)
                   - fix bug (avoiding division by zero)
a5d3c9e070 Mart* o couple pkg/thsice to pkg/seaice:
                   - modify advection in seaice to accomodate new scalar fields to be advected
                   - only muliDimAdection scheme work with seaice/thsice
                   - mapping of thsice-variables to seaice-variables, back and forth
                   - does not break the verification experiments, but does not give the
                     desired results either
                 o pkg/seaice
                   - make (default) second order advection a bit less confusing?
                 
0e6056cd20 Jean* checkpoint58f_post (2006/06/05)
a435e833b1 Mart* o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
                   to pkg/seaice):
25f8242518 Mart*   - new routines thsice_map_exf and thsice_get_exf provide the interface
a435e833b1 Mart*   - add an additional formal parameter to thsice_solve4temp
558a6f8862 Patr* o pkg/exf:
                   - add new fields wspeed, snowprecip (to be able to couple to thsice)
                   - correct Stefan-Boltzmann constant
                   - new parameter for longwave surface emittance
a435e833b1 Mart*   - separate some stuff from exf_bulkformulae into new routines
558a6f8862 Patr*     exf_radiation, exf_wind
a435e833b1 Mart*   - add new parameters and constants: longwave emissivity for ocean, ice
25f8242518 Mart*     and snow, evaporation parameters over ice
51cdae4cbe Mart*   - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
                     either wind from stress or stress from wind
766e50be03 Jean* o pkg/thSIce:
                 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
                 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
                    and THSICE_CALC_THICKN
                 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
                 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
                   to make debugging easier.
                 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
a435e833b1 Mart* o pkg/bulk_force:
                   - clean-up comments and parameters ;
766e50be03 Jean*   - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
086faee439 Jean* o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
                   generate new output for test-experiment: aim.5l_cs.thSI
de56cb35d0 Jean* o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
558a6f8862 Patr*   testreport accordingly
de56cb35d0 Jean* 
0e6056cd20 Jean* checkpoint58e_post (2006/05/17)
23424617f8 Patr* o SEAICE_CGRID adjoint done
f66b450460 Patr* o R_STAR adjoint implemented.
                   * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
                   * need to sort out init. of h0facc, etc.
5ff8d4a5cf Patr* o Make pkg/profile fully independent of ecco,cost, etc. stuff
                   to be able to use it in pure forward.
2619b6fb59 Patr* 
0e6056cd20 Jean* checkpoint58d_post (2006/04/21)
3112405dc7 Jean* o upgrade simple test-experiment to tutorial example:
                  step.1: duplicate the experiment and (step.2) will remove the old copy.
                   tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
                   tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
                   tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
                   tutorial_global_oce_biogeo    <- copy of dic_example
                   tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
                   tutorial_plume_on_slope       <- copy of plume_on_slope
                   tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
                   tutorial_global_oce_optim     <- empty for now (David ?)
                   tutorial_global_oce_in_p      <- copy of global_ocean_pressure
                  some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4c5f492b95 Gael* o correct a sign problem in cost_scat.F
a435e833b1 Mart* o obcs and ptracers: fix boundary conditions for advections schemes
                   with larger stencil
2057f5cbae Patr* o thsice adjoint: start
a435e833b1 Mart* o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
9108661f3b Mart*   completeness
a435e833b1 Mart* o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
562e0a15fe Mart*   and COSINEMETH_III, add comments in default CPP_OPTIONS.h
a4d028af27 Patr* o ptracers adjoint:
                   * avoid extensive recomputatations
                   * fix missing re-init. of gptr (missed by TAF)
a435e833b1 Mart* o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
8ef23b4c75 Mart*   me to turn off the excessive output to STDOUT that this package produces
b030b75637 Jean* o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
                   and add those terms in Vector-Invariant formulation.
a435e833b1 Mart* o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
d4f53c1fd3 Gael*   if the control period (xx_hfluxperiod etc) is 0
                 o in profiles pkg, clean routines and fix details
a435e833b1 Mart* o in ecco pkg, reading ssh data:
d4f53c1fd3 Gael*   fix problem in case the model does not start at iter0=0
587564817e Mart* o fix mnc-pickup/restart for ptracers
b970da0492 Patr* o new package prifiles:
                   code to compute profile-based cost by Gael Forget
01c71301a9 Patr*   (modifs in ecco, ctrl, autodiff)
b970da0492 Patr* o Benign bug fix in initialization (spotted by M. Mazloff) of
                   ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
01c71301a9 Patr* 
0e6056cd20 Jean* checkpoint58c_post (2006/03/23)
5f86d55b22 Patr* o adjoint: finish NLFS adjoint and provide reference output in
                   verification/global_ocean.90x40x15/results_ad_nlfs
a435e833b1 Mart* o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
c401c03915 Mart*   documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
a435e833b1 Mart*   SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
c401c03915 Mart*   with SEAICE_CGRID defined.
eaf6816ef6 Jean* o move calendarDumps from "data" to "data.cal" and clean-up the code
                   with a simple call to pkg/cal S/R: CAL_TIME2WRITE
                 o add useEXF & useCAL flags (for now, set in hard-coded way)
8f72ee0f86 Jean* o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
                   (were missing in NH mode, and wrong in quasihydrostatic mode).
                   waiting for Chris updated version of calc_gw to add those CALLs.
                 o fix bug in quasihydrostatic S/R ;
                   add a test for this option: global_ocean.90x40x15.qshyd
808cde9ea6 Jean* o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
                   (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
                 o add on/off flag useOffLine for package OFFLINE
a435e833b1 Mart* o seaice:
ed94531ee9 Mart*   - modify advection so that it works also on the C-grid
a435e833b1 Mart*   - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
ed94531ee9 Mart*     problem in multi-tile runs with C-grid
362dbfa680 Mart*   - add flags for clipping ice velocities and/or masking solver forcing
8582a6e33f Mart*   - fix drag (ocean on ice) formulation and a bug that caused noise in the
                     C-grid solver
3dce9279c3 Mart*   - added a few comments to seaice_diffusion.F
                   - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
                     are now exclusive)
a435e833b1 Mart*   - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3dce9279c3 Mart*     required re-ordering the code a little:
                    + make DAIRN global variable (defined in SEAICE)
                    + move computation of the viscosities eta and zeta into a new separate
                      routine (because I need to recompute them in seaice_ocean_stress.F)
0946cb6a20 Mart* 
0e6056cd20 Jean* checkpoint58b_post (2006/03/13)
a435e833b1 Mart* o AIM+thSIce: fix sign of Short-Wave through the Ice ;
12cf6f073b Jean*   update output.txt of exp. aim.5l_cs.thSI
9705a0d5c6 Ed H* o various mnc cleanups and improvements:
                   + shrink lookup tables by factor of ~4
                   + better error reporting when running out of lookup space
                   + able to handle longer path/file names (up to 500 chars)
07c24e37c2 Patr* o adjoint:
                   - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
                   - TBD: "hidden" mom_vecinv recomp. in dynamics
3975cf6076 Jean* o change forcing_In_AB to affects both T,S forcing and Momentum forcing
                  (allow to differentiate between forcing components using new integer flags:
                   momForcingOutAB=1/0 & tracForcingOutAB=1/0)
                  and add new flag to put Dissipation tendency out of Adams-Bashforth.
d7e0df64ad Patr* o ecco
                   - enable trend removal from SSH anomaly obs.
                 o adjoint
                   - a fix for PmEpR when #undef EXACT_CONSERV
                   - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
                   - try to fix "hidden" recomp. in forward_step for NLFS
                     (NLFS seems broken sometimes after I checked it in)
a435e833b1 Mart* o seaice:
73792e16df Mart*  - add c-grid version of the dynamic solver:
                    + three new routines that are the c-grid substitute lsr, dynsolver
                      and ostres
                    + put a few fields that were local to dynsolver into global common
                      blocks, so that I can move the computation of stresses etc into
                      seaice_lsr (saves coding but may break the adjoint).
                  - replace more hardwired parameters by runtime parameters
                  - add ice masks that mask the rhs of the implicit solvers where there
                    is no ice (commented out in seaice_dynsolver, because i am not sure
                    if this works properly), eventually this should replace the clipping
                    of ice velocities in seaice_dynsolver to +/-40cm/s.
a435e833b1 Mart* o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2f7dcdd863 Ed H*   include it only where its needed
a69f02f073 Mart* o move balancing of fluxes before the call of external_forcing_surf
6ed81927e7 Mart* o seaice:
                   - correct units of turning angles (now they are really in degrees)
                   - move computation of GWATX/Y out of main routine into dynsolver
                   - initialize GWATX/Y in seaice_init
6f005fadde Jean* o Apply mask on Fresh-Water flux (needed for SSH forcing).
a435e833b1 Mart*   update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
03a9a80809 Mart* o seaice: add runtime flags for turning angles (default to zero)
a435e833b1 Mart* o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4bf6063982 Patr*   and trend from exf forcing and ctrl control adjustments
                 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
                   (since checkpoint57x_post)
f5e99809b0 Jean* o change the default rotation period to 86164.s = the Earth rotation
6fdf842d4f Jean* o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
                   and based on a reference stratification. Tested within hs94.cs-32x32x5.
009bbbd3aa Mart* o seaice advection: add code for choosing between the default (2nd order
                   central differences) and multiDim advection schemes provided by
                   pkg/generic_advdiff
7d6367e3db Mart* o seaice:
a435e833b1 Mart*   - removed all references to SEAICE_GRID.h fields from
7d6367e3db Mart*     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
                     (cubed-sphere configuration will change a little)
                   - grid computations in seaice_init are obsolete now.
                   - cleaned up code a little so that is easier to read (hopefully).
009bbbd3aa Mart*   - added new (better?) discretizations of default advection and diffusion
                     (turn on with SEAICEuseFluxForm)
                   - replace 1 in 3d global fields by kSurface in growth.F
a435e833b1 Mart* 
0e6056cd20 Jean* checkpoint58a_post (2006/02/13)
14e9b6a754 Mart* o seaice:
                   - bug fix in advect.F
a435e833b1 Mart* o shelfice:
                   - separate shelfice load anomaly from pload (breaks with time
70b0991389 Mart*     dependent forcing), => introduce constant field shelficeLoadAnomaly.
                     Its default is 0., but it may be computed more cleverly from (unknown)
                     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
                     done offline. A good approximation of the pressure load anomaly is
a435e833b1 Mart*     necessary to avoid large initial adjustment processes underneath
70b0991389 Mart*     deep-reaching shelfice.
e5cc225f5e Mart*   - small fix in ISOMIP shelfice_thermodynamics
a435e833b1 Mart*   - add more sophisticated thermodynamics of Hellmer (1989), this is
e5cc225f5e Mart*     now the default
                   - give a few constants more intuitive names
d5413e2490 Mart* o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
                   if bulk formulae are used in long integration (especially EmPmR). Turn
                   on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
                   if balancePrintMean, the imbalance that is substracted is printed to
                   STDOUT.
48ddec2149 Jean* o fix bug (typo) in obcs_apply_eta.F
506298a7d9 Mart* o add a new package shelfice which enables us to model the circulation
                   underneath shelf-ice with draughts of hundreds of meters.
                  - works
                  - to do: + include improved thermodynamics
                           + check whether kSurfC (from model/inc/SURFACE.h) can be used
                             instead of new field kTopC
a435e833b1 Mart*           + can we use topoFile, Ro_surf and existing code in ini_depth.F
506298a7d9 Mart*             instead of new field R_shelfIce and new code in ini_depth.F
                             and ini_mask_etc.F?
70b0991389 Mart*           + adjust vertical mixing schemes?
a435e833b1 Mart* o seaice pkg:
                  - add a cpp-flag to include a simple formula for a salinity dependent
f2368faea9 Mart*    freezing point of sea water at the surface
                  - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
                    meridional stresses are now different (and hopefully correct)
da87ea6f08 Jean* o AIM pkg: change threshold on large-scale condensation to conserve Heat.
                    update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
                    and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
a435e833b1 Mart* o pkg/diagnostics: add options and parameters for regional-statistics
                    diagnostics ; define regions by reading a region-mask from a file
575f9a835c Jean*    (might add other options later)
bae467ec49 Jean* o pkg/bulk_force:
                  - add option and parameters to use AIM surface-flux formulae.
                  - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
a435e833b1 Mart*    others forcing fields (defined in PARM05, parameter file "data") are loaded
bae467ec49 Jean*    from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
a435e833b1 Mart*  - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
bae467ec49 Jean*  - use the right EXCH call for uwind,vwind (to work on CS-grid).
                  - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
                    and parameters (note: calcWindStress replaces .NOT.readwindstress).
                  - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
                 
0e6056cd20 Jean* checkpoint58 (2006/01/12)
a435e833b1 Mart* o add "--embed-source" option to genmake2 which, when the supporting
                   tools can be compiled (as determined by genmake2) will turn on the
                   embed_files package which then embeds the entire MITgcm source code
d79bbe5ed9 Ed H*   (*.[fFhc] + Makefile) used for the build within the executable
                   - requested by CNH but off by default
                   - adds a paltry <9MB to the mitgcmuv executable in most cases
                   - only writes the output when useEMBEDSRC in eedata is true
f4ab189f71 Patr* o clean up 3-dim. relaxation codes:
                   * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
                   * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
                   * Thanks to Tom Haine for testing!
                 
0e6056cd20 Jean* checkpoint57z_post (2005/12/31)
b83f88edb2 Jean* o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
                   affects output (@ truncation level) of exp. plume_on_slope ; updated.
b00d0b5f70 Mart* o fix the pickup behavior for obcs in combination with ptracers
                 o fix a bug in ptracers_external_fields_load
                 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
                   affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
                 o transfered surface NH pressure to eta field (if exactConserv).
0330ceca59 Jean* o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
                      and update lab_sea output.txt file.
7276a6414c Patr* o completing 3-dim. relaxation code: additional term
                      1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
                   in S/R EXTERNAL_FORCING_T (file external_forcing.F)
                   * At compile time, in "EXF_OPTIONS.h" set
                       #define  ALLOW_CLIMTEMP_RELAXATION
                       #define  ALLOW_CLIMSALT_RELAXATION
                   * At runtime in "data", under &PARM03 set (e.g., units in seconds)
                       tauThetaClimRelax3Dim = 15552000.0,
                       tauSaltClimRelax3Dim  = 15552000.0,
                   * 3 cases:
                       1) Use a constant-in-time 3-dim. field
                       2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
                       3) Real-time relax. to time-evolving prescribed field
a435e833b1 Mart* o Adding Laplacian-type smoothness constraint on
3ed7687b4d Patr*   initial and boundary (forcing) controls (ic, bc)
a435e833b1 Mart*   * enable at compile-time via
3ed7687b4d Patr*     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
                   * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1014465bd0 Patr*   * Absolute scale somewhat unclear so far
                   * no area weighting was included since no other cost term does so far
0330ceca59 Jean* 
0e6056cd20 Jean* checkpoint57y_post (2005/12/08)
3488aaba5f Patr* First step for a NLFS adjoint
                 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
                 o new init. routines for calc_r_star, calc_surf_dr
                 o still need to deal with ini_masks_etc
                 o testreport seemed happy
0e6056cd20 Jean* checkpoint57y_pre (2005/12/08)
7df36fd6a0 Patr* 
94e76af995 Jean* o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1023fa2ba2 Step* o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
81b06b0cda Step* o add new offset feature to offline pkg (plus minor cleanup)
                 o cfc fixes for final year of integration
                 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
                   be in GCHEM_OPTIONS).
                 
0e6056cd20 Jean* checkpoint57x_post (2005/12/04)
7392df2720 Jean* o fix testreport Pb in multiple test experiment.
4212cfbd21 Ed H* o cleanup our namelist syntax in verification:
                   - make it more F95 standards compliant (some work still needed)
                   - allows the vast majority of our tests to work with gfortran
f3a828f7e4 Jean* o Non-Hydrostatic:
                  - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
                  - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
f56826ff51 Jean* o Allow to apply AB on T,S rather than on AB(gT,gS):
                  - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
                  - use the same arrays (gtNm,gsNm) to hold tracer field at previous
                    time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
                  - need a "clever" read_pickup to restart from the other AB formulation
a435e833b1 Mart* o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
31a33cd878 Jean* o remove some unused variables (reduces number of compiler warnings)
812e613baf Patr* o adjoint
                   * Disable useVariableViscosity for adjoint for time being
                     (there are a number of extensive recomputations)
                   * Initialize certain variables needed for adjoint
31a33cd878 Jean* 
0e6056cd20 Jean* checkpoint57w_post (2005/11/03)
b0d5c3a79b Jean* o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
                              fix the singleCpuIO RS version of MDSWRITEFIELD
                    and add a WARNING if using globalFiles=T with multi-processors.
1b9b94d610 Jean* o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
                   using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
b0d5c3a79b Jean* o tracer advection scheme:
a435e833b1 Mart*   add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
                    those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
dcc36c3b47 Jean*    was not very convenient).
a435e833b1 Mart*   add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
dcc36c3b47 Jean*    (further tests needed for the implicit DST & Flux-Limiter schemes).
1ccb4070a2 Mart* o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
                   and sRef for convenience, handy, when you want to initialize
                   ptracers in a large domain with a constant non-zero value. Also,
                   untangle ptracers_init.F a little.
                 
0e6056cd20 Jean* checkpoint57v_post (2005/10/13)
5e507d5445 Jean* o change dome exp. to use variable viscosity in side-drag terms.
2f98dc7b12 Ed H* o remove all the files from the cfc_offline test since they are now
                   incorporated into tutorial_cfc_offline which has been producing
                   identical results for a few days of testing
7053a0bdbe Jean* o add new parameter: sideDragFactor to enable half-slip-side BC
                   and change side-drag S/R to use viscosity from mom_calc_visc
a435e833b1 Mart*   (can switch back by setting sideDragFactor=0.); affects results at
                   truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
7053a0bdbe Jean*    global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
a435e833b1 Mart* o vorticity & strain are now computed without masking, to account for
cc95ee1c31 Jean*   no-slip-side BC in variable viscosity calculation ; mask is applied
                   anyway later on, before computing advection/coriolis terms.
1ccb4070a2 Mart* o modify exp4 to test new obcs support for reading from external files
58bf89d65c Mart*   and for passive tracers
a435e833b1 Mart* o fix behavior of ptracers_monitor when monitor output is written to a
c760cf3af0 Mart*   netcdf-file; still not independent of monitor.F (writes in the same
                   file).
a435e833b1 Mart* o change default value of tRef (put a uniform, meaningful value for ocean
9807caa0b1 Jean*   & atmos) and initialize sRef (was missing, as Martin mentioned).
a435e833b1 Mart* o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
e2b2bf4d90 Bayl*   to be proportional to enstrophy dissipation length.  Thus,
                    viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
                   This is now consistent with Smagorinsky and with the manual.
                 
ca1cda04e8 Mart* checkpoint57u_post
ae51cb4320 Mart* o OBCS and PTRACERS: add open boundary support for passive tracers
a435e833b1 Mart*   - either use homogenous (pseudo) v.Neumann conditions or prescribe
ae51cb4320 Mart*     OB-values from file; this is not different from the way theta and salinity
                     are treated
                   - however, Orlanski-radiation conditions are not supported, and the model
a435e833b1 Mart*     will stop if you use pTracers and Orlanski at the same time.
ae51cb4320 Mart*   - beefed up the rountine obcs_external_fields_load: now only those open
a435e833b1 Mart*     boundary values are overwritten with values from files for which there
ae51cb4320 Mart*     are really files, otherwise the OB-fields remain untouched. This makes
a435e833b1 Mart*     it possible to use different OBs at different ends of the domain (as
ae51cb4320 Mart*     with EXF)
a435e833b1 Mart* o reduce number of exch calls in shap_filt (s2).
                 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
20e058fdde Jean*   truncation level) 4/5 MLAdjust test results (11&12 digits match).
                 
0e6056cd20 Jean* checkpoint57t_post (2005/10/03)
c126063c4a Jean* o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
                 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
                   same truncation, independent of the face number: affects affects several
                   test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
02b02f5c36 Jean* o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
c126063c4a Jean*   note that biharmonic viscosity + no-slip was not tested in any experiment.
76b60848db Jean* o fix bug in non-linear free-surf side-drag ; generate new output for
                   global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
b22b541fe9 Ed H* o make mnc honor the writeBinaryPrec flag for most kinds of output
8b81bca38d Ed H* o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
f28ad821d5 Jean* o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
                   error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
b39b0f289d Jean* o add brackets in multi-terms sum to get same truncation, independent of
                   the face number (manage to get exactly same value of gU,gV at the cs-edge)
                   affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1e9e8678dd Bayl* o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
                   and viscA4Remax, which allow one to limit the minimum viscosity by specifying
                   a maximum grid-scale Reynolds number.  Also, changes all length calculations
                   in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
a435e833b1 Mart*   Suggested values of viscosity parameters found in mom_calc_visc.
1e9e8678dd Bayl*   Many new viscosity diagnostics available.
96c813b2a5 Jean* 
0e6056cd20 Jean* checkpoint57s_post (2005/09/20)
a435e833b1 Mart* o Add clearing-house for viscosity calculations, mom_calc_visc and
                   correct numerous bugs in LeithD and Smagorinsky discretizations.
                   mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
                   used simultaneously, and to be used in mom_vecinv and mom_fluxform.
188fd32c24 Bayl*   Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
a435e833b1 Mart*   and with Strain-Tension viscous term calculation (mom_hdissip.F).
188fd32c24 Bayl*   The Strain-Tension form is now called with useStrainTensonVisc=.true.
                   ViscAhStrain and viscAhTension are now retired.
96c813b2a5 Jean* o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
f7f6e70984 Ed H* o In response to JMC's bug report, genmake2 now ignores any soft-links
                   that it finds in the *current* directory when searching for files.
                   Soft-links found in any other source directories will still work as
                   they did before.
a435e833b1 Mart* o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
df91541502 Ed H*   a C routine to unlimit the stack size
157ea9ae8e Ed H* o mnc-ify pkg/aim snapshot vars
cf701ea57b Ed H* o mnc-ify pkg/land as requested by Daniel
5bc9611487 Ed H* o various changes to mnc including:
                   - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
a435e833b1 Mart*   - output can now be grouped so that all files within a group
5bc9611487 Ed H*       change the ITER portion of their names in lock-step together
                   - can now read ("global") PER-FACE (in addition to PER-TILE) files
                       and works with both EXCH1 and EXCH2 (but needs more testing)
                   - writing works for all verification test cases w/ g77 on Linux
                 
0e6056cd20 Jean* checkpoint57r_post (2005/09/07)
88d5fee2bf Ed H* o make MNC variable initialization happen earlier
84386989cd Jean* o add diagnostics for (almost) each term of the momentum Eq.
66f83c2ede Jean* o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2be058fac5 Jean* o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
a435e833b1 Mart* o remove MINIMAL_TAVE_OUTPUT option ;
2be058fac5 Jean*   add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
69a417565e Jean* o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
                   allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5d1838d198 Patr* o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
                 o add time-dependent SST, SSS control
7e2510a0ae Patr* o cost terms in ecco/ modularized (new cost_generic.F)
                 o cost_averages routines are modularized (new cost_averagesgeneric.F)
                 o new infrastructure for seaice model vs. obs misfits in seaice/
                   * driver from the_main_loop.F is seaice_cost_driver.F
                   * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
                   * gradient check in Exp. 6a of natl_box_adjoint/
                 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
                   (see README file)
69a417565e Jean* 
0e6056cd20 Jean* checkpoint57q_post (2005/08/19)
fa355923ad Jean* o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1660a6b12d Ed H* o fix annoying months-old bug in mnc/mdsio output for seaice pkg
                   - bug was reported by Jean-Michel and Ian Fenty
e8d8f0b10f Jean* o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
a435e833b1 Mart*   update exp. cpl_aim+ocn output.
9caa94febf Patr* o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
a435e833b1 Mart*   Needed for high-res. runs with large global files
9caa94febf Patr*   to be able to limit tapelev size
                 o Changed some tests for adjoint:
                   * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
                   * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
                   * global_ocean.90x40x15/ back to default 3-level checkpointing
9094bd878c Patr* o Modifications to enable scripted COMMON to MODULE conversion
                   * verification/OpenAD/code/ has necessary scripts and description;
                   * converts, compiles and runs successfully;
9caa94febf Patr* 
0e6056cd20 Jean* checkpoint57p_post (2005/08/01)
62807350a8 Jean* o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
                 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
                   (already the case for some pkgs, including recent MNC_init, e.g. thsice)
                 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
f39b9d8a97 Jean* o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
                   (was already the case for dissipation with mom_vecinv,
                    and also the case for grad.PhiHyd when staggered-timeStep)
                   This will allow to put dissipation out-off the AB time-stepping.
                  Unfortunately, affects truncation error. Update output of exp. that "fails"
                   (cg2d matching number) and leave the others for later: front_relax(10),
                   global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
                   matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
                 
0e6056cd20 Jean* checkpoint57o_post (2005/07/30)
a435e833b1 Mart* o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
50653b81f1 Ed H*   (2) its ready to be documented during the 20050801 DocFest
a435e833b1 Mart* o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
e2d47178e0 Ed H*   for ideal_2D_oce and lab_sea on linux_ia32_g77
f48a8b1137 Patr* o set to #undef CTRL_SET_OLD_MAXCVARS_30
                   in global1x1_tot/code_seaice_adj to access indices 32, 33
                   (worth another tag)
e2d47178e0 Ed H* 
0e6056cd20 Jean* checkpoint57n_post (2005/07/29)
fbb2516727 Patr* o adding precip control xx_precip 32
                 o adding swflux control xx_swflux 33
53a1c5d19a Patr* o Replacing 10 forcing penalty cost routines by 1 generic.
                 o Implementing partitioning in time-mean and variable adjustment
                   for atmos. state.
                 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
08f22f958d Patr* o in natl_box_adjoint:
a435e833b1 Mart*   * updated exp 1 to 10
53a1c5d19a Patr*     (but does not have time-mean vs. variable split results yet)
455751fbdb Patr* o updated global1x1/*_seaice_adj/
                   to incorporate latest changes
df05ad6e2a Patr* o enable useSingleCpuIO for mdsio vector routines
                   (applies in particular to tapelev I/O)
                 o removed inefficient K-loop in all active_file*control*.F
3d0327d769 Patr* 
0e6056cd20 Jean* checkpoint57m_post (2005/07/28)
c0c2091c08 Jean* o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
                   and advect_cs (use EXCH-2 and standard cs-32 grid files).
a435e833b1 Mart* o pkg/exch2: filling of face-corner halo regions is optional
d6f0fdc2ab Jean*   (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
                 
0e6056cd20 Jean* checkpoint57l_post (2005/07/14)
a435e833b1 Mart*  tag before updating tutorials (pre-release-2)
9ce7209758 Jean* o add cos & sin of grid-direction orientation angle (curvilinear grid only,
                    for output and interpolation of input fields onto model grid)
                 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
                    Affects results of exp. rotating_tank ; update output.txt.
27356e724c Jean* o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
6e29458d64 Jean*       and taking the square quantity and/or using a fraction-weight field.
27356e724c Jean* o fix aim_diagnostics_init.F mate numbers.
                 o add mnc output capability to diagnostics/diagstat and update
106a65ba8a Ed H*   our cvsignore files for the ACSII output generated
                 
0e6056cd20 Jean* checkpoint57k_post (2005/07/02)
508b8225ad Patr* o lab_sea now uses diagnostics package and provides a suite of
                   new EXF diagnostics output.
                 
0e6056cd20 Jean* checkpoint57j_post (2005/06/30)
61b6aef6a7 Patr* o exf
                   * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
                     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
                     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
                   * extended diagnostics output
                     - now includes all EXF variables
                     - hs, hl moved to common block
                     - separate S/R for diagnostics, called after ctrl vector is added
                     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
                     - EXFqnet contains true Qnet (i.e. includes qsw)
                   * updated verif. lab_sea, global_with_exf
                   * Rearranging hflux (exf_mapfields -> exf_getforcing)
                     to ensure that diagnostics sees a true EXFqnet
f529aaf45d Jean* o add matlab scripts for CS-grid vectors (in utils/cs_grid)
f4f7b96c0e Jean* o diagnostics pkg: change pointers so that 1 diagnostic can be used
                   several times with different frequencies.
df4e8f7bcf Ed H* o mnc-ify the thsice package as requested by Daniel Enderton
                   - the monitor--MNC output needs work
                   - many attributes need to be added (most are currently blank)
                 o mnc-ify theaim_v23 package as requested by Daniel Enderton
                   - many attributes need to be added (most are currently blank)
24babd248d Jean* o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
cafbc21546 Jean* o add Sadourny like discretization to the 4th.O vorticity advection scheme
a435e833b1 Mart* o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
a3075797a1 Jean*   update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
                      fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
85f899f51b Jean* o fix few little things to avoid floating error with -ftrapuv (ifort v9)
                  (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
                 
0e6056cd20 Jean* checkpoint57i_post (2005/06/19)
d1a9b8a2b9 Andr* o Diagnostics package was changed: diagnostic allocation is now deactivated
                   by setting an empty file name in the namelist (used to be by setting 0 frequency)
78a781bbae Jean* o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
                   add 1rst Order upwind vertical Shear.
eb47174845 Ed H* o add a quick fix for A/B checkpointing in OFFLINE mode
4b08b6ee66 Ed H* o add IGNORE_TIME define and -ignore_time option to genmake2 as an
                   end-run around the C/Fortran linking horror in eesup/src/timers.F
2e9be4c81e Alis* o added pkg/runclock: allows user to terminate run based on wall clock
                 o added non-hydrostatic scaling parameter: nh_am2
8fef4b1a57 Mart* o pkg/my82: futile attempt to make results compiler-independent by adding
                   some "_d 0", etc. no effect.
a435e833b1 Mart* o for mnc output, fill the 'T' coordinate var with myTime and create a
987ff12cb6 Ed H*   separate 'iter' variable for iteration count
a435e833b1 Mart* o pkg/diagnostics:
37224b77cb Jean*   add new capability: output of Global/Regional & per-level statistics ;
                   tested against monitor output (including land & thSIce) on various exp.
                 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
b9d81c4350 Jean* 
0e6056cd20 Jean* checkpoint57h_done (2005/05/19)
a435e833b1 Mart*   tag after changing user customized files (DIAGNOSTICS_SIZE.h,
74630d4888 Jean*   data.diagnostics, data.gchem, data.ptracers) is done.
                 
a435e833b1 Mart* o pkg/diagnostics: prepare for Global/Regional statistics.
                   add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
83f253cab3 Jean* o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
                   and rename it: DIFFERENT_MULTIPLE
                 
0e6056cd20 Jean* checkpoint57h_post (2005/05/14)
8e5ee067a3 Jean* o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
0da48370b7 Jean* o pkg/diagnostics: change output frequency, now in seconds (instead
                   of Nb of iterations). This requires to change data.diagnostics.
0e6056cd20 Jean* checkpoint57h_pre (2005/05/12)
51dd5bf40e Jean* 
41ce3f2380 Ed H* o in mnc, let the user create the output dir if both mnc_outdir_date
                   and mnc_outdir_num are false
06fffa8fd5 Ed H* o add fflags() to pkg/diagnostics which allows one to specify, on a
                   per-file basis, the file precision [default behavior is unchanged]
7e819019d5 Dimi* o added diagnostics to pkg/kpp, including computation of mixed layer
                   depth based on a temperature/density criterion
                 o updated verification/natl_box to test the new pkg/kpp diagnostics
7bc0d239f7 Jean* o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
300c0d54fc Jean* o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
9a87ea5e43 Ed H* o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
                   not mnc -- this mistake was found by JMC and is now corrected
                 
0e6056cd20 Jean* checkpoint57g_post (2005/04/15)
79e87d2e6d Jean* o add Adams-Bashforth 3rd Order time stepping:
                   - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
                   - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
0e6056cd20 Jean* checkpoint57g_pre (2005/04/15)
af908d3f0e Jean* 
5ab5d7f263 Patr* o make lambda[Theta,Salt]ClimRelax spatially varying
                   (default remains spatially uniform constant based on tau)
ce442b4534 Patr* o added new control variables
                   * init. uVel, vVel, etanN
                   * lambda[Theta,Salt]ClimRelax
                 o separate masks used for ctrl_pack/unpack 'from write_grid' output
                   (suggested by G. Forget)
5ab5d7f263 Patr* 
0e6056cd20 Jean* checkpoint57f_post (2005/04/06)
a80a5e8cfd Jean* o add parameter "baseTime" = model base time = time at iteration zero
a435e833b1 Mart*   new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
a80a5e8cfd Jean*   account for baseTime shift
                 o move Coriolis arrays from PARAMS.h to GRID.h
0e6056cd20 Jean* checkpoint57f_pre (2005/04/06)
ee61c20a30 Jean* 
de859229b1 Ed H* o mnc-ifying the seaice package
de01be390b Alis* o introduced an alternative length scale calculation for use in the limiting
                   maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2d80ef5b25 Patr* o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
a435e833b1 Mart* o added modified Leith scheme with viscosity proportional to grad(Hdiv)
b4b9669a6b Bayl*   as well as grad(vort3).  Made it compatible with both approximate form
                   for the cubed sphere and full form of these gradients.  Added flag
a435e833b1 Mart*   useFullLeith to select between approximate and full form.
02718ea810 Jean* o add "d0" in getcon.F to reduce differences between compilers/platforms
                   update output.txt of exp. fizhi-gridalt-hs
5103c42ce9 Jean* o change port_rand funtion to allow to set the seed.
409155d7b6 Ed H* o fix obscure MNC bug involving conversion between reals and integers
a435e833b1 Mart*   - it caused no problems with certain (eg. gcc, ifc) compilers but the
409155d7b6 Ed H*     new version is now more standards-compliant
4645654aba Patr* o adjoint-related modifications
                   * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
                   * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
                   * mom_vi_hdissip: to be able to use Leith scheme in adjoint
409155d7b6 Ed H* 
0e6056cd20 Jean* checkpoint57e_post (2005/02/28)
a4f6b487ba Patr* o Adding eddy stress controls a la Ferreira et al.
5245708a89 Jean* checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
f30908c65d Patr* 
eee5dc53df Jean* o fizhi pkg: fix AtoC and CtoA when called with same input & output array
                   update output.txt of exp. fizhi-gridalt-hs
2cc3b69a26 Ed H* o add more "Z" dimensions and associated coordinate vars to MNC
c098ac3e0d Dimi* o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
fc64655a31 Dimi* o parameter calendarDumps: when set, approximate months (30-31 days) and years
                   (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
                   KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
                   months and years.  Requires pkg/cal.
ee2e7fad64 Ed H* o diagnostics: add pickup functionality
                   - off by default for backwards compatibility
                   - current version only uses MDSIO -- MNC will be added
9723cb5244 Jean* o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
26c7db4c78 Jean* o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
                 
0e6056cd20 Jean* checkpoint57d_post (2005/02/11)
06d5464476 Jean* o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
a435e833b1 Mart* o modify verification/ideal_2D_oce so that it tests the creation of mnc
91cf1175df Ed H*   output from the diagnostics package
24ef99fe7f Jean* o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
6554790d1c Ed H* o make genmake2 more portable by using ".$FS" instead of ".f" for more
                   of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
e8743b4419 Ed H* o add coordinate variables to the MNC output from the diagnostics package
a629410b0b Jean* o change MNC-flags default value: true when useMNC=TRUE
e808c5b132 Ed H* o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
a435e833b1 Mart*   the ability (off by default) to read the grid information using MNC
7a3f7c0b47 Jean* o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
0557aa5c83 Jean* o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
a435e833b1 Mart* o do snap-shot diagnostics at the middle of the time-interval (instead of
fde699a81e Jean*   at the end).
40893cb58a Jean* o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
                   new test for AIM with thSIce + slab-ocean
dd3fb239f5 Jean* o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
440b7157f3 Jean* o move state variable diagnostics to the beginning of the time step ;
                   (note: still needs some work specially for snap-shot diagnostics)
                   duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
                 
0e6056cd20 Jean* checkpoint57c_post (2005/01/27)
c130fcff71 Jean* o Change testing option (-ieee) to get closer agreement between g77 & ifort
                 o generate new output.txt files on faulks with g77 & the new -ieee option
0e6056cd20 Jean* checkpoint57c_pre (2005/01/27)
7ba28f2af1 Jean* 
                 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5a35007c50 Jean*   update output.txt of exp. global_ocean.90x40x15
a435e833b1 Mart* o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
6643de8305 Jean*   results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5f46ec9135 Jean* o add saltFlux(+File) forcing capability with periodicExternalForcing
97038d3c07 Jean* o allow to use pkg diagnostics for GM-Redi & ThSIce output
                 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
35ef3a0982 Ed H* o improvements for the MNC output from DIAGNOSTICS:
                   - correct handling of the unlimitied dimension
                   - all dims now have associated coordinate variables
                   - variables located at U, V, and Corner ("Z") points are now written
a435e833b1 Mart*     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
35ef3a0982 Ed H*     *all* data points are output
8d9f2d1888 Dimi* o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
e1a538cff8 Dimi* o added pkg/seaice/seaice_monitor.F
fcf5946e08 Dimi* o mdsio_readfield.F can now read files visible only to master MPI process.
714116e714 Dimi* o pkg/seaice: some test code for ice-modified ocean stress
4aa81846e7 Dimi* o exf_getffields interpolation defaults to bilinear for all scalar forcing
                   fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
                   spurious negative numbers for precipitation and humidity.  Will cause
                   some small numerical differences for integrations using pkg/exf/exf_interp.F.
a3296ad516 Patr* o pkg/ctrl/
                   * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
                     May be enabled via doPackDiag
a435e833b1 Mart*   *  introduce z-scaling of
                      + gradient (doZscalePack) and
a3296ad516 Patr*      + control (doZscaleUnpack)
                 o pkg/mdsio/
                   * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
                   * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4aa81846e7 Dimi* 
0e6056cd20 Jean* checkpoint57b_post (2004/12/20)
0cf6e0ada1 Jean* o simplify options in diagnostics_fill arguments (remove weird combinations)
2f38f768b3 Ed H* o fix MNC coordinate variables so that they now contain per-face index
a435e833b1 Mart*   values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2f38f768b3 Ed H*   general, EXCH2 grids are only aligned to a "local" coordinate system
34bd0f9de0 Jean* o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
                 o Implement instantaneous output within pkg diagnostics:
                   setting a negative frequency in data.diagnostics produces
                  "snap-shot" output (as opposed to time-average if freq > 0)
ed27c6ee8e Jean* o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
a435e833b1 Mart*   NOTE: change ptracer diagnostics name: use 2 characters to work with
ed27c6ee8e Jean*         more than 9 tracers. Add also diagnostics of advect & diffus flux.
a435e833b1 Mart* o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
18eb3f79fd Ed H*   becomes the coordinate variable for the 'T' dimension
d77e828db7 Ed H* o add CF-style coordinate variables to MNC
a435e833b1 Mart*   - just a first cut:  numbers are meaningless on the cubesphere and
d77e828db7 Ed H*     missing along the T axis but otherwise it works!
e07cbe4110 Dimi* o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
047c5644f3 Jean* o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
9a922069e0 Jean* o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
                   this is based directly on what the model compute, so that the content of
                   each diagnostics might be affected by switching options (e.g., implicitDiffusion)
                 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
a435e833b1 Mart* o clean up build options files for SunOS, in particular
e8f00bfc75 Mart*   - remove -traditional from xmakedepend
                   - change -xarch=v9 to -xarch=native for f77
                   - restore use of make (not gmake)
                   - add CC=gcc if using g77
7af35f0733 Ed H* o changes per discussion of AM, JMC, & EH3 today:
a435e833b1 Mart*   - move redundant "grid" variables out of "state" -- in preparation of
                     creating proper CF-style coordinate variables and in recognition
                     that any/all grid variables can be easily copied (eg. w/NCO) from
7af35f0733 Ed H*     the grid files into any of the other NetCDF files
a435e833b1 Mart*   - *always* output grid variables with MDSIO (this will eventually be
7af35f0733 Ed H*     changed)
                   - output MNC grid file if useMNC is true
a435e833b1 Mart* o every instance of _END_MASTER() has been found and replaced with
                   _END_MASTER( myThid ) in order to satisfy certain picky Sun
ea6e02f692 Ed H*   preprocessors
ee5c9de779 Jean* o re-arrange diagnostics pkg initialisation:
                  - allow each package to extend the available diagnostics list
                  - add some checking and fix small problems (multi-threaded, ...)
                  - new S/R diagnostics_fill (replace fill_diagnostics):
                    look through the short list of active diag. (instead of the long list)
                    create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
617e9c07f6 Ed H* 
0e6056cd20 Jean* checkpoint57a_post (2004/12/10)
6ff6896d7d Patr* o this set of changes restores TAMC compatibility
                   tested for global_ocean.90x40x15 adjoint on trough
                   (what a pain)
                 
0e6056cd20 Jean* checkpoint57a_pre (2004/12/10)
4161b94ac5 Patr* o some modifs in tools/build_options for sunos
                 o call ctrl_pack for ctrl at end for optimcycle=0
                 
0e6056cd20 Jean* checkpoint57 (2004/12/09)
7bcb6cc723 Mart* o add horizontal bi-harmonic viscosity for vertical velocity
                   - new parameter viscA4W (defaults to viscA4)
                   - affects only non-hydrostatic code
                   - to be done: no-slip lateral boundary conditions
af994d39e8 Dimi* o switch back to "sflux = sflux - runoff" in exf_getforcing.F
f9712caa2c Jean* o implement Implicit Vertical advection for pTracers
2c4cea51ae Jean* o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
e97e7f4284 Jean*   (implemented also for implicit vertical diffusion & advection)
5428496056 Mart* o OBCS: extend application of tracer open boundary conditions
                   to a strip beyond the boundary of width Olx/Oly
14137e831b Patr* o add call monitor to TAF set of required calls (flow directives)
                   and include in natl_box_adjoint
                 o untangle a few ifdefs related to cost, ctrl, autodiff
                   untangel a few ALLOW_ECCO_OPTIMIZATION
e5d44c8b0d Patr* o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
                   (theta2, salt2 in ecco_cost_weights)
5428496056 Mart* 
0e6056cd20 Jean* checkpoint56c_post (2004/12/03)
93ea71777b Mart* o OBCS as control variables
                   - update ctrl_ad_diff.list, obcs_ad_diff.list
                   - remove balance of obcs controls from default
                   - fix index bug nobcs in ctrl_init
                   - fix dummy fields filen in ctrl_pack
                   - add dummy weights for obcs
                 o lsopt: comment out fort.94 output
a435e833b1 Mart* o optim:
93ea71777b Mart*   - remove unnecessary header files
                   - adjusted namelists
                   - add xerbla.F to Makefile
a435e833b1 Mart* o exf:
93ea71777b Mart*   - multiple modifications of exf_check_range
                   - unit change in exf_init_runoff from [m/year] to [m/s]
                 o mdsio:
                   - i/o-vector change debugLevel from debLevA to debLevB
                 
0e6056cd20 Jean* checkpoint56b_post (2004/12/01)
8a588e179e Mart* o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
                   is called from DO_THE_MODEL_IO
                   - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
                   - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
                   - clean up PTRACERS_WRITE_TIMEAVE a little
233b414ed8 Mart* o add another verification experiment that tests both the cfc-pkg and
a435e833b1 Mart*   the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
233b414ed8 Mart*   reactive tendencies treated inline with regular timestepping
d8c583b49a Mart* o testreport previously did a lousy job of comparing small numbers, so
                   we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
                   implemented in the little c-progam tmp_cmpnum.c which is embedded in
a435e833b1 Mart*   testreport.
d8c583b49a Mart* o ptracers_monitor: bug fix for MPI
                 
0e6056cd20 Jean* checkpoint56a_post (2004/11/28)
bdb2728325 Mart* o GCHEM: finish reorganizating the package
a435e833b1 Mart*   - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
bdb2728325 Mart*     (introduces another 3D-array for each passive tracer, but only if
                     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
                     gchemTendency is not needed because the timestep is done separately)
                   - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
                   - GCHEM is now---more or less cleanly---separate from PTRACERS
                   - to bo done: handling of surfaceForcingPtr that is needed for KPP not
                     so clear to me how that should be done in a general way.
                 o CFC: improve formatting of output in CFC_ATMOS
                 o PTRACERS:
                   - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
                     that ALL experiments with ptracers enable can be checked. This makes
                     GCHEM_MONITOR obsolete.
                   - include a runtime parameter PTRACERS_monitorFreq that defaults to
                     monitorFreq
a435e833b1 Mart*   - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
68c34fd102 Ed H* o add PTRACERS (PTR0[1-5]) to testreport output
b3bbb0d458 Patr* o exf_check_range:
                   * default changed to .TRUE.
                   * will check values for niter0 if debLevA, every timestep if debLevB
                   * STOP in exf_check_range if 'out of range'
                   * range chosen generous to allow for potential extema
                   TBD: a version with stricter range
                        permitted range would be runtime parameters
5f42c34bbe Jean* o GMredi:
                   - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
                   - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
                   - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
a435e833b1 Mart* o GCHEM:
31940778af Mart*   - move call to GCHEM_FORCING_SEP, so that it is now called before
                     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
a435e833b1 Mart*   - introduced a useGCHEM runtime flag and applied it everywhere.
26bcdcd4f0 Mart*   - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
                     this flag is now only visible within GCHEM-pkg routines.
                   - moved gchem_forcing_int temporarily into ptracers_forcing, this will
a435e833b1 Mart*     be replaced by a 3D array that is computed before thermodynamics; for
26bcdcd4f0 Mart*     this, the tracer ID iTracer had to be included into the parameter list
                     of ptracers_forcing
a435e833b1 Mart*   - set up forward_step to call gchem_forcing, that will replace
26bcdcd4f0 Mart*     gchem_forcing_int in ptracers_forcing
                   - cleaning up
3e021cd85f Jean* o small cleaning of exch2: remove files that are also in eesupp/src
30a55c64a0 Mart* 
0e6056cd20 Jean* checkpoint56 (2004/11/17)
0608749963 Jean* o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2f14a1f812 Ed H* o mnc: cleanup "full" files--fixes out-of-memory problem
c715d0b027 Patr* o ECCO-GODAE
                   * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
                   * fully merged and updated from SIO code
                     windstress sign change affects
                     - exf_inscal_[u/v]stress
                     - sign of xx_tau[u/v] adjustments
                     - signs in cost_scat
                   * ctrl_get_gen: avoid update of tau[u/v] for first few days
                   * natl_box_adjoint updated and compressed
                   * 2-level checkpoint switch added
                     (tested in EXP. 1 of natl_box_adjoint)
                   * new switch doInitXX to avoid init. of xx_... in optimcycle=0
                 o SVD
                   * first complete, non-hacked version for SVD calculations
                   * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
                     performed via direct access files admtlm_vector.it????
                     (via ctrl_[un]pack)
                   * optimcycle is used for ARPACK iteration counter
                     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
                   * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
a435e833b1 Mart*     and add linear transforms where necessary
c715d0b027 Patr*   * controls are initial/final SST, SSS (can be extended; need to check
                     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
                 o mdsio: filename info to both stderr, stdout
                 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
a435e833b1 Mart*   from sign change
2f14a1f812 Ed H* 
0e6056cd20 Jean* checkpoint55j_post (2004/11/10)
4c23dd3d61 Jean* o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
                   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
617e9c07f6 Ed H* o add consistent build directories and .cvsignore files to verification
070e727a0d Dimi* o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
a435e833b1 Mart* o make all subroutines 30 or less characters in length for certain older
                   compilers to work (a thorough search only turns up two routines in
064f472621 Ed H*   pkg/ptracers)
a435e833b1 Mart* o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
7066de6cf6 Jean*   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
                 
0e6056cd20 Jean* checkpoint55i_post (2004/10/28)
92cbe40bc9 Jean* o change arrays for total vertical diffusivity (2.D if explicit,
                   3.D if implicit) ; each ptracer uses its own background value.
73983c4f5f Ed H* o added mnc/NetCDF output capability to ocn_compon_interf
a435e833b1 Mart*   - added bits to verification/cpl_aim+ocn so that it can run on
73983c4f5f Ed H*     ITRDA and other clusters without the mpirun "-wd" option
0de9c264f0 Andr* o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
a435e833b1 Mart*   configuration
                 o give MNC the ability to create additional files rather than
                   exceeding a specified file size limit "MNC_MAX_FILESIZE"
                   - the default is just less than 2GB which is a practical limit
ab11ba1276 Ed H*     on many systems
a435e833b1 Mart* o Compute the non-local term using either KPP vertical diffusivity (=default)
60fa91c126 Jean*    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
9f675e95f9 Jean* 
0e6056cd20 Jean* checkpoint55h_post (2004/10/20)
19afae78f4 Jean* o add verification test "vermix"
ff63a227b0 Ed H* o remove all the *_ioinc flags and replace with the single global
                   outputTypesInclusive flag
69377f8682 Jean* o allow to set a vertical profile of vertical diffusivity for T & S
19afae78f4 Jean* o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
                 o useMNC moved from data.mnc to data.pkg
69377f8682 Jean* 
0e6056cd20 Jean* checkpoint55g_post (2004/10/14)
6b1c25ae7b Patr* o Renaming carbon AD experiments to comply with testreport conventions
                 o Updating adjoint of Held-Suarez hs94.1x64x5
                 o Fixing directives for non-ECCO forward_step, after ECCO directives
                   have been fixed to avoid recomp. of do_oceanic_phys
                   Works well for global_ocean.90x40x15,
                   but recomp. issue remains for carbon
a435e833b1 Mart* o Updating adjoint output for natl_box_adjoint after
6b1c25ae7b Patr*   pkg/ecco has been modified (see taga c55d_post)
                 
0e6056cd20 Jean* checkpoint55f_post (2004/10/13)
8a3e9d877a Ed H* o rename to timeave_init_fixed
                 
0e6056cd20 Jean* checkpoint55e_post (2004/10/13)
d6be6cad8f Patr* o some delicate re-shuffle of store directives to avoid one
                   extra call of do_oceanic_physics
                   affects ecco_the_main_loop.F, do_oceanic_physics.F
                   checkpoint_lev1_directives.h
                 o NB: this may break global_ocean adjoint temporarily,
                   but it is clear how to fix it. Will do later, need this now.
                 
0e6056cd20 Jean* checkpoint55d_post (2004/10/11)
75d667876f Patr* o ECCO specific cost function terms (up-to-date with 1x1 runs)
                 o ecco_cost_weights is modified to 1x1 runs
                 o modifs to allow observations to be read in as
                   single file or yearly files
                 o enable to read exf forcing fields as either
                   single file or yearly files (flag useExfYearlyFields)
0e6056cd20 Jean* checkpoint55d_pre (2004/10/08)
75d667876f Patr* 
                 o switch between 2-level and 3-level checkpointing
a435e833b1 Mart* o add ability of MNC to write local and "partial" (eg. 2D slices where
cb356b4c5f Ed H*   the full 3D field is never actually stored) arrays to NetCDF files
a435e833b1 Mart*   with the correct (that is, the complete multi-dimensional) set of
cb356b4c5f Ed H*   array indicies
                   - used in mom_vecinv() to write the diagFreq output
                   - tested (demonstrated) in verification/aim.5l_cs
c9c3d7103f Ed H* o further mnc-ification
                   - add verification/lab_sea to the list with mnc setups
                   - fix undefined mnc v-names in cd_code
                   - add kpp to mnc output (both snapshot and timeave)
6deb815953 Mart* o non-hydrostatic code
                   - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
                     in calc_gw.F
                   - defaults to viscAh
                   - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
a435e833b1 Mart*     friction or Leith) in non-hydrostatic mode, as long as there is
6deb815953 Mart*     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
449f3c105b Patr* o pkg/cost
                   extend simple cost functions to treat time mean quantities
                   (T,U,V) via cost_accumulate_state from cost_tile
4ddf54cc90 Jean* o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
                     be 2 times larger than the minimum size the advection scheme requires.
                     now get a perfect conservation of salt in advect_cs test-exp (updated)
76f580e1f0 Mart* o GGL90 (Gaspar's TKE mixed layer)
a435e833b1 Mart*   - add horizontal diffusion of TKE, requires exchanges in
                     do_fields_blocking_exchanges, horizontal diffusivity is zero by
                     default. In OPA there is no horizontal diffusion of TKE but the
76f580e1f0 Mart*     mixing coefficients are computed from a horizontal average of TKE of
                     6 points or so. I think that diffusion has a little more physical
                     justification.
a435e833b1 Mart*   - clean up ggl90_calc in the hope of reducing memory usage (this hope
76f580e1f0 Mart*     was in vain)
                   - mask tke-variable in ggl90_init
3c38934f04 Jean* o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
                 o fix biharmonic diffusion on CS-grid.
78800a222d Mart* o more obcs stuff
                   - added obcs_external_fields_load as an alternative to the EXF-pkg option
a435e833b1 Mart*     for reading boundary values. This routine is called from
78800a222d Mart*     obcs_prescribe_read
                   - updated obcs_check
965df15d92 Mart*   - changed sponge layer relaxation parameter units for days to seconds
                   - turned off sponge layer by default
5720994acc Patr*   - changed argument list of OBCS_CALC to myTime+deltaTclock
b67ae883c8 Mart*   - fixed about 35 bugs in obcs_external_fields_load
78800a222d Mart* 
0e6056cd20 Jean* checkpoint55c_post (2004/09/23)
38224ac59a Patr* o obcs stuff
                   - new runtime flags useOBCSprescribe, useOBCSbalance
                   - re-arranged obcs_calc
                   - moved exf_getobcs to obcs_prescibe_read
                     obcs_prescibe_read is called after ORLANSKI stuff
                     and independent of it (executable can contain all).
                   - updated obcs_check
64e4c8fd27 Patr*   - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
                     These may be necessary only if tangential velocities are
                     prescribed at OB, not sure, needs testing.
2509c39694 Ed H* o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
                   which simplifies the calls and passes the ifc check-bounds test
                 
0e6056cd20 Jean* checkpoint55b_post (2004/09/22)
6fdcc18f80 Jean* o add a 2D scalar, Z location, exchange_2 routine.
9f675e95f9 Jean* o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
                   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
                   affects advect_cs results (for the wrong reason): update output.txt
a435e833b1 Mart* o use a more standard discretization for biharmonic viscosity ;
df39a169f0 Jean*  (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
a435e833b1 Mart*   affects results of dome set-up: update output.txt
df39a169f0 Jean* o fix gad_advection.F (CubedSphere part), back to version 1.23
                 o fix bug in mom_vi_del2uv.F (CubedSphere part).
58031354dd Mart* 
0e6056cd20 Jean* checkpoint55a_post (2004/09/20)
a435e833b1 Mart* o merged code to
96bbd4e2a5 Patr*   * prescribe/read time-dependent open boundaries
                     (works in conjunction with exf, cal)
                   * sponge layer code for open boundaries
                   * each boundary N/S/E/W now has its own CPP option
                     (healthy for the adjoint)
                 
0e6056cd20 Jean* checkpoint55 (2004/09/17)
334b55a5b0 Patr* o up-to-date adjoint of previous breaks
                   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
                   - global_ocean_ebm: adjoint still needs fix (TLM ok)
                   - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
                   - carbon: * remove tr1-related adjoint verification
                             * add ptracer as control variable
                 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
                   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
                 
0e6056cd20 Jean* checkpoint54f_post (2004/09/16)
d3c81fef04 Patr* o in verification/carbin/ remove experiment related to
                   ALLOW_PASSIVE_TRACER (array tr1 etc)
                   code_ad/ input_ad/ results_ad
                 
b8e554ea44 Mart* o add two new packages
                   - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
                     + subject to optimization (memory)
                   - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
                     + subject to reordering (many GOTOs in the original code)
                     + so far opps is called for every (i,j) point, and then operates in
                       the vertical; one may want to reorder the scheme in order operate in
a435e833b1 Mart*       horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
b8e554ea44 Mart*       fields)
e05d966902 Ed H* o overhaul of IO so that we now have flags for MDSIO and/or MNC
                   - all verification tests compile and run with linux_ia32_g77
a435e833b1 Mart*   - defaults are compatible with current input files--nothing
e05d966902 Ed H*     should change if you were not previously using MNC
                   - MNC output has been added in numerous places (eg. timeave)
                     but there are still a few writes not yet do-able with MNC
                     (this is in progress)
a435e833b1 Mart*   - flags now allow for either/or/both use of MDSIO and MNC and
e05d966902 Ed H*     documentation will soon follow
                   - numerous small formatting cleanups for ProTeX
1f6288729b Ed H* o add version info (via BUILD_INFO.h) to MNC and stdout
                 
0e6056cd20 Jean* checkpoint54e_post (2004/09/02)
58031354dd Mart* o add two new packages
a435e833b1 Mart*   - pp81 (Packanowski and Philander, 1981), Richardson number and
58031354dd Mart*     stratification dependent mixing
                   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
a435e833b1 Mart*   - these scheme operate in a similar manner as KPP (without ghat, of
58031354dd Mart*     course), however there is only one diffusivity that is used for both
58378fc26e Mart*     temperature and salinity (and passive tracers)
ff0dde6fdb Step* o add offline package
c7bf664228 Ed H* o add "verification/dic_example" which contains a dic-gchem-ptracer setup
                   provided by Stephanie Dutkiewicz
e8a04cb645 Ed H* o genmake2: add ability to search for C compilers and cleanup test output
                   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
                 
0e6056cd20 Jean* checkpoint54d_post (2004/07/27)
999e18a3ba Alis* o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
a435e833b1 Mart* o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
1c7ec5d18e Jean*   leading to additional shift by 5 days each year of integration
                    (i.e. leading to considerable offset over the years)
3eb6e74bad Jean* o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
                 o start with no AB and no initial filtering (staggerTimeStep):
                   change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
                 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
                   (external loading & cpl import/export stay in forward_step.F)
                 o update coupling interface to work with new staggerTimeStep
                 o change MDSIO ptracers_pickup.
f8f693c946 Jean* o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
353dc202ae Ed H* o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
f8f693c946 Jean* o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
353dc202ae Ed H* 
0e6056cd20 Jean* checkpoint54c_post (2004/07/18)
1a73c8a0cc Jean* o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
                   this affects (truncation error) output.txt of test-exp:
                    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
                 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
b59159bd17 Jean* o change Qnet to always be the net heat flux, (+upward).
                   affects (truncation error) output of natl_box exp.: updated
43f9f92e51 Jean* o define the max number of passive tracers in PTRACERS_SIZE.h
                 o start to test mnc routinely in exp0
                 o add sea-ice loading (sIceLoad) as a new forcing field.
                 
0e6056cd20 Jean* checkpoint54b_post (2004/07/08)
a435e833b1 Mart* o add testreport "-j JOBS" option for parallel builds (tested and pretty
8c9e835c69 Ed H*    impressive on Altix and Opteron systems)
bc1bd3388a Ed H* o diagnostics can now write NetCDF files through the mnc package
b71b8cc969 Jean* o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
a435e833b1 Mart* o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
f04695194c Jean* o staggerTimeStep & NLFS: rescale T & S surface tendencies.
                   affects (truncation error) output of lab_sea & natl_box exp.: updated
                 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
                 
0e6056cd20 Jean* checkpoint54a_post (2004/07/06)
89aa0d86bf Jean* o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
                 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
                 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
                 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
                   + internal_wave (shift in writing cg2d_ini_res)
0e6056cd20 Jean* checkpoint54a_pre (2004/07/05)
33e1cd7241 Jean* 
0f1d4cfc8d Dimi* o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
                   - modified verification/lab_sea and natl_box_adjoint accordingly
                 
0e6056cd20 Jean* checkpoint54 (2004/07/02)
                 checkpoint53g_post (2004/07/02)
e5b80f023f Jean* o prepare splitting of thermodynamics: store convect.counter in common block
8ac0de89ba Jean* o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
                   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
e73e2206ff Dimi* o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
1cf497b67b Jean* o new parameter "nShapS": allow to treat differently S from T (nShapT)
                 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
9e38639d14 Patr* o restore adjointability
1cf497b67b Jean* 
0e6056cd20 Jean* checkpoint53f_post (2004/06/25)
f4437bef13 Jean* o modifications that affect AIM experiment results (update output.txt):
a435e833b1 Mart*   - no advection of S at top interface Nr (pkg/generic_advdiff)
f4437bef13 Jean*   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
71989a1d2f Jean* o AIM pkg:
                   - include stability function into surf.Flux derivative relative to Tsurf
                   - calculate clear-sky radiation & surface temp. change (for diagnostics)
a435e833b1 Mart* 
9583d821f1 Andr* checkpoint53e_post
                 o merged cylindrical coord configuration
                 o added rotating_tank experiment
db2e27b728 Andr* checkpoint53e_pre
                 
0e6056cd20 Jean* checkpoint53d_post (2004/06/14)
27134ca433 Jean* o faulks upgraded: re-generate output.txt that have changed:
                    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
19ec94aecc Alis* o Added Bryan and Lewis, 1979, vertical diffusivity profile
a435e833b1 Mart* o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5d5fff3a81 Alis* o added Sadourny discretization of Coriolis
                   - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
                   - re-enabled use of omega3 (useAbsVorticity)
e46ec53fc5 Alis* o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
52f1ebc9d7 Jean*   vector-invariant equations
e46ec53fc5 Alis*   - note: does *NOT* yet use same variable visc. for no-slip BC's.
8a9329e700 Mart* o recoded the lateral boundary conditions for non-hydrostatic w, this time
                   hopefully without new bugs
                   - still to do: biharmonic friction for non-hydrostatic w
4855f667f0 Alis* o bug fix for mom_*_sidedrag: rA -> rAs,rAw
                 o regenerated output for global_ocean_ebm (using -ieee)
647a06f20c Alis* o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
                   of mom_common/
                   - simple re-arrangement of instructions within computing loop
0e6056cd20 Jean* checkpoint53d_pre (2004/05/21)
647a06f20c Alis* 
0e6056cd20 Jean* checkpoint53c_post (2004/05/21)
1ad8306ce0 Jean* o new version of coupler for AIM+thSIce and Ocean models
                  - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
                  - land: change Evaporation of snow
                  - aim with thSIce: fix bug in snow-precip.
fbdf55c31a Mart* o changes to calc_gw.F
                  - bug fix for w^2 term near the bottom boundary
                  - (hopefully) improve the lateral slip boundary condtions for use with
                     partial/looped cells
                   - because the bug fix changes two verification experiments anyway (exp5
                     and plume on slope), change the lateral boundary condition from half slip
                     to the value of no_slip_sides
4e8c9bded2 Patr* o ebm package wasnt quite up to the parallel task. Fixed that.
8c7ad6d151 Patr* o Adjoint of EBM package + verification
                   * TLM OK
                   * ADM not sufficient accuracy yet (needs further testing)
fbdf55c31a Mart* 
0e6056cd20 Jean* checkpoint53b_post (2004/05/14)
f86a3c0e0c Patr* o Commiting new energy balance model to repository
                   * package is pkg/ebm
                   * verif. is verification/global_ocean_ebm
                   * references are in ebm_driver.F
                 C      * X. Wang, P. Stone and J. Marotzke, 1999:
                 C        Global thermohaline circulation. Part I:
                 C        Sensitivity to atmospheric moisture transport.
                 C        J. Climate 12(1), 71-82
                 C      * X. Wang, P. Stone and J. Marotzke, 1999:
                 C        Global thermohaline circulation. Part II:
                 C        Sensitivity with interactive transport.
                 C        J. Climate 12(1), 83-91
                 C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
                 C        Destabilization of the thermohaline circulation
                 C        by atmospheric eddy transports.
                 C        J. Climate 7(12), 1870-1882
                 o Will need long integration testing.
0e6056cd20 Jean* checkpoint53b_pre (2004/05/14)
89dadec0f0 Patr* 
9c05b3873e Alis* o created pkg/mom_common in preparation for variable viscosity code
                 o renamed and split ini_mnc_io
f4a07a4bc7 Jean* o pkg/land: only liquid water can diffuse or run-off
                 o AIM using land: soil wetness availability account for snow
53c7d996f6 Dimi* o added printMapIncludesZeros to EEPARMS namelist
                 
0e6056cd20 Jean* checkpoint53a_post (2004/05/11)
e7f1536c88 Patr* o restore TAMC compatiility for exf_constants.h
                   (no usage of _d in .h)
                 o Additional storing in KPP in an attempt to fix
                   TAMC problem with adjoint of KPP code.
                   (no success...)
                   Identical code works fine with TAF.
0b07ed3507 Dimi* o Fixed verification/natl_box_adjoint experiments.
                   Initial conditions for Experiments 4 and 5 are now
                   set to "SEAICE_initialHEFF=0", which is more reasonable,
                   and hence gives results closer to that of Experiment 2.
                   Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
e7f1536c88 Patr* 
0e6056cd20 Jean* checkpoint53 (2004/05/06)
8522e3c798 Chri* o stable checkpoint with up to date adjoint
                   TLM tests only run for 1st grdchk at the moment. Its unclear if
                   this is a code problem or a problem with resetting code for g_
                   variables that is being autogenerated wrong.
                   Otherwise:
a435e833b1 Mart*    o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
                    o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
8522e3c798 Chri*      are both still in chaos following their security messes.
                 
0e6056cd20 Jean* checkpoint52n_post (2004/05/06)
f989ca6313 Ed H* o various build (mostly genmake2) changes including:
                   - ability to build/run more easily within Cygwin and MacOS X
                   - more complicated Makefiles with a stronger dependence on Gnu Make
4634ed4578 Dimi* o pkg/seaice modifications
f4fcd985ee Dimi*   - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
                     of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
                     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
a435e833b1 Mart*   - changed proxy for geostrophic velocity and updated
28d826540b Dimi*     verification/lab_sea/results/* accordingly
4634ed4578 Dimi*   - removed ADI dynamic solver from pkg/seaice
                   - replaced all occurrences of 1/CSTICE or 1/CSUICE
                     they caused a segmentation fault under certain circumstances
9976df0ac5 Mart*   - removed unused field WATR
b055761890 Mart* o bug fix in exf-package:
                   -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
                      now reflect that.
386eadb044 Mart* o small fixes in the cal-package:
                   - set reference date to first of January for the 'model'-calendar
                   - failing of cal_CheckDate in cal_FullDate now actually results in a
                     warning
df66ce88b0 Mart* o small modifications in exf-package to increase flexibility:
                   - change climtempfreeze from a constant to a runtime parameter that
                     is specified in data.exf_clim (default = -1.9)
                   - introduce runtime parameter windstressmax (default = 2.0) that is
                     specified in data.exf
351ee82bec Jean* o fix in pkg/thsice:
                   - update Evap (Tsf changes) to be consistent with Latent heat flux
                   - maintain snow precipitation unchanged (even if Tsf >=0).
                  both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
                 
0e6056cd20 Jean* checkpoint52m_post (2004/04/18)
329dcc48c4 Mart* o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
                   this does not change any of the results, because myIter=0 in swfrac always
                   lead to jwtype=2 (the default anyway), but the call makes little sense
                   as a default
222786db83 Jean* o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
1395c36e8a Jean* o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
                   atmospheric model (AIM) to use it ; add a "slab ocean" component.
                 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
                 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
7b6ef96a80 Dimi* o extending useSingleCpuIO option to work with new exch2 I/O format
                   - old-style, missing-tile I/O is still accessible by defining CPP
                     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
7e019df062 Ed H* o monitor package can write to NetCDF files and/or STDOUT
                 o fix re-definition bug in MNC_GRID_INIT_ALL()
8a37d3da43 Ed H* o doc/api_reference added
                   - a framework for building an API Reference Manual using all
                     the "protex" comments embedded in the code
                   - see pkg/generic_advdiff, pkg/mnc for examples
b297381f9a Ed H* o MNC:
                   - make myThid the last argument for all subroutines
                   - new default for the grid files: NO halos
cba009f524 Ed H*   - add useMNC and other run-time flags
                   - separate per-file-group handling of the unlimited dimension
a435e833b1 Mart*   - early initialization of MNC w/ flags read at the eeboot stage
cba009f524 Ed H*     and lookup tables set in initialize_fixed
                   - write all MNC output to a freshly-created directory
47e4defd15 Jean* o thermodynamics sea-ice (thsice) is now tested with testreport.
                 o test exp. advect_cs: use the standard cs32 grid ; update output.
cd56948b28 Patr* o Added functionality to grdchk:
                   pick global i,j,k position (or nearest wet) where to perform check.
9fa8dff5bb Jean* 
0e6056cd20 Jean* checkpoint52l_post (2004/03/11)
63585e25d4 Jean* o new land formulation:
                   a) use ground enthalpy as prognostic variable to ensure exact
                      energy conservation.
                   b) account for water temperature and for latent heat of freezing
                      in all processes (rain, run-off, ground storage)
                   c) compute surface and ground temperature implicitly.
                 o aim_v23 modification for new land model:
                   a) Treat separately land / ocean / sea-ice surface fluxes
                      to allow implicit computation of land & sea-ice surface temp.
                   b) add snow precipitation.
0e6056cd20 Jean* checkpoint52l_pre (2004/03/11)
9fa8dff5bb Jean* 
af5663a801 Jean* o fix problem (when 1 tile is empty) in min/max monitor.
a435e833b1 Mart* o fix bug in timeAve (u,vZetatave in common block)
76a3a9dce3 Dimi* o no restoring terms under ice for pkg/seaice
36f6faaf99 Dimi* o moved SEAICE_DO_DIAGS to S/R do_the_model_io
                 o bug fix for pkg/seaice pickups
070ec0f1ad Ed H* o change MNC call locations and add coordinate attributes
3777bd4e33 Jean* o mask vorticity at the corner ; affects global_ocean.cs output
                 o fix ini_curvilinear_grid ; test CS experiments with mpi
831771ecb4 Jean* o aim.5l_cs: modify sea-ice fraction input file ; update output
73ca73937b Patr* o exf: Adding simple range check routine for exf fields after read
e06eab71ce Jean* 
0e6056cd20 Jean* checkpoint52k_post (2004/02/23)
c99437d93a Alis* o removed top-level directory "diags"
                   - we migrated these functions to pkg/timeave a long time ago
                 o fixed bug introduced in pkg/monitor
171b0dbf72 Patr* o accuracy ctrlprec = 32 insuffient for gradient checks using
                   averaged fields (I/O via cost_averages)
                   -> use ctrl.h in active_file*.F to control I/O precision.
                 o paramter list of CALL ADTHE_MAIN_LOOP
                 o added initial do_the_model_io to ecco
                 o set all ...Freq to zero after cost_final
                   taveFreq, dumpFreq, pChkptFreq
4f02768964 Patr* o MAIN and ECCO differentiability restored
c99437d93a Alis* 
0e6056cd20 Jean* checkpoint52j_post (2004/02/18)
37b568618c Patr* o fix nchklev in tamc.h for global_ocean...
                 o Bringing flow and store directives up-to-date
                 o Really weird thing!
                   call do_the_model_io from the_main_loop with parameters
a435e833b1 Mart*   starttime, niter0, instead of mytime, myiter, screws up the adjoint:
37b568618c Patr*   TAF places a faulty re-call of initialise_varia
                   after cost_final call which should not be there!
0e6056cd20 Jean* checkpoint52j_pre (2004/02/03)
37b568618c Patr* 
63ae023a6f Andr* o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
                   error messages
e06eab71ce Jean* o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
7ecbd3c2aa Andr* o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
                   debug output
bd481ce0ad Andr* o modfied mdsio_writefield.F to handle non-global files under exch2
65c905ad22 Jean* o update AIM Cubed-Sphere exp (aim.5l_cs):
                   use land, p*, and Franco.M forcing fields with fractional land-sea mask.
                 o update AIM Equatorial Channel exp:
                   use standard aim_v23 pkg and change the SST fields to be more realistic.
6b7f81d27b Andr* o globalFile now works with exch2
a435e833b1 Mart* o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
e06eab71ce Jean*   mon_vort3.F to make exch2 friendly with >1 tile per cube face
e7f0a9dbe1 Dimi* o limit timeave output for hi-res integrations
404487e0d3 Andr* 
0e6056cd20 Jean* checkpoint52i_post (2004/01/21)
6989afdf96 Alis* o removed CPP_EEOPTIONS.h from verification/*/code
                 o updated the tiling for global_ocean_pressure
0e6056cd20 Jean* checkpoint52i_pre (2004/01/20)
6989afdf96 Alis* 
a435e833b1 Mart* o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
1e2193d0c9 Jean*   the old pkg/aim).
                 
0e6056cd20 Jean* checkpoint52h_pre (2004/01/20)
27e400a76e Andr* o shortened offending lines in exch2_send_rx?.template
8c93ce9839 Andr* o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
65592d1bf7 Ed H* o genmake2: add build & execute test for NetCDF code
52d06eb5f9 Andr* o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
                   old grid files, moved CPP_EEMACROS.h to pkg/exch2
f02794c1c2 Dimi* o added useSingleCPUIO flag to monitor.F and mon_out.F
d3ec31b5f6 Dimi* o added temporary hack for sea-ice dynamics on the cube:
                   metric terms are ignored and it is assumed that
                   there is no sea-ice on cube faces 1, 2, 4, and 5.
f02794c1c2 Dimi* 
0e6056cd20 Jean* checkpoint52f_post (2004/01/09)
046fd16d1c Andr* o added exch2 cube routines to pkg/exch2
                 o modified hs94.cs-32x32x5 to use it
                 o added new grid files to hs94.cs-32x32x5
0e6056cd20 Jean* checkpoint52f_pre (2004/01/07)
046fd16d1c Andr* 
0e6056cd20 Jean* checkpoint52e_post (2004/01/07)
67b14118a3 Jean* o first attempt to solve vertical advection (momemtum & T,S) Implicitly
                   for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
1cead955c0 Jean* o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
                   to work with implicit vertical advection and AB ;
                 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
                 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
                  front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
0e6056cd20 Jean* checkpoint52e_pre (2004/01/02)
caad9f4c67 Jean* 
                 o fix bug in impldiff when Nr=1 or Nr=2.
7d401e1f11 Jean* o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
                 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
157d0c5b42 Jean* o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
                   ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
7e230c5c02 Dimi* o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
7fd609fd20 Dimi* o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
                 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
7e230c5c02 Dimi* 
0e6056cd20 Jean* checkpoint52d_post (2003/12/16)
8b7b5f4e88 Alis* o re-tiled many expts to allow comparison in multi-processor mode
                   - updated output accordingly
                   - changed hs94.128x64x5 to use intial T from file rather than use the
                     random number generator
bcea5a4765 Andr* o add infrastructure in model routines for fizhi and gridalt packages
6b0a2bb136 Jean* o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
8ac0e9b3ce Dimi* o changes to permit hi-res, cubed-sphere, configuration
                   - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
                   - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
                   - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
                     of surface winds for the cube
                   (A verification experiment, based on global_ocean.cs32x15, but with
                    pkg/seaice turned on and with on-the-fly interpolation from the NCEP
                    Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
                    complete with example surface forcing files and matlab scripts to look
                    at the output and compare it with that of global_ocean.cs32x15.)
4b82b202ac Jean* o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
                    but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
                    to conform to the common rule.
a435e833b1 Mart* o check-in the first version of the coupler + interfaces for multi-components
bf18de4739 Jean*    set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
                    - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
a435e833b1 Mart*    - atmosphere: use pkg aim_v23 ; no sea-ice for now.
bf18de4739 Jean*    - ocean and atmos. share the same horizontal grid (no interpolation).
                    - exchanges between component and coupler is done in forward_step
a435e833b1 Mart* o new verification experiment, cpl_aim+ocn:
                    coupled ocean - AIM atmosphere on cs32 grid.
6b0a2bb136 Jean* 
0e6056cd20 Jean* checkpoint52d_pre (2003/12/06)
a435e833b1 Mart* o surface flux time-av diagnostic modified for NLFS & RealFreshWater
803573887e Jean* o add call to AIM pendant S/R in external_forcing & external_fields_load.F
269d31530a Jean* 
0e6056cd20 Jean* checkpoint52c_post (2003/11/25)
7c799abcad Patr* o Fixing OPTIONS files for use of exf:
                   - ALLOW_ECCO not needed
                   - ECCO_CPPOPTIONS.h should not be included from
                     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
                     as has been the case in the past
                   - All cal/exf related options are currently set in
                     single header file. Should remain so until we
                     agree on a consistent new policy.
2a563ee529 Patr* o Removed all CPP options for cal package.
                   cal has no more CPP options.
9682a51356 Patr* o modified STOREs in GAD_ADVECTION
                 o corrected key comp. for passkey
7c799abcad Patr* 
0e6056cd20 Jean* checkpoint52b_post (2003/11/23)
dfac86e1ec Jean* o new version: "thsice" of thermodynamic sea-ice pkg:
a435e833b1 Mart*  - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
dfac86e1ec Jean*  - modify fluxes but do not change theta directly;
                  - light cleaning of bulk_force pkg (still needed with thsice).
a435e833b1 Mart*  - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
dfac86e1ec Jean*    + output_thsice.txt to test thsice & bulk_force pkgs.
                 o put back grid & coriolis monitor output.
0e6056cd20 Jean* checkpoint52b_pre (2003/11/23)
7966caf364 Jean* 
a435e833b1 Mart* o call "do_the_model_io" at the beginning (=> dump initial state)
7966caf364 Jean* o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6dbdc867be Patr* o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
                   (need info on NUMBER_OF_PTRACERS)
                 o missing PTRACERS headers in some routines
                 o default tamc.h in pkg/autodiff supposed to crash
                   to ensure proper customization
                 
0e6056cd20 Jean* checkpoint52a_post (2003/11/17)
fa690556aa Jean* o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
9d36aec500 Dimi*   - moved surfaceTendencyTice from pkg/seaice to main code
fa690556aa Jean*   - subroutine FREEZE_SURFACE now limits only surface temperature
                     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
                     => new output.txt for global_ocean.cs32x15 & global_with_exf
                   - keep the old version of FREEZE for backward compatibility;
                     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
915eb1cffa Patr*   - corresponding modifs for TAF directives
9d36aec500 Dimi* o added surface flux output variables to TIMEAVE_STATVARS
                 o time-averaged output for pkg/ptracers
915eb1cffa Patr* o fix problem with ECCO-related divided adjoint
                   snapshot file was missing some ad-variables,
                   but no warning issued by TAF
fa1dae9534 Dimi* 
0e6056cd20 Jean* checkpoint52a_pre (2003/11/12)
fa1dae9534 Dimi* o some bug fixes for #undef REAL4_IS_SLOW
                 
aca4df70a2 Patr* checkpoint52 = ecco_c52_e35
                 o after testing adjoints of checkpoint51u_post
                 
0e6056cd20 Jean* checkpoint51u_post (2003/11/06)
909a9f878d Patr* o this is the post-merge tag of the ecco-branch
                   (needs another clean checkout and re-testing)
                 o various natl_box_adjoint configs and results
                   but no input fields
                 o obcs adjoint not yet merged!
                 o adding ECCO global 1x1 and 2x2 degree configs
                 o updated/extended some store directives for seaice
                 o pkg/ecco now containes ecco-specific part of cost function
                 o top level routines the_main_loop, forward_step
                   supersede those in model/src/
                   previous input data.cost now in data.ecco
                   (new namelist ecco_cost_nml)
                 o in ctrl/ cleaned some cross-dependencies and updated CPP options
                 
0e6056cd20 Jean* checkpoint51t_post (2003/11/04)
909a9f878d Patr* o this is the pre-merge tag of the ecco-branch
                 
0e6056cd20 Jean* checkpoint51s_post (2003/11/04)
ef651d0d5f Ed H* o cleanup: removed various obsolete #define-s
909a9f878d Patr* o pkg/grdchk
                   - renamed 'ph-grd 3' to 'grad-res'
a435e833b1 Mart*   - merged from ecco-branch
909a9f878d Patr*     (remaining bug fixes for obcs gradient checks)
                   - additional high-precision output for testreport
                     (grep for 'precision_grdchk_result')
ef651d0d5f Ed H* 
0e6056cd20 Jean* checkpoint51r_post (2003/11/03)
16add2227d Ed H* o cleaned up or removed CPP_OPTIONS.h files
                 o updated results for some of the tests to reflect the new
                   optfiles (-ieee: -O0 instead of -O3)
                 
0e6056cd20 Jean* checkpoint51q_post (2003/10/30)
cb574bfa04 Patr* o cd_code:
                   - moved cd_scheme.F -> cd_code_scheme.F
                   - separate read_checkpoint from cd_code_ini_vars.F
                   - separated cd_code part from write_checkpoint
                   - updated AD_SOURCE, generated .flow
                   - added CD_CODE_VARS.h to the_main_loop
                   - Moving cd_code specific store dir.s to pkg/cd_code
                 o ctrl package totally restructured
                   - pack/unpack now optional and decoupled from
                     xx_/adxx_ I/O
                   - ctrl_pack/unpack cleaned
                     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
                   - confined inclusion of AD_CONFIG.h to where necessary.
                 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
                 
0e6056cd20 Jean* checkpoint51p_post (2003/10/30)
138482fdf6 Ed H* o create initial cd_code package
a5bd9cbb61 Ed H*   - WARNING: the initialization of fields within packages
                     is broken because INI_FIELDS (where READ_CHECKPOINT is
                     called) is called *before* PACKAGES_INIT_VARIABLES.
                     This seems to be backwards since
a435e833b1 Mart*     1) its important to initially zero the entire field including
a5bd9cbb61 Ed H*        the "halo" region
                     2) zeroing needs to be done *before* reading pickup info
a435e833b1 Mart*        and the pickup call might or might not happen in any
a5bd9cbb61 Ed H*        particular run
                   - this needs an overhaul for R2
138482fdf6 Ed H* o cleanup verification/*/code/GMREDI_OPTIONS.h
                 o cleanup testreport
                 
0e6056cd20 Jean* checkpoint51o_post (2003/10/27)
8a8c81fb3e Patr* o bringing AD-related verif's up to date with genmake2
                   - carbon/
                   - global_ocean.90x40x15/
                   - hs.94.1x64x5/
                   - (front_relax/ )
                 o (more) consistent directory structure for AD-related verif.'s
                 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
                 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
                 o bug fix in find_alpha.F for MDJWF:
                   - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
                     change rho -> rho-rhoConst
                   - replace call find_rho to find_rhonum
                 o initialisation of rFlx extended to full array (required by TAF)
                   and shifted to thermodynamics
                 o removed PTRACERS.h in ptracers routine
                 o added surfacetendencyPtr to S/R parameter list pracers_forcing
                 o Correcting initialisations for fVerU, fVerV.
                 o helping TAF to recognize dependency on kUp for
                   fVerU, fVerV
                 o Replacing delZ by delR in pkg/ctrl/
0e6056cd20 Jean* checkpoint51o_pre (2003/10/24)
8a8c81fb3e Patr* 
51701379d8 Ed H* o undid all of cp51 pending some cleanups and discussion
a435e833b1 Mart* o added the [#include "AD_CONFIG.h"] statement to all files that need
406902c2ea Patr*    it for adjoint/tl #defines
                  o re-worked the build logic in genmake2 to support AD_CONFIG.h
                  o removed tools/genmake since it no longer works
c9cb668a47 Dimi* 
0e6056cd20 Jean* checkpoint51n_post (2003/10/23)
c9cb668a47 Dimi* o modifications to make FREEZE flux visible to pkg/kpp
                   - moved surfaceTendencyTice from pkg/seaice to main code
                   - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
                   - subroutine FREEZE now limits only surface temperature
                     (this means new output.txt for global_ocean.90x40x15,
                      global_ocean.cs32x15, and global_with_exf)
                 o added surface flux output variables to TIMEAVE_STATVARS
                 
0e6056cd20 Jean* checkpoint51n_pre (2003/10/23)
d7f6e03355 Dimi* o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4a967b9107 Ed H* o added [#include "AD_CONFIG.h"] to all files that use the following
                   defines:
                   - ALLOW_ADJOINT_RUN
                   - ALLOW_TANGENTLINEAR_RUN
                   - ALLOW_ECCO_OPTIMIZATION
d7f6e03355 Dimi* 
0e6056cd20 Jean* checkpoint51m_post (2003/10/21)
668b211e58 Ed H* o incorporating changes to get TAMC/TAF working in genmake2
                   - added new TAMC/TAF targets to the Makefile
                   - various cleanups related to package handling
fea3c3e36d Ed H*   - these changes should have no impact on the forward model
668b211e58 Ed H* 
0e6056cd20 Jean* checkpoint51l_post (2003/10/20)
c84f6b7c89 Dimi* o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
                  - faster algorithm for cal_addtime.F
                  - higher precision arithmetic, where needed
                  - pkg/exf *startdate variables changed from calendar date to
                    model integration time
                 
0e6056cd20 Jean* checkpoint51l_pre (2003/10/17)
d33aea2a79 Jean* o add salt flux to forcing fields (used when salty sea-ice forms or melts)
                 o enable to apply restoring on S & T only in a latitude band.
                 o update output (external_forcing_surf modif. change truncation errors)
                    global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
06c869d156 Patr* 
0e6056cd20 Jean* checkpoint51k_post (2003/10/16)
f9e188eb72 Jean* o change default to: useNHMTerms=.FALSE.
                  - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
                    adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
                  - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
                     exp1, ideal_2D_oce
                  - change data file of oceanic exp (leave the results unchanged for now)
                    exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
                 o set gravitySign automatically according to the vertical coordinate used
                   (and change sign: back to "logical" value: +1 when R increases downward)
a435e833b1 Mart* o added an include barrier to the default CPP_OPTIONS.h and
9eb494b0cb Ed H*   removed the #include "PACKAGES_CONFIG.h" from it
f9e188eb72 Jean* o fix a bug in mom_fluxform (from chk51j_post)
9eb494b0cb Ed H* 
0e6056cd20 Jean* checkpoint51j_post (2003/10/10)
0b85d93038 Patr* o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
                 o adjusted some flow directives (dynamics, thermodynamics)
                 o added cubed-sphere case to test cost function
                 o heckpoint_lev?_directives.h now include
                   pkg-specific directives, whenever those are enabled.
                 o Moving pkg-specific flow directives to corresponding pkg
                   Moving pkg-specific differentiation list to corresponding pkg
                   Moving pkg-specific checkpoint-lev storing to corresponding pkg
                   ---> conventions are
                        - pkg_ad.flow
                        - pkg_ad_diff.list
                        - pkg_ad_check_lev?_dir.h
                 
0e6056cd20 Jean* checkpoint51i_post (2003/10/09)
6d54cf9ca1 Ed H* o merge of the branch-genmake2
                   - knowingly breaks the older genmake
                   - automatic generation of all ALLOW_${PKG_NAME} defines
                   - new testreport supersedes older testscript
                 o large number of package inclusion and header cleanups
0e6056cd20 Jean* checkpoint51i_pre (2003/10/08)
6d54cf9ca1 Ed H* 
b95c3843ab Ed H* o new output for adjoin of global ocean vector invariant
                 o fix for checkpoint of thermodynamic seaice and bulk_force
                 o Steph gchem various cleanups
                 
46a4243beb Step* checkpoint 51h_pre
b95c3843ab Ed H* o fixed some single quotes
46a4243beb Step* o modify gchem pkg to be more versatile
                 o modifications to clean up dic pkg
                 o add pkg/cfc
                 
0e6056cd20 Jean* checkpoint51g_post (2003/10/02)
8c13754326 Patr* o provide links for ARPACK and ADM*TLM
                 o start removing verification/vero/
                 o update AD-related stuff
                   (in particular some IF-statements in model/src/ routines)
                 o adding to verification/global_ocean.90x40x15/ adjoint of
                   vector invariant setup
                 
0e6056cd20 Jean* checkpoint51f_post (2003/10/02)
57c1eda489 Jean* o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6eb9516f3f Dimi* o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
34fdea0d95 Dimi*   of tracer Green's fucntions for ocean inversion project.
                 
0e6056cd20 Jean* checkpoint51f_pre (2003/08/07)
981f32514d Dimi* o Added on-the-fly spatial interpolation capability
                     "USE_EXF_INTERPOLATION" to pkg/exf.
bda7c25f4a Dimi*   - This is a temporary Cartesian-grid hack until
981f32514d Dimi*     the super-duper ESMF coupler becomes available.
bda7c25f4a Dimi*   - See verification/global_with_exf/README for usage example.
                   - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
                     flags and modified pkg/seaice accordingly.
981f32514d Dimi* o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
                     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
                     non-local transport term.
                 
0e6056cd20 Jean* checkpoint51e_post (2003/08/03)
a435e833b1 Mart* o pkg/mom_vecinv:
542c6d36a4 Jean*   - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
                   - add time-ave diagnostic of vorticity advection.
                 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
a435e833b1 Mart* o atmospheric geopotential: - include water vapor effect;
542c6d36a4 Jean*                             - use p^kappa in p* scaling.
c886fcc85e Jean* o land pkg: read initial state from files.
                 o AIM : add stratospheric drag in the upper level
                 
0e6056cd20 Jean* checkpoint51d_post (2003/07/18)
c886fcc85e Jean* o change function ILNBLNK (=> last non-blank char.) to return zero
                   (instead of the string length) when the string. char is empty
8cd26a84aa Jean* o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
06c869d156 Patr* o modif's to restore TAMC compatibility
                   - avoid "_d" constructs in PARAMETER declarations
                   - avoid interrupting lines by comment lines
                 o Use cluster local disks for purely local I/O
                   vs. globally visible disks needed for ctrl stuff
                   (merged from ecco-branch)
                   - new active_file_loc... and mdsio_..._loc routines
                   - affected packages: autodiff, ctrl, grdchk, mdsio
f171be8f2a Alis* 
0e6056cd20 Jean* checkpoint51c_post (2003/07/08)
494ad43bae Patr* o introducing integer flag debugLevel
                   - debLevZero: suppress all output
                   - debLevA: standard
                   - debLevB: equivalent to current debugMode=.TRUE.
                 o introducing pathname variable mdsioLocalDir for mdsio
                   that can be specified at runtime
                   (relevant for cluster I/O to local disk)
                 `
f35a23c575 Patr* >>>checkpoint51b_post
                 adjoint of ptracers
                 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
                 o extended state in checkpoint_lev?, etc.
                 o alternative ctrl/cost with tr1 or ptracer
                 o new comlev1_bibj_ptracers
                 o new ptracers.flow
                 o made ptracers_forcing same as external_forcing_s
                 o added verification for adjoint with ptracers
                   - adm. grdchk fail so far
                   - tlm. grdchk OK
                   - checked tapelev/comlev recomputations: OK
                 <<<checkpoint51b_pre
                 
0e6056cd20 Jean* checkpoint51a_post (2003/06/25)
f04468175c Step* o added code for biogeochemistry package
                   - new pkgs: dic, gchem
                   - new subroutine in ptracers
                 o modify code for biogeo packages
                   - in model/src and pkg/ptracers
                 
0e6056cd20 Jean* checkpoint51 (2003/06/24)
5949b565e2 Patr* o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
                   - autodiff, ctrl, exf, grdchk, seaice
                   kept separate packages
                   - cost, ecco, obcs
f535eb56d5 Patr* o updating verification/internal_wave, verification/lab_sea
                   (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5949b565e2 Patr* 
0e6056cd20 Jean* checkpoint50i_post (2003/06/23)
3cd89c6ea4 Patr* o Preparing next differentiable checkpoint and sync
                   of MAIN vs. ecco-branch
                   - 1st step: this one is differentiable
a435e833b1 Mart*   - 2nd step: next(! not this) checkpoint will have updated packages
3cd89c6ea4 Patr*               from ecco-branch)
                 
0e6056cd20 Jean* checkpoint50h_post (2003/06/20)
8f5c8e08bc Jean* o new package "land": provide surface BC for AIM.
                 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
a435e833b1 Mart* o AIM: use true log-P extrapolation for near surface temp (= as in
568bb87ebb Jean*     F.Molteni paper) ; update aim.5l_cs output.
8aafdaabe9 Alis* o New variable in PARM03 for more flexible pickups
61893791a0 Patr* o somewhat cleaned package initialisation sequence for
                   ctrl/ cost/ ecco/ in packages_... routines
568bb87ebb Jean* 
0e6056cd20 Jean* checkpoint50g_post (2003/05/23)
09510da3bb Dimi* o merged with release1_p17 (pkg/seaice and verification/lab_sea)
                   - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
                   - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
                     made the default because of faster convergence than ADI
                 
0e6056cd20 Jean* checkpoint50f_post (2003/05/23)
5192502418 Patr* o exf totally restructured
                   - replaced all exf_set_ routines by one generic exf_set_gen.F
                     and made sure it's still differentiable
                   - split exf_getffields.F into new exf_bulkformulae.F
                   - exf_inscal_/exf_outscal_ suffixes consistent with field names
                   - updated adjoint/makefile and relevant verif. accordingly
                 
0e6056cd20 Jean* checkpoint50f_pre (2003/05/23)
b8d7339ac7 Jean*  o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
                       + change Evap over land. (update aim.5l_cs output)
f171be8f2a Alis*  o added missing .cvsignores and made uniform across expts
                  o changed configuration of tidal_basin_2d expt
                  o added pkg/debug functions for tracing code in fatal crashes
                  o tidied pkg/monitor to use MONITOR_OPTIONS.h
                  o new fn in pkg/monitor to stop model if solution grows too big
                  o removed lots of single quotes from comments
                 
0e6056cd20 Jean* checkpoint50e_post (2003/05/14)
1a1e1d268a Mart* o make KPP work with PTRACERS
                  - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
                    nearly a copy of kpp_transport_s
a435e833b1 Mart*  - there is no analogue to SurfaceTendencyS, so I have to use
1a1e1d268a Mart*    gPtr(of the surface layer) instead
                 o add a new platform SunFire+mpi (SunFire 15000) to genmake
0e6056cd20 Jean* checkpoint50e_pre (2003/05/13)
1a1e1d268a Mart* 
0e6056cd20 Jean* checkpoint50d_post (2003/05/13)
a435e833b1 Mart* o change kpp output from multiple-record state files to single-record state
3ff61f337e Mart*   files analogous to write_state.F
a435e833b1 Mart* o reduce the output frequency of cg3d-related stuff to the monitor frequency,
                   analogous to the cg2d-related output.
                 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
1a1e1d268a Mart*   so that writing to internal file fn (with length 512) fails.
0e6056cd20 Jean* checkpoint50d_pre (2003/05/12)
dd4e4e2846 Patr* 
0e6056cd20 Jean* checkpoint50c_post (2003/05/12)
36b01f3eb4 Jean* o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
a07df11acd Jean* o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
956742bd08 Jean* o add time-average diagnostic of U*V and vertical diffusive flux for theta.
                 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
                 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
                 
0e6056cd20 Jean* checkpoint50c_pre (2003/04/30)
460cb5f999 Dimi* Merging from release1_p13:
                 o bug fix for pkg/seaice dynamic solver
                 o Added SEAICE_initialHEFF to pkg/seaice
                 
0e6056cd20 Jean* checkpoint50b_post (2003/04/17)
b95ba5a50f Jean* o store u*,v* in gU,V instead of in guNm1,gvNm1
                 o in order to put the momForcing out of the Adams-Bashforth:
                   move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
                   to timestep.F
                 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
                 o re-generate output for highly sensitive test-exp:
                    global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
                 
0e6056cd20 Jean* checkpoint50b_pre (2003/04/17)
3228e22c96 Jean* o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
a435e833b1 Mart* o corrected CPP option mismatch in exf_Bulk... functions for case
5ef1561d49 Patr*   #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
                 
0e6056cd20 Jean* checkpoint50a_post (2003/03/21)
011884106d Patr* o Bug fix for merging between c50 and KPP.
                   ikey was passed from thermodynamics to kpp_calc via
                   common block rather than being recomputed in kpp_calc,
                   in contradiction with new key itdkey.
                   New key ikppkey created, and tamc.h headers updated.
                 
0e6056cd20 Jean* checkpoint50 (2003/03/08)
19c7b39f75 Patr* - 2nd step of merge with ecco-branch:
                   merge changes in ecco-branch back into main trunk
                 - bug fix in find_alpha
                 - more storing in gmredi_calc_tensor.F, kpp_routines.F
                 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
                 - merged some sliced AD support routines
                 
0e6056cd20 Jean* checkpoint49 (2003/03/06)
a2ac993b88 Patr* merged from ecco-branch:
                 o exf:
a435e833b1 Mart*   - Enable initialisation of forcing fields to constant
a2ac993b88 Patr*     (runtime) values.
                   - in exf_getffields.F
                     Reduce i-/j-loop to interior domain, discarding overlaps.
                     That also fixes wrong TAF-key computations for key_1, key_2
                     with bulf formulae.
                   - exf_init.F modify #ifdef for exf_init_evap
                   - exf_getffieldrec.F, ctrl_getrec.F
                     The following INT-usages are not safe:
                       fldsecs  = int(fldsecs/fldperiod)*fldperiod
                       fldcount = int(fldsecs/fldperiod) + 1
                     and were modified.
                 o autodiff: checkpoint_lev...
                   - updated storing for bulk formulae (some arrays were missing)
                   - added state for seaice package
                   - synchronized with main branch
                 o DIVA:
                   Modif.s in
19c7b39f75 Patr*   - the_main_loop.F
                   - the_model_main.F
a2ac993b88 Patr*   and added cost_final_restore.F cost_final_store.F
                   o With these changes, it is possible to fully separate
                     the first forward run to compute the cost function (mdthe_main_loop)
                     and adjoint runs over individual DIVA intervals (adthe_main_loop)
                     into separate model executions.
                     This enables better tuning of DIVA to given queue sizes.
                   o Loss of cost function value in consecutive DIVA runs is
                     fixed by storing to 'costfinal' file.
a435e833b1 Mart*   o Appropriate call of ctrl_unpack/_pack,grdchk_main at
a2ac993b88 Patr*     beginning/end of adjoint integration is accounted for.
                   The current changes apply to TAF-1.4.26.
                   TAF has one remaining bug, requiring one manual change
                   (see MITgcm manual).
                 o cal: synchronized between MAIN and ecco-branch
                 
0e6056cd20 Jean* checkpoint48i_post (2003/03/05)
eae13cfd04 Patr* o Changes to restore differentiability of code w.r.t. previous tag
                   (mostly adding new routines to make list and replacing
                   pressure by totPhiHyd).
                 o Updated and merged grdchk package
                   - has both ADM and TLM checks
                   - works for single- and multi-proc.
                   - output cleaned
                   - worked successfully for parallel DIVA
                 o genmake:
                   - Adding -platform=SP4
                   - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
                 o Modif. for DIVA:
                   ctrl_unpack should not be called in intermediate DIVA interval.
                   (similar thing would apply for active files such as
                   tbar, sbar, psbar, which should not be reinitialised;
                   only relevant for ecco-branch)
                 
0e6056cd20 Jean* checkpoint48h_post (2003/02/28)
c05a259eac Jean* o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
190e1777cb Dimi* o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
                 o Added SEAICE_initialHEFF to pkg/seaice
d0702b49e9 Dimi* o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
190e1777cb Dimi* 
0e6056cd20 Jean* checkpoint48g_post (2003/02/18)
2959c7b521 Jean* --- EOS:
                 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
                   store total Potential in totPhyHyd for diagnostics & EOS.
                 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
                 --- Pressure/geopotential gradient:
                 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
                 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
                   ( changes results of global_ocean_pressure )
                 o NLFS + z-coord.: add eta*Rho' contribution.
                 o accurate phiHyd when using interface-W at the middle between 2 centers
                  ( changes results of ideal_2D_oce )
                 o includes r* 2nd term in potential gradient.
                 
0e6056cd20 Jean* checkpoint48f_post (2003/02/18)
6060ec2938 Dimi* Merging from release1_p12:
                 o Modifications for using pkg/exf with pkg/seaice
                   - improved description of the various forcing configurations
                   - added basic radiation bulk formulae to pkg/exf
                   - units/sign fix for evap computation in exf_getffields.F
                   - updated verification/global_with_exf/results/output.txt
                 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
                   (SBO) core products, including oceanic mass, center-of-mass,
                   angular, and bottom pressure (see pkg/sbo/README.sbo).
                 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
                   to avoid negative values in shallow regions.
                   - updated verification/natl_box/results/output.txt
                   - updated verification/lab_sea/results/output.txt
                 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
                 o Added useSingleCpuIO option (see PARAMS.h).
                 o Updated useSingleCpuIO option in mdsio_writefield.F to
                   work with multi-field files, e.g., for single-file pickup.
                 o pkg/seaice:
                   - bug fix in growth.F: QNET for no shortwave case
                   - added HeffFile for specifying initial sea-ice thickness
                   - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
                 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
                   kpp_transport_t.F, forward_step.F, and the_main_loop.F
                 o pkg/seaice:
                   - adjoint-friendly modifications
                   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
                 
0e6056cd20 Jean* checkpoint48e_post (2003/02/12)
6f90d97ce9 Jean* o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5f7a0a65d1 Jean* o dynamics: change definition of computational domain & adapt mom_fluxform
a435e833b1 Mart*   accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5f7a0a65d1 Jean* o following exp works with Olx=Oly=2 (and pass through checkbounds option):
                     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
bc5ef4cea8 Jean*     exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
a435e833b1 Mart*     global_ocean.90x40x15 global_with_exf global_ocean_pressure
5f7a0a65d1 Jean*     inverted_barometer solid-body.cs-32x32x1
                   (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6f90d97ce9 Jean* 
0e6056cd20 Jean* checkpoint48d_post (2003/02/09)
fa86c7bd0e Jean* o in preparation for r*:
                  a) use pre-computed gradient of hydrostatic potential:
                     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
                  b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
a435e833b1 Mart*     => affects results of glob_oce_pressure (different truncation error)
fa86c7bd0e Jean*   update output.txt of ideal_2D_oce & global_ocean_pressure
                 
0e6056cd20 Jean* checkpoint48d_pre (2003/02/08)
395300a99d Jean* o in preparation for r*:
                   new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
                   pass the 2 comp. of the grad. as arguments to momentum S/R.
a435e833b1 Mart*   but for the moment, only used if it does not change the results.
395300a99d Jean* o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
                 
0e6056cd20 Jean* checkpoint48c_post (2003/02/06)
da25c1b1f0 Patr* Modifications in treatment of initial flux forcing controls
                 to avoid extra storing of flux fields.
                 
0e6056cd20 Jean* checkpoint48c_pre (2003/01/21)
6201ebed0f Alis* o Added tidal_basin_2d experiment (currently 1D!)
a435e833b1 Mart* o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
ed1ae133b9 Jean* 
0e6056cd20 Jean* checkpoint48b_post (2003/01/27)
1bf124dbfd Jean* o r* coordinate added in #ifdef NONLIN_FRSURF block.
                  (modification to pressure gradient not yet implemented)
                 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
                   (for U & V) that are used for vertical advection of momentum.
                 
0e6056cd20 Jean* checkpoint48a_post (2003/01/24)
5c72e2cee7 Jean* o In preparation for r*, use temp. array to compute vertical transport
a435e833b1 Mart*    in flux-form momentum pkg. => change results of few test-exp.
                   Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5c72e2cee7 Jean*                     lab_sea, natl_box & plume_on_slope
                 
0e6056cd20 Jean* checkpoint48 (2003/01/23)
3fa5200144 Jean* o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
                 
0e6056cd20 Jean* checkpoint47j_post (2003/01/21)
d15fa5f8eb Jean* o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
dd4e4e2846 Patr* o moved adexch from forward_step to addummy_in_stepping
                 o added exch in ctrl_map_...
                 o aveFreq.=0. at end of cost_final to avoid overwrite in
                   reverse checkpointing loop
                 o Yet more changes in gmredi:
                   * adgmredi_calc_tensor
                     avoiding all recomputation of gmredi_slope_limit
                   * adgmredi_x/y/rtransport
                     added flag for excessive storing to avoid recomp. of
                     u/v/rtans, dTdx/y/z
                     -> this is not really necessary and very memory-consuming
                   * adgmredi_slope_psi:
                     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
                   * gmredi_slope_limit
                     re-activated full calculation of taperfct for case 'ac02'
                 o updating verification/ adjoints of carbon, global_ocean.90x40x15
d537a7f0b2 Patr* 
0e6056cd20 Jean* checkpoint47i_post (2003/01/13)
a934d97f06 Jean* o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
                 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
                   default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
a435e833b1 Mart* o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
a934d97f06 Jean* o gmredi: fix few bugs.
                 
ba5e34915b Alis* checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
d537a7f0b2 Patr* This will be a good checkpoint to plug into the ecco-branch.
                 o few modif.'s to get latest version adjointed
                   (mainly kick out code in ini_linear_phisurf)
                 o modif's to run adjoint with exactConserv
                 o case GM_BOLUS_ADVEC should be cleaned
                   S/R gmredi_slope_psi should be cleaned
                 o verification/carbon now has exactConserv=.TRUE.
0501ef9fb3 Patr* 
0e6056cd20 Jean* checkpoint47g_post (2003/01/10)
6d8d3f40dd Jean* o time-average AIM output: becomes independent from statvars time-average
                   (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
88844f54ad Patr* o After TAF bug fix:
                   Tested adjoint of gmredi package.
                   Tests were done with checkpoint47 rather than with latest
                   checkpoint47f_post since the latter is broken for the adjoint
                   verification/carbon/ contains both ADM and TLM gradient checks.
                 Here they are, before they get changed/lost/stolen.
                 Mostly modif.'s to fix numerical sensitivities.
                 Gradient checks OK for
                 - GM_taper_scheme:
                   * clipping
                   * ac02
                   * linear
                   * glw91
                   * dm95
                   * ldd97
                 - GMREDI_OPTIONS:
                   * GM_VISBECK_VARIABLE_K
                   * GM_NON_UNITY_DIAGONAL
                   * GM_EXTRA_DIAGONAL
                   * GM_BOLUS_ADVEC
                 in conjunction with data.gmredi parameters to be checked in
                 in a few minutes under verification/carbon/code/
6d8d3f40dd Jean* 
0e6056cd20 Jean* checkpoint47f_post (2002/12/28)
cee16b76ae Dimi* Merging from release1_p10:
                 o modifications for using pkg/exf with pkg/seaice
                   - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
                     and SEAICE_EXTERNAL_FLUXES
                   - pkg/exf CPP options EXF_READ_EVAP and
                     EXF_NO_BULK_COMPUTATIONS
                   - usage examples are Experiments 8 and 9 in
                     verification/lab_sea/README
                   - verification/lab_sea default experiment now uses
                     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
                 
0e6056cd20 Jean* checkpoint47e_post (2002/12/27)
2d0f62a494 Curt* o created a tag prior to creating a branch
                 
0e6056cd20 Jean* checkpoint47d_post (2002/12/16)
a435e833b1 Mart* o fixed bug in the oceanic pressure coordinates code: vertical viscosity
2672305b1d Mart*   at the bottom boundary had an erroneous half slip boundary condition
a435e833b1 Mart* o added bottom drag and no slip boundary condition capabilities to
2672305b1d Mart*   oceanic pressure coordinates code
                 o added new verification experiment global_ocean_pressure, this experiment is
                   also described in the tutorial section of the manual
0e6056cd20 Jean* checkpoint47d_pre (2002/12/16)
2672305b1d Mart* 
0e6056cd20 Jean* checkpoint47c_post (2002/12/16)
03456d021e Curt* o Added a verification experiment for a global cubed-sphere ocean run
                   -  verification/global_ocean.cubed32x32x30
                   -  uses pkg/therm_seaice and pkg/bulk_forcing
                 
4195ef17c2 Jean* o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
                 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
                   when using P-coordinate; only implemented for atmospheric config.
                 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
                   NOTES: requires option NONLIN_FRSURF to be "#define".
                 o update advect_xz/results/output.txt (left from checkpoint44g_post)
                 
0e6056cd20 Jean* checkpoint47b_post (2002/12/05)
baa476eeba Dimi* Merging from release1_p9:
                 o pkg/seaice
                   - removed GOTO's and added taf directives
                   - double precision constants to reduce the g77 (Linux)
                     to F77 (SGI) differences reported in release1_p8
                 o tools/genmake
                   - added SGI options
                 o verification/testscript
                   - updated to that of checkpoint47a_post
                 o verification/global_ocean.90x40x15/input/eedata
                   - modified for SGI f77 compatibility
                 o verification/lab_sea
                   - added description of sea-ice model
                   - added missing matlab routines
                   - added test of thermodynamics parallelization
                 
0e6056cd20 Jean* checkpoint47a_post (2002/11/23)
a435e833b1 Mart* o new pkg: aim_v23
                  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
9a923a4cdc Jean*    for now, keep the same surface forcing as before.
                  - Part-Cell implemented into AIM; check that Heat & Water are conserved
                  - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
                  - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
                 o add diagnostic of surface correction term in monitor output
                 
a435e833b1 Mart* o bulk_force and therm_seaice
c9bad82272 Curt* - Two packages:  bulk_force (Bulk forcing)
                   and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
                 - Earlier integration from Stephaine Dutkiewicz
                   and Patrick Heimbach.
                 - Two ifdef statements for compile time,
                    ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
0ae80337bd Jean* 
0e6056cd20 Jean* checkpoint47 (2002/11/15)
d66d6a3f19 Patr* differentiable version of checkpoint46n_post
                 o bug fix in quasihydrostaticterms
                 o * "clean" adjoint code (in terms of extensive recomputations)
a435e833b1 Mart*     can now be obtained for all GMREDI options (i.e. for
d66d6a3f19 Patr*     - GM_VISBECK_VARIABLE_K
                     - GM_NON_UNITY_DIAGONAL
                     - GM_EXTRA_DIAGONAL
                     - GM_BOLUS_ADVEC )
                   * However, wrong gradient check problem remains unsolved.
                   * New CPP options have been introduced for different
                     tapering schemes
                 o external_fields_load now part of differentiation list
                 o pressure needs multiple storing;
                   would be nice to have store_pressure at beginning or
                   end of forward_step, e.g. by having phiHyd global (5-dim.)
                   (NB: pressure is needed for certain cases in find_rho,
                   which is also invoked through convective_adjustment).
a435e833b1 Mart* o recomputations in find_rho for cases
d66d6a3f19 Patr*  'JMD95'/'UNESCO' or 'MDJWF' are OK.
                 o #define ATMOSPHERIC_LOADING should be differentiable
                 o ini_forcing shifted to begining of initialise_varia
                 o Incorporating QNVS line search routines into MITgcm
                   (this is separate code, and therefore not under pkg)
                   lsopt/, optim/
                 o Updated verification/carbon/
                   - #define GM_VISBECK_VARIABLE_K
a435e833b1 Mart*   - GM_taper_scheme    = 'ldd97'
d66d6a3f19 Patr* 
0e6056cd20 Jean* checkpoint46n_post (2002/11/12)
5553098c72 Patr* Merging from release1_p8:
                 o verification/natl_box:
                   updating new external_fields_load routine
                 o New package: pkg/seaice
                   Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
                   The sea-ice code is based on Hibler (1979-1980).
                   Two sea-ice dynamic solvers, ADI and LSR, are included.
a435e833b1 Mart*   In addition to computing prognostic sea-ice variables and diagnosing
                   the forcing/external data fields that drive the ocean model,
5553098c72 Patr*   SEAICE_MODEL also sets theta to the freezing point under sea-ice.
a435e833b1 Mart*   The implied surface heat flux is then stored in variable
                   surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
                   kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
                   non-local transport term.  Because this call precedes model
                   thermodynamics, temperature under sea-ice may not be "exactly" at
5553098c72 Patr*   the freezing point by the time theta is dumped or time-averaged.
                   N.B.: fairly large differences in accuracy occur across
                         different platforms/compilers; comparison between
a435e833b1 Mart*         g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5553098c72 Patr*         generated output gives:
                    T           S           U           V
                   C D M    c        m  s        m  s        m  s        m  s
                   n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
                   f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
                   g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
                 
                   Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
a435e833b1 Mart* o GAD:
5553098c72 Patr*   - generated new common blocks to account for call of
                     same gad routines with differing traceridentities
                     (needed to modify tracerIdentity indices in GAD.h)
                   - generated separate common blocks for case useCubedSphereExchange
                     (Department of Futurology)
                   - parameter lists to gmredi_?transport: added tracerIdentity
                   - added new key indices to tamc.h
                 o external_fields_load:
                   - added this routine to TAF list
                   - needed to make some common blocks global and additional storing
                     along the same lines as exf package (checkpoint_lev?_directives.h)
                 o exf:
                   updated external forcing package
                   - bug fixes carried over from ecco-branch
                     (missing OBCS_OPTIONS.h in two routines)
                   - enable easy to use "no forcing".
                   - added exf I/O for atmospheric loading
                   - added exf I/O for runoff data
                   - transfered scaling between exf <-> MITgcm to exf namelist
                 o Adding new verification experiment global_with_exf.
                   This verification experiment is almost identical to the
                   global_ocean.90x40x15 experiment, except that it uses
                   the exf (and cal) package instead of the
                   external_fields_load routine (cf README file).
                 
0e6056cd20 Jean* checkpoint46m_post (2002/11/07)
a435e833b1 Mart* o modified testscript to return -- when there are no lines of "%MON" output
775ad00e06 Alis* o added new flag "quasiHydrostatic" for QH mode
                   and new routine quasihydrostaticterms()
c5990018f4 Alis* o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
                   New routine: mom_u_coriolis_nh()
8d87f02f4b Alis* o fixed sign of non-hydrostatic metric terms in u and v equations.
                   Depend on correct sign of gravitySign.
574be91465 Alis* o added work.pc* to .cvsignore in aim directories using ifc
faaa70ed68 Alis* o introduced flag for controllin non-hydrostatic metric terms
a22df31c5b Alis* o removed gravitySign from PARM04
4cc3ac93d0 Alis* o switched to g77/ifc from pgf77 in aim experiments
                 
0e6056cd20 Jean* checkpoint46l_post (2002/11/01)
59e59b79d8 Mart* o made convective adjustment work with pressure coordinates:
                  - changed the direction of k-loop in convective_adjustment.F for the
                    case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
                  - adjusted the reference pressure k-index in convective_adjustment.F
                  - adjusted the convection condition in convect.F (in analogy to
                    calc_ivdc.F)
                  - convective_adjustment no longer computes anything on the halos
                  - removed the warnings about negative salinity from find_rho.F and
                    find_alpha.F; instead the new routine look_for_neg_salinity, called
a435e833b1 Mart*    at the beginning of find_rho, find_alpha, and find_beta, does a
                    check of the entire slice, if CPP-option
59e59b79d8 Mart*    CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
0e6056cd20 Jean* checkpoint46l_pre (2002/10/23)
59e59b79d8 Mart* 
0e6056cd20 Jean* checkpoint46k_post (2002/10/23)
19ec7ca2f5 Mart* o fixed the verification/global_ocean.90x40x15 experiment:
                  - new bathymetry (the world according to A., JMC, and M.)
                  - new initial fields and forcing fields (*.bin files)
                  - new POLY3.COEFFS (for the next release one should switch to a full
                    equation of state: JMD95P or MDJWF)
                  - fixed several errors and redundancies in the data file
                  - experiment uses looped cells
                  - added matlab directory with diagnostic scripts for plotting of output
                 
1b947e4f16 Jean* o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
                  - read AIM physics parameters from a file (data.aimphys)
                  - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
                 
0e6056cd20 Jean* checkpoint46j_post (2002/10/07)
3d1716969e Jean* o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
                 o move wVel computation at the end of the time step, in S/R integr_continuity
                 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
                 o update timeave pkg for wVel diagnostic.
0e6056cd20 Jean* checkpoint46j_pre (2002/09/27)
3d1716969e Jean* 
0e6056cd20 Jean* checkpoint46i_post (2002/09/25)
e16ef9be6a Jean* o Clean up AIM package (and keep the results unchanged):
a435e833b1 Mart*   include CPP_OPTION and use IMPLICT NONE in all routines ;
e16ef9be6a Jean*   declare all the variables _RL ; use _d 0 for all numerical constants.
                   use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
e305438401 Mart* 
0e6056cd20 Jean* checkpoint46h_post (2002/09/25)
a435e833b1 Mart* o cleaned up the use of rhoNil and rhoConst.
                   - rhoNil should only appear in the LINEAR equation of state, everywhere
e305438401 Mart*     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
                     and the dynamical equations are all divided by rhoConst
a435e833b1 Mart* o introduced new parameter rhoConstFresh, a reference density of fresh
e305438401 Mart*   water, to remove the fresh water flux's dependence on rhoNil. The default
                   value is 999.8 kg/m^3
                 o cleanup up external_forcing.F and external_forcing_surf.F
                   - can now be used by both OCEANIC and OCEANICP
0e6056cd20 Jean* checkpoint46h_pre (2002/09/18)
e305438401 Mart* 
                  Added code to convert surface volume flux (fresh water) into
                  a mass flux when using P coordinates in the ocean (OCEANICP).
                  Note: It assumes you have set rho0=rhoConst=density of fresh water.
                 
0e6056cd20 Jean* checkpoint46g_post (2002/09/18)
60c223928f Mart* o Include a new diagnostic variable phiHydLow for the ocean model
                   - in z-coordinates, it is the bottom pressure anomaly
                   - in p-coordinates, it is the sea surface elevation
                   - in both cases, these variable have global drift, reflecting the mass
                     drift in z-coordinates and the volume drift in p-coordinates
                   - included time averaging for phiHydLow, be aware of the drift!
a435e833b1 Mart* o depth-dependent computation of Bo_surf for pressure coordinates
60c223928f Mart*   in the ocean (buoyancyRelation='OCEANICP')
a435e833b1 Mart*   - requires a new routine (FIND_RHO_SCALAR) to compute density with only
                     Theta, Salinity, and Pressure in the parameter list. This routine is
60c223928f Mart*     presently contained in find_rho.F. This routine does not give the
                     correct density for 'POLY3', which would be a z-dependent reference
                     density.
                 o cleaned up find_rho
                   - removed obsolete 'eqn' from the parameter list.
                 o added two new verification experiments: gop and goz
                   (4x4 degree global ocean, 15 layers in pressure and height coordinates)
0e6056cd20 Jean* checkpoint46g_pre (2002/09/16)
60c223928f Mart* 
0e6056cd20 Jean* checkpoint46f_post (2002/09/16)
77d659325b Patr* o Enable tangent linear (forward mode) gradient checks:
                   - extended active file handling to g_... files
                   - added TANGENT_SIMULATION to theSimulationMode
                   - extended grdchk package accordingly
                 o added tangent linear setup in verification/carbon/code_ftl
                 o added adjoint setup in verification/front_relax/code_ad
                 
0e6056cd20 Jean* checkpoint46e_post (2002/09/05)
31a5949e20 Mart* o Added new equation of state -> MDJWF
                   - EOS of McDougall et al., 2002, JAOT, submitted
                   - caveat: the equation of state is only valid for a smaller (more
                     realistic?) range of values than JMD95P/Z and UNESCO
                   - added masks to the calculation of pressure in store_pressure
a435e833b1 Mart*   - added more check values for density in check_eos (ini_eos.F), some of
31a5949e20 Mart*     the old check values are out of the range of the MDJWF-eos, so don't
a435e833b1 Mart*     expect perfect matches for those
0e6056cd20 Jean* checkpoint46e_pre (2002/08/19)
31a5949e20 Mart* 
0e6056cd20 Jean* checkpoint46d_post (2002/08/19)
9b1fb10894 Mart* o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
a435e833b1 Mart*   'OCEANICP', also initialised field pressure correctly in ini_eos in the
                   case of pressure coordinates. eosType='JMD95Z' in
9b1fb10894 Mart*   combination with buoyancyRelation='OCEANICP' now causes an error.
                 o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
                   in find_alpha/beta.
0e6056cd20 Jean* checkpoint46d_pre (2002/08/15)
9b1fb10894 Mart* 
                 o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
a435e833b1 Mart*   so that JMD95Z and JMD95P give approptiate static stability in find_rho.
9b1fb10894 Mart* 
0e6056cd20 Jean* checkpoint46c_post (2002/08/15)
9e5f2093d3 Alis* o Changes necessary for ocean in p-coordinates
                  -  Added new buoyancy relation = 'OCEANICP'
                  -  Added new parameters = gravitySign (this used to be contained inside
                     the factor dRdZ which I added when we first switched to R coordinates).
                  X GM/Redi is not compatible (yet)
                  X bottom drag and no-slip need to be debugged.
0e6056cd20 Jean* checkpoint46c_pre (2002/08/07)
9e5f2093d3 Alis* 
0e6056cd20 Jean* checkpoint46b_post (2002/08/07)
a37a13034c Mart* o Added new equation of state -> JMD95Z and JMD95P
31a5949e20 Mart*   - EOS of Jackett and McDougall, 1995, JAOT
a37a13034c Mart*   - moved all EOS parameters into EOS.h
                   - new routines ini_eos.F, store_pressure.F
a435e833b1 Mart* o Added UNESCO EOS, but not recommended because it requires
a37a13034c Mart*   in-situ temperature (see JMD95)
                 o Modified formatting for knudsen2.f in utils/knudsen2 and added
                   unesco.f to be used with POLY3
0e6056cd20 Jean* checkpoint46b_pre (2002/07/31)
a37a13034c Mart* 
0e6056cd20 Jean* checkpoint46a_post (2002/07/31)
395b093796 Mart* o Added (atmospheric) pressure loading
                   - new field in FFIELDS.h, etc...
                   - new cpp flag ATMOSPHERIC_LOADING
                 o Changed hFacC to _hFacC in calc_phi_hyd.F
                 o Added SHORTWAVE_HEATING to some files for consistency
0e6056cd20 Jean* checkpoint46a_pre (2002/07/13)
395b093796 Mart* 
0e6056cd20 Jean* checkpoint46 (2002/07/13)
0501ef9fb3 Patr* further merges from release1_p5
                 o new ctrl package
                   - adopted from ECCO environment to enable optimization
                   - added Eliassen Palm fluxes to controls
                 o added Eliassen Palm flux controls to gradient check package
                 o cost package
                   - Compatible with new ctrl package
                   - added Eliassen Palm cost hooks
                   - modif's of existing cost functions
                 o Adjoint-related bug fixes in kpp:
                   - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
                   - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
                 o autodiff package
                   - flow directives:
                     + new for S/R do_the_model_io
                     + enhanced for S/R checkpoint
                     + new gmredi.flow
                   - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
                     disable adcommon.h/g_common.h by default.
                   - fixed problem for adjoint of global_max
                 o modified verification/carbon/
                 o New setup for adjoint of global_ocean
                 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
                 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
                 o incorporated hooks for sponge layer code (external_forcing.F)
                 
0e6056cd20 Jean* checkpoint45d_post (2002/07/12)
9d1e859170 Jean* o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
fe84d1c123 Jean* o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
                   (affects plume_on_slope "cg2d" output)
9d1e859170 Jean* o add new parameter deltaTfreesurf for free-surface time stepping
a435e833b1 Mart* o exchange gT,gS when using staggerTimeStep & GM & Oly<4
40a013c787 Jean* o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
5a6e38b5cb Jean* o change phiMin in exp1 (to agree with documentation)
a435e833b1 Mart* o add new flags:
5a6e38b5cb Jean*  - T,S forcing inside/outside Adams-Bashforth
                  - turn off temp,salt advection and/or forcing
                  - for each tracer, define internal flag for multiDimAdvection & A-B
                 o monitor: change definition of KE to check conservation of Energy
fda4da40f3 Jean* 
0e6056cd20 Jean* checkpoint45c_post (2002/05/30)
cda7963c0f Patr* o Removed f90 comments ("!")
                 o Modified initialisations to enable exf package for MITgcm
                   (without invoking ECCO_PACKAGE).
                 o modifications to gradient check package (Martin Losch)
                   - enable centered differences
                   - modified format of standard output
                 
0e6056cd20 Jean* checkpoint45b_post (2002/05/30)
778263fdd2 Patr* o cleaned exchange calls in cg2d
                 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
                 o included CPP option SINGLE_LAYER_MODE in thermodynamics
                   to configure barotropic setup (Martin Losch)
                 o moved some initialisations within bi,bj loop in dynamics
                   (TAF flow dependency)
                 o in initialise_varia, moved call packages_init_variables
                   before convective_adjustment_init
                   (corresponding adjustment of TAF tape initialisation).
                 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
                 
0e6056cd20 Jean* checkpoint45a_post (2002/05/01)
23b8953dcb Jean* o compute Rho over the whole domain (extend iMin,jMin indices)
                 o specific exchange for X-slice domain (case Ny=1)
58071f7ded Jean* o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
                 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
                 
f2f05cab96 Patr* checkpoint44h_post = checkpoint45
                 o Fix to restore differentiability:
                   place at which packages_init_variables is called in
                   initialise_varia is crucial for reverse control flow.
                 o modifications in GMRedi to enable stable adjoint
                   (corresponding modif's in thermodynamics, dynamics)
                 o added missing hook for sponge layer code in external_forcing
                 o modified test cost functions
                 o storing in gad_advection (plus removal of write(0,*)!
                 o missing headers TR1.h added in convective_adjustment routines
                 o errorMessageUnit set non-equal zero in eeboot
                   (conflict on some platforms, e.g. IBM SP3)
                 o modified carbon verif.
                 
0e6056cd20 Jean* checkpoint44h_pre (2002/03/14)
e5968d5db8 Jean* o vertical grid option: allow to put the Interface at the middle between
                   2 cell-centers ; replace delZ in pkg/kpp by drF.
3f61bba06d Jean* o GM Advective form: Tracers are advected using the residual transport (=
                   Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
                 
0e6056cd20 Jean* checkpoint44g_post (2002/03/05)
a435e833b1 Mart* o fix surface correction term in multiDimAdvection (affects plume_on_slope
d459353a4c Jean*   results) ; ifdef missing in thermodynamics.F
                 
5c43c390b6 Alis* checkpoint44f_pre,checkpoint44f_post
                 o added PTRACERS package
                   This allows an arbitrary number of passive tracers to be integrated
                   forward simultaneously with the dynamicaly model.
                   + Implemented so far:
                     - basic forward algorithm (time-stepping, advection, diffusion, convection)
                     - I/O and checkpointing
                     - GM/Redi  *but*  using the GM/Redi coefficient of Salt
                   + Not implemented so far:
                     - KPP
                     - OBCS
                   + No specific example supplied (yet) but global_ocean.90x40x15 has the
                     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
                     line in data.pkg.
                   + This package is disabled by default since it increases storage.
                 
                 
658a1753bb Alis* o testscript: added -cleanup option
f4ba6d3695 Jean* o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
                              b) enable to filter 2D fields.
d427b861ca Jean* 
3e6bf4af46 Alis* checkpoint44e_pre,post
                 o re-wrote convective adjustment to use pre-calculated weights
                   Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
                   Adds:    model/src/convective_weights.F, convectively_mixtracer.F
                   Original calls to convect() still in place.
                 
2014c6d62b Patr* chkpt44d_pre,post
                 o added missing EXCLUDE_MONITOR flags
                 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
                   (incompatible typ in MIN/MAX expressions caused problems
                   on IBM SP3)
                 o in genmake added variable MAKEDEPEND
                   plus resetting for case SunOS
                 o added timer_stats.c routine for IBM SP3
                 o removed variables in dynamics
                 !!! I forgot to create tag chkpt44d_pre !!!
                 !!! But chkpt44d_pre = chkpt44c_post    !!!
                 
f4ba6d3695 Jean* o real fresh water flux implemented with non-linear free-surface.
                 
d645283517 Jean* chkpt44c_pre,post
a435e833b1 Mart* o few fix (mask in shap_s2, EmPmR in external_field_load,
                   USE_NATURAL_BCS in solve_for_P);
d645283517 Jean* o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
                 
de416ebcde Patr* checkpoint44b_pre/_post
                 o merge of relevant stuff from the ecco-branch:
                   - genmake: removed $S64 overwrite for case SunOS
                   - pkg/exf: update and corrections for field swapping and obcs
                   - pkg/ecco: parameter lists for the_model_main, the_main_loop
                               harmonized between ECCO and MITgcm
                   - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
                                   updated checkpointing_lev... lists for obcs
                   - model/src: minor changes in forward_step, plot_field
                                added directive for divided adjoint in the_main_loop
                   - pkg/mdsio: added mdsio_gl_slice
                 
fda4da40f3 Jean* o check parameters & config (chkpt44a_pre,post)
5fc9e00fa1 Jean* o OBC and NonLin_FrSurf.
                 
0e6056cd20 Jean* checkpoint44 (2002/01/18)
beeff87535 Jean* o fix bug in mom_vi_del2uv
5fc9e00fa1 Jean* o select when filters are applied ; add options to zonal_filter (data.zonfilt)
                 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
                 o update AIM experiments (NCEP input files)
                 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
b07345cdda Patr* o added some stuff for AD
84a1eca0f1 Patr* 
0e6056cd20 Jean* checkpoint43 (2001/09/28)
7205c731d1 Alis* o added two new advection tests
                 o added global 4x4 degree ocean test
                 o added test of H&S94 with free surface on cube
                 o some final mods for gradient check, adjoint,...
                 
0e6056cd20 Jean* checkpoint42 (2001/09/27)
9620337c26 Patr*   Fixed AD-related problems:
                 o Store directives up-to-date with re-arranged Adams-Bashforth
                   (mainly thermodynamics.F)
                 o New store directives for multi-dim. advection schemes
                   * new CPP flag ALLOW_MULTI_DIM_ADVECTION
                   * new common block and key passkey
                   (mainly gad_advection.F)
                 o Modified store directives for split of dynamics/thermodynamics
                   for the case ALLOW_KPP
                 o Cleaned argument list for timestep_tracer.F
                 
0e6056cd20 Jean* checkpoint41 (2001/09/27)
aafb52f44c Alis* o re-formatted/added comments in prologues of key subroutines
                   to work with protex
                 
0e6056cd20 Jean* checkpoint40 (2001/09/27)
07eb89f7e7 Alis* o moved calc_gs, calc_gt and calc_tr1 back to model/src
                 o added FLT (floats) package from Arne along with demo. experiment
                 o re-arranged Adams-Bashforth scheme for tracers to allow easier
                   implementation of forward-in-time forcing terms
                 o more mods for non-linear free-surface including new variable
                 o modified multi-dim method to work on cube
                 o bug fix in KPP (from DM)
                 
0e6056cd20 Jean* checkpoint40pre9 (2001/09/27)
76bfa80e3f Alis* o added DST advection schemes
                 o fix MPI bug on SGI's
                 o modifications for non-linear free-surface
                 o fixed conditionals for fixed flow/passive tracer only mode
                 o added tension/strain form of stress tensor
                 o changes to commenting of arguments for TAF/TAMC
                 o added/updated many matlab scripts
07eb89f7e7 Alis* o added multi-dimensional advection method for tracers
a435e833b1 Mart* 
0e6056cd20 Jean* checkpoint40pre8 (2001/09/05)
c710cbecfb Patr* o new package rw/
                   Added method for dumping intermediate local arrays:
                   mdsio_writetile - same as mdsio_writefield except works from inside
                                     bi,bj loop
                   mdsio_writelocal - same as mdsio_writetile except works for local
                                      arrays
                   write_local_r? - higher-level wrapper for mdsio_writelocal
                   Controlled by diagFreq. Defaults to zero (ie. no dumps)
                   Example given at end of mom_vecinv.F that dumps some local arrays.
                 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
                   control flux-form versus vector invariant code.
                   Switch is runtime flag vectorInvariantMomentum (defaults to false)
                   or genmake -DISABLE ...
                 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
                   (additional storing is now needed for case vecinv;
                   currently nothing implemented to switch this storing off
                   in case fluxform is used since no CPP flag available).
                 
0e6056cd20 Jean* checkpoint40pre7 (2001/08/14)
11252a3870 Patr* o bug fix in dynamics.F
                   calc_viscosity called before k=1,Nr loop.
                 o added some #ifdef's ALLOW_PASSIVE_TRACER
                 o cleaned initialisations in ctrl_map_ini
                   related to TAF
                 
0e6056cd20 Jean* checkpoint40pre6 (2001/08/13)
b2d3fccd49 Patr* o split dynamics into thermodynamics & dynamics
                 o corresponding split of calc_diffusivity into
                   calc_diffusivity, calc_viscosity
                   (kpp_calc_diff, kpp_calc_visc).
                 o Added diffkr, kapgm to control variables
                 o bug fix in gmredi_slope_limit for ldd97
                 
0e6056cd20 Jean* checkpoint40pre5 (2001/07/31)
2277c012d1 Alis* o proper initialization of Adams-Bashforth time stepping
                   + uses forward step for very first step of model (iter=0)
                 o re-generated *all* output since almost all output is modified by this
                   change (sorry but we've been putting this one off for about 2 years)
                   + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
                     *not* regenerated since they are already out of date and I don't
                     want to create the impression that they are suddenly working.
                 o removed KAP stuff for DEC's
                 o modified/added many .cvsignore files in */code and */input
                 o added new expt "solid-body.cs-32x32x1"
                   + this uses an alternative form of ini_curvilinear_grid.F which
                     is not necessarily any better than the current one...
                 
0e6056cd20 Jean* checkpoint40pre4 (2001/07/30)
84a1eca0f1 Patr* o added re-initialisations of utrans,vtrans,rtrans in
                   calc_common_factors which are crucial for TAF.
                 o extended iMin,jMin range for calc_common_factors,
                   calc_diffusivity
                 o added option ALLOW_PASSIVE_TRACER
                 o a few minor updates and fixes
                 
0e6056cd20 Jean* checkpoint40pre3 (2001/07/13)
8970237877 Patr* o created calc_gtr1.F for gad package
                 o split the_main_loop and re-introduced forward_step
                 o some recomputations of nIter0 for TAMC
                 
0e6056cd20 Jean* checkpoint40pre2 (2001/07/13)
12b269a63b Patr* o Updated to latest branch of AJA, JMC
                 o Added gradient check package
                 o Added routines for passive tracer handling
                 o Added carbon sequestration sensitivity experiment
                 
0e6056cd20 Jean* checkpoint39 (2001/05/14)
0a8108926c Patr*  o Modifications and fixes to support TAMC
                    (mainly missing or wrong directives)
                  o Corrected common blocks when fooling TAMC to produce adjoint I/O
                    in addummy_in_stepping
                  o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
                  o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
                  o Included following packages:
                    cal: calendar
                    exf: external forcing
                    ecco: essential routines to control use of cal, exf
                          (NB: this is not the full ECCO environment)
160e0619c9 Patr*  o disabled some packages by default in genmake
0a8108926c Patr* 
0e6056cd20 Jean* checkpoint38 (2001/04/10)
2cfc9d59a2 Patr*  o see notes_c37_adj.txt
                  o corrected wrong layer index in external_forcing_t
                  o replaced the_main_loop/forward_step by the_main_loop
                  o removed forceoutput from write_state
                    (replaced criteria for initial/final state)
                  o added runtime flag for pre-C35 pickups: usePickupBeforeC35
b7a12fbe29 Chri* 
0e6056cd20 Jean* checkpoint37 (2001/03/13)
2a60a6d948 Jean*  o mdsio.F routine split and packaged in pkg/mdsio
                    (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
                     used unless genmake -disable=mdsio)
                  o allow a more precise surface-geopotential gradient for the atmosphere
                    taking into account the change in space of Alpha (=1/rho) at the surface.
                  o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
                    (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
                  o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
                    Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
                    [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
                  o Time-Average diagnostics defined as a pseudo package "timeave".
                  o pickup files : old pickup (before c35) did not work with new code (c35
                    and after) unless activating 2 commented lines in initialise-varia.
                  o Non-Hydrostatic pickup file Pb fixed.
a435e833b1 Mart*  o bug with Rigid-lid version (since c35) fixed.
2a60a6d948 Jean* 
0e6056cd20 Jean* checkpoint36 (2001/02/20)
2a60a6d948 Jean*  o implement Crank-Nickelson barotropic time-stepping
3d3ffaaedb Jean*  o recover Time-Average diagnostics
a435e833b1 Mart*  o fix Pb in checkpoint (PR#19)
3d3ffaaedb Jean*  o AIM become a standard package ; clean unused CPP_kees
                 
0e6056cd20 Jean* checkpoint35 (2001/02/08)
47b446e27e Jean*  o subtantial rewrite of dynamics.f
                  o allows staggered time-stepping
                  o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
                  o added bottom drag (linear + quadratic)
                 
0e6056cd20 Jean* checkpoint34 (2001/01/30)
ea8b6560ce Patr*  o Modified exchange routines for correct reverse simulation.
                  o Added verification output to comply with bug fix in impldiff.F
                    as of c33 (exp2, natl_box).
                  o Corrected store directives in dynamics.F
                  o Corrected array boundaries in impldiff.F
                  o Corrected array dimensions in gmredi.
                    Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
c3ddfd9c4c Patr*  o Added routine GLOBAL_SUM_INT to global_sum.F
ea8b6560ce Patr*  o Added mdsio_gl.F for ECCO purposes.
                 
0e6056cd20 Jean* checkpoint33 (2000/11/30)
7a9ddade78 Alis*  o Fixed bug in lower BC in impldiff.F
                  o Fixed confusion about units of forcing arrays in FFIELDS.h
                    namely Fu,Fv,Qnet,Qsw,EmPmR:
                    - Removed verification/natl_box/code/external_fields_scale.F
                      (did not differ from that in model/src)
                    - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
                      (see FFIELDS.h for description)
                    - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
                      kpp_calc.F and kpp_transport_t.F
                    - Removed model/src/external_fields_scale.F and calls to it
                    - verification/natl_box uses flux data with "atmospheric" sign so
                      a special version of external_fields_load.F is used to
                      change the data as it's read in. This way, the arrays
                      have the right units and signs at all times tha a user could
                      possibly use them.
                  o Corrected genmake to delete a temporary file during configuration
                 
0e6056cd20 Jean* checkpoint32 (2000/11/13)
cfb3cd1ea2 Patr*  o Scaling of forcing fields moved from external_forcing.F to
                    external_fields_scale.F, called directly after loading fields.
                  o Surface relaxation terms added to surface tendency fields in
                    extra subroutine.
                  o impldiff.F changed to avoid storing by TAMC of huge intermediate
                    fields.
                  o Changes in GMRedi to comply with packaging structure.
                  o Modifications and bug fixes in KPP package.
                  o Verification experiment for KPP added (verification/nat_box/)
                 
0e6056cd20 Jean* checkpoint31 (2000/09/11)
dde6192d54 Patr*  o Packages interface brought in line with defined standard
                    -> new routines packages_...F
                    -> changes in initialise_fixed.F, initialise_varia.F
                    -> enables initialisation interface for ECCO package
                  o Rescaling of external forcing fields immediately after read
a435e833b1 Mart*    (removed from external_forcing.F)
dde6192d54 Patr*    -> new: surface_fields_scale.F
                    -> affects ini_foorcing.F, external_fields_load.F
                  o Computation of surface tendencies before tendency updates.
                    -> new: external_forcing_surf.F
                  o Change of variable names useGMRedi, useKPP, useECCO
                  o Further changes in dynamics.F, impldiff.F for TAMC
                  o Tested for experiments 0, 2, 4.
                    - not yet tested for GMRedi.
                    - not yet tested for KPP.
                 
0e6056cd20 Jean* checkpoint30 (2000/07/13)
7eedb26c3d Alis*  o Updates for OBCs
                  o New experiment for test OBCs (internal_wave)
                  o New output.txt in verification/exp4/results/
                  o Updates for KPP: calculation of viscosity corrected, new variables
                    kpp_dumpFreq and kpp_taveFreq
                  o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
                    and entry for T90 in genmake
                 
0e6056cd20 Jean* checkpoint29 (2000/06/21)
c53ad8dc62 Alis*  o packaged KPP and GM/Redi
                 
0e6056cd20 Jean* checkpoint28 (2000/06/09)
56096ca40a Patr*  o Corrected initialization of hFacMin for difference vertical coordinates
                  o Modified calculation of partial cell thickness to more robust algorithm
                  o config_summary.F: replaced write_1D_... by write_0D_...
                    read_write.F: added subroutines write_0D_...
                  o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
                    included some initialisations required for TAMC.
a435e833b1 Mart*  o routine calc_isoslopes: modified sqrt computation to make it
56096ca40a Patr*    differentiable for zero argument.
                  o routines dynamics, impldiff:
                    included store directives and tape key computations required for TAMC.
                  o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
                 
0e6056cd20 Jean* checkpoint27 (2000/04/10)
5b679adde0 Alis*  o fixed calc_isoslopes() to so that cancellation of terms in tensor
                    formulation works properly with variable resolution.
                  o restructured the calling tree between the_model_main() and dynamics()
                  o split initialise() into initialise_fixed() and initialise_varia()
                  o introduced initialization file pSurfInitFile for free surface (cg2d_x)
                    in new routine ini_psurf()
                 
0e6056cd20 Jean* checkpoint26 (2000/04/05)
ab1673a65c Alis*  o moved some #ifdef in optional routines to encompass everything
                    except the argument declarations. This was using up some memory.
                  o fixed macros like _ADT to work with both versions of Linux cpp
                  o cleaned up some unused and uninitialized variables
                    (helps when debugging with strict compile options)
                  o split up CPP_EEOPTIONS.h into options and macros
                    (macros are now in eesupp/inc/CPP_EEMACROS.h)
                  o patch for 2 processor JAM mode
                 
0e6056cd20 Jean* checkpoint25 (2000/03/15)
c19cdd9408 Alis*  o updates for OBCs and NH
                  o dramatically reduced memory usage
                  o added "JAM" routines for use on Artic network
                  o parameterization of convection by implicit vertical diffusion
                  o added a diagnostic of convective index
                  o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
                    (this is was partly for OBCs and NH but also in anticipation of
                     an explicit free-surface option)
                  o initial state input files for U and V
                 
0e6056cd20 Jean* checkpoint24 (1999/08/02)
090b7007c7 Alis*  o Removed some spurious "REAL"s
                  o Updated KPP to latest version from JPL
                  o Added a COS(latitude) in horizontal viscosity
                 
0e6056cd20 Jean* checkpoint23 (1999/05/26)
8f6e5ef29b Alis*  o Added del^4 diffusion for salt and temperature
                  o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
                 
0e6056cd20 Jean* checkpoint22 (1999/05/18)
b3d4b567f6 Alis*  o Made many small changes: implicit none, format(i5), etc...
                  o Introduced KPP mixing scheme (compiles and runs but *not* tested)
                 
0e6056cd20 Jean* checkpoint21 (1999/05/18)
dccdad8bbd Alis*  o Introduced new I/O package that supports direct-access records (mdsio.F)
                  o Split-up mid-level I/O routines
                  o Updated input data for experiments 0,1,2,4 and 5
                  o Finally removed the genmake.* scripts (everyone seems happy with genmake)
                 
0e6056cd20 Jean* checkpoint20 (1999/03/22)
e92aabed24 Alis*  o Tidied up open-boundaries some more
                  o Added non-hydrostatic code
                  o Fixed some input data
                  o Modified MPI start-up to work in "coupled" context.
                 
0e6056cd20 Jean* checkpoint19 (1998/12/15)
337ad8328b Alis*  o Tidied up directory structure for verification experiments.
                  o Added new code for open boundaries.
                  o Corrected advective terms near boundaries.
                  o Added CPP flag for "old UV" geometry and corrected spherical geometry.
                  o Implemented free-slip/no-slip BCs and del^4 dissipation.
e92aabed24 Alis*  o Split default parameters out of ini_parms.F into set_defaults.F.
337ad8328b Alis* 
0e6056cd20 Jean* checkpoint18 (1998/11/30)
a435e833b1 Mart*  o Further changes for optional code generation with
632baf6c85 Chri*    CPP - ugh!
                 
0e6056cd20 Jean* checkpoint17 (1998/11/03)
6d71ac9cce Chri*  o Beginning to incorporating modularity
                    for supporting atmos. and ocean configs.
                  o Small changes for TAMC complinace
                  o New ultra simple test case. Barotropic box
                    configuration "exp0".
                 
0e6056cd20 Jean* checkpoint16 (1998/10/28)
a435e833b1 Mart*  o Minor changes to exchange routines to support
8c88443df3 Chri*    accumulation in reverse mode. Adjoint of an
                    assignment is an addition.
a435e833b1 Mart*  o Changes to support compilation by TAMC (LR(1)
8c88443df3 Chri*    syntax) and by g77 under Linux ( 72 character
                    limit ).
                 
0e6056cd20 Jean* checkpoint15 (1998/09/29)
048ce7bdb7 Chri*  Rewrote exchange routines to allow
                  o General tile <-> tile connectivity.
                  o TAMC reverse mode flag ( is this really needed? )
                  o Variable width overlap and exchange region widths.
a435e833b1 Mart*  o Hooks for sharing data via DMA, Arctic, Memory Channel,
                    shmput/shmget, VIA, SYSV shmem and every other cool
048ce7bdb7 Chri*    communication method.
                 
0e6056cd20 Jean* checkpoint14 (1998/09/09)
e83f632bdc Chri*  Consistent isomorphism chages made. These allow dynamical core
                  to support both pressure and meters as a vertical coordinate.
                 
0e6056cd20 Jean* checkpoint13 (1998/07/17)
b472be50f6 Chri*  Release which corrects global_max problem and a couple
                  of KGM time-averaging diagnostic errors. Also contains
                  a double-gyre experiment setup as well as the baseline
                  4 degree global template. The double gyre template is
                  organised to allow it to be applied automatically to
                  the baseline configuration.
                 
6b85e5319c Alis* branch-point-rdot
                  A few tidy-ups have been made bt the real point of this
                  check-point (excuse the pun) is to allow a branch to be
                  made for the purposes of adding the rDot alterations.
                  I don't want to commit the rDot to the main-trunk until
                  we've actually tested it...
                 
0e6056cd20 Jean* checkpoint12 (1998/07/08)
713eeb0b71 Chri*  Tidy up and added generic genmake script (formerly
a435e833b1 Mart*  configure script).
713eeb0b71 Chri*  Released to testers.
                 
0e6056cd20 Jean* checkpoint11 (1998/07/02)
8e14856263 Alis*  Re-arranged initialise() and introduced ini_vertical_grid()
                  and ini_masks_etc().
                 
0e6056cd20 Jean* checkpoint10 (1998/07/01)
bef276faee Alis*  Introduced the configure script.
                  Separated out the diags package.
                  Added template for writing time-averages of tile/intermediate quantities.
                  Updated SIZE.h in exp2 and made the data big-endian.
                 
0e6056cd20 Jean* checkpoint9 (1998/06/22)
455e14887b Alis*  MPI fix. Filename changes (meta/data). salbin*y stuff.
                  General tidy-up.
                  SST.bin SSS.bin added to verification/exp2
                 
0e6056cd20 Jean* checkpoint8 (1998/06/22)
81be42c716 Alis*  Inludes time-dependant forcing and time-averaging.
                  Works at 4x4 and 2.8125x2.8125 global
                 
                 checkpoint7-4degree-ref
                  Branch from checkpoint7. Released for application to
                  global modeling and general modeling - process studies, regional
a435e833b1 Mart*  model etc..
81be42c716 Alis*  Configured for verification/exp2 - 4 degree global, two process.
                 
0e6056cd20 Jean* checkpoint7 (1998/06/15)
42bd47f06f Chri*  Created by cnh
a435e833b1 Mart*  Simple 4 degree global simulation
42bd47f06f Chri*  configuration.
a435e833b1 Mart*  Includes climatological wind,
42bd47f06f Chri*  hydrography, bathymetry etc
                  Does not include Heat Flux and E-P
                 
0e6056cd20 Jean* checkpoint6 (1998/06/08)
a82990e8c1 Chri*  Created by cnh
a435e833b1 Mart*  merged checkpoint5 with CD and
                  spherical polar code.
a82990e8c1 Chri*  Still some problems with GM Redi
                  abd full topography.
                 
0e6056cd20 Jean* checkpoint5 (1998/06/08)
41a4b13446 Chri*  Created by AJA
                  contains updates to GM Redi
                  and reordered timestepping loop
                  for Implicit Diffusion.
                 
0e6056cd20 Jean* checkpoint4 (1998/05/30)
b7a12fbe29 Chri*  Created by cnh
                  Contains memory saving macros ( _rdxc etc..) for when
                  grid variations are limited.
                  Contains polynomial coeffs for EOS and knudsen program
                  for generation.
                 
0e6056cd20 Jean* checkpoint3 (1998/05/26)
addde852ed Chri*  Created by cnh
                  Added extra flags for runtime options
                  Added this file
                  Added implicit free-surface
                  Added pre-conditioner
                  Put compare01 into repository ( compare01/... )
                  Put data and eedata into repository ( verification/exp1 )
                 
                 checkpoint2
                  Created by AJA
                  Added GM/Redi
                 
                 checkpoint1
                  Created by AJA
                  Restructured kloop in dynamics.F
                  Added non-linear EOS
                 
b7a12fbe29 Chri* baseline
                  Original checked in code