Warning, /doc/tag-index is written in an unsupported language. File is not indexed.
view on githubraw file Latest commit c1b8648b on 2026-07-23 18:05:57 UTC
addde852ed Chri*0001 Notes on tags used in MITgcmUV
0002 ==============================
5dda98cf07 Jean*0003
c1b8648b4c Jean*0004 o verification:
0005 - remove all OpenAD test dir and files (code_oad, input_oad*, output_oadm.*)
0006 and update docs in few places.
ee5aaa9a62 dngo*0007 o pkg/streamice:
0008 - fix Tapenade adjoint for simple SOLVE_FP use (same fix as for OpenAD)
0009 and update halfpipe_streamice Tap adj & tlm ref. output.
ca3a717dfb Jean*0010 o pkg/seaice:
0011 - comment out debug print in seaice_cost_test.F and reduce overlap size
0012 (from 3 to 2) in experiment "1D_ocean_ice_column".
e4aef62d49 Mart*0013 o pkg/exf:
0014 - fix time-invariant exf field (fldPeriod=0) when used as ctrl variables
0015 (xx_gentim2d), by resetting it (ALLOW_GENTIM2D_CONTROL) from fld0,fld1 in
0016 exf_set_fld.F ; simplify "data.exf" in AD experiment "offline_exf_seaice".
de8e498dc9 Oliv*0017 o tools/ci:
0018 - remove OpenAD tests from GitHub actions; add other Adjoint Tapenade test
0019 experiments to CI (only run with label "adjoint"); update docs.
0020
e4aef62d49 Mart*0021 checkpoint69o (2026/07/06) last version to support OpenAD
1c3b30160d Jean*0022 o testreport:
0023 - add process-id number to tar-file name when sending output with "scp".
4b8b6dffc3 Jean*0024 o pkg/obcs(sponge):
0025 - fix bug in sponge relaxation time-scale for Salinity at the Southern OB;
0026 - remove special condition (non zero T / S) for temp and salt relaxation.
9b89fcf692 antn*0027 o pkg/layers:
24d87fa921 Mart*0028 - fix bug in LAYERS_THERMODYNAMCS surface term code for LinFSConserveTr=F
0029 o pkg/layers:
9b89fcf692 antn*0030 - new header file "LAYERS_P2SHARE.h" with new parameter "layers_useThermo"
0031 allows calling S/R layers_fill only when it is necessary;
0032 - fix bug that leads to zero output for some of the LAYERS_THERMODYNAMCS
0033 diagnostics (LaTz, LaSz, LTto, LSto,LaTs,LaSs).
0034
a2d7de1ac7 Jean*0035 checkpoint69n (2026/05/08)
3f0f10fc37 Mart*0036 o pkg/seaice:
0037 - move seaice grid-variables from SEAICE.h into new header "SEAICE_GRID.h";
0038 - add missing metric terms to stress divergence (bug fix); new run-time parms
0039 SEAICEselectMetricTerms, default=2, =1 recover previous partial metric-terms
0040 (i.e., old results), tested in lab_sea.salt_plume ;
0041 - update all affected reference output (in cpl_aim+ocn, global_ocean.cs32x15,
0042 lab_sea & seaice_obcs, 19 total).
242228367a Mart*0043 o pkg/mdsio:
0044 - when using pkg/cal, add date and time to ".meta" output file.
f39e9f371c Mart*0045 o pkg/shelfice:
0046 - use alternative way to compute freshWaterFlux based on heat balance ;
0047 keep old code under CPP option SHI_SALTBAL_FWFLX, and define this option
0048 in verification exp. shelfice_2d_remesh; update docs;
0049 - fix potential division by zero in saltFreeze & freshWaterFlux expressions;
0050 - fix bug related to SHELFICEadvDiffHeatFlux=T.
ea437dae83 Hugo 0051 o pkg/obcs:
0052 - fix CPP logic in obcs_cost_driver.F to avoid compilation error.
0053
8d6ec7ca68 Jean*0054 checkpoint69m (2026/03/30)
df0999b5dc Jean*0055 o pkg/cost:
0056 - change ordering of calls in `cost_final.F`, profiles before ecco, as
0057 before PR 946 ; refine printing of cost per tile value to STDOUT.
0058 - drop condition on "useECCO" in shelfice_cost_final.F ; fix few missing
0059 or inconsistent CPP #ifdef.
6fc9daf8e1 Jean*0060 o verification/global_ocean.cs32x15 & offline_exf_seaice:
0061 - in exp. "global_ocean.cs32x15", turn off useCAL in remaining FWD and AD
0062 tests and skip compilation of pkg/cal in FWD built. Also shift "nIter0"
0063 + rename pickup files in few secondary tests.
0064 - similarly, in exp. offline_exf_seaice, turn off and skip compilation of
0065 of pkg/cal in AD tests.
0066 - fix missing useCAL in 2 pkg/ctrl src files.
69361556c2 Mart*0067 o pkg/cost,ctrl,ecco,obcs:
0068 - final cost-function always computed in "cost_final.F" (even if useECCO=T),
0069 calling individual {PKG}_COST_FINAL, each writing its own "costfunction_*"
0070 summary file. Similar changes in new "cost_driver.F", calling individual
0071 pkg "{pkg}_cost_driver.F";
0072 - make ctrl-cost (and obcs-ctrl-cost) available without pkg/ecco ; move all
0073 obcs-cost S/R from pkg/ecco to pkg/obcs ; and move+rename "data_errfile"
0074 (formerly in data.ecco) to "obcs_data_errfile" in "data.ctrl";
0075 - retire ALLOW_COST_DEPTH (covered by generic controls);
0076 - no changes to results ; adjust few namelists for special cases (obcs_ctrl,
0077 bottom_ctrl_5x5);
0078 - adjust store directives for combinations of pkgs kpp, seaice, shelfice
0079 with ALLOW_DEPTH_CONTROL.
0080
932fd2f667 Jean*0081 checkpoint69l (2026/03/01)
15ec4b1e94 Jean*0082 o verification:
0083 - for secondary tests, change testreport to only run a single "prepare_run"
0084 from run-dir, after linking files from both ../input.${sfx}/ and ../input/.
0085 - adjust several verification exp. secondary tests accordingly and update
0086 instructions in README files + in the docs.
decd05a68a dngo*0087 o pkg/streamice:
0088 - fix typo and S/R argument list within #ifdef ALLOW_PETSC adjoint code.
0ecb64d391 Jean*0089 o tools:
0090 - fix PR 949 changes (location of "flow_tap") in Tapenade ad-optfile by
0091 using Makefile variable "TOOLSDIR".
642de41482 dngo*0092 o pkg/tapenade:
0093 - fix for Tang-Lin: add missing handwritten code for some pkg/streamice S/R
0094 and fix issues in ACTIVE_READ_XY/XYZ_D ;
0095 - turn back on Tapenade TLM test for experiment halfpipe_streamice.
6a9e386e2e dngo*0096 o tapenade & genmake2:
0097 - in genmake2, import Tapenade command arguments from ad-optfile (adjoint_tap)
0098 - allow additional extra arguments with TAP_EXTRA, which can also be set using
0099 new command line option "-tap_extra" ;
0100 - add support for Tapenade to skip checkpointing with new "_FWD" and "_BWD"
0101 versions of manually written subroutine derivatives ;
0102 - test new "no-checkpointing" feature in halfpipe_streamice experiment
0103 with new reference output.
a3ffb3b677 Jean*0104 o pkg/gmredi:
0105 - remove OLD_VISBECK_CALC code ; rename S/R GMREDI_CALC_PSI_B ;
0106 - unless restricted to only uniform Kappa (including 2-D & 1-D scaling),
0107 define local 3-d vars for Kappa-Redi and Kappa-GM to simplify Tensor
0108 setting and Psi-Bolus code.
0109
db6c4bb05b Jean*0110 checkpoint69k (2026/01/25)
b15f6f1e9f Jean*0111 o model/src:
0112 - fix scaling from cg2g/cg3d TargetResWunit to CG-Tolerance (exact scaling
0113 if rAc is uniform) by using few more domain global quantities (in GRID.h).
0114 - adjust accordingly cg2g/cg3d TargetResWunit in all forward test exp. to keep
0115 identical results but switch off cg2dTargetResWunit in most AD exp. (except
0116 if using useNSACGSolver=T) to use cg2gTargetResidual (normalize cg2d RHS).
f1b47febb7 Jean*0117 o verification:
b15f6f1e9f Jean*0118 - after moving/merging (PR 944) fwd & adm tests from global_ocean_ebm into new
0119 host-exp global_oce_latlon, move former input dir and ref. output to replace
0120 sym-link in new host-exp and remove remaining files/dir in global_ocean_ebm.
b4e9a6eb7c aver*0121 o pkg/obsfit:
0122 - fix allocation of 2 local vars in obsfit_init_fixed.F
6a83a78373 Jean*0123 o pkg/profiles:
0124 - fix typo ; this allows to compile ALLOW_PROFILES_SAMPLESPLIT_COST code.
2a2b7d0c36 Mart*0125 o pkg/gchem:
0126 - new routine gchem_insolation.F to replace pkg/bling & pkg/dic code,
0127 and now also usable on Curvilinear-Grid.
8dee4b5b73 dngo*0128 o tools/ci:
0129 - add two tapenade AD test experiments to GitHub action CI test.
0130
2578cc1182 Jean*0131 checkpoint69j (2025/12/20)
75cb2ff809 Jean*0132 o optim:
0133 - fix outdated ALLOW_SHIFWFLX_CONTROL option in "optim_read/writedata.F".
ad59256d7d aver*0134 o pkg/obsfit:
0135 - new package "obsfit" for for model-observations comparisons (and cost
0136 contribution);
0137 - add secondary "obsfit" test in TAF-AD exp. global_oce_biogeo_bling.
036aee8265 Mart*0138 o verification:
0139 - move "global_ocean_ebm" experiment forward tests to "global_oce_latlon" and
0140 adjust AD test for merging in global_oce_latlon, as a secondary "ebm" test.
0141 - disable test of global_ocean_ebm (to be removed later).
6b145becaf Jean*0142 o pkg/seaice:
0143 - fix compilation of untested SEAICE_MODIFY_GROWTH_ADJ code.
47ecd1025a Jean*0144 o model/src:
0145 - add a STOP if using selectPenetratingSW > 0 in Atmospheric set-up.
feb7fa5d1e dngo*0146 o pkg/streamice & Tapenade:
0147 - introduce fixed-point treatment of Goldberg et al 2016 (GMD) for streamice
0148 nonlinear solver using Tapenade FP-LOOP pragma ; used in halfpipe_streamice
0149 exp. (with #define ALLOW_STREAMICE_FP_ADJ) ;
0150 - rename: streamice_vel_solve_openad.F --> streamice_vel_solve_fp.F
0151 + CPP option ALLOW_STREAMICE_OAD_FP --> ALLOW_STREAMICE_FP_ADJ
0152 - skip differentiation of streamice_cg_solve.F with Tapenade, calling instead
0153 adstreamice_cg_solve (update "flow_tap" and stubs_tap_adj.F, add
0154 adFixedPoint.c in ADFirstAidKit/ + links in pkg/tapenade);
0155 - for now, disable halfpipe_streamice exp. Tapenade Tang.-Lin test.
61b91e10c1 Ivan*0156 o pkg/grdchk:
0157 - fix grdchk location to allow to span several vertical level k ; test this
0158 in secondary test exp. "global_ocean.90x40x15.kapredi".
e6feef680a Ivan*0159 o pkg/mnc:
0160 - update grid-variable names in pkg/mnc NetCDF files (mostly matching GRID.h)
0161 and provide backwards compatibility in MATLab "load_grid.m" and for Python
0162 MITgcmutils (restore_MNC_keys).
204068be6a R. S*0163 o pkg/seaice:
0164 - new parameter "SEAICE_evpAreaReg" for regularizations of denomU/V in EVP
0165 solver ; tested in exp. seaice_obcs new secondary test "regDenom".
0166
58fb4fd147 Jean*0167 checkpoint69i (2025/11/14)
c9c019d2e0 Jean*0168 o pkg/cost:
0169 - fix multi-proc initialization of Tapenade adjoint cost-function.
b7411f1a84 Jean*0170 o pkg & model:
0171 - remove pkg/timeave ; remove all ALLOW_TIMEAVE code ; remove all timeave
0172 related parameters from common blocks (in header files) and from src code
0173 and disable/retire these params.
0174 - also updates model_ad.flow, TAP_support/flow_tap, OAD_support and most
0175 */code_oad/cb2mFiles from verification.
626c6ac944 Jean*0176 o tools (Tapenade):
0177 - implement "-ncad" genmake2 option for Tapenade Makefile (similar to TAF),
0178 to append each forward src file to corresponding Tapenade-generated AD file,
0179 using new short script "append_fwd_src"; otherwise (default), put all
0180 adjoint (or Tang.Lin.) tapenade fortran files "_b.f" (or "_d.f") into a
0181 single "adj/tlm/_tap_all.f" file, to be compiled to get an object file.
0182 - simply add symbolic-links within pkg/tapenade/ to the few files from
0183 "tools/TAP_support/ADFirstAidKit/" that are needed.
0184 - fix for case-insensitive file systems (e.g., on Mac-OS) and update optfile
0185 "darwin_arm64_gfortran" to use Tapenade on Mac-OS using with "docker".
78dc053d11 Jean*0186 o pkg/diagnostics:
0187 - add diagnostic "VSHEARSQ" for the square of vertical shear.
0188
66720c264e Jean*0189 checkpoint69h (2025/10/23)
4b300c49e1 Jean*0190 o pkg/ctrl:
0191 - account for shift in record number between original xx_gentim2d_file full
f9b5d1eb8f Jean*0192 time-series and "effective" sub-set version ; this was previously missing.
4b300c49e1 Jean*0193 Also enable some debug print from ctrl_get_gen_rec.F (if debugLevel >= 3).
0fa8d50cfc Jean*0194 o pkg/seaice:
0195 - fix compilation of seaice_growth_adx.F (left from PR #750).
c3be04357d Jean*0196 o model, pkgs:
0197 - remove code within "#ifndef EXACT_CONSERV / #endif" bracket and remove
0198 completely CPP option EXACT_CONSERV.
e9828181c3 Yixi*0199 o pkg/bling:
0200 - allows to specify a 2D field of light attenuation coefficient (k0_2d) from
0201 file "bling_k0_2dFile".
0202
bbbca756c9 Jean*0203 checkpoint69g (2025/09/12)
d4a066fa68 Jean*0204 o verification/short_surf_wave:
0205 - fix Non-Hydrostatic pressure initialization issue with implicSurfPress=1/2
0206 by re-starting (nIter0=1) from pickup generated with implicSurfPress=1.
bb357ea692 Jean*0207 o tools/mpack-1.6:
0208 - fix compilation for recent version of gcc, to pass the compiler test in
0209 "configure" and md5 compilation with v15 (comply with C23 standard).
a5926ff804 dngo*0210 o pkg/streamice:
0211 - for OpenAD, adjust streamice_write_pickup.F to only write the forward
0212 components of state arrays to the binary pickups for later use.
5e44d2ea81 Jean*0213 o verification:
0214 - remove all pkg/timeave params from all exp. and no longer compile this
0215 pkg in any exp. ; also skip pkg/mnc compilation in 4 fwd test exp ;
0216 - switch few remaining exp. to #define EXACT_CONSERV so that no exp is
0217 compiled with this option undefined anymore.
13ce79fe94 Ivan*0218 o pkg/profiles:
0219 - fix "profilesDoNcOutput" feature (writing NetCDF model equivalents) so
0220 that it can be use with pkg/grdchk. Switch profilesDoNcOutput" to True in
0221 adjoint test exp. global_oce_biogeo_bling (both in TAF & Tapenade test).
0222 - improve code readability, rename cost_profiles.F to profiles_cost.F
0223 and fix obvious multi-threading issues.
0224
214bfe91bf Jean*0225 checkpoint69f (2025/07/10)
00c7090dc0 Mart*0226 o model/src, pkg/kpp:
0227 - store shortwave penetration fraction in 3D field SWFrac3D and add run-time
0228 params "selectPenetratingSW" to chose between different short-wave heating
0229 options (only =1 currently implemented);
0230 - remove local (buggy) solution in pkg/seaice ;
0231 - add runtime-flag "KPPuseSWfrac3D", set to F by default, because this code
0232 can only approximately replace the original pkg/kpp-code ;
0233 - update TAF directives in pkg/kpp (mostly related to the code changes);
0234 - fix "global_ocean.cs32x15" exp bug in "in_p" and "seaice" tests, update FWD,
0235 ADM & TLM ref. output ; set KPPuseSWfrac3D to True in "1D_ocean_ice_column"
0236 (both FWD & ADM) test exp. with updated ref. output.
b74a470d07 Jean*0237 o pkg/streamice:
0238 - fix "new_partial" initialisation in streamice_adv_front.f (helps Tapenade)
b26a461de7 Mart*0239 o pkg/bling, pkg/dic:
0240 - additional store directives to avoid hidden recomputations.
6a6c83f9ac Hajo*0241 o pkg/longstep:
0242 - add remaining GM-Redi matrix coefficients (extra-diagonal & diagonal terms)
0243 and Bolus transport stream function for time-averaging in longstep pkg and
0244 use saved values in longstep time-stepping.
871ac80009 Jean*0245 o pkg/seaice:
0246 - fix 3 output formats to allow to run with gfortran v.15
0247 - also add "deep_anelastic.vecinv" to multi-threaded tests.
31fb0e0e6d Jean*0248 o pkg/mom_{common,fluxform,vecinv}:
0249 - mom_fluxform, new option, selectCoriScheme=4: use hFac averaged transport in
0250 Coriolis term so that column integral of tendency match Coriolis time
0251 column integral U,V.
0252 - mom_vecinv, new option, selectVortScheme=4: by-pass division by hFacZ and
0253 instead apply recip_hFacW/S on final tendency. Note: this fixes Angular-Mom
0254 (AM) conservation but breaks vorticity tendency matching advection of vort.
0255 - new 3-d Coriolis option, select3dCoriScheme=2,3: Alternative discretization
0256 using averaged transport; =3 (vs 2), an other alternative discretization of
0257 vertical momentum tendency gW.
0258 - deep-model, put gU,gV NH-metric terms inside vertical advection, to exactly
0259 conserves AM (+ simplify & speed up by skipping NH metric-terms gU,gV
0260 calculation). Add CPP option "MOM_USE_OLD_DEEP_VERT_ADV" (in
0261 MOM_COMMON_OPTIONS.h) to recover the explicit NH metric-term calculation.
0262 - mom_fluxform, new spherical Metric-terms option, selectMetricTerms=2,3: More
0263 accurate discretization similar to manual eq. 2.102 & 2.103 but centered at
0264 grid-cell corner; Also option (selectMetricTerms=3) to skip the gU spherical
0265 metric term by advecting uVel*dxC (simpler, faster and exactly conserve AM).
0266 - add diagnostics for Metric-Terms.
0267 - verification exp. "deep_anelastic", new secondary "vecinv" test + also
0268 update primary test ref output.
0269
69c3e78b15 Jean*0270 checkpoint69e (2025/05/01)
86f389907b Jean*0271 o pkg/atm_ocn_coupler:
0272 - update local copy of setdir.c and CPP_EEOPTIONS.h (were left behind);
0273 - improve "run_cpl_test" step 1 (pass options to genmake2) and step 2.
c296d11a59 Jean*0274 o tools/genmake2:
0275 - use specific "ad_config.template{0,1,2}" in different stages of TAF
0276 AD/TL built to avoid race condition issue with "make -jN".
79b5d5775c Jean*0277 o model/src:
0278 - no "addMass" contribution to initial (iter=0) vertical velocity ;
0279 - with selectAddFluid=1, fix missing implDiv2DFlow factor in "addMass"
0280 contribution to solver RHS ;
0281 - add a STOP if implDiv2DFlow < 1 with exactConserv=F, (was not right with
0282 useRealFreshWaterFlux=T or selectAddFluid=1) and remove untested pieces
0283 of code dealing with this case ;
0284 - when using cg2d/cg3dTargetResWunit, add missing implDiv2DFlow factor to
0285 solver tolerance setting (cg2d/cg3dTolerance) ;
0286 - upgrade "global_ocean.cs32x15.viscA4" exp. to test selectAddFluid=1
0287 with implDiv2DFlow=1/2 ; also update "short_surf_wave" exp. output.
8908c6917c Jean*0288 o tools/genmake2:
0289 - with Tapenade, remove list NON_AD_F77_SRC_FILES from Makefile (not used),
0290 remove processing of "dontCompile", "keepOriginal" and "cb2mFiles" lists ;
0291 - otherwise, in Makefile, move NON_AD_F77_SRC_FILES and NON_AD_F90_SRC_FILES
0292 lists after AD_FILES and AD_F90FILES ;
0293 - simplify (remove intermediate targets) and improve the "-ncad" Makefile
0294 to ends cleanly when "staf" command fails.
f460f9a57e Ivan*0295 o utils:
0296 - improve gluemnc description (usage, dependencies, and example).
fbb692b4e1 Jean*0297 o tools:
0298 - replace (obsolete) "egrep" with "grep -E" (or without "-E" if not needed).
7fe51dd492 Jean*0299 o verification:
0300 - After merging (5 fwd tests + 2 AD) few exp. into new host-exp. (PR #830),
0301 move input dir and ref. output from merged exp. to replace sym-link in new
0302 host exp. and remove remaining files/dir (code, build, run) in merged-exp;
0303 - Add or update README.md in new host-exp and update list of exp. in the docs.
c8ce5f710c Jean*0304 o pkg/rbcs:
0305 - fix error/warning cases and messages.
29b81f1d21 Jean*0306 o pkg/autodiff:
0307 - alternative way (printResidualFreq >=0) to get CG2D output from cg2d_mad.F
0308 - remove 2 unused CPP options.
b7b61e618a Mart*0309 o tools, autodiff and others:
0310 - remove TAMC features, untested, unused and probably broken.
0311
b2c8bc6cea Jean*0312 checkpoint69d (2025/03/01)
5b53130725 Ivan*0313 o tools:
0314 - changes to genmake2 to allow TAF to process F90 files with modules, for now
0315 only with "-ncad" option;
0316 - re-order list of src files sent to TAF (needed with current version of TAF);
0317 - add new scrip "f90mkdepend_taf" to add dependencies form TAF generated src
0318 code (Adjoint and Tang.Lin) in a file included into Makefile.
0319 - more logical and consistent ordering in Makefile target, *.F90 first then
0320 *.F77, *.c and *.h
0321 - add 2 new variables TAF_F77_FLAGS and TAF_F90_FLAGS (set from genmake_local
0322 or adjoint-optfile) to go into the TAF command.
701e10a905 Mart*0323 o model/src and forcing:
0324 - for TEOS10, add new S/R to convert model surface Conservative Temperature
0325 to in-situ Temperature (SST) and compute and store model SST in new model
0326 field (in FFIELDS.h) "gcmSST", just a copy of model Pot.Temp with other EOS.
0327 - use model SST to compute surface forcing over open ocean in pkg/exf and
0328 pkg/bulk_force ; for now, leave ice/seaice freezing/melting unchanged.
0329 - switch test exp. global_ocean.cs32x15.in_p to use TEOS10 + update lab_sea
0330 Tapenade ref. output (affected @ machine truncation level).
f955de4ba2 Jean*0331 o tools:
0332 - remove old backward compatibility feature, so that env.var ROOTDIR is no
0333 longer recognized by genamke2 ;
0334 - re-write "suggest_optfile_names" to use parts from "genmake2".
83a53713c2 Oliv*0335 o utils/python:
0336 - make MITgcmutils compatible with numpy 2.0.0 again.
c908a600ca Jean*0337 o testreport:
0338 - improve way of sending results tar file with "scp", now allowing to combine
0339 "ssh" then "scp".
0340
efc7ba3160 Jean*0341 checkpoint69c (2024/12/06)
7bb5a8a109 Jean*0342 o pkg/mom_common,fluxform,vecinv:
0343 - remove ISOTROPIC_COS_SCALING code from pkg/mom_vecinv/mom_vi_hdissip.F (was
0344 not right); add warning (or stop if side-drag) if used with pkg/mom_vecinv.
0345 - move 2 Cos-Scaling CPP options from CPP_OPTIONS.h to MOM_COMMON_OPTIONS.h
0346 to be used in horizontal viscosity formulation; more consistent use of
0347 GAD_OPTIONS.h where these 2 CPP options are used for horizontal diffusion.
0348 - update all verification exp. customized version of CPP_OPTIONS.h,
0349 GAD_OPTIONS.h and MOM_COMMON_OPTIONS.h.
4287557481 Jean*0350 o verification/atm_gray:
0351 - gray atmosphere test exp moved from "verification_other".
80fd556159 Ou W*0352 o model/src:
0353 - add few missing option header files (RBCS, SALT_PLUME, SHELFICE) in few
0354 src files ; also illustrate how to catch these (see SALT_PLUME.h and
0355 shelfice_ad_check_lev{1,2,3,4}_dir.h).
27ce1202c5 Jean*0356 o eesupp + model:
0357 - remove FAST_BYTESWAP code and option
0358 - remove empty file AUTODIFF_MYFIELDS.h
cb406db96c Ou W*0359 o pkg/ctrl:
0360 - add a STOP when ALLOW_CTRL_OBCSN/S/W/E is defined but corresponding
0361 ALLOW_OBCS_NORTH/SOUTH/EAST/WEST is undef ; and fix the code so that, in
0362 that case, it will compile and reach the stop before running 1rst time-step
0e6a4460e5 Ivan*0363 o model,pkg:
0364 - minor spell checking and formatting updates.
9edc0e3a85 aver*0365 o pkg/bling:
0366 - size-dependent phytoplankton growth code cleaned up and related parameters
0367 can now be specified in data.bling;
0368 - clean up OPTIONS in pkg/bling code ( SIZE_NUT_LIM merged with SIZE_DEP_LIM,
0369 MULT_NUT_LIM merged with MIN_NUT_LIM ) and switch USE_QSW to #undef ; this
0370 fixes FWD exp. global_oce_biogeo_bling which a) use default BLING_OPTIONS.h
0371 and b) since no short-wave is provided, light was zero with USE_QSW defined.
d3172737dc aver*0372 o pkg/profiles:
0373 - add option to write model-equivalent profiles in a netcdf file, thus
0374 removing the need for post-processing tiled output files.
9f85ea262e Mart*0375 o pkg/grdchk:
0376 - write either "grd_ratio_ad" or "grd_ratio_ftl" depending on type of run
0377 and remove limitation to "useSingleCpuIO=F" when writing 2D files ;
0378 - write "costfunction0000" only once, from pkg/ecco.
0379
7a6b0d88e9 Jean*0380 checkpoint69b (2024/10/31)
8b7be8db08 Mart*0381 o pkg/autodiff:
0382 - TAF-store directives for saltFlux (needed for #define EXCLUDE_FFIELDS_LOAD)
0383 - little cleaning of ctrl_map_forcing.F (remove duplicated EXCH calls, ...).
71b7a3e5ac Mart*0384 o tools/genmake2:
0385 - remove step that generates *.flowdir
c9bf163375 Ivan*0386 o pkg/profiles:
0387 - fix missing pieces in this pkg for Tang-Lin model and get this tested in
0388 verification exp. global_oce_biogeo_bling.
ee480e7782 amc2*0389 o pkg/seaice:
0390 - if SEAICEaddSnowMass=T, include HSNOW in diagnostics "SIenph ".
58679b5a83 Esta*0391 o utils/python/MITgcmutils/:
0392 - augment (llc, examples, ...) and update python utils
c7a06a2c29 Mart*0393 o tools/build_options:
0394 - update darwin_arm64_gfortran to be able to compile free-format F90 files.
0395 o pkg/seaice:
5bb179ddc2 Mart*0396 - add new lateral drag parameterisation for landfast ice (Liu etal 2022, JGR)
3a00e4dea9 Jean*0397 o verification/*/results:
0398 - update 5 adm + 3 tlm ref. output affected by TAF new version 6.4.5 & 6.5.0
4c91ca28d5 Ou W*0399 o pkg/ecco:
0400 - implement sea-ice freeboard cost "m_freeboard".
f79ba37af1 Mart*0401 o tools/xmakedepend:
0402 - fix xmakedepend to accept suffix longer than 1.c and add dependencies to
0403 Makefile from included headers in F90 src files.
e6e223b277 Jean*0404 o model/src:
0405 - Add new param "cg3dTargetResWunit" to skip the normalization of cg3d RHS
0406 by specifying the CG3D target residual in term of vertical-velocity units ;
0407 - Remove header files SOLVE_FOR_PRESSURE{3D}.h ; clean-up "post_cg3d.F" ;
0408 - switch test exp. global_ocean.cs32x15.viscA4 & short_surf_wave to use new
0409 param "cg3dTargetResWunit".
95cd2dedde Ivan*0410 o tools/f90mkdepend:
0411 - add arguments to f90mkdepend to specify alternative file suffix (e.g.,
0412 for MacOS) + minor improvement in error message.
0413
b537eb461d Jean*0414 checkpoint69a (2024/09/08)
0524b7d1ff Mart*0415 o tools/genmake2:
0416 - list of src files to Differentiate: change from simply "*.list" to commonly
0417 adopted "*_ad_diff.list" (to avoid accidents).
0418 - change Makefile to enable TAF to generate Tangent-Linear code from a mix
0419 of fixed-form (.F) and free-form (.F90) src code.
0420 - test free format *.F90 code in hs94.1x64x5/code_ad/ exp. for AD and TLM.
ae2be6150b Jona*0421 o pkg/dic:
0422 - save 3D pH (for calcite saturation calculation, useCalciteSaturation=T)
0423 for next time-step and store it in pickup files (for restart).
5237154b93 Jean*0424 o eesupp/src:
0425 - new set of Global-Sum vector routines working with shared buffer
0426 (=> no needs for input/output to be in common block) and with
0427 GLOBAL_SUM_ORDER_TILES implemented ; and remove older versions.
ea893758ea Patr*0428 o tools/genmake2:
0429 - change Makefile to enable TAF to generate adjoint from a mix of fixed-form
0430 (.F) and free-form (.F90) src code. Also fix for alternative suffix (e.g.,
0431 used on MacOS) to work without -ncad.
6d7b0906cb Ivan*0432 o tools/adjoint_options:
0433 - allow to pass -f08 flag to TAF by setting TAF_FORTRAN_VERS to "F08".
a340904e5a Ou W*0434 o pkg/mom_vecinv:
0435 - add more 3-D momentum tendency diagnostics (originally from Helen Pillar)
0436 for harmonic/bi-harmonic dissipation and for bottom + top friction
0437 tendency (under new CPP option: ALLOW_MOM_TEND_EXTRA_DIAGS).
0438
6519d60651 Jean*0439 checkpoint68z (2024/07/27)
acacc28f7f Jean*0440 o pkg/diagnostics:
0441 - to allow to use ADJ-diags in DIVA runs, change call sequence regarding
0442 TURNOFF_MODEL_IO and DIAGSTATS_INI_IO and simplify (fewer tests for
0443 "costfinal") the_model_main.F (+ shorten pkg/openad version) ;
0444 - restore the use of "diag_pkgStatus" (switch & check) in AD backward sweep
0445 with new small S/R for DIVA runs ;
0446 - turn on FWD and ADJ-diags in secondary lab_sea AD test "noseaice".
4dea327916 aver*0447 o pkg/bling:
0448 - clean-up "bling_light.F" (fix typo related to PHYTO_SELF_SHADING option,
0449 move k-loop outside) ; add CHL to bling_ad_check_lev{2,3,4}_dir.h and
0450 fix TAF storage directives ;
0451 - change "global_oce_biogeo_bling" AD test exp. (both TAF & Tapenade) to
0452 use PHYTO_SELF_SHADING (with #undef USE_QSW) and update ref. output.
0453 - also clean-up MDSIO_BUFF_WH.h (avoid common block that mixes r4 & r8 vars).
af61e5eb16 Mart*0454 o pkg/obcs:
0455 - Neumann boundary conditions for sea ice variables, activate by setting
0456 new runtime parameter useSeaiceNeumann=.TRUE. in data.obcs ;
0457 - fewer (hidden) recomputations and no recomputation warnings when
0458 both ALLOW_OBCS_BALANCE and ALLOW_OBCS_STEVENS are defined.
0459 o pkg/cost:
0460 - new runtime flag for pkg/cost "cost_mask_file", which can be used
0461 for flexible cost function definition.
0462
976081d885 Jean*0463 checkpoint68y (2024/06/05)
6518e4ecc5 aver*0464 o pkg/bling:
0465 - fix bigR setting when option CARBONCHEM_TOTALPHSCALE is defined.
00f81e6785 Ou W*0466 o pkg/steep_icecavity + shelfice:
0467 - new package to be used together with pkg/shelfice to also account for
0468 melting at the vertical faces of a steep ice-shelf interface ;
0469 - allows to use non-zero (but constant) ice-shelf salinity ;
0470 - new FWD and (TAF) AD secondary test exp. (in isomip) using new pkg.
82e538d851 aver*0471 o pkg/bling:
0472 - fix/improve initialization of biomass for the 3 phytoplankton groups ;
0473 - add 2D diagnostics of optically integrated chlorophyll concentration
0474 within local-time window to be compared with satellite observation ;
0475 - improve TAF store directives (reduce recomputations).
672b822630 Jean*0476 o pkg/obcs (tides):
0477 - more efficient implementation of OB barotropic tidal velocity components,
0478 with both Cos & Sin of phase times Amplitude stored in common block ;
0479 - more flexible specification of OB tidal-components (only read-in components
0480 with non-zero tidal period) ;
0481 - allows to specify tangential component of barotropic tidal velocity at OB ;
0482 - rename all OBC tidal component input parameter (period, amplitude and
0483 phase of each OB barotropic tidal velocity component input files) ;
0484 - upgrade OB tidal example (in seaice_obcs/input.tides) with fewer tidal
0485 components (only 4) but including few tangential components.
0c90ef582a Jean*0486 o verification:
0487 - changing domain decomposition (more tiles) in global_with_exf experiment
0488 (both FWD & AD) and update ref. output ;
0489 - use correct CD-Scheme time-stepping in FWD exp. global_ocean_ebm and update
0490 ref. output ;
672b822630 Jean*0491 - simplify global_ocean.90x40x15/code_ad (undef ALLOW_GENTIM2D_CONTROL,
0c90ef582a Jean*0492 ALLOW_DIFFKR_CONTROL & ALLOW_3D_DIFFKR); remove kpp from global_oce_latlon
0493 (from both TAF & Tapenade code) ;
0494 - after adjusting new host experiment code, merge forward test:
0495 flt_example --> exp4.with_flt
0496 global_with_exf --> global_ocean_ebm.w_exf
0497 global_with_exf.yearly --> global_ocean_ebm.yearly
0498 natl_box --> lab_sea.natl_box
0499 natl_box.longstep --> lab_sea.longstep
0500 and TAF & Tapenade tests:
0501 global_with_exf --> global_oce_latlon.w_exf
0502 For now, keep original set-up in place and add symbolic links into new
0503 host exp. for input dir and ref. output to run these as secondary test.
9e0fdb4065 Garr*0504 o pkg/obcs:
0505 - fix unusual division by zero in all 4 (N,S,E,W) orlanski main S/R.
41c4545f8f Jean*0506 o pkg/diagnostics:
0507 - new header file "DIAGNOSTICS_P2SHARE.h" (for now, just for useDiag4AdjOutp),
0508 and remove DIAGNOSTICS.h in any src code outside pkg/diagnostics;
0509 - new params "diag_dBugLevel" (default = main model "debugLevel");
0510 - add new arg "seqFlag" to DIAGNOSTICS_SWITCH_ONOFF and DIAGNOSTICS_SUMMARY
0511 and prevent "diagnostics_status" to be overwritten when using ADJ-diags.
0512
5f2d22066e Jean*0513 checkpoint68x (2024/04/30)
8fabf86828 Jean*0514 o model/src:
0515 - more precise specific-volume anomaly expression for Ocean in P-coord;
0516 update reference output of all 3 Ocean in P test experiments.
598aebfcee Mart*0517 o pkg/generic_advdiff:
0518 - adjust 2 SOM (Prather advection) store directives to reduce memory overhead
0519 - include OS7MP (advScheme 7) in AD code ; switch AD test experiment
0520 isomip.htd to use this advection scheme for Temp and Salt.
720a211d38 Ou W*0521 o pkg/ecco, ctrl:
0522 - put active_read calls within #ifdef ALLOW_AUTODIFF (missing in few places)
0523 and fall back to non-active read (from pkg/rw) if undef;
0524 - change argument order in few obcs related pkg/ecco S/R.
20e951135e Mart*0525 o pkg/seaice:
0526 - for seaice-dynamics, add missing mapping of (pkg/thsice) snowHeight to HSNOW
0527 - this affects results (unless SEAICEaddSnowMass=F); update seaice parameters
0528 in test global_ocean.cs32x15.icedyn and update reference output.
0529
7456fbd729 Jean*0530 checkpoint68w (2024/03/05)
5cf4364659 Mart*0531 o pkg/ctrl, grdchk & optim:
0532 - clean and improve list of ctrl-var settings (in common blocks) and update
0533 ctrl-pack header files:
0534 a) define new character fields "ncvartype" for ctrl-var shape type and
0535 save ctrl-var (file) name "ncvarfname" ;
0536 b) re-define "ncvarindex" to point directly to genArr index (according to
0537 ncvartype) or 1,2,3,4 for N,S,E,W obcs-ctrl ;
0538 so that map of index (and grdchkvarindex) to file name, array shape and
0539 genArr specification is direct, code is simpler, more robust and efficient.
0540 - allow to specify grdchk ctrl-var by name in "data.grdchk" (more robust) ;
0541 - write ncvartype list to ctrl-pack header files ;
0542 - simplify definition of maxcvars to get much shorter "ncvar"-field lists ;
0543 - remove unnecessary common blocks, rename ctrl_init.F -> ctrl_init_fixed.F,
0544 call TURNOFF_MODEL_IO only once ;
0545 - adjust optimisation utility optim and provide backward compatibility
0546 regarding changes to ctrl-pack files ; also improve build process ;
0547 - update all "data.grdchk" in verification experiments.
a4576c7cde Juli*0548 o pkg/gmredi:
0549 - add GEOMETRIC parameterization (Mak etal, JPO, 2018) for GM coefficient,
0550 under GM_GEOM_VARIABLE_K CPP-option, turned on with "GM_useGEOM=T" and
0551 tested in exp. ideal_2D_oce, secondary test "geom".
35c4fdc74b Emma*0552 o pkg/ecco:
0553 - add option ECCO_VARIABLE_AREAVOLGLOB to use the total time-varying volume
0554 to weight contributions to m_boxmean cost functions
0555
285cda8c7b Jean*0556 checkpoint68v (2024/02/03)
427e24e121 Jean*0557 o model/src:
0558 - change param "metricTerms" to integer param "selectMetricTerms" and change
0559 param "use3dCoriolis" to integer param "select3dCoriScheme" but keep former
0560 parameters in namelist (backward compatible).
0561 - remove un-used param "writeStatePrec" + also in experiment param file "data"
0562 - rotateGrid: fix missing 3-D Coriolis term to gV ; adjust usage restriction.
d4b64b229a Jean*0563 o pkg/ecco:
0564 - remove call to ECCO_CHECK from ecco_cost_init_fixed.F (but keep the other
0565 call from packages_check.F) and move ECCO_SUMMARY call to ecco_check.F
005af54e38 Jean*0566 o pkg/shelfice:
0567 - put the update of kTopC code within "#ifdef ALLOW_SHELFICE_REMESHING/#endif"
0568 and add run-time switch "SHI_update_kTopC" to allow to turn it off.
0569 - Change the initial setting of "kTopC" to remain unaffected by machine
0570 truncation error and if using SHELFICEMassStepping, set it according to
0571 shelficeMassInit.
aef96ed361 Jean*0572 o verification/solid-body.cs-32x32x1:
0573 - update set up (faster flow, smaller planet ..) and fix initial Ps condition.
9af873c532 Hajo*0574 o pkg/ggl90:
0575 - revisit Langmuir Circulation (LC) mixing-length calculation: fix bugs in
0576 some "mxlMaxFlag" implementation and ensure it works with P-coordinate.
0577 Update vermix.gglLC ref. output and add new secondary AD test (with LC on)
0578 in global_oce_latlon experiment.
0579
fca39df4c8 Jean*0580 checkpoint68u (2023/12/10)
143d9ce879 Dami*0581 o pkg/seaice:
0582 - new/improved LSR convergence criteria (CPP: SEAICE_ALLOW_LSR_FLEX, run-time:
0583 SEAICEuseLSRflex) accounting for both Non-Lin and Linear solver residual;
0584 tested in offline_exf_seaice.dyn_lsr; also add 2-D diagnostics for residual.
f0ff6e912a dngo*0585 o pkg/streamice:
0586 - rename STREAMICE_PETSC.h to STREAMICE_PETSC_MOD.h and rename
0587 STREAMICE_ARG_PETSC_mod code module to STREAMICE_PETSC_mod;
0588 - include STREAMICE_PETSC_MOD.h in src files rather than the module directly:
0589 this obviates the need for alphabetical order in names or serial compilation
15ec8028f7 aver*0590 o pkg/bling:
0591 - fix 2 small bugs in carbonate and aragonite saturation states: a) both Ksp
0592 coeff are fct of log of temperature (and not log10); b) add missing unit
0593 conversion factor to carbonate variable in OmegaC & OmegaAr calculation.
1052c30783 Jean*0594 o pkg/grdchk:
0595 - new S/R to get CTRL var/file name from grdchk-index ; use it to simplify
0596 (with new arguments) the 3 routines that handle CTRL var/file perturbations
0597 - rename grdchk_init to grdchk_get_mask ; move GRDCHK_SUMMARY call ;
0598 - report (in summary & in results section) CTRL var/file name used in grdchk.
51e381e9c9 Jean*0599 o pkg/dic:
0600 - fix loading of forcing file for the case DIC_forcingCycle = 0 ;
0601 - fix inconsistent timing params for loading initial surface-silica file ;
0602 - clean-up initialise-varia level S/R, now all called from dic_init_varia.F
0603 and move all forcing field initialisation to dic_ini_forcing.F ;
0604 - read and process pickup_dic meta file with error/warning (depending on
0605 pickupStrictlyMatch = T/F) if missing file or field.
65754df434 Mart*0606 o pkg/ctrl:
0607 - reduce pkg/ctrl/optim.h to just "optimcycle" and rename into OPTIMCYCLE.h ;
0608 - keep optim_readparms.F namelist unchanged and define variables locally.
0609
ec9548c9e7 Jean*0610 checkpoint68t (2023/10/28)
a2c35952f2 Jona*0611 o pkg/dic:
0612 - improve carbonate dissolution options (new params: selectCalciteDissolution)
0613 and fix a minor bug in dissolution rates according to Keir et al (1980);
0614 - change exp. so_box_biogeo secondary tests caSat0/3 to test option 2 & 3.
f5509be190 Mart*0615 o pkg/gmredi:
0616 - fix setting of GM_ExtraDiag that was not (always) turned on with 3D Kappa
0617 read from file, with Bates-K3d or QG-Leith, therefore missing 2 terms in
0618 isopycnal diffusion tensor; update ref. output of MLAdjust.QGLthGM test ;
0619 - add more check and stop for the case #undef GM_NON_UNITY_DIAGONAL ;
0620 - add runtime parameter GM_isoFac_calcK to allow to scale dynamically computed
0621 Kappa contribution in the Redi-tensor (default = 1.).
018c28d301 Jean*0622 o pkg/autodiff:
0623 - adjust call to S/R DIAGNOSTICS_SWITCH_ONOFF in autodiff_inadmode_set_ad.F
0624 so that snap-shot Adjoint diagnostics are filled within the same time-step
0625 as they are written to output file.
4d72283393 Mart*0626 o pkg/ctrl:
edcd27be69 Mart*0627 - rename ctrl_dummy.h to CTRL_DUMMY.h, remove unused variables & common blocks
0628 - retire CPP-flag ALLOW_HFACC/HFACC3D_CONTROL and remove related code.
0629 o pkg/ctrl:
4d72283393 Mart*0630 - rename header file "ctrl.h" to "CTRL.h".
4ec37fd829 Jean*0631 o utils/matlab/cs_grid:
0632 - update some basic matlab-scripts for CS-grid (split_*_cub.m,
0633 rotate_uv2uvEN.m, mk_psiLine_CS.m & use_psiLine.m) to a) also work with
0634 compact-format input; and (b) always assume "long-vector" are stored one
0635 face after the other (compact-format compatible);
0636 - new script to generate broken-lines (for computing meridional transport
0637 stream-function), simpler than the previous version in cs_grid/bk_line/;
0638 - update RGB-dims in 2 latloncap/ scripts to match pkg/exch2 convention.
172933ad7e Mart*0639 o pkg/ctrl:
0640 - simplify file name handling in ctrl_map_ini_gentim2d.F to please TAF (fixes
0641 hs94.1x64x5 TL test) without upsetting Tapenade & OpenAD.
85c224e862 Ou W*0642 o pkg/autodiff + ecco:
0643 - fix a typo in AD-var output file name (addummy_in_stepping.F);
0644 - fix and improve weight output in pkg/ecco/cost_generic.F
96b006450c dngo*0645 o pkg/streamice:
0646 - implementation of parameterized depth-dependent ice-shelf melt rate ;
0647 - new subroutines added to accumulate misfit cost based on time-dependent
0648 surface elevation and velocity observations (+ calls in pkg/cost) ;
0649 - fix generic ctrl (ctrl_map_ini_{genarr,gentim2d}.F) for OpenAD and
0650 add mapping of STREAMICE arrays to generic controls ;
0651 - update exp. halfpipe_streamice OAD & Tap setup (remove customized *.F)
0652 and switch on new CPP option ALLOW_COST_STREAMICE (+adjust params files).
910e5c3e29 Mart*0653 o pkg/autodiff:
0654 - fix a bug in ALLOW_AUTODIFF_WHTAPEIO code with ALLOW_DIVIDED_ADJOINT ;
0655 - refine grad-check + update output for AD test "lab_sea.noseaicedyn".
0656
26e63756eb Jean*0657 checkpoint68s (2023/09/11)
19ced9bf8f Mart*0658 o verification:
5a54dbbd56 Jean*0659 - change default ALLOW_IB_CORR (in pkg/ecco/ECCO_OPTIONS.h) to "#undef" and
0660 test that this code compiles in experiment global_oce_biogeo_bling ;
0661 - clean/update AD related CPP header files across all experiments and reduce
0662 differences with standard version in pkg autodiff, cost, ctrl and ecco.
0663 o verification:
19ced9bf8f Mart*0664 - change global_oce_latlon TAF set-up to multi-tiles (4 tiles, as in code_oad
0665 & code_tap) and add SIZE.h_mpi to enable MPI tests (in all 3 code_* dir).
7448700841 Mart*0666 o model/src & pkgs, TAF storage dir:
0667 - rearrange and add storing of variables to reduce number of (unwarned)
0668 recomp. in fluxform & vecinv pkgs and in model/src (e.g., calc_phi_hyd.F) ;
0669 - add store directives in solve_tri/pentadiagonal.F to avoid recomputation
0670 warnings with SOLVE_DIAGONAL_KINNER defined ;
0671 - add CPP condition inside GAD SOM advection S/R (-> empty ".f" file if
0672 neither GAD_ALLOW_TS_SOM_ADV nor PTRACERS_ALLOW_DYN_STATE is defined ) ;
0673 - clean-up/refine many unnecessary store directives -> less TAF warnings ;
0674 - remove unnecessary checkpointing code from pkg/smooth_diff2/3d.F
b038e3cc4f Mart*0675 o pkg/ggl90:
0676 - move computing the mixingLength to a dedicated routine ggl90_mixinglength.F
0677 - adjust/add TAF store directives to avoid hidden recomputations.
45315406aa Mart*0678 o pkg/seaice:
0679 - new option SEAICE_BGRID_DYNAMICS allows to remove/replace
0680 SEAICE_ALLOW_DYNAMICS by ( SEAICE_CGRID or SEAICE_BGRID_DYNAMICS ) ;
0681 - exclude more code if SEAICE_CGRID is undefined and clean up/rearrange
0682 SEAICE.h to form more consistent groups and common-blocks ;
0683 - update SEAICE_OPTIONS.h in verification experiments.
57622776fd Jean*0684 o pkg/mdsio:
0685 - Add 2 new arguments (kLo & kHi) to pkg/mdsio Slice I/O routines that allow
0686 to select which levels in Slice-array to read-in or to write-out to file.
0687
2a22bb531b Jean*0688 checkpoint68r (2023/08/02)
5bc996898d Mart*0689 o verification:
0690 - adjust amplitude of perturbation (grdchk_eps) to improve Fwd/Adj gradient
0691 check comparison in exp. global_ocean.90x40x15, global_with_exf & lab_sea ;
0692 - change location of grad-check (away from freezing Temp) in exp. OpenAD
0693 and rename experiment "OpenAD" to "global_oce_latlon".
444da61630 Mart*0694 o pkg/ctrl + pkg/grdchk:
0695 - define PARAMETER nobcs = 4 in CTRL_OBCS.h instead of SIZE.h ; update SIZE.h
0696 of all code_ad/oad/tap verification exp.
0697 - in pkg/grdchk, rename grdchk.h to GRDCHK.h and adjust src code to work
0698 without "nobcs" when OBCS_ALLOW_CONTROL is undefined.
44c9a33d03 Jean*0699 o verification:
0700 - Remove duplicated parameter files from input_tap/ dir and adjust prepare_run
0701 accordingly ; remove few untested additional files (in OpenAD/ & lab_sea/).
d73d15cdef antn*0702 o pkg/seaice:
8e32c48b8f Mart*0703 - rename ZMIN/ZMAX into SEAICE_ZMIN/ZMAX to avoid potential conflicts with kpp
0704 variables with the same name ; rename swfracb into SEAICE_SWFrac ;
0705 - fix a bug in computing SEAICE_SWFrac in pressure coordinates ; update exp.
0706 global_ocean.cs32x15.in_p reference output.
0707 o pkg/seaice:
d73d15cdef antn*0708 - SEAICE_USE_GROWTH_ADX: fix a bug related to flooding and fix budget closure
0709 for linear free-surface case.
025a9bb173 antn*0710 o pkg/ecco:
0711 - in cost_gencost_sshv4.F, enable to also process monthly data (previously,
0712 only daily) for SSH cost.
c61a47f63f Mart*0713 o pkg/ctrl:
0714 - remove left-over and unused code within ALLOW_NONDIMENSIONAL_CONTROL_IO
0715 (except in OBCS_CONTROL pack/unpack code); as a consequence, switch back
0716 ALLOW_PACKUNPACK_METHOD2 to #undef in exp. tutorial_global_oce_optim.
0717 o pkgs:
de57a2ec4b Mart*0718 - for local filenames, replace character*(80) by character*(MAX_LEN_FNAM)
0719 declaration, where possible, especially in pkgs: autodiff, ctrl, ecco,
0720 profiles, smooth & grdchk.
0721
acbfbd3bbd Jean*0722 checkpoint68q (2023/06/29)
5b0716a6b3 Mart*0723 o pkg/ggl90:
0724 - non IDEMIX code: fix bug (missing hFac) in matrix coefficient computation ;
0725 - fix RI-Number calculation for IDEMIX ; new flag GGL90_IDEMIX_CVMIX_VERSION
0726 (defined by default) to update IDEMIX to CVMix version ;
0727 - add new diagnostics ;
0728 - update Fwd ref. output of exp. isomip.obcs, global_ocean.90x40x15.idemix
0729 and global_ocean.cs32x15.in_p.
b4daa24319 Shre*0730 o pkg/tapenade + other Tapenade addition:
0731 - add new capability to use Tapenade to generate Adjoint & Tang-Linear model:
0732 new package (pkg/tapenade), new tools (tools/TAP_support), update genmake2
0733 and testreport ; add some docs (in progress);
0734 - modify src code & packages to work with tapenade ; add new code_tap/ &
0735 input_tap/ dirs (+ ref output) in 9 verification experiments to get
0736 tested with tapenade.
0737
8c2ab294fc Jean*0738 checkpoint68p (2023/05/07)
8377b8ee87 Mart*0739 o pkg/seaice:
0740 - fix compile error related to ALLOW_AUTODIFF_TAMC/ALLOW_AUTODIFF mix-up
0741 in seaice_evp.F; also replace many ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF
0742 where code is not specific to TAF/TAMC;
0743 - call S/R seaice_get_dynforcing every timestep to always have valid TAUX/Y;
0744 - move most of routine body of seaice_dynsolver.F inside the
0745 SEAICE_ALLOW_DYNAMICS block.
b0b45f2373 Ou W*0746 o pkg/ecco:
0747 - fix "sterGloH" output after a restart (issue related to Greatbatch
0748 correction) by writing & reading (small) new "pickup_ecco" files.
b938a3c63b antn*0749 o pkg/ctrl:
0750 - fix record number (mostly in ctrl_map_ini_gentim2d.F) in case of restart,
0751 using corresponding xx_gentim2d_startdate1/2 as specified from data.ctrl;
0752 this finalizes (+ fix) changes made in PR #260 and #380;
0753 - also add more debug print (+new CPP option ALLOW_CTRL_DEBUG);
0754 - improve generic-control documentation in Chap.10 (State Estimation).
ab47de63dc Mart*0755 o pkg/mom_common:
0756 - new expression for quadratic drag coefficient, function of cell thickness &
0757 roughness length (logarithmic law of the wall); for now, only for z-Coords.
0758 Turned on with CPP option ALLOW_BOTTOMDRAG_ROUGHNESS (MOM_COMMON_OPTIONS.h)
0759 and run-time setting zRoughBot > 0 in data, PARMS01 namelist.
0760 Tested in exp. tutorial_plume_on_slope, new secondary test "roughBot".
cda1c18f72 Jean*0761 o model/src & pkgs:
0762 Finish to remove code within retired CPP options:
0763 - remove orphan code within (many) removed ALLOW_()_CONTROL (as listed in
0764 PR #689 comments); remove seaice_ctrl_map_ini.F;
0765 - remove code within retired CPP options, remove call to COST_TRANSPORT,
0766 remove ALLOW_ECCO_BARSTORES and the 4 "ecco_ad_check_lev?_dir.h" files;
0767 - remove (check & stop) "using_cost_bp" & "using_cost_scat" from "data.ecco";
0768 - avoid few unused variables; use default CTRL_OPTIONS.h in exp. hs94.1x64x5.
a4e168e012 antn*0769 o pkg/seaice:
0770 - SEAICE_USE_GROWTH_ADX: fix diagnostic SIatmFW and add diagnostic SIeprflx
0771 to close seaice mass and heat budgets.
a17ca5331e Jean*0772 o pkg/dic:
0773 - remove TAF storage dir for variable "OmegaC" (within wrong CPP option).
0774
628b4a6c85 Jean*0775 checkpoint68o (2023/03/13)
d9efc637ba Mart*0776 o model/src:
0777 - salt/temp/ptracer_integrate.F: optimise store directives
0778 - add mising "obcs_seaice_sponge.f" to obcs_ad_diff.list
4890e8ebab antn*0779 o pkg/ecco:
0780 - smoothing in gencost_bpv4: allow to choose between a) call to smooth_basic2D
0781 (using a constant length, with run-time params replacing hard-coded values)
0782 or b) call to smooth_hetero2D (using a 2D field to be read in).
e99fa9b078 Mart*0783 o pkg/obcs:
0784 - update OBCS configuration summary.
806785c928 Jean*0785 o eesupp/inc, model/inc & pkgs:
0786 Clean CPP header files:
0787 - remove ALLOW_GENCOST_CONTRIBUTION from COST_OPTIONS.h (is already set in
0788 ECCO_OPTIONS.h);
0789 - move ALLOW_PACKUNPACK_METHOD2 from AUTODIFF_OPTIONS.h to CTRL_OPTIONS.h;
0790 - set EXCLUDE_WHIO_GLOBUFF_2D in MDSIO_OPTIONS.h (found in some customized
0791 AUTODIFF_OPTIONS.h);
0792 - list CPP options in pkg CPP header file (as undef) when used in any
0793 experiment local set-up;
0794 - fix typo in 2 CPP option names ; rename few (unused) pkg/fizhi CPP options;
0795 - update pkg dependence rule for pkg/bling ; avoid few unused variables.
28038c27d5 Lois*0796 o pkg/kl10:
0797 - get stratification from variable "SigmaR" (passed as argument) instead of
0798 recomputing locally in-situ density (less efficient and inaccurate when
0799 using Non-Linear EOS); update (kl10) ref output for internal_wave exp.
38d78826c7 Ciar*0800 o pkg/ecco:
0801 - add new generic integral cost function "m_boxmean_vol" (e.g. to track
0802 volume of isoycnal layer); add it to lab_sea secondary AD test "noseaice"
0803 and update ref. AD output file.
c26ad343d2 Jean*0804 o tools/build_options:
0805 - fix OpenMP option in ifort optfiles for modern intel compiler.
0806
f6d206d1bd Jean*0807 checkpoint68n (2023/02/08)
2b959ba38e Mart*0808 o pkg/seaice:
0809 - make all seaice-cost code independent of pkg/ecco and remove few
0810 SEAICE_COST.h from pkg/ecco ;
0811 - remove unused code related to ALLOW_SEAICE_COST_SMR_AREA (formerly used
0812 with ECCO_CTRL_DEPRECATED, seaice_cost_driver.F and S/R called from there),
0813 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION + ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION,
0814 and retire associated parameters.
2e3e8c330d Jona*0815 o pkg/dic:
0816 - rename CPP: CAR_DISS -> DIC_CALCITE_SAT and AD_SAFE -> DIC_AD_SAFE and put
0817 all carbonate-saturation code and 3D arrays inside #ifdef DIC_CALCITE_SAT
0818 block and time-ave arrays within #ifdef ALLOW_TIMEAVE ;
0819 - add run-time params: useCalciteSaturation, calcOmegaCalciteFreq, nIterCO3,
0820 selectCalciteBottomRemin, KierRateK, KierRateExp and WsinkPIC ;
0821 - switch order of arguments to "myTime, myIter, myThid" in few remaining
0822 pkg/dic S/R + S/R calls in pkg/gchem ;
0823 - update exp. so_box_biogeo (define CARBONCHEM_TOTALPHSCALE & DIC_CALCITE_SAT)
0824 + add 2 new secondary tests (caSat0 & caSat3) with useCalciteSaturation=T
0825 and using 3-D silicate input file.
edb6656069 Mart*0826 o TAF tape keys:
0827 - rename many local taf keys to use shorter and more consistent names ;
0828 - pkg/thsice: fix bug in key computations.
1d99daeaf6 Oliv*0829 o pkg/diagnostics (+doc):
0830 - fix index-loop range in diagnostics_sum_levels.F and document "fileFlags"
0831 and associated features (vertical interpolation & integral & hFac scaling).
5a6997640b Mart*0832 o pkg/gmredi:
1d99daeaf6 Oliv*0833 - in gmredi_slope_limit.F, fix tape keys by using local tapes.
9293d3c672 Hajo*0834 o pkg/ggl90:
1d99daeaf6 Oliv*0835 - cleaning: remove maskS multiplication in ggl90_calc_visc.F (no equivalent
0836 for KappaRU) and update "output_oadm.ggl90.txt" in OpenAD exp.
ea7679383f Jean*0837 o pkg/ggl90:
9293d3c672 Hajo*0838 - Add code in pkg/ggl90 to parameterize Langmuir Circulation (LC) effects on
0839 vertical mixing (useLANGMUIR=T); follows: Tak et al, Ocean Modelling, 2023;
0840 - Primary effect is to increase mixing length scale due to LC ; the stokes
0841 velocity term is also included in the momentum equation (Coriolis term);
0842 - Tested in new secondary test "gglLC" in exp. "vermix".
0a1233e81a Ou W*0843 o pkg/ecco:
0844 - fix out-of-bound array index issue in cost_gencost_sshv4.F;
0845 - fix a small bug in same S/R (skipping call to smooth_hetero2d(anom_slaobs, )
0846 if gencost_outputlevel(igen_lsc)=0.);
0847 - in same S/R, skip output of "_smooth" file when smoothing is not applied.
c69ccc91fb antn*0848 o pkg/ctrl:
0849 - enable initial sea ice area/heff controls with correct definition of control
0850 indices;
0851 - move condition on useSEAICE inside seaice_init_varia.F (always initialize to
0852 zero) when compiling pkg/autodiff. Similar changes to shelfice_init_varia.F;
0853 - fix out-of-bounds index issue in ctrl_map_ini_genarr.F (igen_shiCDrag=0).
a1d0e455fd Hann*0854 o pkg/dic:
0855 - enable to read in prescribed 3d silicate fields for calcite-saturation
0856 calculation and 3-D pH calculation (#define CAR_DISS).
0857 - add 5 new 3-D diagnostics related to calcite-saturation calculation.
0858 - fix 2-D silica input file from tutorial_global_oce_biogeo and add 3-D silica
0859 input file to so_box_biogeo exp. (currently unused).
0860
af3e3bca65 Jean*0861 checkpoint68m (2022/12/05)
5b172de0d2 Jean*0862 o pkg/gmredi:
0863 - update Redi diffusion and GM (skew-flux or advective form) to also work with
0864 P-coordinates and most current tapering schemes ; change sign of sigmaR (for
0865 now, only within pkg/gmredi) to always be the same as stratification, i.e.,
0866 positive if stratified ; add 2 arguments to GMREDI_SLOPE_LIMIT for 'ldd97'.
0867 - with p-coord, keep sign of slope component unchanged (same as dSigmaX,Y)
0868 and flip sign (-gravitySign) of Redi-tensor extra-diagonal terms ; also keep
0869 stream-function components GM_PsiX & GM_PsiY unchanged and flip sign when
0870 computing bolus-transport (left handed coord).
a1d0e455fd Hann*0871 - add unit conversion factor between p and z coord. at level center, function
0872 of vertical profile of ref. density ; used inside slope-limiter and tapering
0873 function.
5b172de0d2 Jean*0874 - stop if trying to use P-coord with not yet updated gmredi pieces of code.
0875 - add a simple secondary test in front_relax exp. using GM and p-coord.
20dee61641 Mart*0876 o pkg/autodiff:
0877 - cleanup tamc.h: remove unused parameters and nthreads_chkpkt as it is (and
0878 should be) always one; update all verification exp. code_ad versions.
0879 - simplify tape-key dependence on tile indices (remove thread grouping).
f9d7cbfb72 Ou W*0880 o pkg/ctrl:
0881 - add run-time variable ctrlDir to specify a directory different from default
0882 current directory for I/O of controls adjustment and adjoint gradient (xx
0883 and adxx), and other active files; used (as example) in lab_sea experiment.
0884 o pkg/smooth:
0885 - add run-time variable smoothDir to specify a directory different from
0886 default current directory for I/O of smoothing operators.
0887
1575dc0796 Jean*0888 checkpoint68l (2022/10/26)
cc9097e522 Oliv*0889 o pkg/longstep:
0890 - fix initialization of LS_fwFlux ;
0891 - move params report & check to new S/R LONGSTEP_CHECK.
dbb54b7d7a Jean*0892 o model/src:
0893 - fix ocean r-star pressure gradient in case model top is not uniformly at r=0
0894 - update ref output of secondary test "isomip.obcs".
d220271442 Oliv*0895 o tools/genmake2:
0896 - Remove unnecessary awk escape sequence ; this avoids a warning with recent
0897 GNU awk (5.0.1 and newer).
3924ebfa1b Mart*0898 o tools/adjoint_options:
0899 - merge five ad-optfiles into single one with compact list of generic control
0900 variables and obcs-control variables ;
0901 - to use divided adjoint (DIVA), in genmake_local, set new flag USE_DIVA=1
0902 (replacing "adjoint_diva");
0903 - select which Fortran version is sent to TAF by setting TAF_FORTRAN_VERS
0904 to either F77, F90, or F95 (replacing "adjoint_f95") ;
0905 - to replace "adjoint_tamc_compatibility", in genmake_local, set new flag
0906 TAMC_COMPATIBILITY_MODE=1 ;
0907 - remove "-server fastopt.net" to use the default server (fastopt.de)
0908 - use the staf default server (currently "fastopt.de") instead of specific
0909 server "fastopt.net" ;
0910 - remove more commented lines (remove_comments_sed) in src code sent to TAF ;
0911 - remove obsolete "ad_taf_output.f.*" diff-patches in tools/ ;
0912 - remove "ad_optfile.local" files from some verification experiments ; keep
0913 example how to specify local optfile in verification/bottom_ctrl_5x5 ;
8a34959769 dngo*0914 o pkg/streamice:
0915 - changes related to PETc solver interface to be compatible with PETSc
0916 version 3.8 and above and also available without MPI;
0917 - also make sure PETSc is not used at runtime by default.
0918
4cf519afc7 Jean*0919 checkpoint68k (2022/08/17)
cf705a6c8e Mart*0920 o pkg/ctrl, ecco, ... :
0921 Remove untested and obsolete ECCO_CTRL_DEPRECATED code: From now on it is
0922 only possible to specify control parameters through generic controls.
0923 - retire associated pkg/ctrl and pkg/autodiff flags, such as: ctrlUseGen,
0924 xx_hflux_file, xx_hflux_startdate1, ..., ctrlSmoothCorrel2D/3D,
0925 useSmoothCorrel2DinAdMode. Most of these did not have any effect with
0926 undefined ECCO_CTRL_DEPRECATED, but were still allowed in data.ctrl.
0927 Now specifying them is an error and stops the run.
0928 - remove code that assumes ctrlUseGen=F
0929 - remove empty and unused subroutines:
0930 * pkg/ctrl: ctrl_weights.h, ctrl_map_ini_gen.F, ctrl_smooth.F,
0931 ctrl_map_ini.F, ctrl_map_ini_ecco.F, ctrl_map_ini.F, ctrl_map_ini_ecco.F
0932 * pkg/ecco: cost_forcing.F, cost_hyd.F, cost_internal_params.F, cost_ssh.F
0933 ecco_cost_summary.F
0934 * pkg/smooth: smooth_correl2dw.F
0935 * pkg/seaice: seaice_cost_areasst.F
0936 - adjust parameters in verification experiment that still contained retired
0937 parameters
0938 - switch global_ocean.cs32x15.thsice to using generic control variables
0939 Note: some untested code (notably pkg/admtlm, which did not compile before)
0940 will be more difficult to resurrect without the ECCO_CTRL_DEPRECATED code.
f18a893d42 Mart*0941 o pkg/ggl90:
0942 - adjust code to also work under an ice-shelf (with pkg/shelfice); idemix
0943 under ice-shelf not fixed yet.
0944 - turn on ggl90 in isomip experiment secondary test "obcs" and update
0945 reference output file.
94a8024bbe Jean*0946 o pkg/gmredi:
0947 - allow to read-in 3-D background isopycnal (Redi) and thickness (GM)
0948 diffusivity without pkg/ctrl: new 3-D arrays, new CPP options:
0949 GM_READ_K3D_REDI & GM_READ_K3D_GM and new input files: GM_K3dRediFile &
0950 GM_K3dGMFile (replacing retired GM_isopycK3dFile & GM_background_K3dFile).
0951 - update code for ALLOW_KAPGM_CONTROL & ALLOW_KAPREDI_CONTROL to use
0952 these new 3-D arrays (from GMREDI.h) and move setting of 3-D control arrays
0953 from from ini_mixing.F to gmredi_init_varia.F (+ adjust call condition);
0954 Note: need to define new option GM_INPUT_K3D_GM and/or GM_INPUT_K3D_REDI
0955 to use KAPGM_CONTROL and/or KAPREDI_CONTROL.
0956 - remove obsolete code & CPP option ALLOW_KAPGM/KAPREDI_CONTROL_OLD
0957
f03a2f5e21 Jean*0958 checkpoint68j (2022/06/28)
cc60455fbb Mart*0959 o pkg/exf:
0960 - implement drag coefficient of Large and Yeager (2009), Climate Dynamics, 33,
0961 pages 341-364, within #ifdef ALLOW_DRAG_LARGEYEAGER09
fe1862e69b Mart*0962 o autodiff(TAF):
0963 - fix few taf recomputation and conflict warnings in: calc_3d_diffusivity.F
0964 (PCELL_MIX_CODE), pkg/bling & dwnslope_apply.F ; update reference AD output
0965 of exp. that use pkg/dwnslope (lab_sea).
f6de6620bc Mart*0966 o pkg/thsice:
0967 - fix bug in computation of ustar (case velocity=0) in thsice_calc_thickn.F;
0968 - introduce & document THSICE_REGULARIZE_CALC_THICKN flag.
20a156cdce Mart*0969 o pkg/generic_advdiff (TAF):
0970 - in gad_advection.F, replace global tapes "comlev1_bibj_k_gad" &
0971 "comlev1_bibj_k_gad" by local tapes; avoid unnecessary recomputations, but
0972 recompute full routine (only) once in ad-routine;
0973 - this affects results when useApproxAdvectionInAdMode=T, since now all tapes
0974 are computed using approximate Adv-Scheme (inAdMode=T); udate AD ref. output
0975 of exp. global_ocean.cs32x15.seaice.
3bafcf6020 Timo*0976 o pkg/shelfice:
0977 - Remove ALLOW_SHIFWFLX_CONTROL and all xx_shifwflx related code in favor of
0978 already implemented gentim2d;
0979 - move update of shelficeLoadAnomaly inside shelfice_step_icemass.F (within
0980 IF (SHELFICEMassStepping) ...);
0981 - fix storage dir for SHELFICEMassStepping, allowing to realFreshWaterFlux=T
0982 with ALLOW_AUTODIFF defined (remove STOP there). Still not working with
0983 OpenAD (add a STOP in shelfice_check.F).
0984
9bcb497701 Jean*0985 checkpoint68i (2022/04/27)
6b551785d1 Jean*0986 o eesupp/src:
0987 - simplify reading parameter file, using single scratch file (instead of 2).
2e7aec9951 dngo*0988 o verification, OpenAD:
0989 - make all OpenAD experiments use generic control variables, so that from now
0990 on, the ECCO_CTRL_DEPRECATED code is no longer tested in verification
0991 (neither in verification_other, where it never was tested), except for
0992 global_ocean.cs32x15.thsice (this is intentioal).
113b21cd45 Mart*0993 o autodiff(TAF):
0994 - avoid unnecessary local recomputations and associated warnings by storing to
0995 local tapes in: seaice/advect.F, gad_dst3fl_impl_r.F, gmredi_slope_limit.F,
0996 shap_filt_uv_s2.F, solve_pentadiagonal.F
a85293d087 Mart*0997 o pkg/thsice:
0998 - fix store directives + modify code of thsice_calc_thickn.F, thsice_extend.F
0999 and thsice_solve4temp.F to avoid 28 recomputation warnings and recomputing
1000 the state unnecessarily;
1001 - define new tape and retire two old thsice related tapes (commented out for
1002 now) in the_main_loop.F;
1003 - change offline_exf_seaice.thsice experiment to be more sensitive to changes;
1004 - fixing a bug leads to smaller gradient errors and correct TLM cost function
1005 values and requires updating (both ADM and TLM) offline_exf_seaice.thsice
1006 and global_ocean.cs32x15.thsice reference output;
07b7562e86 Ou W*1007 o pkg/ctrl:
1008 - fix issue in S/R CTRL_MAP_GENARR3D by explicitly set xx_gen to zero where
1009 wgenarr3d is zero ; also replacing 10^xx_gen with EXP(log(10)*xx_gen) for
1010 log10ctrl produces small differences at machine truncation level.
3d93c0a01e Ou W*1011 o eesupp & pkg/mdsio:
1012 - new (CPP) Macro to open read-only files with ACTION='read', added to
1013 most pkg/mdsio S/R (+ exf_interp_read.F); disable this in few old compiler
1014 optfiles (g77, pgf77) by adding EXCLUDE_OPEN_ACTION to DEFINES list.
51575f66de Mart*1015 o model:
1016 - new CPP option to exclude (= default) S/R CONVECTIVE_ADJUSTMENT_INI;
1017 to reproduce old results, define new option INCLUDE_CONVECT_INI_CALL in
1018 two verification experiments: exp2 and tutorial_tracer_adjsens.
1019 - add a check for INCLUDE_CONVECT_CALL if cAdjFreq <> 0.
fefbff5637 Mart*1020 o tools/build_options:
1021 - new optfile "darwin_arm64_gfortran" for Mac ARM 64-bit processor.
6514215240 Jean*1022 o pkg/gmredi:
1023 - add deep-factor to pkg/gmredi code to work with "deepAtmosphere=T".
a99d705983 Jean*1024 o verification/cpl_aim+ocn:
1025 - add secondary test set-up using seaice dynamics (pkg/seaice) as part of
1026 ocean component and update script to handle option to run multiple test.
adac922254 dngo*1027 o verification/halfpipe_streamice:
1028 - update OpenAD test by removing ECCO_CPPOPTIONS.h (but, for now, keep local
1029 version: ctrl_map_gentim2d.F & ctrl_map_ini_genarr.F in code_oad).
64811cb024 Jean*1030 o pkg/mypackage:
1031 - improve description (for a coding style example).
7e00d7e8f9 Jean*1032 o model:
1033 - add option to apply a correction for net global fresh-water flux imbalance
1034 proportional to, fixed in time, 2-D weight field that is read-in from file ;
1035 - new integer selector "selectBalanceEmPmR" (=0: off, =1: uniform correction,
1036 =2: correction scaled by weight) that replaces logical switch "balanceEmPmR"
1037 with backward compatibility setting.
1038
479cbc238b Jean*1039 checkpoint68h (2022/03/22)
aa93ca8e85 Ciar*1040 o pkg/ecco:
0cd0083da8 Ou W*1041 - new src files: ecco_init_fixed.F & ecco_diagnostics_init.F ;
1042 - new SSH diagnostics: SSH,SSHNOIBC (with & w-out Inv.Barometer corr.: SSHIBC)
1043 STERICHT (steric height anomaly); and Bottom-Pressure/Mass: OBP & OBPGMAP ;
1044 - add arg myTime & myIter to S/R ECCO_PHYS and adjust calls ; change to use
1045 model "rhoInSitu" (instead of recomputed rho) for Greatbatch correction ;
1046 this affects cost "m_eta".
1047 o pkg/ecco:
aa93ca8e85 Ciar*1048 - add new feature (within gencost) to evaluate cost-function contribution
1049 over specified density range (instead of depth range, see issue #483);
1050 - add few run-time parameters including logical switch: gencost_useDensityMask
1051 - test this new feature in lab_sea/input_ad.noseaice and update ref. output.
ef7fa68a19 Jean*1052 o pkg/ptracer (adjoint):
1053 - remove AUTODIFF_PTRACERS_SPLIT_FILES as it has no effect.
1054 o pkg/generic_advdiff & seaice (adjoint):
1574069d50 Mart*1055 - avoid recomputation in Second-Order Moment (SOM) advection S/R by using
1056 local tapes ; reduce local tapesize in seaice_solve4temp.F ;
479cbc238b Jean*1057 - fix key and size of tapes in multi-dimensional advection routines and adjust
1574069d50 Mart*1058 maxcube value (2 or 3 if using CubedSphereExchange) in few exp. "tamc.h".
30ad0459d6 Jean*1059 o pkg/mdsio:
1060 - retire all S/R from mdsio_rw_slice.F after replacing the last 2 calls to
1061 MDSWRITEFIELD{X,Y}Z in pkg/ctrl/ctrl_set_globfld_{x,y}z.F with calls to
1062 S/R WRITE_REC_{X,Y}Z_RL (from pkg/rw).
1063 - remove src file mdsio_rw_field.F & mdsio_rw_slice.F from NOOPTFILES list
1064 in few linux_amd64_ifort* optfiles.
1065 - move if statement out of "lengthBuff" loop in mdsio_{read,write}_whalos.F
16cc32c739 Mart*1066 o verification AD exp.:
1067 - remove ECCO_CPPOPTIONS.h from global_ocean_ebm/ and halfpipe_streamice/
1068 code_ad/ dir and replace by appropriate AUTODIFF/CTRL/COST_OPTIONS.h ;
1069 - for halfpipe_streamice AD exp., make necessary adjustments in pkg/streamice
30ad0459d6 Jean*1070 and remove ALLOW_GENTIM2D_CONTROL from store directive header files
16cc32c739 Mart*1071 streamice_ad_check_lev?_dir.h ;
1072 - remove customized version of ctrl_map_gentim2d.F & ctrl_map_ini_genarr.F
1073 from halfpipe_streamice/code_ad/ and add corresponding code to pkg/ctrl.
1074
ec9af22855 Jean*1075 checkpoint68g (2022/02/19)
0bad585a21 Navi*1076 o doc:
1077 - fix some math notation in docs.
385da9f3ec Jean*1078 o pkg/obcs:
1079 - avoid division by zero when useOBCStides=.True. and tidalPeriod=0.
8233d0ceb9 Jean*1080 o pkg/gmredi:
1081 - fix basic code to also work with dry grid cells near the top (e.g., under
1082 ice-shelf) and in this case, for now, stop if unsafe features are used ;
1083 - fix tapering 'ac02' and 'stableGmAdjTap' ;
1084 - add a secondary test, "input.top", in verification exp. front_relax to test
1085 GM with dry cells at the top (+ also 'ac02' tapering) ;
1086 - update few adm & tlm & oad ref. output from exp. global_ocean.90x40x15
1087 since adding better masking in gmredi_s{x,y}rtransport.F does affect AD &
1088 TLM gradient (@ machine truncation level).
3c775cbf98 Mart*1089 o pkg/autodiff:
1090 - new CPP-flags allow to turnoff (default) autodiff_store/restore entirely:
1091 * New flags AUTODIFF_USE_STORE_RESTORE, AUTODIFF_USE_STORE_RESTORE_OBCS to
1092 turn on autodiff_store/restore, undefined by default ;
1093 * AUTODIFF_EXCLUDE_ADEXCH_RS to skip calls to some AD-exch (if missing).
1094 - improve comments in AUTODIFF_OPTIONS.h, fix some store directives for new
1095 default, which are:
1096 #define ALLOW_AUTODIFF_WHTAPEIO
1097 c#define AUTODIFF_USE_MDSFINDUNITS
1098 #undef AUTODIFF_USE_STORE_STORE_RESTORE
1099 #undef AUTODIFF_USE_STORE_STORE_RESTORE_OBCS
1100 and update local AUTODIFF_OPTIONS.h files from verification experiments.
1101 - experiment specific setting:
1102 * define AUTODIFF_EXCLUDE_ADEXCH_RS in exp.: hs94.1x64x5, obcs_ctrl & OpenAD
1103 * increase "nWH" value in local MDSIO_BUFF_WH.h for exp.:
1104 global_oce_biogeo_bling, offline_exf_seaice & tutorial_dic_adjoffline
1105 - add a TAF "INCOMPLETE" directive for TICES and wVel to avoid a TAF bug.
1106 - fix a TAF store directive to avoid extra call of "load_fields_driver"
1107 with EXF_SEAICE_FRACTION defined.
f2389c73b0 Jean*1108 o pkg/gmredi:
1109 - rename S/R, CPP option (GM_BATES_K3D), on/off switch (GM_useBatesK3d),
1110 parameters (GM_Bates_*) and 3-D var (GM_BatesK3d) of Bates etal (JPO, 2014)
1111 scheme that computes 3-D field GM/Redi diffusivity (analog to Visbeck etal
1112 variable/option naming example).
1113
65dd265852 Jean*1114 checkpoint68f (2022/01/14)
f2389c73b0 Jean*1115 o pkg/exf:
56d13a40ed Mart*1116 - clean-up relative wind implementation so that uwind and vwind are kept
1117 unchanged (always vanilla atmospheric winds after interpolation) while
1118 relative wind is computed locally; add diagnostics for relative wind.
1119 - adjust pkg/seaice relative-wind code (+ clean-up SEAICE_GREASE code).
0c240d16ef Jean*1120 o pkg/kpp:
1121 - avoid updating input argument "kmtj" in S/R BLDEPTH (in: kpp_routines.F);
1122 this also remove/avoid 3 recomputation warnings for kmtj in adm (TAF) built.
0fbff46b46 dngo*1123 o pkg/streamice:
1124 - fix regularised coulomb basal stress impl to avoid issues with adjoint ;
1125 - cancel metric terms in stress tensor for cartesian grid ;
1126 - allow (time-indep) velocities to be imposed from external file rather than
1127 solved for ;
1128 - allow for specification of log of controls as well as sqrt ;
1129 - allow termination of adjoint fixed point loop based on relative and absolute
1130 error ;
1131 - terminate adjoint fixed point loop when change between most recent iterates
1132 begins to increase (a sign of unstable growth from linear solve errors ?);
1133 update OAD output of exp. halfpipe_streamice (affected by this modif).
c704c5a1ef Mart*1134 o pkg/seaice:
1135 - replace hard-coded parameters for JNKF line search by new runtime parameters
1136 SEAICE_JFNK_lsGamma and SEAICE_JFNK_lsLmax ;
1137 - increment line search counter after reporting and fix an if statement, so
1138 that zeroth step is not counted for more consistent debugging output.
f397060a05 dfer*1139 o tools/build_options:
3ee2cce2f5 Jean*1140 - update pleiades optfile "linux_amd64_ifort+mpi_ice_nas"
f397060a05 dfer*1141 - rename/update optfile for UK HPC Archer2.
9f5240b52a Jean*1142 o pkgs:
1143 - remove/avoid unused variables from AD verification exp. built except from
1144 halfpipe_streamice (pkg/streamice); also clean-up a bit pkg/smooth.
3b6c79e4de Mart*1145 o pkg/autodiff:
1146 - introduce separate tapes for integer arrays: the corresponding routines
1147 just convert between integer and double precision arrays and call the
1148 original adread/adwrite routines.
934d981c17 Jean*1149 o pkg/atm_compon_interf:
1150 - only with Atm-Phys pkg, allow "regional coupling", i.e. coupled only where
1151 there is ocean, keeping Atm-Phys basic mixed-layer elsewhere.
1152
d7c15ab3ba Jean*1153 checkpoint68e (2021/12/10)
ae17457769 Andr*1154 o lsopt & optim:
1155 - update Makefiles and README.
c7de4e3cb2 antn*1156 o pkg/ctrl:
37e373688b Mart*1157 - remove unused flag ALLOW_ECCO_OPTIMIZATION and associated code, always save
1158 "fcloc" to gradient vector file and save fcloc=0 to initial ctrl vector file
1159 (which is never used); also remove it from any code*/CTRL_OPTIONS.h.
1160 o pkg/ctrl:
c7de4e3cb2 antn*1161 - replace few calls to MDS_READ/WRITE_FIELD with corresponding call to
1162 pkg/rw READ/WRITE_REC_3D_RL ; also clean-up: ctrl_map_ini_gen.F
7855a13227 Mart*1163 o tape related code (adjoint):
1164 - clean-up tape code in the init-phase, mainly in the_main_loop.F and in
1165 ctrl_map_ini_gentim2d.F ;
1166 - remove unused (ecco) cost_averages_bar_directives.h ;
1167 - adjust comments in (autodiff) adread_adwrite.F & in main_do_loop.F
c3d0b098ae Lars*1168 o eesupp:
1169 - fix scratch file names when using PDAF.
6e2befed03 Oliv*1170 o pkg/exf:
1171 - fix issue in interannual monthly forcing addition (case ${fld}period=0)
bb459eb78c Jean*1172 o model/src:
1173 - skip reading kapGM and kapRedi from ini_mixing.F when useGMRedi is .FALSE.
deacece587 Oliv*1174 o pkg/exf:
1175 - add option for interannual monthly forcing with pkg/cal by setting
1176 ${fld}_period=-1. (like -12. indicates climatological monthly forcing),
1177 available with or without useExfYearlyFields ; update exp. global_with_exf
1178 SST forcing to test this new option with and without useExfYearlyFields.
d68b36a485 Mart*1179 o model/src:
1180 - define local arrays cg2d_q/v/z without overlaps in all 4 cg2d*.F
1181 and skip initialisation of cg2d_q in cg2d.F
9d0c386f0c dngo*1182 o tools/genmake2:
1183 - new option to call OpenAD compiler in a singularity container (if provided);
1184 add option to testreport too and update OpenAD doc (in section 7.5).
1185
4300da6d2c Jean*1186 checkpoint68d (2021/11/05)
71a2d60687 Jean*1187 o verification/*/results:
1188 - update few adm and tlm refence output to get closer agreement.
75c5b64bda Jean*1189 o verification/global_ocean.90x40x15:
1190 - no longer use old bug (fixed in Oct 2015) in KAPGM_CONTROL & KAPREDI_CONTROL
1191 code and update AD & TL ref. output for kapgm & kapredi tests ;
1192 - other small cleaning: finish removing OLD_THSICE_CALL_SEQUENCE code ; remove
1193 "cost_yftype" from experiments "data.ecco" ; move ALLOW_ECCO_OPTIMIZATION
1194 to the right header file.
016b84c482 Mart*1195 o pkgs pp81, my82, opps & ggl90:
1196 - remove pkg/timeave and pkg/mnc output from these mixing packages (since
1197 this functionality is available with pkg diagnostics); add 1 diagnostics
1198 to pkg/opps (to replave TAVE output).
7ea6a3439c Jean*1199 o tools/build_options:
1200 - add "-DAUTODIFF_USE_MDSFINDUNITS -DPROFILES_USE_MDSFINDUNITS" to DEFINES
1201 in g77 optfile ; this allows to run set-up with AUTODIFF_WHTAPEIO and/or
1202 with pkg/profiles using g77 (with S/R MDSFINDUNITS) while other compilers
1203 continue to use local version with extended range of I/O units number.
ebcc29af97 Jean*1204 o pkg/ecco:
1205 - fix halo initialisation for argument "active_var" in cost_genread.F ;
1206 - change "facNum" expression in cost_gencost_transp.F, to be consistent with
1207 comment in src code, by adding missing factor "nSx"; also avoid division
1208 in PARAMETER statement.
1c2b1fa3bc Mart*1209 o model/inc:
1210 - move potentially time dependent grid variable from GRID_RS to new common
1211 block GRID_VAR_RS (hFacW/S/W, etc.) and split common block CG2D_I_R into
1212 a _RL and a _RS part ; adjust AD common block accordingly.
11c3150c71 Mart*1213 o verification AD experiments:
1214 Update TAF AD exp. so that none relies anymore on ECCO_CTRL_DEPRECATED code:
1215 - remove #define ECCO_CTRL_DEPRECATED from experiments: 1D_ocean_ice_column,
1216 bottom_ctrl_5x5, global_with_exf, lab_sea, OpenAD, tutorial_dic_adjoffline,
1217 tutorial_global_oce_biogeo & tutorial_global_oce_optim ; use instead generic
1218 control and generic cost.
1219 - for now, keep experiment global_ocean.cs32x15 with both ECCO_CTRL_DEPRECATED
1220 code and generic control + generic cost.
1221 - also remove ECCO_CPPOPTIONS.h (use instead set of pkg specific OPTIONS
1222 header files) from these experiments above.
1223 - results unchanged except few digits in cost & ad-monitor for lab_sea &
1224 obcs_ctrl ; and few minor recomp. warnings count changes for
1225 tutorial_global_oce_biogeo (-4) and for tutorial_dic_adjoffline (+2).
1226 Update pkgs as needed:
1227 - pkg/ecco: fix field declarations for ecco_toolbox routines and cost_readgen,
1228 new toolbox routines ecco_offset, ecco_maskmindepth, make argument lists
1229 more consistent between ecco_toolbox routines and remove unused subroutines;
1230 - pkg/cost: fix ALLOW_COST_DEPTH contribution;
1231 - pkg/ctrl: add more "ifdef ECCO_CTRL_DEPRECATED" where necessary;
1232 - pkg/exf: add xx_snowprecip as generic control, adjust CPP-flags.
d97a730ee3 Jean*1233 o pkg/gmredi:
1234 - remove condition (ifdef GM_NON_UNITY_DIAGONAL) around 3-D arrays Kux & Kvy
1235 to simplify how GMREDI is applied (e.g., gmredi_x/ytransport); fill up these
1236 2 arrays with constant value (gmredi_calc_tensor.F & offline_get_diffus.F)
1237 when GM_NON_UNITY_DIAGONAL is undef (to reproduce old results).
1238 - also with GM_NON_UNITY_DIAGONAL undef, fix ALLOW_KAPREDI_CONTROL averaging.
c59dd234b1 Jean*1239 o tangent-linear:
1240 - fix few hand-written tangent-linear src code (in autodiff & ctrl pkgs);
1241 - add new target "ftlobj" to Makefile (similar to "obj" & "adobj" for forward
1242 and AD built) and corresponding switch in testreport ;
1243 - fix non-standard sed command (for Mac) in TLM testreport.
1244
2ffc13e2be Jean*1245 checkpoint68c (2021/10/02)
dc26f158aa Mart*1246 o pkg/seaice:
1247 - update some dynamics solver default so that now:
1248 a) SEAICEuseEVPstar = .TRUE. ; b) SEAICEuseEVPrev = .TRUE. ;
1249 c) LSR_ERROR = 1.e-5 (previously was 1.e-4) ;
1250 - put back old default in exp. lab_sea (primary test);
1251 - modify (simplify?) logic in seaice_readparms.F and seaice_check.F.
cf8a0ac466 Jean*1252 o pkg/grdchk:
1253 - allow to use "recglo" to specify a particular control time record for
1254 gradient check (was previously inactive).
f4a4b4841b Jean*1255 o pkg/exf:
1256 - new parameters to reduce AD-exf monitor output:
1257 1) exf_adjMonFreq (def= adjMonitorFreq), = 0. suppresses all output
1258 2) exf_adjMonSelect: =1 (def): less output ; =3 as before, =0 : no output
1259 - fix some AD-common block name + content to match TAF directives (in
1260 common.flow) and TAF generated code.
1261 - skip monitor of model forcing AD-variables (unless monitorSelect=4).
44d3986245 Jean*1262 o pkg/ecco + other:
1263 - fix few non-standard syntax (+ repeated setting of "gencost_msk_is3d").
7fbec11c25 Jean*1264 o pkg/bling:
1265 - fix call to S/R BLING_BIO_NITROGEN when USE_SIBLING is defined.
13d362b8c1 Ou W*1266 o pkg/ecco:
1267 - put various dimensions related to gencost out of "ecco.h" into specific
1268 (new) header file "ECCO_SIZE.h" and rename "ecco.h" to "ECCO.h" ;
1269 - add gencost param "gencost_kLev_select" to select a vertical level (from 3-D
1270 array) to form 2-D gencost ; currently only used in drifter velocity cost ;
1271 - add a couple of costs based on 1) inverse barometer (IB) corrected model sea
1272 level for altimetry data comparison 2) OBP excluding contribution from
1273 global mean atmospheric pressure for comparisons with GRACE data.
7f5c807389 Jean*1274 o pkg/autodiff:
1275 - fix type (_RS vs_RL) of AD-vars in hand-written AD routine cg2d_mad.F and
1276 in adcommon.h, common block adgrid_rs.
042d2503e1 Jean*1277 o model/src:
1278 - fix missing initialisation of local working arrays that were previously
1279 in common block in CG2D.h (needed when using blank tiles).
6b3f5dbce1 Hann*1280 o pkg/dic:
1281 - fix calculation of carbonate saturation state (with CAR_DISS defined) when
1282 #define CARBONCHEM_SOLVESAPHE ; no current test run with #define CAR_DISS.
aecc8b0f47 Mart*1283 o pkg/autodiff:
1284 - add code for Full-Adjoint of cg2d in renamed (from cg2d_sad.F) routine
1285 cg2d_mad.F (cg2d manual adjoint) ;
1286 - new runtime params cg2dFullAdjoint (data.autodiff), useNSACGSolver (data,
1287 default to "FALSE"), cg2dMinItersNSA (data, defaults to 0) ;
1288 - new sub-verification experiment bottom_ctrl_5x5.facg2d to test new
1289 Full-Adjoint capability ;
1290 - update primary test experiment bottom_ctrl_5x5 to always use a minimum
1291 number of 10 CG2D iterations (changes results but improves accuracy) ;
1292 - modify AD-experiment global_ocean.90x40x15.bottomdrag to use full nonlinear
1293 free surface (nonlinFreeSurf=4) and cg2dFullAdjoint=True.
042d2503e1 Jean*1294 - move CG2D working arrays out of CG2D.h common blocks (not necessary)
1295 to local arrays within each cg2d S/R.
aecc8b0f47 Mart*1296
93664352be Jean*1297 checkpoint68b (2021/08/24)
906a61c194 Ou W*1298 o pkg/ecco:
1299 - add time-series output of global mean steric height change at each time step
1300 (variable: sterGloH, with #define ALLOW_PSBAR_STERIC) ; turned on
1301 with run-time switch "ecco_output_sterGloH=T" ; add option to keep file open
1302 (+ single meta file writing) with "ecco_keepTSeriesOutp_open=T" switch.
31f96e9372 Jean*1303 o pkg/ggl90:
1304 - fix EXCH calls in pkg/ggl90 when IDEMIX is used: no additional EXCH when
1305 using zero horizontal diffusion of IDEMIX_E (IDEMIX_tau_h=0) but with
1306 IDEMIX_tau_h > 0, EXCH both IDEMIX_E and GGL90TKE ; this affects results
1307 of test experiment cs32.in_p and fix restart issue ;
1308 - more consistent/simpler idemix code: use model parameter value for PI,
1309 reduce number of IDEMIX global array, add TKE tendency from IDEMIX as output
1310 of S/R GGL90_IDEMIX ; use double product of IDEMIX_E instead of power of 2
1311 which affects results at machine truncation level ;
1312 - update some IDEMIX default param values (following Pollmann et al., 2017)
1313 but keep old default values in global_ocean.90x40x15.idemix ;
1314 - apply also option calcMeanVertShear to uStarSquare calculation (wind-stress
1315 magnitude) and switch on calcMeanVertShear in test experiment cs32.in_p.
0320e25227 Mart*1316 o model/src + pkgs ggl90, exf & seaice: ocean in P-coordinate
1317 - read geopotential anomaly directly into phi0surf instead of via pLoad (was
1318 a hack), specified with new input filename "geoPotAnomFile" in data&PARM05 ;
1319 - adjust MXLDEPTH diagnostic for pressure coordinates ; make sure sigmaR is
1320 computed the same way in P-coord as it is in Z-coord.
1321 - for penetrating Short-wave and geothermal heating as well as for exf forcing
1322 and seaice, use the correct P-coord vertical index for bottom and surface ;
1323 - add a flag sIceLoadFac (in "data", default=1.) to be able to turn off
1324 seaice surface pressure loading, mainly for Z-coord (since not currently
1325 supported in P-coord) ;
1326 - use diagnostics "phiHydLow" for seaice dynamics with P-coord ocean to get
1327 surface tilt term (instead of using ETAN as in Z-coord); fix restart by
1328 adding phiHydLow (only if useSEAICE and usingPCoords) to main pickup file ;
1329 - in pkg/ggl90, apply simple scaling to get mixing-length in meters (from
1330 pressure) so that no parameter changes are necessary ; significant code
1331 changes regarding surface & bottom index + direction of vertical k loop ;
1332 - add secondary test "in_p" to experiment global_ocean.cs32x15 (similar to
1333 Z-coord secondary test "seaice" but using pkg/ggl90 and without pkg/gmredi).
62748458e3 Jeff*1334 o tutorial_reentrant_channel:
1335 - add python notebook (for analysis), add python script to generate input
1336 files (+ update matlab version) and update this tutorial docs.
9c166ce5bb Jean*1337 o verification/vermix:
1338 - change ggl90 secondary test to use (pkg/ggl90) mxlMaxFlag=3 (instead of 2)
1339 and update reference output.
a78204c019 Mart*1340 o pkg/ctrl:
1341 - move S/R CTRL_MAP_GENARR2D/3D out of file "ctrl_map_ini_genarr.F" into
1342 a new file "ctrl_map_genarr.F" ;
1343 - clean-up local versions of ctrl_map_gentim2d.F and ctrl_map_ini_genarr.F
1344 from code_ad dirs (i.e., minimize diff with standard version from pkg/ctrl).
375581a429 Jean*1345 o model/src:
1346 - improve REMOVE_MEAN_RL/RS subroutines (address issues raised in issue #501)
1347 including results independent of tile to proc mapping, correction extended
1348 to overlap regions, improve accuracy of _RS version when RS is real*4 and
1349 and enable the use 2-D mask maskInC/W/S when applied to 3-D array. Change
1350 argument list (add myIter, flip order + change mask arg from 3-D to 2-D).
def7daa328 Jean*1351 o verification/global_ocean.90x40x15:
1352 - increase "grdchk_eps" from 1e-7 to 10 in AD test kapgm to improve
1353 accuracy of FD gradients ; update reference output.
ac8f9c9b75 Jean*1354 o verification/OpenAD:
1355 - add ggl90 pkg to code_ad/packages.conf to get it tested in one TAF-AD exp.
39fa6219cc Oliv*1356 o doc:
1357 - require sphinxcontrib-bibtex 2.0.0 or higher
1358
073783ff30 Jean*1359 checkpoint68a (2021/07/16)
16b9a002a2 Mart*1360 o pkg/seaice:
bcc88b4b54 Jean*1361 - clean up and simplify TAF store directives in do_oceanic_phys.F
1362 for seaice_model to avoid unnecessary recomputations ;
1363 - in testreport, count and report number of times s/r seaice_model is called.
1364 o pkg/seaice:
16b9a002a2 Mart*1365 - fix (untested) multi-threading and recomputations in seaice_solve4temp.F
4e4ad91a39 Jean*1366 o files that include "tamc.h":
1367 - add missing declaration of local keys for TAF store-dir in pkg/obcs
1368 (ALLOW_OBCS_STEVENS) and pkg/bling (USE_BLING_V1, PHYTO_SELF_SHADING) ;
1369 - add missing AUTODIFF_OPTIONS.h in few places (e.g., in pkg/ebm), needed to
1370 get ALLOW_AUTODIFF_TAMC defined ;
1371 - change few ALLOW_AUTODIFF <-> ALLOW_AUTODIFF_TAMC ;
1372 - remove included "tamc.h" in few files from pkgs seaice, streamice, bling, +
1373 in exf_radiation, longstep_thermodynamics, obcs_sponge & pp81_ri_number S/R.
1374 - define ALLOW_OBCS_STEVENS in AD exp. obcs_ctrl (to check it compiles).
93de14eac5 Jean*1375 o pkg/ecco:
1376 - fix incorrect order of array indices for "objf_gencost" and "num_gencost"
1377 in 2 gencost v4 S/R (bpv4 & sstv4).
4351f9c554 Jean*1378 o eessup/inc & pkg/thsice:
1379 - Remove 2 CPP options for deprecated code and remove corresponding code:
1380 a) USE_OLD_MACROS_R4R8toRSRL (added in May 2009) and
1381 b) OLD_THSICE_CALL_SEQUENCE (added in Jan 2013).
dcd3df3e6a Ou W*1382 o pkg/shelfice:
4351f9c554 Jean*1383 - fix missing local keys declaration in shelfice_thermodynamics.F for TAF
dcd3df3e6a Ou W*1384 storge dir. with SHI_ALLOW_GAMMAFRICT defined ;
1385 - remove included PACKAGES_CONFIG.h in many verification exp. "tamc.h".
11d5e9fc04 Gael*1386 o tools/build_options:
1387 - update gfortran optfile for MacBook Pro "darwin_amd64_gfortran" to work with
1388 gfortran version 10 (or higher), similar to linux version update.
7c50f07931 Mart*1389 o pkg/ctrl & other:
dcd3df3e6a Ou W*1390 - cleanup: move declarations of local variables from header files ctrl.h and
7c50f07931 Mart*1391 AUTODIFF.h to the local variables section in the respective routines ;
dcd3df3e6a Ou W*1392 - move declaration of local keys and variables from header file tamc.h to
1393 subroutines where they are used.
1394 ==> IMPORTANT: This requires updating all customised versions of "tamc.h",
1395 from each and every TAF-AD setup.
7c50f07931 Mart*1396 - remove tamc_keys.h + remove tamc (+tamc_keys) from all "cb2mFiles" lists ;
1397 - disentangle ALLOW_AUTODIFF/ALLOW_AUTODIFF_TAMC/ALLOW_OPENAD a bit more ;
1398 - remove unused variables where this is straightforward ;
1399 - remove a few i/jmin/max variables.
1400
b7589390f2 Jean*1401 checkpoint67z (2021/06/12)
49a029e3de Mart*1402 o veritication:
1403 - make testreport count and report the number calls of S/R load_fields_driver
1404 and do_oceanic_phys in AD-code (similar to TAF error & warning count).
2b4c90c108 Mart*1405 o pkg/kpp:
1406 - add CPP-flags to turn off diffusivity matching at bottom of boundary layer ;
1407 - add CPP-flag to turn on taper shear mixing in the case of very small shear ;
1408 - add FLAG to turn on smooth regularisation of divisions by small numbers:
1409 1/(var+eps) instead of 1/MAX(var,eps) ;
1410 - fix a small masking error ;
1411 - fix some unfortunate loop ordering and spurious recomputations ;
1412 - add new diagnostics KPPshsq, KPPdVsq ;
1413 - update exp. vermix (which has KPP_ESTIMATE_UREF defined) reference output.
aa6b2555c8 Jean*1414 o model/src:
fb2c52cfd4 aver*1415 - in the main code, add option and code for sound speed calculation with
1416 corresponding diagnostics ; turned on in exp. global_oce_biogeo_bling.
1417 o model/src:
aa6b2555c8 Jean*1418 - fix few loop range to allow to run with OLx,y=1 when momStepping=F ;
1419 - add check and stop if momStepping=T and overlap-size is smaller than 2.
1420 o pkg/ggl90:
ce9abcce9d Jean*1421 - add 3 store directives for gg90tke in ggl90_calc.F and break some loops
1422 in two to help TAF without extra storage requirements.
2383f7d4e9 Mart*1423 o pkg/seaice:
1424 - adjust store directives in seaice_growth_adx.F:
1425 *) add store directives to avoid calling seaice_solve4temp in AD-mode
1426 *) adjust/remove/reorganise for good balance between storing and recomputing
1427 *) fix a small bug (full 4D arrays were stored instead of 2D for each bi,bj)
1428 *) local option "SEAICE_GROWTH_ADX_STORE_MORE" (not recommended)
1429 reduces the recomputations but increases the memory requirements.
1430 - update ref. AD output of experiment offline_exf_seaice (the only one using
1431 SEAICE_GROWTH_ADX): no Grad-Check changes but differences in AD-Monitor.
7b8b86ab99 Timo*1432 o pkg/ctrl & pkg/shelfice:
1433 - generalize masking procedure for control parameters, fixes procedure for
1434 ice-shelf controls ;
1435 - add ability to control base 10 logarithm in generic control arrays ;
1436 - add shiTransCoeffT, shiTransCoeffS, and shiCDrag as control variables ;
1437 - add ability to compute shelfice freshwater and heat fluxes through ecco
1438 package.
9c41af81f6 Timo*1439 o store directives (model/src, pkg/exf, ...):
1440 - By adding many store directives for variables after they have been computed
1441 the corresponding s/r load_fields_driver, oceanic_phys, solve_for_pressure
1442 no longer need to be called in the AD-routine forward_step_ad.
1443 A as a consequence the forward part of forward_step is not recomputed,
1444 and there are far fewer store statements in the AD-code.
1445 - Most of the new store directives and many of the old ones are collected in
1446 two new files "check_lev1_dir_forcing.h" and "check_lev1_dir_ocephys.h" to
1447 avoid clutter in forward_step.F
1448 - More store directives in pkg/exf allow it to store the forcing fields
1449 instead of the level0/1 (e.g. aqh instead of aqh0 and aqh1), thereby
1450 reducing the number of stored exf-forcing variables by about two. This is
1451 also necessary to avoid calling load_fields_driver from forward_step_ad.
1452 - Additional small tweaks of store directives in forward_step.F have the
1453 effect that the recomputations are kept to a minimum in all of the AD
1454 verification experiments (and in verification_other/global_oce_[llc/cs32])
1455 and calling potentially expensive forward routines are not called (e.g.
1456 do_stagger_fields_exchange, which involves unnecessary exchanges).
1457 - Remove storage of gchemTendency in all checkpoint levels.
1458 - Results unaffected except if using real*4 storage (isbyte=4, e.g., in
1459 offline_exf_seaice, small changes in AD-monitor).
1460
2389d48735 Jean*1461 checkpoint67y (2021/05/05)
c96d63ff5a Jean*1462 o pkg/shelfice:
1463 - Update kTopC when using SHELFICEMassStepping if ice-shelf retreat completely
1464 from one column or advance to cover new grid-cell ; add 4 levels TAF storage
1465 of kTopC (to prevent major recomputations).
1466 - Also prevent ice-shelf mass to become negative.
70ceddf25f Timo*1467 o pkg/mom_common & gmredi:
1468 - Adjust Smag and Leith code for use in Adjoint:
1469 a) protect against derivative of SQRT(0) in mom_calc_visc.F and
1470 gmredi_calc_qgleith.F ;
1471 b) add GM-Redi QG Leith routines to ad_diff lists.
0a637c269e Ou W*1472 o pkg/gmredi:
1473 - fix/remove 2 TAF recomputations in GMREDI_WITH_STABLE_ADJOINT code.
6463ae49bb Jean*1474 o pkg/generic_advdiff:
1475 - improve "slope" calculation in DST2 Flux-Limiter advection scheme to avoid
1476 potential over-flow arithmetic in division by small slope (issue #459),
1477 similar to what has been done in gad_dst3fl_*.F routines.
e9b2d4871a Timo*1478 o pkg/diagnostics:
1479 - use Integer*8 conversion in diagnostics_out.F to get time-record to write
1480 in meta file (avoid integer overflow with large time & small diag-freq).
342b4ea43e Mart*1481 o pkg/mom_common:
1482 - initialise again hdiv in mom_calc_hdiv.F (in case it got dropped by TAF in
1483 calling S/R).
dd54a44307 Mart*1484 o model/src:
1485 - fix a bug in convective_adjustment.F AD code by adjusting store directives
1486 for theta and salt ; update experiment isomip reference AD output.
1487 - a little bit of cleanup: remove unnecessary store directives and options.
9f55dac2bf Jean*1488 o pkg/shelfice:
1489 - change expression of pLoc in shelfice_thermodynamics.F to be simply the
1490 weight of the ice-shelf (= shelficeMass * gravity) replacing inaccurate
1491 estimate from "R_shelfIce". Add TAF directive storage of prognostic
1492 variable "shelficeMass" in all 4 checkpointing levels. Update all reference
1493 output of experiments that use pkg/shelfice (isomip & shelfice_2d_remesh)
d81415648f Jean*1494 o verification/testreport
1495 - add ad-monitor of 3-D state variables to testreport summary output
638b7d19dd Jean*1496 o pkg/ggl90:
1497 - avoid division by zero in adjoint of S/R GGL90_CALC (sqrt related)
1498
aa29a5fd58 Jean*1499 checkpoint67x (2021/04/12)
c512e371cc drin*1500 o pkg/seaice:
1501 - Addition to the sea ice package of 6 sea ice rheologies with different yield
1502 curves and flow rules ;
1503 - Add 4 new verification tests in offline_exf_seaice using new rheologies ;
1504 - Update documentation with description of new rheologies and how to use them.
ba0b047096 Mart*1505 o model, pkg & doc:
1506 - replace all occurrences of incorrect "psu" and "PSU" by "g/kg" in units and
1507 comments ; update the documentation accordingly.
698b6992ee Jean*1508 o pkg/ctrl:
1509 - move to pkg/ctrl the local copy of ctrl_map_ini_genarr.F from verification/
1510 global_oce_biogeo_bling/code_ad/ with ptracers generic control. Improve for
1511 general number of ptracers control.
1512 - add missing diagnostics fill for diagnostics 'Um_ImplD' & 'Vm_ImplD' in
1513 impldiff.F (otherwise not filled when pkg/autodiff is compiled).
9c8f6b90ac Jean*1514 o pkg/autodiff:
1515 Include TICES of pkg/seaice into StoreSEAICE:
1516 - split AUTODIFF.h into two to be able to use nITD in the new AUTODIFF_STORE.h
1517 - rearrange and cleanup declarations, add CPP flags ALLOW_SEAICE/OBCS/EXF ;
1518 - clean up seaice section of autodiff_store/restore.F to remove unused storage
1519 space ;
1520 - changes AD results of global_ocean.cs32x15.seaice & seaice_dynmix, lab_sea &
1521 lab_sea.noseaicedyn => output_adm updated.
cab62edf37 Ou W*1522 o model/src:
1523 - make sure the 3 recip_hFac{C,W,S} are reset after resetting the 3 hFac
1524 in ini_nlfs_vars.F when using Non-Lin FreeSurf with pkg/autodiff compiled
1525 (#define ALLOW_AUTODIFF): this fix problems in gradient-check if recip_hFac
1526 is used, e.g., in one {PKG}_INIT_VARIA S/R.
a10c595eb6 Timo*1527 o pkg/autodiff & diagnostics:
1528 - Add interface routines to write to binary file and fill diagnostics of
1529 single (or pair) of Adjoint variable.
1530 - Rewrite addummy_in_stepping.F using set of new interface S/R to make it
1531 more compact and easier to add new control variables.
1532 - Add all current adjoint variables in addummy_in_stepping, ptracers_ad_dump,
1533 seaice_ad_dump & exf_adjoint_snapshots_ad to work with diagnostics package.
1534 - turn on Adjoint-variable diagnostics in adjoint verification experiments:
1535 *) global_oce_biogeo_bling (with ptracers AD-var diagnostics) and
1536 *) global_ocean.cs32x15.seaice (with seaice and exf AD-var diagnostics).
84cf551a2a Jean*1537 o model/src + pkg/mom_common:
1538 Fix AB time-stepping of QuasiHydrostatic with staggerTimeStep.
1539 - involves new CPP option "ALLOW_QHYD_STAGGER_TS" for storage of previous
1540 time-step Quasi-Hydro tendency to enable AB extrapolation in time when
1541 using staggerTimeStep.
1542 - field added to pickup file for restart ; allows to restart (but not perfect
1543 restart) if field is missing and pickupStrictlyMatch=F.
1544 - switch to staggerTimeStep=T in experiment "global_ocean.90x40x15.dwnslp"
1545 that uses QuasiHydrostatic to test this code; update corresponding output
1546 (as well as primary test output due to machine truncation).
1547 o verification:
1548 In experiments: global_ocean.cs32x15, isomip, obcs_ctrl and offline_exf_seaice
1549 replace CPP flag ECCO_CTRL_DEPRECATED by the much nicer generic control
1550 variables GENARR/GENTIM2D variant.
1551 Also replace ECCO_CPPOPTIONS.h by CTRL/AUTODIFF/COST/ECCO_OPTIONS.h files.
1552 This required a number of changes to the general code to make the generic
1553 control variables work in a non-ecco context:
6b47d550f4 Mart*1554 - pkg/thsice: add AUTODIFF_OPTIONS.h and COST_OPTIONS.h header files to
84cf551a2a Jean*1555 numerous routines ;
6b47d550f4 Mart*1556 - pkg/seaice: mask tendencies of HEFF/AREA/HSNOW in seaice_growth_adx.F to
84cf551a2a Jean*1557 reproduce cost function values ;
1558 - pkg/shelfice: enable GENARR/GENTIM2D methods ;
6b47d550f4 Mart*1559 - pkg/obcs: move reading control variable out of S/R obcs_prescribe_read into
1560 S/R obcs_calc to be independent of parameter values unrelated to the
84cf551a2a Jean*1561 adjoint ;
6b47d550f4 Mart*1562 - pkg/ctrl: make generic control variable work without pkg/cal (works only for
1563 time independent control variables), but issue a warning, bonus: make
84cf551a2a Jean*1564 ctrlprec a runtime parameter that defaults to 64 ;
6b47d550f4 Mart*1565 - pkg/ctrl: fix flow directives for S/R ctrl_bound_2d/3d and add tangent
84cf551a2a Jean*1566 linear versions of these subroutines ;
6b47d550f4 Mart*1567 - pkg/ecco: reorder CPP flags in ecco_cost_weights.F and remove unused
1568 variable 'wbaro', move calling S/R cost_obcs out of ECCO_CTRL_DEPRECATED
1569 code block in S/R ecco_cost_driver, reorganise CPP flags in
1570 cost_averagesinit.F, include CTRL_OPTIONS.h wherever ECCO_OPTIONS.h is
84cf551a2a Jean*1571 included, because ECCO_CTRL_DEPRECATED is now set in CTRL_OPTIONS.h ;
6b47d550f4 Mart*1572 - model/src/the_main_loop.F: fix tape initialisation, bonus: suppress a
84cf551a2a Jean*1573 benign warning ;
6b47d550f4 Mart*1574 - for each of the verification experiments remove ECCO_CPPOPTIONS.h and
1575 replace by CTRL_OPTIONS.h, CTRL_SIZE.h, sometimes COST/ECCO_OPTIONS.h,
84cf551a2a Jean*1576 EXF_OPTIONS.h, adjust data.ctrl, data.grdchk, data.ecco ;
6b47d550f4 Mart*1577 - for global_ocean.cs32x15 compile both variants by keeping
1578 ECCO_CTRL_DEPRECATED in CTRL_OPTIONS.h and use runtime parameter ctrlUseGen
1579 to switch between methods (in global_ocean.cs32x15.thsice). This involves an
1580 extra (benign) recomputation warning in this verification experiment because
1581 of an if statement with ctrlUseGen in ctrl_init_variables.F
1582
e856cdc61b Jean*1583 checkpoint67w (2021/03/06)
4b1d371a30 Jean*1584 o verification/global_ocean.cs32x15:
1585 - fix Adjoint set-up by turning off CPP option "ALLOW_AUTODIFF_INIT_OLD" (that
1586 was intended to put back an old bug) and update all 4 ADM and all 4 TLM
1587 reference output files.
1e291a3f4c Jean*1588 o pkg/exf:
1589 - replace wrong CPP option EXF_SALTFLX with ALLOW_SALTFLX in exf_monitor.F.
a5ae6d70cb Jean*1590 o model/src:
1591 - Output dxF, dyF, dxV, and dyU fields to mdsio grid output files.
dc280143ed Oliv*1592 o tools/build_options:
1593 - improve intel optfile for engaging (linux_amd64_ifort+impi_engaging).
0d75a51072 Mart*1594 o pkg/autodiff:
1595 - Improve, extend & clean-up switch to a simpler advection-scheme in AD-Mode
1596 with new parameter "useApproxAdvectionInAdMode to replace inAdMode:
1597 * If useApproxAdvectionInAdMode is True and advection scheme is set to 33
1598 use advection scheme 30 in AD-model in seaice_advection, gad_advection
1599 and gad_calc_rsh ; model stops when parameters are set inconsistently.
1600 * Defaults to False, but is reset to True if inAdExact = False to be
1601 backwards compatible.
1602 - Important change in the meaning of variable inAdMode: now it is always true
1603 after calling S/R AUTODIFF_INADMODE_SET_AD and always false after calling
1604 S/R AUTODIFF_INADMODE_UNSET_AD.
1605 The non-intuitive flags inAdTrue and inAdFalse, which could be T or F, have
1606 been removed from the code.
1607 - Remove unnecessary TAF related and inAdMode code from seaice_lsr.F, remove
1608 SOLV_MAX_TMP in LSR S/R and adjust SEAICElinearIterMax default accordingly.
1609 - Change AD exp. global_ocean.cs32x15.seaice to test this new functionality;
1610 gradient checks necessarily are poorer because AD advection is approximated.
1e25bc2551 Jean*1611 o tools/build_options:
1612 - update standard optfile "linux_amd64_gfortran" to enable to be used with
1613 gfortran version 10 (or higher); update comments and clean-up for missing
1614 "nf-config".
2ac762dbee Jean*1615 o model/src & pkg/generic_advdiff:
1616 - Implement simple isotropic 3D Smagorinsky diffusivity:
1617 Smag diffusivity is assumed to be linearly dependent on 3D Smag viscosity
1618 (just scaled by inverse of a constant Prandtl number); setting involves:
1619 a) CPP Option: ALLOW_SMAG_3D_DIFFUSIVITY in CPP_OPTIONS.h (def. #undef)
1620 b) switching on 3D Smagorinsky by setting "useSmag3D = .TRUE." in first
1621 namelist of main parameter file "data" ; and, in the same namelist,
1622 c) setting smag coeff. "smag3D_diffCoeff" for diffusivity (similar to
1623 smag coeff. "smag3D_coeff" for viscosity), which results in constant
1624 Prandtl number = smag3D_coeff/smag3D_diffCoeff.
1625 Note: Since Smag3D_diffK is lagging by 1 time-step, needs to be stored
1626 in pickup files (for restart) when using synchronous time-stepping.
1627 - code is compiled in experiment tutorial_deep_convection and ready to use
1628 except smag3D_diffCoeff setting in input.smag3d/data is commented out.
1629 - also add few missing initialisations in "ini_dynvars.F" (just for
1630 consistency with coding practice but no practical side effect).
fef3c33926 Jean*1631 o pkg/ecco:
1632 - fix type of argument in S/R MDS_READVEC_LOC call inside cost_gencost_moc.F
9b38007ffc Jean*1633 o verification/lab_sea:
1634 - change lab_sea.hb87 from testing EVP to testing aEVP with some sensible
1635 parameters ; update reference output "output.hb87.txt"
df462307fb Timo*1636 o pkg/ecco:
1637 - Addition of meridional streamfunction maximum (MOC) as objective function
1638 within ecco/gencost code ;
1639 - MOC objective function tested in verification_other/global_oce_cs32.sens ;
1640 - allows to compute sensitivity to hflux/sflux with prescribed atmospheric
1641 state (not fluxes) with new flags CALC_HFLUX_SENS and CALC_SFLUX_SENS.
1642
830e1a2c4c Jean*1643 checkpoint67v (2021/02/03)
66fe84e647 Oliv*1644 o tools/build_options:
1645 - add optfile for engaging similar to linux_amd64_ifort+impi but with -xAVX
d5254b4e3d Mart*1646 o pkg/seaice:
1647 - move store directives of uice/vice to after calling S/R SEAICE_DYNSOLVER to
1648 avoid calling this routine in S/R seaice_model_ad which may trigger
1649 potential recomputation problems (e.g., with non-exact AD) ;
1650 - move if statement inside S/R SEAICE_BOTTOMDRAG_COEFFS : this enables to
1651 remove storage of "CbotC" without triggering recomputations ; compile this
1652 code in the AD-experiments of global_ocean.cs32x15 ;
1653 - remove unnecessary store directives related to pkg/seaice ;
1654 - fix/extend diagnostic "SIenph " to work with all parameter configurations.
4240547d2d Mart*1655 o pkg/autodiff: fix/improve viscFacAdj
1656 - fix treatment of viscFacAdj in mom_vecinv.F by removing storage of 2D
1657 viscosities if new flag AUTODIFF_ALLOW_VISCFACADJ is defined ;
1658 - add a runtime parameter "viscFacInFw" in autodiff_inadmode_unset_ad.F to
1659 replace hard-coded one ;
1660 - apply viscFacAdj to both viscAh/4_D and _Z ;
1661 - test compiling this code in tutorial_global_oce_optim.
f92f728545 Jean*1662 o model/src:
1663 - move if statement out of i/j-loops in solve_tridiagnoal/pentadiagonal.F:
1664 *) this reduces TAF recomputation warnings by 4 ;
1665 *) potentially easier to optimise/vectorise for some compilers.
1666 o tools/build_options:
1667 - adjust floating point options in: linux_ia64_ifort_ollie:
32ce3e9e96 Mart*1668 o pkg/ctrl:
f92f728545 Jean*1669 - fix two bugs related to writing and reading control variables and
1670 corresponding gradients:
1671 a) replace too large loop range endrec by diffrec in ctrl_map_ini_gentim2d.F;
1672 b) skip writing meta-files in REVERSE_SIMULATION mode (active_file_control.F)
32ce3e9e96 Mart*1673
82ad7f2b88 Jean*1674 checkpoint67u (2020/12/30)
616d857f4a Mart*1675 o utils/python/MITgcmutils
f92f728545 Jean*1676 - add code to compute horizontal divergence of a vector field, gradient of a
1677 scalar field, and averages to c-points on an llc grid.
4a08d54d3a Mart*1678 o pkg/seaice:
f92f728545 Jean*1679 - fix bug in seaice_lsr, spotted by Martin Vancoppenolle, that lead to solving
1680 stationary momentum equations (du/dt -> 0) for SEAICEnonLinIterMax>2 ;
1681 - fix minor bug in seaice_bottomdrag_coeffs.F: replace OLy with correct OLx ;
1682 - changing ordering of addition (to FORCEX,FORCEY) in seaice_lsr.F results in
1683 output differences at machine truncation level: update referece output of
1684 several experiments that use LSR solver.
8fc117ecb7 Mart*1685 o pkg/autodiff: fix flow directives for self-adjoint cg2d
f92f728545 Jean*1686 - new self-adjoint cg2d routine cg2d_sad.F mimics AD-code, but neglects
1687 (purposefully) the proper sensitivity propagation
1688 - extra storage of cg2d solver coefficients and preconditioner is required
1689 - change 2 AD-verification experments (global_ocean.cs32x15 and
1690 global_ocean.cs32x15.seaice) to test this code a little better:
1691 use full NLFS and nchklev_1 = 2
8fc117ecb7 Mart*1692
8b41e6235c Jean*1693 checkpoint67t (2020/11/30)
a67734cba4 Mart*1694 o pkg/kpp:
1695 - with CPP-option KPP_ESTIMATE_UREF, fix compilation errors + fix mixed layer
1696 depth determination ;
1697 - define KPP_ESTIMATE_UREF in verification/vermix ;
1698 - a little bit of cleanup.
1699 o pkg/seaice:
4dd39c50d9 Mart*1700 - small modifications of seaice_growth_adx.F to avoid recomputation warnings
1701 and to avoid potentially inefficient code ;
1702 - remove duplicate version of seaice_solve4temp ;
1703 - exclude code of seaice_growth.F if ALLOW_SEAICE_GROWTH_ADX defined ;
1704 - switch on SEAICE_USE_GROWTH_ADX AD in experiment offline_exf_seaice and
1705 update "output_adm.txt".
76d0c749c4 Jean*1706 o eesupp/src:
1707 - add missing "stdio.h" in src code setdir.c
5dda98cf07 Jean*1708 o tools/do_tst_2+2 & tst_2+2:
08bbaa9f0f Mart*1709 - bug fix: replace some non-standard sed command with POSIX compatible syntax
5dda98cf07 Jean*1710 - remove second blank at beginning of 2 new lines in file "data".
dae83699f8 Jeff*1711 o doc:
1712 - add new SO channel tutorial
0a8794f5ee Mart*1713 - update pkg/shelfice documentation
7a4abe9124 Jean*1714 o optim:
1715 - fix a small bug by initialising myX/YglobalLo=1 in optim_nummod.F
44af98263c Jean*1716 o tools/do_tst_2+2:
1717 - for sending restart test output, add same hack in "send" option as in
1718 testreport, allowing to use "scp" (instead of an email).
1719 o model/src:
1720 - fix 2 missing TAF initialisation directives in file "the_main_loop.F";
1721 this allows to use TAF recent version 5.0.9 (that does check for missing
1722 initialisation).
6de16ba22c Jean*1723 o pkg/seaice:
1724 - fix diagnostics additions (from PR #348) for case _RS is real*4.
1725
ede86f4989 Jean*1726 checkpoint67s (2020/07/30)
b9dadda204 Mart*1727 o eesupp/src:
1728 - Improve formatting of output for large grids and many processors:
1729 adjust formats to actual length of nPx*nPy or Nx and Ny but
1730 keep minimal lengths to avoid changing the format for smaller domains;
1731 - also increase number of digits for printing tile & proc number in pkg/exch2
1732 log files and report to STDOUT.
a284455135 Matt*1733 o pkg/bling:
1734 - cleaning: remove USE_QSW_Z code ;
1735 - few more CPP options (NEW_FRAC_EXP & SIZE_DEP_LIM defined, SIZE_NUT_LIM
1736 undef) related to phytoplankton size and sinking organic matter ;
1737 - fix tiled TAF storage directives (were not right for multi-tile per proc);
1738 update ADM reference output of experiment global_oce_biogeo_bling (now
1739 gradient check are identical whether run on 1 proc - 4 tiles or 4 procs
1740 1 tile each).
5867b94c2f Mart*1741 o pkg/seaice:
1742 - Replace hard-coded minimum for DWATN by runtime parameter "SEAICEdWatMin":
1743 * allows to have zero drag by setting both SEAICEdWatMin and
1744 SEAICE_waterDrag to zero. Non-zero drag had been implemented because
1745 previous LSR solver could not handle zero entries on the main diagonal.
1746 * this fixes a bug (unexpected behavior) reported at MITgcm-support by
1747 Kaley Shrestha, but also allows to modify the somewhat arbitrary
1748 default minimum value of SEAICEdWatMin = 0.25 ;
1749 * freedrift code still requires non-zero drag coefficients,
1750 S/R SEAICE_CHECK catches this case.
3770720c1f Jean*1751 o verification/*/packages.conf
1752 - Cleaning verification experiment "packages.conf":
1753 1) add a 1 line description at the top
1754 2) use pkg group "adjoint" in some experiments
1755 3) use similar ordering of pkgs in packages.conf:
1756 a) eesupp pkgs (e.g., exch2, coupler-pkgs)
1757 b) dyn-core pkgs (e.g., gfd pkgs, mom pkgs, cd_code, gad, obcs ...)
1758 c) SGS-scheme (+ atm physics) pkgs (filters, gmredi, vert.mixing ...)
1759 d) forcing pkgs (e.g., rbcs, exf, cal, ebm, cheapaml)
1760 e) other component pkgs (e.g., ice, land, ptracers, biogeo, flt)
1761 f) diagnostics pkgs (e.g., sbo, profiles, layers, diagnostics, timeave)
1762 g) I/O pkgs, e.g., mnc (+ mypackage at the end)
1763 -- blank line --
1764 h) adjoint related pkgs (e.g., autodiff, ctrl, cost ...)
1765 4) remove unused pkgs: kpp, sbo, timeave ; this results in reduced number of
1766 TAF recomputation warning for AD exp: bottom_ctrl_5x5 & global_ocean_ebm;
1767 o tools/build_options:
1768 - add a symbolic link for optfile "linux_amd64_ifort" to "linux_amd64_ifort11"
7deacd640c Jeff*1769 o doc:
1770 - fix link and plot in doc/examples/baroclinic_gyre
5fe78992ba Mart*1771 o pkg/seaice:
1772 - Add new mechanical energy diagnostics ;
1773 - Move computation of stress diagnostics to seaice_dynsolver.F ; this change
1774 affects diagnostics SIpress, SItensil, SIpress, SIzeta, SIdelta, SIshear,
1775 because they are now filled after the current time step update, when they
1776 are actually available. Note: previously, for the first time step, these
1777 variables (and diagnostics) were not properly defined (or zero).
1778
2bc8ced27d Jean*1779 checkpoint67r (2020/06/04)
cd9df85f4a Jean*1780 o pkg/ecco:
1781 - fix character length when checking for m_trHeat, m_trSalt & m_horflux_vol.
04904a066e Timo*1782 o pkg/autodiff:
1783 - add active read and write routines for global 1D vectors, to be used for
1784 compressed cost function vectors (note: not used yet, example to come soon).
42032b6c9d Jean*1785 o model/src & pkg/exf:
1786 - Reference atmospheric pressure for seawater EOS was assumed but was not
1787 explicitly set. New constant "eosRefP0" is added to make this more clear ;
1788 - Add main model reference surface pressure (surf_pRef) so that pLoad
1789 is now defined as the atmospheric pressure anomaly relative to surf_pRef ;
1790 - Account for differences in 2 ref pressure in EOS S/R ;
1791 - Fix few EOS references (in comments) ; fix and simplify S/R EOS_CHECK ;
1792 - Keep exf "apressure" field unchanged (still full atmospheric surface
1793 pressure) but now initialised to "surf_pRef" and fill "pLoad" with atmos.
1794 pressure anomaly relative to surf_pRef.
07e785229e dngo*1795 o pkg/streamice:
1796 - add option to specify "regularised coulomb" sliding law to better reflect
1797 dependence on subglacial water pressure close to the grounding line ;
1798 - above requires CPP option (due to new arrays) STREAMICE_COULOMB_SLIDING
1799 and r/t param streamice_allow_reg_coulomb ;
1800 - add diagnostic for streamice melt rate (BDOT_SI )
1801 - add parameter STREAMICEAdotFile to specify surface mass balance ;
1802 - add parameter streamice_maxnliter_Petsc to specify maximum no. of
1803 linear solves using PETSc in a single time step (not incl. in doc
1804 since PETSc is not part of standard build) ;
1805 - update references to PETSC_DEFAULT_DOUBLE_PRECISION to PETSC_DEFAULT_REAL in
1806 streamice_cg_solve_petsc.F; former seems to be deprecated in some versions
1807 of PETSc while latter is backward compatible ;
1808 - for BJACOBI (block jacobi) PETSc preconditioner, use PCICC (incomplete
1809 cholesky) rather than PCILU (incomplete LU) ;
1810 - for BJACOBI add parameter streamice_petsc_pcfactorlevels to control level
1811 of factor fill-in.
1812
18fff58a99 Jean*1813 checkpoint67q (2020/03/19)
e1e000e69f Jean*1814 o pkg/shelfice, remeshing code:
1815 - simplify/clarify merging S/R call sequence: all done/called from main
1816 remeshing S/R SHELFICE_REMESHING :
1817 - remesh_c_mask : now only update geometry & surface fields at grid-cell
1818 center and compute merging remeshing weights for tracers;
1819 - remesh_uv_mask : now only update geometry & surface fields at grid-cell
1820 edges and prepare merging remeshing weights for velocity;
1821 also fix thin-wall setting without reading again thin-wall files ;
1822 - calls directly CALC_SURF_DR and UPDATE_SURF_DR
1823 - move adjustment of state variables into (new) dedicated
1824 S/R SHELFICE_REMESH_STATE and change loop range so that no further EXCH
1825 calls are needed ; also add missing code for ALLOW_ADAMSBASHFORTH_3 ;
1826 - move update of Rmin_surf (formerly in shelfice_remesh_rminsurf.F)
1827 before first call to S/R CALC_SURF_DR (where Rmin_surf is used)
1828 and in-line S/R SHELFICE_REMESH_RMINSURF into shelfice_remesh_uv_mask.F
1829 - add argument "wFld" and "myIter" to S/R SHELFICE_REMESH_CALC_W
1830 - fix so that it compiles and run when _RS is real*4 (#undef REAL4_IS_SLOW).
7d270b85fa Jean*1831 o model/src:
1832 - Fix for special value of R_low with pkg/shelfice:
1833 When bathymetry field value is just rF(k)+hFacMindrF(k)/2, R_low will
1834 deepen (by hFacMindrF(k)/2 ) to satisfy the hFacMin criteria. In this case:
1835 o if R_shelfIce value (from file) was exactly equal to initial bathymetry
1836 depth, original code would create a very thin grid cell of thickness
1837 factor hFacMin. Fix this problem by preventing deepening of R_low when
1838 initial R_low >= R_shelfIce.
1839 o if R_shelfIce value is deeper than original value, the problem does not
1840 show up for hFacC (column remains dry) but because of erroneous resetting
1841 of rSurfW/S (to be the MAX of rSurfW/S, rLowW/S) this could trigger the
1842 same type of artificial deepening at Western and Southern column edges
1843 (for hFacW and hFacS). Remove early resetting of rSurfW/S to fix this
1844 second issue (see issue #324).
1845 - Simplify correction for miss-match between Sum of level thickness at
1846 W & S edges and top minus bottom r-position: only adjust rSurfW/S
1847 (and not rLowW/S) as done previously for the case useMin4hFacEdges=T;
1848 - Non-lin free-surf in r coordinate: for consistency, use rSurfW & rSurfS
1849 (which account for adjustment, if any) instead of MIN of adjacent Ro_surf
1850 when calculating new thickness factor: hFac_surfW & hFac_surfS ;
1851 - Make thin-wall implementation available for sigma-coordinate ;
1852 - Record thin-wall position as kSurfW/S = Nr+2 (instead of = Nr+1 for
1853 a dry column).
1854 o tools/build_options:
1855 rename optfile "linux_amd64_ifort" to "linux_amd64_ifort10-"
9acfcdc58c Jeff*1856 o verification:
1857 - new reentrant channel tutorial experiment, doc will follow soon.
1858
260efc476e Jean*1859 checkpoint67p (2020/02/12)
bdf98ce602 Edwa*1860 o model/src:
af65683301 Jean*1861 - rename array "surfaceForcingTice" to "adjustColdSST_diag" and change the
1862 description to better reflect what it is: a diagnostic for SST adjustment.
1863 - remove most of the TAF storage directive for "adjustColdSST_diag" that were
1864 not necessary once it's properly initialized.
bdf98ce602 Edwa*1865 o pkg/gmredi:
1866 - improve error handling
1867 - additional QGLeith config checks
1868 - standardise variable name capitalizations
af65683301 Jean*1869 o pkg/mom_common, mom_vecinv, mom_fluxform:
bdf98ce602 Edwa*1870 - protect QGLeith code with ifdefs
af65683301 Jean*1871 - additional QGLeith config checks (in model/src/config_check.F)
40933c9dd3 Jean*1872 o verification:
1873 - rename dir "rotating_tank" to "tutorial_rotating_tank".
7a05b40c01 Jeff*1874 o pkg/flt:
1875 - improve pkg/flt doc and CPP brackets
1c8cebb321 Jeff*1876 o doc:
1877 - new front-page to tutorial chapter, also listing all verif experiments ;
1878 - add new section in ch3 about input file format.
1879
45ac9863cf Jean*1880 checkpoint67o (2019/12/23)
9952f046d7 dngo*1881 o pkg/shelfice:
75f34d1991 Jean*1882 - implement implicit ice-shelf drag, in the same way as implicit bottom drag,
1883 using the same run-time switch "selectImplicitDrag".
1884 - change 3-D diagnostics of ice-shelf drag tendency (SHIUDrag & SHIVDrag) to
1885 2-D diagnostics of ice-shelf drag stress (SHI_TauX & SHI_TauY).
1886 - update 4 forward reference output files of experiment "isomip".
1887 - switch on implicit drag in experiment shelfice_2d_remesh (to get it tested).
1888 o pkg/shelfice:
9952f046d7 dngo*1889 - addition of functionality described in Jordan et al (2017), "Ocean-Forced
1890 Ice-Shelf Thinning in a Synchronously Coupled Ice-Ocean Model";
1891 allows "remeshing" of grid-cells in vertical in response to changing free
1892 surface due to ice shelf mass change:
1893 At SHELFICEremeshFrequency interval, checks for cells that are too thick or
1894 too thin and adjusts R_surf & eta accordingly, and updates state variables ;
1895 - new main remeshing S/R SHELFICE_REMESHING calling additional S/R in files
1896 shelfice_remesh_c_mask.F, shelfice_remesh_uvmasks.F,
1897 shelfice_remesh_rminsurf.F and shelfice_remesh_calc_w.F
1898 and called directly from top of FORWARD_STEP ;
1899 - all new code and call protected under #define ALLOW_SHELFICE_REMESHING ;
1900 - add field "R_shelfice" to pkg/shelfice pickup files for restart ;
1901 - verification/shelfice_2d_remesh/*: new verification experiment
1902 to test remeshing functionality.
1903 - additional options to SHELFICEboundaryLayer:
1904 a) SHI_withBL_uStarTopDz, to compute uStar from uVel,vVel avergaged over
1905 top Dz thickness first and then average horizontally ;
1906 b) SHI_withBL_realFWflux, to use real Fresh-Water flux (and adjust
1907 advective surface flux) with SHELFICEboundaryLayer.
f4206cb08a Jean*1908 o pkg/ecco:
1909 - change S/R ECCO_READWEI to read in uncertainty file and compute weight
1910 as 1/sigma if nosumsq is provided as a preprocessing option, or 1/sigma^2
1911 if not. This is the expected behavior based on the "generic cost function"
1912 section of the documentation.
fb6db187ae Jean*1913 o verification:
1914 - new experiment "global_oce_biogeo_bling" move here from verification_other.
b62dee2337 Jean*1915 o pkg/cheapaml:
1916 - rewrite advection-diffusion of BL atmospheric variables to use Flux-Form
1917 formulation. Affects results (unless cartesian grid is used).
1918 - apply special treatment of diffusive flux at Northern & Southern boundaries
1919 only if .NOT.cheapamlYperiodic (previously unconditional, gad_diff_2d_y.F);
1920 - Skip calls to AB-2 when using "useFluxLimit=T" option since advection scheme
1921 used then is DST3FL which does not need AB at all. Affects results if
1922 useFluxLimit=T" is used.
1923 - clean-up (rename/remove all "gad_*.F" files) and simplify by using few more
1924 pkg/generic_advdiff S/R (instead of local copies).
1925 - update output of experiment "cheapAML_box" (and in separated PR, experiment
1926 "offline_cheapaml" in verification_other)
c8767af0b6 Timo*1927 o pkg/ctrl:
1928 - Tangent Linear mode: allows to initialise g_xx fields with user-provided
1929 g_xx file (default unchanged, i.e., initialised to zero).
1930
6bdcb6b877 Jean*1931 checkpoint67n (2019/11/26)
9906b3fb84 Jean*1932 o pkg/ctrl:
1933 - add doc & storage dir for initial velocity control option.
788c57c2b5 owan*1934 o pkg/autodiff:
1935 - sort out checkpoint_lev1_dir header file for when pkg/ecco is used
1936 with #undef NONLIN_FRSURF ; similar update in pkg/cd_code & pkg/ptracers;
1937 this fixes issue #68.
1938 - clean-up and fix pkg/autodiff checkpoint_lev?_dir to be able to compile
1939 with #define EXCLUDE_FFIELDS_LOAD.
540437b870 Jean*1940 o model/src:
1941 - allows to specify time-dependent (periodic) geothermal heat-flux
1942 with "periodicExternalForcing".
6dfad62739 Jean*1943 o pkg/diagnostics:
1944 - add diagnostics for thickness factor hFacC, hFacW & hFacS.
8dfb9d9b4c Jean*1945 o pkg/dic:
1946 - Fix carbonate chemistry coefficient issues (#269). This affects results when
1947 either CARBONCHEM_TOTALPHSCALE or CARBONCHEM_SOLVESAPHE are defined.
1948 Update output of verification experiment "so_box_biogeo".
a435e833b1 Mart*1949 o doc:
1950 - fix description of zero-layer thermoydnamics
94f0474fee Jean*1951 o verification/*/results/output.txt:
1952 - update reference machine from baudelaire.mit.edu (running fc13)
1953 to villon.mit.edu (running Ubuntu 18 LTS) and update few output.txt
1954 - change travis Docker settings accordingly + update documentation.
1955
5523dc659e Jean*1956 checkpoint67m (2019/10/16)
d67096e55c Jeff*1957 o doc/examples:
1958 - Convert remaining old doc tutorials from latex to rst files and add them
1959 to current MITgcm documentation.
18d2df1f7f Jean*1960 o pkg/ptracers:
1961 - new diagnostics Tp_gTr01, ... for ptracer total transport tendencies
1962 (before gchem_forcing_sep); this includes advection and diffusion terms,
1963 but also anything added in gchem_add_tendency.
94151a9b18 Jeff*1964 o doc & verification/tutorial_baroclinic_gyre:
1965 - split doc for tutorial experiments into separate files
1966 - update configuration for baroclinic gyre tutorial
1967 - update documentation for baroclinic gyre tutorial
1968 - formatting and font changes in algorithm chapter
5752d89cac Ed D*1969 o doc:
1970 - add rtfd config file to control build behaviour and options.
1971
b6c7ea7cf3 Jean*1972 checkpoint67l (2019/08/29)
b90cc7fedb Ed D*1973 o QG-Leith viscosity:
1974 - pkg/mom_common: bug fix for QG Leith viscosity
1975 - pkg/gmredi: bug fix for QG Leith coefficient
1976 - update output of experiments MLAdjust.QGLeith & MLAdjust.QGLthGM
abfe198bce Mart*1977 o pkg/obcs:
1978 - new feature to balance surface flux of freshwater or ice shelf mass by
1979 outflow through open boundary conditions:
1980 * requires splitting S/R obcs_calc to move call to S/R obcs_balance and S/R
1981 obcs_add_tides after S/R external_forcing_surf call in do_oceanic_phys.F
1982 * add contribution for EmPmR of the current time step and the
1983 shelficeMassDynTendency (new S/R shelfice_netmassflux_surf).
1984 - add new secondary test exp. "isomip.obcs" to text this new feature.
a004e35329 Ed D*1985 o pkg/mom_common & model/src:
1986 - new S/R MOM_U/V_BOTDRAG_COEF used both for explicit and implicit bottom drag
1987 computation (thus replacing both MOM_U/V_BOTTOMDRAG in explicit case and
1988 MOM_U/V_BOTDRAG_IMPL in implicit case) to return a drag coefficient.
1989 This modification affects results at machine truncation level.
1990 - change diagnostics 'Um_dPHdx' & 'Vm_dPHdy' to 'Um_dPhiX' & 'Vm_dPhiY'
1991 for full pressure gradient tendencies (including surf & NH contribution);
1992 - remove bottom drag tendency diags (UBotDrag & VBotDrag); add bottom stress
1993 diagnostics and implicit viscous tendency diagnostics, both accurate also
1994 if using implicit bottom drag (selectImplicitDrag=2).
d7b89710f7 Oliv*1995 o pkg/exf:
1996 - re-arrange EXF interpolation header files: move setting of "MAX_LAT_INC"
1997 from EXF_PARAM.h to EXF_INTERP_SIZE.h (more logical place). But to avoid
1998 having to include EXF_INTERP_SIZE.h each time EXF_PARAM.h is included,
1999 move EXF interpolation parameters outside EXF_PARAM.h in new header file:
2000 EXF_INTERP_PARAM.h
2001 - add S/R to define input grid setting (stored in EXF_INTERP_PARAM.h) to be
2002 used for EXF interpolated fields as default input grid.
ebbe8cf013 Jean*2003 o compon_interf pkgs:
2004 - fix bi loop range in few initialisation subroutines (2 in each pkg),
2005 fixing issue #270
2006
02b4c39948 Jean*2007 checkpoint67k (2019/07/19)
80f7dda68b Jean*2008 o model/src:
2009 - fix format in printing 1 error message from S/R SET_PARMS
9d49c8b5d1 Matt*2010 o pkg/bling:
fbb6fdf8a5 mmaz*2011 - add missing components of SIBLING
2012 - add Manizza et al 2005 light attenuation. Enable with PHYTO_SELF_SHADING
c9238c91a3 Jean*2013 - Replace hard coding of max mixing depth with runtime parameter MLmix_max
fbb6fdf8a5 mmaz*2014 o pkg/ctrl:
796fd0e220 Jean*2015 - fix reccord number setting in S/R CTRL_GET_GEN_REC ("startrec" substracted
2016 for no reason).
bc74f5a574 Jean*2017 o doc:
2018 - add a sub-section about optim_m1qn3
6c44cdc71d Jean*2019 o pkg/ctrl:
2020 - fix in rescaling option for control vector ("doscaling/noscaling" option,
2021 S/R CTRL_MAP_INI_GENARR & CTRL_MAP_INI_GENTIM2D); proper counting of
2022 non-zero control vector when weight-mask is different from ocean-mask.
2023 Expect differences only when (a) weight-mask is different from ocean mask
2024 and (b) xx_genarr2d_preproc='noscaling' (doscaling=.false.).
899473f061 Jean*2025 o pkg/exf:
2026 - new run-time parameter "diags_opOceWeighted" (default=T) to weight some exf
2027 surface diagnostics (all net and upward fluxes) with open-ocean fraction.
2028 Option is turned off when no sea-ice pkg (seaice or thsice) is used.
2029 - new S/R EXF_WEIGHT_SFX_DIAGS to do some exf diags as open-ocean weighted
2030 according to input argument ice fraction. Called from the right location
2031 in time-stepping to get diagnostics that are consistent with wind-stress
2032 and buoyancy fluxes that ocean receive.
2033
d1306ef812 Jean*2034 checkpoint67j (2019/06/18)
e0f9a7ba0b Matt*2035 o pkg/bling:
2036 - Cleanly seperate NBLING (default), BLING_V1 (enabled with USE_BLING_V1),
2037 and also add Silica option (enabled with USE_SIBLING);
2038 - New algorithm for calculating mixed layer depth (old enabled with
2039 BLING_USE_THRESHOLD_MLD);
2040 - Options for updated carbon chemistry (from J. Lauderdale) enabled with
2041 CARBONCHEM_SOLVESAPHE or CARBONCHEM_TOTALPHSCALE ;
2042 - And other minor spring cleaning changes;
2043 - update calls in pkg/gchem for BLING(V1) or NBLING (with Silica).
352c2064d4 antn*2044 o pkg/salt_plume:
2045 - fix calculation index range in salt_plume_apply.F (#ifdef SALT_PLUME_VOLUME)
3a78078268 Aras*2046 o pkg/ecco:
2047 - fix/simplify local file names in ecco_cost_init_barfiles.F (within
2048 #ifdef ALLOW_GENCOST_CONTRIBUTION ).
7843dde2de jm-c 2049 o pkg/mom_vecinv:
2050 - add 2 Coriolis schemes which satisfy: d/dt U = f V ; d/dt V = -f U
2051 (with U,V = vertically integrated flow).
2052 - add new run-time coriolis-scheme selector "selectCoriScheme" to replace
2053 "useJamartWetPoints" and "useEnergyConservingCoriolis"; but keep these 2
2054 in namelist (backward compatible) to set "selectCoriScheme" accordingly.
77f894c517 Timo*2055 o pkg/ctrl:
2056 - Fix bug in ctrl_map_ini_genarr.F regarding missing initialization of
2057 igen_uvel & igen_vvel (just like all the other variables).
6acab690ae Jona*2058 o pkg/dic:
2059 - Implement SolveSAPHE (Munhoven, 2013), a robust algorithm to calculate
2060 oceanic pH/pCO2 ; compiled when CARBONCHEM_SOLVESAPHE is defined (in
2061 DIC_OPTIONS.h) and used when (in data.dic) selectPHsolver > 0 ;
2062 Add several options for selecting dissociation coefficients, available
2063 when CARBONCHEM_SOLVESAPHE is defined.
2064 - Change experiment "so_box_biogeo" to compile with CARBONCHEM_SOLVESAPHE
2065 defined and add secondary test "saphe" (dir: input.saphe) to this experiment
2066 to test GENERAL pH solver (selectPHsolver=1).
dc54d31829 Ian *2067 o pkg/seaice:
2068 - add alternative version of seaice thermodynamics two routines that provide
2069 accurate adjoint. Switched by defining CPP option: ALLOW_SEAICE_GROWTH_ADX
66046ae6a1 Brun*2070 o pkg/mdsio:
2071 - in meta file, write number of records with longer format (10 digits vs 5
2072 previously) to accommodate large number of floats.
2073
aa900cad7e Jean*2074 checkpoint67i (2019/05/08)
f2a88c9ff8 jm-c 2075 o autofdiff:
2076 - fix to avoid TAF recomputations in ggl90 & salt_plume pkgs
2077 and in model/src PCELL_MIX_CODE.
f59d76b0dd Ed D*2078 o pkg/mom_common & pkg/gmredi:
2079 - add quasi-geostrophic variant of Leith dynamic visocity
2080 - use the quasi-geostrophic Leith dynamic visocity as GM diffusivity
2081 - new verification experiment to test QG-Leith (variant of MLAdjust)
2082 - updated documentation about new option
39cd4ae623 Ed D*2083 o pkg/seaice:
2084 - add Hlimit to seaice namelist in data.seaice
2085 - use verification seaice_itd.thermo to test this feature with default
2086 values (experiment does not change)
2087 - clean up related output in seaice_init_fixed.F a little
aad71d9e67 Mart*2088 o verification/testreport:
2089 - for file run_ADM_DIVA, fix sed search syntax so that it works with BSD-sed
6b48f6d519 Mart*2090 o model/src:
2091 - fix small bug (wrong balanceEmPmR report) in config_summary.F, spotted by
2092 Christopher Wolfe ; add report of balancePrintMean to summary.
1f2be90d9e Ed D*2093 o verification/verification_parser.py
2094 - ensure Travis test suite fails when a build or a run fails.
2095
fba140841d Jean*2096 checkpoint67h (2019/03/21)
db0c10dd53 jm-c 2097 o tools/genmake2:
2098 - fix option "-nocat4ad" for latest version of TAF: now needs to add TAF
2099 option "-fixed" to process *.flowdir files with newer (after 4.1.1) version
2100 of TAF (otherwise assumed now to be in free format).
b98355c8c5 jm-c 2101 o model/src:
dc54d31829 Ian *2102 - remove argument tFld & sFld from S/R CALC_PHI_HYD and from 2 related S/R
bcbb675387 jm-c 2103 o tools/genmake2:
2104 - allow to skip "check_fortran_compiler" part (as, e.g., in opt-file:
2105 tools/build_options/linux_ia64_cray_archer).
1c87316fba Jeff*2106 o verification/tutorial_barotropic_gyre:
2107 - add 1rst tutorial documentation to new manual and update corresponding setup
8b07a23c92 Jean*2108 o pkg/atm_phys:
2109 - add 3-D input file for stratospheric ozone
2110 - add code from Matt Kasoar for SW absorption by stratospheric ozone,
2111 based on following papers:
2112 Lacis and Hansen (JAS, 1974) and Forster and Shine (JGR, 1997).
2113 - turned on using 2 local run-time parameter: ozone_in_SW (downward)
2114 and two_stream_SW (also in upward); default are off.
2115 - clean up S/R "radiation_up": rename "net" to "flux_lw" (better name)
2116 and remove un-used local (dyn-allocated) arrays.
2117 - also avoid division by zero in Rel-Humid diagnostics (atm_phys_driver.F)
bfae2ee370 jm-c 2118 o pkg/seaice:
2119 - fix missing update of sIceLoad in the case usePW79thermodynamics=F.
80d7ca01bb Jona*2120 o pkg/dic:
2121 - Adjust unit conversions for dissociation coefficients aks, aksi, and akf
2122 (#define CARBONCHEM_TOTALPHSCALE).
516b08a580 jm-c 2123 o tools/genmake2:
2124 - improve Fortran Compiler check, section: running MPI executable ; also
2125 refine the "conclusion" printed message.
2126
29a542dcab Jean*2127 checkpoint67g (2019/01/03)
2128 o doc:
2129 - add documentation for pkg/streamice
148dd84005 jm-c 2130 o model/src:
2131 - change ordering of pkg calls in initialisation: streamice / shelfice and
2132 then seaice / salt_plume / thsice;
2133 - fix thin ice-shelf issue with pkg/seaice ; implemented by updating (recently
2134 added) seaice masks (requiring new ordering of calls).
c87895a3f5 jm-c 2135 o pkg/shelfice:
2136 - allow to include thin ice-shelf (i.e., such that hFacC(k=1) > 0 ) when
2137 using pkg/thsice, by preventing seaice to form where there is an ice-shelf.
2138 - prevent short-wave heating below an ice-shelf (previously still happening
2139 below thin ice-shelf); also fix Qnet there (but only for diagnostics).
ec0d7df165 Mart*2140 o pkg/seaice:
2141 - move initialisation of masks and metric coefficients and KGEO from
2142 seaice_init_varia.F to seaice_init_fixed.F
2143 - remove all reference to global masks maskC/maskW/maskS:
2144 * introduce new masks SIMaskU/V
2145 * initialise HEFFM/SIMaskU/V as copies of surface maskC/W/S
2146 * replace maskC/W/S with HEFFM/SIMaskU/SIMaskV; in some places this requires
2147 including SEAICE.h and as a consequence renaming a few local variables to
2148 avoid name overlap
2149 - remove TAF storage directives for "heffm" (no longer needed) and simplify
2150 seaice calls and TAF storage dir in do_oceanic_phys.F
73c0056d2e Oliv*2151 o pkg/monitor:
2152 - fix local array declaration in mon_stats_latbnd_rl.F
49fc9b4095 Oliv*2153 o tools/example_scripts:
2154 - remove all files in tools/example_scripts/
2155 (updated testing scripts are all in MITgcm_contrib/test_scripts)
2156 o verification:
2157 - remove un-tested experiments: cpl_atm2d+ocn, tidal_basin_2d and
2158 tutorial_offline
2159
9636f5994f Jean*2160 checkpoint67f (2018/11/23)
83ddf5a6c6 Mart*2161 o pkg/seaice:
2162 - add advection ppm and pqm advection schemes ;
2163 - test new scheme in verification/offline_exf_seaice.dyn_lsr
2164 o pkg/generic_advection:
2165 - regularize ppm and pqm advection schemes:
2166 - replace unsafe division in the case of numerical underflows by
2167 regularized expression sign(max(abs(uCFL),1.d-20),uCFL) and similar,
2168 in anology to other advection routines, e.g. gad_os7mp_adv_x/y/z.F
2169 - affects verification/advect_xz at truncation level -> updated
2170 o eesupp & model:
2171 - add entry points for 2-way nesting pkgs.
95edbf0004 chri*2172 o pkg/dic:
2173 - fix out-of-bounds error in S/R CAR_FLUX_OMEGA_TOP (#define CAR_DISS)
68432e7ba3 dngo*2174 o pkg/streamice:
2175 - new implementation of grounding line smoothing by smoothing of basal
2176 traction in partly grounded cell, in streamice_upd_ffrac_uncoupled.F
2177 - rename CPP directives: previous smoothing functionality now enabled with
2178 STREAMICE_SMOOTH_FLOATATION2, new functionality enabled via
2179 STREAMICE_SMOOTH_FLOATATION
2180 - affects verification/halfpipe_streamice, FWD, TAF and OpenAD adjoint.
fcc5c8b844 jm-c 2181 o pkg/atm_phys:
2182 - change IR absorption formulation regarding the dependence on Water-Vapor
2183 in the case wv_exponent = -1 ; update results of experiment "atm_gray.ape"
2184 from verification_other repos.
e0fa1cecbf Mart*2185 o pkg/seaice: clean up advection and SEAICE_ITD
2186 - make SEAICEmultiDimAdvection a global variable that is set in
2187 seaice_readparams.F
2188 - do not allow SEAICE_ITD with old 2nd order advection scheme anymore
2189 - re-organize SEAICE_ITD code in seaice_advdiff.F
2190 - make it possible to compile pkg/seaice without pkg/generic_advdiff
52dd931a85 Timo*2191 o pkg/autodiff:
2192 - created addummy_for_etan.F to correctly print adjoint variable for etaN
2193
901d0c4f7d Jean*2194 checkpoint67e (2018/10/16)
2195 o pkg/seaice:
2196 - fix possible division by zero if LSR_mixIniGuess > 0
85b328ee93 dngo*2197 o pkg/streamice:
2198 - fix bugs relating to ice front advance:
901d0c4f7d Jean*2199 streamice_advect_thickness.F -- overlap update of array passed to
85b328ee93 dngo*2200 streamice_adv_front which was leading to spurious ice area values
2201 streamice_init_varia.F -- proper initialisation of area_shelf_streamice
2202 which is used for ice front advance (only affects diagnostics)
1c882252b0 Ed D*2203 o verification/*/data
2204 - set "rhoConst" instead of "rhoNil" (unless using Linear EOS)
2205 - for net surface heat flux, set "surfQnetFile" instead of "surfQfile"
2206 (unless net surface shortwave is also specified).
2207 - fix OpenAD/input_oad.kpp set-up where net surface heat flux was used
2208 as net heat-flux minus short-wave and update the output.
2209
2df144911f Jean*2210 checkpoint67d (2018/09/04)
dcaaa42497 Jeff*2211 o doc:
2df144911f Jean*2212 - update few pieces of documentation including addition (in "getting_started"
dcaaa42497 Jeff*2213 section) of main CPP OPTIONS description and main code full list of
2214 run-time parameters.
a60aeb96a0 Oliv*2215 o pkg/generic_advdiff:
2216 - move masking of (explicit) vertical diffusive flux to S/R that compute each
2217 contribution (pass maskUp as a new argument): This ensures that diagnostics
2218 of explicit vertical diffusive flux are properly masked.
faf4966244 jm-c 2219 o tools/do_tst_2+2
2220 - Fix up to use absolute paths for results directories.
b8665dacca Mart*2221 o pkg/seaice: some new and hopefully more sensible defaults:
2222 - SEAICEscaleSurfStress = .TRUE.
2223 - SEAICEaddSnowMass = .TRUE.
2224 - SEAICEadvScheme = 77
2225 - SEAICE_useMultDimSnow = .TRUE.
2226 - SEAICE_Olx/y = Olx/y - 2
2227 - SEAICEetaZmethod = 3
2228 - SEAICE_drag = 0.001
2229 - CPP-flag SEAICE_ZETA_SMOOTHREG defined by default
2230 - change SEAICE_waterDrag default to 5.5e-3 and add reference density
2231 rhoConst to scale it. Add a warning if SEAICE_waterDrag > 1.
2232 This change also involves a slight re-organization (= simplification)
2233 in seaice_oceandrag_coeffs.F
2234 - all verification experiments are affected, so that all but four
2235 data.seaice are adjusted to restore the old defaults. The four experiments
2236 that use the new defaults are
2237 + global_ocean.cs32x15.seaice
2238 + offline_exf_seaice
2239 + offline_exf_seaice.dyn_jfnk
2240 + offline_exf_seaice.dyn_lsr
2241 - updated documentation
b4d50d3323 Oliv*2242 o pkg/dic:
a60aeb96a0 Oliv*2243 - Promote constants in S/R CARBON_COEFFS_PRESSURE_DEP and
2244 S/R CAR_FLUX_OMEGA_TOP to double precision.
1cf5741c70 Jean*2245 o pkg/seaice:
2246 - fix bug in seaice B-grid code (call to seaice_advdiff, see issue #134);
2247 Note: B-grid code not tested in any verification exp. (only compiled in one)
2248 so no need to update any output.txt
a5ec81ed49 Timo*2249 o pkg/diagnostics:
2250 - Print adjoint variables for theta, salt, uvel, vvel, wvel, and etan
2251 through diagnostics package.
4f8baf0351 Kait*2252 o pkg/shelfice:
2253 - fix ice shelf mask for very-thin ice shelf case, when hFacMin
2254 and hFacMinDr criteria leave no room for ice (hFac(k=1)=1).
2255 Note: thin ice-shelf that results in 0< hFac(k=1) <1 still need
2256 to be fixed when using any seaice pkg.
736e27304c Timo*2257 o pkg/ecco:
2258 - Replace "mskTrVol" and "gencost_errfile" with "gencost_mask" in
2259 "cost_gencost_transp", mirroring "m_horflux_vol".
2260 - Document and warn user (via STDERR) of potential issues with using
2261 "cost_gencost_transp" to compute volume, heat, or salt transport.
2262
00ab3a8557 Jean*2263 checkpoint67c (2018/06/26)
63eaf06b6a Jean*2264 o pkg/generic_advdiff:
2265 - Add per tracer run-time param to switch on/off Smolarkiewicz-Hack:
2266 Run-time switch for Temp & Salt are set from main param file "data"
2267 (default value = FALSE); and for pTracers, they are set from parameter
2268 file "data.ptracers" (default value = TRUE).
2269 - Add a test in verification exp. global_ocean.90x40x15.down_slope for
2270 Smolarkiewicz-Hack (switched on for Salt and pTracer(1)) but results
2271 remains unchanged since, in this exp., Salt & pTr(1) are well above 0.
f149b16d6e Jean*2272 o pkg/mdsio:
2273 - apply same substitution to remaining calls to MDSREADFIELD/MDSWRITEFIELD
2274 in pkg/ctrl and in pkg/seaice.
2275 - disable the use of obsolete MDSREADFIELD and MDSWRITEFIELD S/R (unless
2276 USE_OBSOLETE_MDS_RW_FIELD is defined).
f8e779c983 antn*2277 o pkg/ecco:
2278 - replace calls to (obsolete) MDSREADFIELD and MDSWRITEFIELD with calls to
2279 pkg/rw S/R: READ_REC_3D_RL and WRITE_REC_3D_RL ; this enable to use pkg/ecco
2280 without pkg/autodiff.
a51428376c jm-c 2281 o verification exp:
2282 - update few (10) adm & tlm output after latest TAF update, from version 3.9.0
2283 to version 3.9.6 on May 16-18.
2284
9ba62b8274 Jean*2285 checkpoint67b (2018/05/05)
502f242cbd Mart*2286 o pkg/exf/exf_wind.F:
9ba62b8274 Jean*2287 - fix a bug detected by Stanislav Martyanov: replace wStress by SQRT(wStress)
2288 in computing ustar ; this bug does not appear to affect the verification
2289 experiments but has been around for a while (inherited from the ecco-branch)
210ee8461e jm-c 2290 o pkg/seaice:
2291 - new run-time parameter to skip the update of ocean surface stress ; could be
2292 useful for testing or when seaice-dynamics is off (add a warning otherwise).
2293
411fbe7664 Jean*2294 checkpoint67a (2018/03/10)
2295 o pkg/layers
2296 - add Moist Static Energy coordinate in layers package
455d18a2e4 Jean*2297 o pkg/aim_v23:
2298 - change parameter "aim_abs_pCO2" default value (used if aim_select_pCO2=1,3)
2299 to calibrated value (from David Ferreira).
3ba991b895 chri*2300 o pkg/layers
210ee8461e jm-c 2301 - fixed up units reported in diagnostics for THETA and SALT term induced layer
3ba991b895 chri*2302 thickness changes.
17bd6b9422 jm-c 2303 o pkg/seaice:
2304 - move wind-stress over seaice out of SEAICE.h into local seaice_dynsolver.F
2305 common block ; move initialisation of TAUX & TAUY accordingly and add them
2306 to argument list of S/R SEAICE_OCEAN_STRESS (like SEAICE_GET_DYNFORCING).
2307 This enable to remove CPP option "SEAICE_EXCLUDE_WIND_STRESS" (hack from
2308 June 2016) in pkg/dic/dic_fields_update.F
034fdcf01f Jean*2309 o doc:
2310 - first addition of reST/sphinx documentation (formerly in
2311 https://github.com/altMITgcm/MITgcm/doc/), converted from original MITgcm
2312 LaTeX manual in: https://github.com/MITgcm/manual-archive with edits
2313 (including new sections) from @jrscott and @edoddridge ;
2314 - update section on Ocean State Estimation packages by @gaelforget ;
2315 - updated seaice pkg description by @mjlosch.
2316
78abfc2fd0 Oliv*2317 checkpoint67 (2018/02/05)
2318 o add Sphinx configuration for documentation on https://mitgcm.readthedocs.io
2319 o add Travis configuration for testing pull requests
7c72f3fed9 Oliv*2320 o migrate from CVS to Git (2018/01/31)
2321
e1a9cfe6da Jean*2322 checkpoint66o (2018/01/30)
2323 => Final CVS tag ; disable CVS check-in.
2324
9f8d0cd292 Jean*2325 checkpoint66n (2018/01/18)
4dedbda92a Jean*2326 o pkg/seaice & down_slope:
2327 - remove few files from ${pkg}_ad_diff.list (when calling S/R is not in
2328 any *_ad_diff.list)
2329 o pkg/shelfice:
2330 - account for "shelficeLoadAnomaly" in computation of initial pressure
2331 that is used in EOS (case selectP_inEOS_Zc >= 2).
457ca81085 Jean*2332 o pkg/aim_v23:
2333 - merge namelist "AIM_PAR_CO2" into "AIM_PARAMS" and replace Aim_CO2_Flag=2
2334 option with aim_select_pCO2=2 (using #define ALLOW_AIM_CO2);
2335 - add option to derive LW absorption in CO2 band as function of pCO2,
2336 using either prescribed pCO2 (aim_select_pCO2=1), or computed pCO2
2337 from well-mixed atm-box (aim_select_pCO2=3).
a88d8cd2fb Jean*2338 o pkg/gchem, changes to enable to use several geo-chemistry pkgs together:
2339 - new CPP option GCHEM_ADD2TR_TENDENCY around definition of gchemTendency
2340 array (replacing #ifndef GCHEM_SEPARATE_FORCING) ;
2341 - in GCHEM_FIELDS.h, change dimension of array "gchemTendency"
2342 from PTRACERS_num to GCHEM_tendTr_num ; this later one is set in new header
2343 file: GCHEM_SIZE.h, to be included anytime GCHEM_FIELDS.h is included ;
2344 - new set of S/R, called from GCHEM_TR_REGISTER, to record rank (in pTracer
2345 array) and number of tracers for each geo-chemistry pkg ;
2346 - check that GCHEM tracers all fit in pTracer and gchemTendency arrays ;
2347 - initialise gchemTendency array in gchem_init_vari.F ;
2348 - fix storage directives for gchemTendency ;
2349 - add some entry points for new geo-chemistry pkg SPOIL.
b82264afff Jean*2350 o verification/isomip:
2351 - update secondary test (input.htd): a) drop cd_scheme, useJamartWetPoints=T
2352 and increase viscAh ; b) use ivdc_kappa with implicit Diff & Visc ;
2353 c) switch off SHELFICEboundaryLayer, turn on pCellMix_select (=20) and
2354 use SHELFICEselectDragQuadr=1 ; add new set of pickup files.
0ce06cdb80 Jean*2355 o pkg/shelfice:
2356 - Replace CPP option: SHI_USTAR_WETPOINT with run-time parameter:
2357 SHELFICE_oldCalcUStar (default=F <--> #define SHI_USTAR_WETPOINT)
2358 but keep only original (old) formula in SHELFICEboundaryLayer code.
2359
e699be221d Jean*2360 checkpoint66m (2017/12/12)
40b8e0222d Mart*2361 o add another hook (S/R PDF_FINALIZE) for the Parallel Data Assimilation
2362 Framework PDAF (http://pdaf.awi.de/) in the_main_loop.F
d5d280a154 Jean*2363 o pkg/autodiff:
2364 - fix pkg/exf AD variable output (mainly ADJprecip), left from pkg/exf modif
2365 on Jan 27, 2017. Try also to fix ADJrunoff and TLM output (but less clear).
2366 o pkg/obcs:
2367 - add simpler setting (single value) of OB indices for the case where
2368 indices are uniform over the full section (Bruno Deremble contribution).
5421b78870 Jean*2369 o pkg/rbcs:
2370 - increase size of "relaxMaskFile" to read-in from namelist and save it
2371 (+check) into new (renamed) "relaxMaskTrFile" array.
fe8f61a7d2 Jean*2372 o model/src:
2373 - option (interViscAr_pCell, interDiffKr_pCell) to account for true vertical
2374 distance (including hFac) in vertical viscous flux and diffusive flux ;
2375 - add option to increase vertical mixing (for both momentum and tracers)
2376 near surface and/or bottom where partial cell is too thin ;
2377 - for now, both additions above are within: #ifndef EXCLUDE_PCELL_MIX_CODE ;
2378
1a6d19a1b5 Jean*2379 checkpoint66l (2017/10/24)
408a6af91c Jean*2380 o pkg/kpp, ggl90 & ebm:
2381 - read namelist without IOSTAT=errIO to force to stop if there is an error
2382 in the parameter file namelist.
11fedddd87 Jean*2383 o pkg/cheapaml: major changes to relaxation coefficient setting:
2384 - rename parameters cheapaml_taurelax & cheapaml_taurelaxocean (in days)
2385 to cheap_tauRelax & cheap_tauRelaxOce (now in seconds);
2386 - if using cheapMaskFile, set relaxation coeff to: cheapMask/tauRelax
2387 (instead of 1/cheapMask over ocean and 1/tauRelax over land);
2388 - with cheapMaskFile unset: set relaxation coeff according to land/ocean mask
408a6af91c Jean*2389 (unchanged) but skip increase near domain edges for periodic domain (in X
11fedddd87 Jean*2390 or Y dir) when cheapamlX/Yperiodic=T ; also fix linear increase (over
2391 Cheapaml_mask_width grid points) of coeff towards domain edges (previously
2392 was increasing away from edges). Update output of experiment "cheapAML_box".
2393 o pkg/cheapaml:
2394 - move setting of (fixed in time) relaxation coefficient
2395 from cheapaml_init_varia.F to cheapaml_init_fixed.F
dc84b236da Jean*2396 o pkg/exf:
2397 - add specific forcing field for tides to feed model new geopotential anomaly
2398 forcing, for now within #ifdef EXF_ALLOW_TIDES.
2399 - remove from common block unused params: exf_inscal_sst & exf_inscal_sss.
1faed850cb Jean*2400 o model:
2401 - add new 2-d forcing field for time-dependent geopotential anomaly (e.g.,
2402 tidal forcing), in m^2/s^2 ; add run-time param to allow to turn it off.
2403 o eesupp/src:
7727ad69a9 Dimi*2404 - shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F
2405 for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h
2406
3cac0e158e Jean*2407 checkpoint66k (2017/09/20)
2408 o model/src:
0442cf0340 Gael*2409 - add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F
2410 and the_model_main.F)
2411 o ctrl:
2412 - use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F)
3cac0e158e Jean*2413 - call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated
0442cf0340 Gael*2414 mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F,
2415 ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F )
dd5f25c34f Jean*2416 o eesupp:
2417 - add CPP option to activate some pieces of code for coupling to GEOS AGCM;
2418 - shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM.
59cd39d469 Matt*2419 o pkg/bling:
dd5f25c34f Jean*2420 - bling_production: Fix typo in calcium carbonate uptake. Also rearranging
2421 and cleaning
8880ed1f7d Jean*2422 o model/src:
2423 - move k loop inside correction_step.F (+ update calling S/R)
2424 - collect implicit pressure gradient tendencies in local 2-D array;
2425 affect results (at machine truncation level) when using 3-D solver; update
2426 output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
2427 rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
2428 & tutorial_plume_on_slope.
2429
32f5cbc73c Jean*2430 checkpoint66j (2017/08/15)
ba2a21739f Jean*2431 o pkg/ptracers:
2432 - fix surface forcing under ice-shelf (useShelfIce=T).
2433 o pkg/atm_phys:
2434 - use hFac weighted average when applying A-grid atm-phys momentum tendency
2435 to C-grid dynamics; this ensures wind-stress match mom tendency.
03aacdc90f Mart*2436 o eesupp/src:
157398927a Mart*2437 - change default for opening scratch files to avoid STATUS='SCRATCH'
4a3a90a659 Jean*2438 - close scratch files with STATUS='DELETE'
03aacdc90f Mart*2439 - changes affect eeset_parms.F and open_copy_data_file.F and many routines
2440 that read namelists (because they close the scratch files)
4a3a90a659 Jean*2441 - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
2442 in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
d39315aba7 Jean*2443 o pkg/atm_phys:
2444 - fix unset arguments in (unused) S/R surface_flux_0d.
5261466e31 Jean*2445 o eesupp/src:
2446 - add argument "procId" to S/R EESET_PARMS to fix scratchFile1 & 2 setting
2447 (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
2448 called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
234f0840d6 Mart*2449 o pkg/streamice:
2450 - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
2451 preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
2452 streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
7d973b58e2 Jean*2453 o pkg/diagnostics:
2454 - new option to allow to cumulate thickness-factor (hFac) weighted field
2455 (if field permitted); implemented by changing sign of "jdiag" pointer
2456 (> 0: cumlulate field, < 0: cumulate hFac weighted field).
2457 a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
2458 center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
2459 b) for now, activated by setting fileFlags 3rd character to 'h'.
2460
d0fc06a0a4 Jean*2461 checkpoint66i (2017/07/18)
2462 o pkg/cheapaml:
2463 - add parameter "useRelativeWind", default set to False; this change the
2464 previous setting which was always using relative wind.
036ec33ebd Mart*2465 o add hooks for the Parallel Data Assimilation Framework PDAF
d0fc06a0a4 Jean*2466 (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
2467 to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
fc55955988 Jean*2468 o pkg/exf:
2469 - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
a435e833b1 Mart*2470 of South-Pole mean value.
d0fc06a0a4 Jean*2471 - interpolation near the poles, case where second additional row is at the
04a6d3d2ba Jean*2472 pole (or beyond the pole and moved to the pole): change first addition row
d0fc06a0a4 Jean*2473 value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
04a6d3d2ba Jean*2474 row (instead of just a copy of it).
fc55955988 Jean*2475 o pkg/seaice:
f720d02ca0 Mart*2476 - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
fc55955988 Jean*2477 - add the option to compute no-slip du/dy, dv/dx (i.e.
2478 the offdiagonal strain rate e12) by a second order approximation
2479 on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
2480 it is too messy to implement for the implicit LSR matrix.
f720d02ca0 Mart*2481 SEAICE_2ndOrderBC = .FALSE. by default
50ab531fad Mart*2482
6a3f62c6cb Jean*2483 checkpoint66h (2017/06/02)
2484 o pkg/seaice:
2485 - add new routines to compute stress tensor components and stress tensor
e228c48bba Mart*2486 divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
2487 - change names of diagnostics SIsigI/II (commonly used for invariants)
2488 to SIsig1/sig2 (more common for principal components) to avoid confusion
5d66a6a2ec Jean*2489 o pkf/exf:
2490 - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
2491 similarly, stop if rotateStressOnAgrid with constant wind-stress.
caa3182bae Jean*2492 o pkg/seaice:
2493 - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
2494 EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
2495 - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
2496 fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
2497 o pkg/diagnostics:
2498 - small piece of code to rename (old) diagnostics, when namelist is processed.
e9ff366891 Jean*2499 o model/src:
2500 - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
2501 originally, set as minimum of adjacent hFacC factor ; now (new default)
2502 computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
2503 Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
caa3182bae Jean*2504 o pkg/seaice:
e9ff366891 Jean*2505 - add momemtum advection, off by default, still in test phase
2506 most of the momentum advection code is adapted and reused from mom_vecinv
caa3182bae Jean*2507 o pkg/mom_vecinv:
2508 - pass these runtime flags:
e9ff366891 Jean*2509 selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
caa3182bae Jean*2510 as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
e9ff366891 Jean*2511 so that these routines can also be used in pkg/seaice.
fc0cb18620 Mart*2512
4207dc8bfb Jean*2513 checkpoint66g (2017/04/24)
d9c26da9d2 Jean*2514 o model/src:
2515 - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
2516 to get same expression (regarding machine truncation) in different places
2517 in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
2518 Update forward output of experiments: global_ocean.cs32x15 (all 5 except
2519 viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
e3622e8a9f Jean*2520 o pkg/shelfice:
2521 - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
2522 to shelfice_init_fixed.F
2523 - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
2524 ini_masks_etc.F for now) to update ocean upper boundary position according
2525 to ice-shelf topography (instead of directly updating hFacC).
559a8104ea Jean*2526 o model/src:
2527 - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
2528 packages_init_fixed.F to allow other pkgs to set mask and weight fields.
2529
902eadea41 Jean*2530 checkpoint66f (2017/04/06)
4fcf953981 Jean*2531 o model/src:
2532 - add specific run-time param to select level of printed plot-field-maps,
2533 set by default to debugLevel. Remove internal param "printDomain".
2534 o pkg/seaice:
c854efd521 Mart*2535 - add flag to add snow mass to seaiceMassC/U/V, the default is
2536 SEAICEaddSnowMass=.FALSE., not to change previous results
7d18c8ad21 Matt*2537 o pkg/bling
2538 - Bug fix in bling_production regarding unit conversion for diagnostics
2539 being put in the wrong place
bc982d58e8 Jean*2540 o model/src:
2541 - add back recomputation of rSurfW & S to ensure consistent column thickness
2542 (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
2543 when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
2544 revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
fe1663a66d Jean*2545 o pkg/autodiff:
2546 - clean-up "checkpoint.flow"
2547 o pkg/rw (Contribution from Jody Klymak):
2548 option to set mds file suffix as function of time in simulation:
2549 *) new input parameter "rwSuffixType" (read from PARM03 namelist)
2550 to select file suffix format; by default (=0), use iteration number;
2551 *) add simple routine to return file suffix according to rwSuffixType;
2552 *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
2553 use new S/R to get file suffix, except for debug output file (diagFreq)
2554 and pkgs offline & rbcs input files.
2555 o pkg/rw:
2556 - uniform processing of "I10" suffix across writing fld routines; used to
2557 simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
2558 (similar to cg3d.F, cg3d_ex0.F)
a94e0175c9 Jean*2559 o pkg/mom_vecinv:
2560 - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
2561 vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
1906a8e7f8 Matt*2562 o pkg/bling:
a94e0175c9 Jean*2563 - Many small changes intended to clean the code.
2564 Unnecessary ADJOINT_SAFEs removed ;
2565 removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
2566 diagnostics added.
1906a8e7f8 Matt*2567
a035b63002 Jean*2568 checkpoint66e (2017/03/14)
78a0667e15 Jean*2569 o pkg/exf:
2570 - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
2571 definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
2572 use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
728f4c76b4 Jean*2573 avoid any dynamic allocation ;
2574 - S/R EXF_CHECK: add new check & stop when file-name is defined but not
2575 read-in ; add warning when file is read-in but not used within pkg/exf ;
2576 + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
2577 - update exf_summary.F (print {FLD}RepCycle).
78a0667e15 Jean*2578 o verification/global_with_exf:
2579 - switch on exf interpolation in AD test (just like the forward test)
52e8352d39 Gael*2580 o pkg/mom_vecinv:
2581 - add storage directives to avoid recomputations within mom_vecinv.F
78a0667e15 Jean*2582 which were generating seg. fault with gfortran -devel
52e8352d39 Gael*2583 o pkg/ctrl, pkg/smooth:
78a0667e15 Jean*2584 - initialize array halos which were generating seg. fault with
52e8352d39 Gael*2585 gfortran -devel in adjoint mode
df8491dd93 Jean*2586 o pkg/exf:
ab74fbfba7 Jean*2587 - for each input field, enable to specify a field specific repeat-cycle
2588 ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
2589 o verification/lab_sea:
2590 - update AD results of primary test and noseaicedyn test after switching
2591 to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
2592 check stays about the same.
2593 o pkg/exf:
df8491dd93 Jean*2594 - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
d1272ed847 Dimi*2595 - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
1a68cdf63d Jean*2596 o pkg/bling, USE_EXFCO2 code:
2597 - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
2598 - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
38dcf987c9 Jean*2599 o pkg/exf:
2600 - rename S/R EXF_INIT to EXF_INIT_VARIA ;
2601 - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
2602 repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
2603 and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
2604 - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
2605 EXF_INIT_FLD) and update calls in exf_init_varia.F
2606 - For now, for backward compatibility, keep a simplified version of S/Rs
2607 EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
2608 - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
2609 to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
2610 o tools/genmake2:
2611 - replace "bc -l" (only used once) by "expr" (already used).
0e208b4985 Jean*2612 o verification/global_ocean.cs32x15:
2613 - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
2614 Note: exf setting (data.exf) can be compared to other exf secondary exp
2615 "seaice" (kept with useCAL=T) which has same time dependent forcing.
2616
68b2841201 Jean*2617 checkpoint66d (2017/02/13)
2618 o pkg/exf:
2619 - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
2620 early on (in packages_boot.F) to stress this change in pkg setting.
2621 - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
e88a30daa9 Jean*2622 o model/src:
39fa77e8d0 Gael*2623 - move call to ecco_phys to end of time step; this may induce minor
2624 cost function changes by shifting time averages by one time step
2625 for some variables; this revision resulted in changed adjoint results
2626 in MITgcm_contrib/verification_other/global_oce_cs32
e88a30daa9 Jean*2627 o pkg/exf:
2628 - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
2629 this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
2630 e.g. precip, are not available.
2631 o pkg/flt:
2632 - flt_init_varia.F: use pickupSuff if specified
2633 - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
2634 intermediate, step towards completing pkg/exch2 support within pkg/flt;
2635 ifdef DEVEL_FLT_EXCH2 then:
2636 - flt_init_fixed.F: comment out stop
2637 - flt_exch2.F: conserve ipart, jpart (grid coordinates)
2638 - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
2639 - flt_mapping.F: attempt to fix longitude diagnostic near date-line
2640 - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
ea11a19a76 Jean*2641 o tools/genmake2 & pkg/pkg_depend:
2642 - define new type of pkg dependency rule ("=pkg_x"), less strict than
2643 the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
2644 (-pkg_x in packages.conf).
2645 - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
2646 - add "+cal" to dependency list of pkg/ecco (needed to compile).
2647 - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
127047c0ca Dimi*2648 o utils/matlab:
2649 - adding ocean_basin routines for defining basin masks.
6a96fcda5d Jean*2650 o pkg/exf:
450d2d2f88 Jean*2651 - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
2652 arguments, allowing to check (and stop) if parameter setting of
2653 {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
2654 useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
2655 for backward compatibility.
2656 - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
2657 exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
2658 o pkg/bling (USE_EXFCO2 code):
2659 - fix missing setting of apco2StartTime according to apco2startdate1 & date2
2660 by adding a call to S/R EXF_GETFFIELD_START.
2661 o pkg/exf:
40e5c4acf5 Jean*2662 - allows to compile without pkg/cal (but disabled by current dependency
2663 rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
2664 run with useCAL=F ; this involves setting directly {FLD}StartTime instead
2665 of {FLD}startdate1 & date2 ; consistency check not yet coded.
2666 o verification/global_ocean.cs32x15:
2667 - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
2668 corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
2669 o pkg/exf:
2670 - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
2671 calculations); change FWD experiment global_ocean.cs32x15
2672 (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
2673 o pkg/exf:
2674 - In preparation for addition to NAMELIST, rename internal (_RL) parameter
053dccd244 Jean*2675 {FIELD}startdate to {FIELD}StartTime
2676 Note: new name also fit better the content, i.e, a start time in second.
40e5c4acf5 Jean*2677 o eesupp/src:
2678 - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
053dccd244 Jean*2679 o pkg/exf:
6a96fcda5d Jean*2680 - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
2681 to allow to read-in Sensible & Latent Heat flux ;
2682 - simplify pkg/exf main options:
2683 1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
2684 exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
2685 compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
2686 2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
2687 ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
2688 3) improve options documentation in EXF_OPTIONS.h.
c63b11972e Gael*2689 o pkg/ecco:
6a96fcda5d Jean*2690 - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
2691 ecco_summary.F: add passive tracer cost functions to gencost;
c63b11972e Gael*2692 m_ptracer and m_boxmean_ptracer
2693 o pkg/ctrl:
6a96fcda5d Jean*2694 - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
c63b11972e Gael*2695 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
2696 of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
2697 xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
2698 o model/src:
6a96fcda5d Jean*2699 - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
c63b11972e Gael*2700 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
2701 o pkg/exf:
6a96fcda5d Jean*2702 - exf_getffields.F: add to list of implemented gentim2d contol parameters:
c63b11972e Gael*2703 xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
2704
6b39d139af Jean*2705 checkpoint66c (2017/01/19)
8611775bfe Jean*2706 o verification:
2707 - add new option "-src" to testreport to only produce source code (*.f),
2708 including taf output src code (if using '-adm'/'-tlm' option).
66f021d63a Gael*2709 o pkg/exf:
2710 - add saltflx :: Net upward salt flux in psu.kg/m^2/s
2711 o pkg/diagnostics:
bd9df6a12d Jean*2712 - add run-time variable diagMdsDir to specify a subdirectory for
66f021d63a Gael*2713 diagnostic output when mds is being used and mdsioLocalDir is not.
c34b076d9e Gael*2714 o pkg/mnc:
9922871071 Gael*2715 - mnc_utils.F: edit stop message
c34b076d9e Gael*2716 o pkg/autodiff:
66f021d63a Gael*2717 - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
2718 add HAVE_SYSTEM bracket around system call to mkdir
c34b076d9e Gael*2719 o pkg/profiles:
bd9df6a12d Jean*2720 - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
c34b076d9e Gael*2721 profiles_readparms.F: call ALL_PROC_DIE before 'stop'
66f021d63a Gael*2722 - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
2723 add HAVE_SYSTEM bracket around system call to mkdir
c34b076d9e Gael*2724 o pkg/smooth:
2725 - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
2726 - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
2727 - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
7b97f426d4 Jean*2728 o pkg/exf:
2729 - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
bd9df6a12d Jean*2730 issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
2731 generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
7b97f426d4 Jean*2732 - summary: skip detailed field report if not used (empty file-name).
93424431c1 Jean*2733 o tools/xmakedepend:
2734 - In case line editor "ed" is missing, switch to "sed" command to clean-up
2735 Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
5d59af6b6c Jean*2736 o pkg/exf:
2737 - change definition of "hflux" input file to always include Short-Wave;
93424431c1 Jean*2738 this is now consistent with hflux computation (if using bulk-formulae)
5d59af6b6c Jean*2739 and hflux diagnostic & documentation (in EXF_FIELDS.h).
2740
cd57923099 Jean*2741 checkpoint66b (2016/12/01)
3706e6143e Jean*2742 o model & momentum pkgs:
2743 - implement fully implicit bottom friction combined with implicit surf.
2744 pressure, for now, only in hydrostic formulation:
2745 + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
2746 and run with selectImplicitDrag=2 ;
2747 + currently missing diagnostics of bottom drag and vert. viscosity tendency;
2748 - partial implicit time-stepping (bot. friction + vert. visc first, then
2749 surf. press) corresponding to selectImplicitDrag=1 should be applicable
2750 to NH formulation but not available until we solve for surf. pressure
2751 increment (instead of full etaN).
499c3c4540 Jean*2752 - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
2753 with implicit vertical viscosity.
ff74c947d1 Mart*2754 o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
2755 - this is a first version that includes many regularisations that may
2756 not all be necessary, to be sorted out,
2757 - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
2758 - change one verification experiment in seaice_itd to use and test new code
3706e6143e Jean*2759 - seaice_growth: catch a case where the argument of log can be zero
ff74c947d1 Mart*2760 or smaller (important for code stability)
c68e15e2a9 Jean*2761 o model/src:
2762 - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
2763 & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
2764 similar A.X'=Y' system (with same matrix A) in subsequent calls;
2765 switch based on errCode (In/Out) argument value; in calling routines,
2766 initialise errCode before first call.
2767
4a59b36843 Jean*2768 checkpoint66a (2016/10/18)
2661ed7c00 Matt*2769 o pkg/bling:
4a59b36843 Jean*2770 - BLING package now loads in atmospheric pCO2 file using exf package routines
2771 Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
8372d9421d Jean*2772 o model/src & pkg/ptracers:
2773 - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
2774 GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
2775 implicitDiffusion (respectively) are used (even without momImplVertAdv
2776 or temp,salt,PTRACERS_ImplVertAdv).
25215968c0 Jean*2777 o model/src & generic_advdiff:
2778 - add parenthesis in main diagonal calculation of implicit vertical
2779 diffusion matrix (impldiff.F & gad_implicit_r.F).
2780 This affects results at machine truncation level; update output of many
2781 verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
caec104026 Jean*2782 o pkg/mom_commom & generic_advdiff:
2783 - add deep atmosphere and anelastic scaling factor in implicit vertical
2784 advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
2785 o model/src:
2786 - remove few unnecessary temp array copies in solve_tridiagonal.F
2787 & solve_pentadiagonal.F
2788
434f2a808d Jean*2789 checkpoint65z (2016/09/28)
2790 o pkg/seaice: fix multithreading for seaice_fgmres.F
4d686fb526 Mart*2791 - remove unecessary variables from common blocks
434f2a808d Jean*2792 - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
2793 basis, that are stored in commom blocks (including integer variable i1)
2794 - clean up code a little by removing commented lines that refer to
4d686fb526 Mart*2795 original code
434f2a808d Jean*2796 - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
6c3fcd2d73 Gael*2797 o MITgcm manual:
caec104026 Jean*2798 - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
2799 preliminary documentation for generic controls (8.3; ctrl.tex),
2800 a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
2801 ecco_costfunction.tex
b3b78d9534 Gael*2802 o pkg/ecco:
caec104026 Jean*2803 - update and cleanup list of CCP options
2804 - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
2805 is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
2806 - add checks that retired run-time options are not used, and in relation
2807 to gencost_mask and gencost_errfile
2808 - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
2809 gencost_nrecperiod
2810 - fix m_eta computation for virtual salt flux case
2811 - add m_horflux_vol case (selected via gencost_barfile) that computes
2812 transports via cost_gencost_boxmean (gencost_flag=-3)
2813 - use gencost_flag more systematically (i.e., avoid using gencost_name)
2814 for code switches (aside from physical variable selection)
290bbecc29 Mart*2815 o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
2816 attempt appears to be a bit of a hack and my need some repair down the road
423bece461 Jean*2817 o pkg/exf:
2818 - interpolation near South Pole: fix criteria on input field latitude.
772c88b829 Jean*2819 o pkg/icefront & pkg/exf:
2820 - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
2821 from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
6708d8dfd2 Jean*2822 o pkg/exf:
2823 - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
2824 "exf_output_interp" (in namelist: EXF_NML_04); change output file name
2825 (add suffix "_out" instead of a prefix); keep same record number as in
2826 input file but always write record 1 first (to avoid a STOP in I/O S/R).
2827 Change output file content by writing interpolated field before applying
2828 land-sea mask (helpful for debug).
2829 - 2 compon. vector interpolation with rotation: apply scaling factor on
2830 each compon. (Eastward and Northward) just before rotation.
7e2b7aaecb Matt*2831 o pkg/bling:
6708d8dfd2 Jean*2832 - Cleaned package. Removed not needed code and comments.
2833 - adjoint example now works
7e2b7aaecb Matt*2834 (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
33d60f0145 Jean*2835 o pkg/ptracers:
2836 - add Bruno Deremble's code to complete the linear surface correction
2837 for tracer conservation;
0aacb0e819 Oliv*2838 - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
c16ff5b7c8 Mart*2839
94ff1e4393 Jean*2840 checkpoint65y (2016/07/29)
92de52e82f Jean*2841 o pkg/debug (stats):
2842 - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
2843 proc/thread mapping);
2844 - fix Min & Max for case where 1 thread has only empty tiles;
2845 - use RL variable to count number of wet grid points (with big domain,
2846 can be too large to fit into integer*4).
c21a057aef Jean*2847 o pkg/monitor:
92de52e82f Jean*2848 - use RL variable to count number of wet grid points (but used only for del2)
c21a057aef Jean*2849 - add new routine to compute Advective CFL within tracer time-stepping with
2850 writing delayed until next monitor output.
880a06ccd8 Jean*2851 o pkg/obcs:
2852 - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
33d60f0145 Jean*2853 o pkg/cal:
2854 - calandar-dump: treat case myTime < timePhase in the same way as in
2855 eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
20bafebaa1 Jean*2856 o pkg/dic & seaice:
2857 - fix compilation of ocean component for coupled atm+ocn model with
2858 seaice dynamics & dic.
2859
1fc3f67886 Jean*2860 checkpoint65x (2016/06/11)
2861 o add a license text file in main MITgcm tree.
dca45a136c Matt*2862 o added pkg/bling:
c721362620 Jean*2863 - intermediate complexity biogeochemical model
dca45a136c Matt*2864 - see bling_description.txt for details
c721362620 Jean*2865 - verification experiment is global_oce_biogeo_bling (for now, in
2866 Contrib/verification_other/); tested daily on baudelaire with gfortran.
2867 - add entry point in pkg/gchem for new pkg "bling".
dd56bd054f Mart*2868 o pkg/seaice: fix tensile stength computation
2869 - replace global field tensileStrength by tensileStrFac
2870 - tensileStrFac can be computed once in S/R seaice_init_varia
2871 - fortunately that does not affect any verification results
2872
4973639fa7 Jean*2873 checkpoint65w (2016/05/12)
b509abd770 Mart*2874 o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
2875 with ECCO_CTRL_DEPRECATED defined
9cecfd71bf Jean*2876 o verification/global_ocean.cs32x15:
2877 - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
2878 with "selectNHfreeSurf=1".
99dd8840a4 Jean*2879 o model/src (non-hydrostatic free-surface):
2880 - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
2881 was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
2882 - Calculate surface vertical velocity after 2-D solver adjustment (accounts
2883 for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
2884 and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
2885 This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
2886 - Update output (changes at machine truncation level) of verification exp:
2887 exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
2888 short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
ca41d54747 Mart*2889 o pkg/seaice: ITD code
99dd8840a4 Jean*2890 - fix picking up from a single category model by initialising
ca41d54747 Mart*2891 heff/area/hsnowITD = 0. in seaice_itd_pickup.F
2892 - split a long warning message in seaice_check_pickup.F into two lines,
2893 because NEC SX-ACE cannot deal with the long line.
8c8ba31314 Jean*2894 o model/src:
2895 - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
4ecb7ca1c7 Mart*2896 o pkg/seaice:
2897 - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
8c8ba31314 Jean*2898 o pkg/seaice:
02ecb7194f Mart*2899 - add basal stress as parameterisation for grounding ice
2900 following Lemieux et al. (2015)
8c8ba31314 Jean*2901 - turn on by setting new parameter SEAICEbasalDragK2 to a value
2902 larger than 0. Lemieux et al. (2015) recommend 15.
02ecb7194f Mart*2903 - The adjoint complains with extra recomputations so there is also a
2904 new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
2905 order to postpone the problem
2906 - compile the new code in lab_sea
026b44969e Jean*2907 o verification/halfpipe_streamice:
2908 - update both TAF and OpenAD adm output (machine truncation differences)
2909
8692139b79 Jean*2910 checkpoint65v (2016/04/08)
77f624c4e1 Jean*2911 o verification/advect_xz:
2912 - increase overlap size from 3 to 4 and add new secondary test for PQM
2913 advection scheme (with mono & wino limiter).
2914 - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
ef0910b248 Jean*2915 o model/src:
2916 - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
2917 added phi0Ref) to set vertical axis origin and phiRef origin;
2918 keep Ro_SeaLevel for backward compatibility (with a warning).
2919 According to coordinate and fluid type:
2920 OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
2921 ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
2922 OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
2923 ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
77f624c4e1 Jean*2924 - remove Ro_SeaLevel from ATM experiment parameter files;
2925 - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
2926 complement; update output.txt (changes at machine truncation level).
9af9059269 Mart*2927 o pkg/seaice/seaice_evp.F
2928 - simplify computation of deltaZ and zetaZ to simple averaging following
2929 Bouillon et al. (2013). This removes a lot of code, but also changes
2930 verification experiment lab_sea.hb87 -> updated
2931
1ec3766700 Jean*2932 checkpoint65u (2016/03/14)
2c76214192 Jean*2933 o pkg/generic_advdiff:
2934 - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
2935 with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
2936 Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
2937 testing and not for actual use.
fc40089cb1 Jean*2938 o model/src:
2939 - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
2940 origin r = rF(1);
2941 - add options (parameter selectP_inEOS_Zc) to select which pressure to use
2942 in EOS for height coordinate: enable to include NH Pressure or to use
2943 more accurate pressure vertical profile; options not linked to EOS type
2944 (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
2945 - start to implement variable gravity (along vertical): for now, only with
2946 z-coords (not even z*).
2947 - add Ideal Gas equation of state for height coordinate.
2c76214192 Jean*2948 - update OpenAD output (affected at machine truncation level) of exp:
2949 global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
564694d02e Gael*2950 o pkg/exf:
2951 - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
fc40089cb1 Jean*2952 of exf interpolation (before any rescaling, rotation or interpolation
2953 to velocity point) for each field that gets loaded from file. This option
2954 identically mimics the input file organization (e.g. record numbers in year
2955 by year input files) besides the change in horizontal grid.
564694d02e Gael*2956 - add rotateStressOnAgrid run-time switch so that wind stress fields
fc40089cb1 Jean*2957 can be provided on the A-grid in zonal/meridional direction and
2958 rotated on the fly. This only applies to the case when the exf
2959 interpolation is off and rotateStressOnAgrid is false by default.
dc293ceb82 Jean*2960 o model/src:
2961 - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
2962 it's also used with pkg/atm_phys) and add few more parameters (but still
2963 inactive, src code yet to come)
2964
388e260d1d Jean*2965 checkpoint65t (2016/02/10)
6eeba9ca6b Jean*2966 o pkg/atm_phys:
2967 - from Ruth Geen: add optical depth dependence on CO2 concentration.
74dbf591da Jean*2968 o model/src:
2969 - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
2970 for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
2971 Update output of exp. deep_anelastic (changes at truncation level).
42d6c3122b Jean*2972 o tools:
2973 - add a hack in "remove_comments_sed" (used only with TAF) for recent
2974 version of OpenMPI (shipped with FC.23): comment out the new header
2975 file "mpif-sizeof.h" which causes problems to TAF.
142f5afeb1 Mart*2976 o pkg/seaice:
c9f636aca9 Mart*2977 - change the termination criterion so that maxits (SEAICElinearIterMax)
2978 has an effect
142f5afeb1 Mart*2979 - unify iteration parameters for implicit solvers (JFNK and Picard)
2980 SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
2981 SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
2982 SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
2983 SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
2984 SEAICEnonLinTol replaces JFNKgamma_nonlin
2985 - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
2986 - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
2987 use with SEAICEuseKrylov
2988 o pkg/seaice/seaice_lsr.F
42d6c3122b Jean*2989 fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
2990 relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
2991 an effect.
e42d0c73e8 Mart*2992 o pkg/seaice: add two new parameters
42d6c3122b Jean*2993 - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
e42d0c73e8 Mart*2994 parameter is not in any namelist)
42d6c3122b Jean*2995 - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
2996 a preconditioner for the non-linear Newton iteration of the JFNK
e42d0c73e8 Mart*2997 solver
2d057da76f Mart*2998 o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
42d6c3122b Jean*2999 affects some experiments at truncation level:
3000 - global_ocean.cs32x15.icedyn (11 digits),
3001 - global_ocean.cs32x15.seaice (11 digits),
2d057da76f Mart*3002 - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
3003 - also update global_ocean.cs32x15 adjoint and tangent-linear results
3d01549ccd Jean*3004 o pkg/salt_plume & pkg/thsice:
3005 - for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
3006 connect salt_plume flux to ATM-OCN coupling pkgs interface:
3007 a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
3008 export to coupler interface) even without compiling pkg/salt_plume ;
3009 b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
3010 (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
467753bb05 Jean*3011 o pkg/dic:
3012 - use the updated seaice fraction (from seaice pkgs) for DIC forcing
3013 instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
3014 called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
3015 - move also update with values from ATM-OCN Coupler in the same new S/R
3016 (previously done in ocn_apply_import.F).
3017 o tools/adjoint_options:
3018 - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
3019 has been changed on Jan 14, 2016.
3020 o pkg/ggl90:
3021 - add alternative discretisation of vertical shear (off by default), to
3022 compute the mean (@ grid-cell center) of vertical shear compon instead of
3023 vertical shear of mean flow (@ grid-cell center).
3024 - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
3025 results on adjacent faces of cubed-sphere grids; this fix the restart.
86104489ad Jean*3026 o pkg/atm_compon_interf:
467753bb05 Jean*3027 - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
86104489ad Jean*3028 pass last value, stored directly before export to CPL ;
3029 Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
3030 - remove atmSLPr from pickup files (no longer needed for restart)
3031
96ead4aa58 Jean*3032 checkpoint65s (2016/01/13)
9d1bad620f Jean*3033 o eesupp & genmake2:
3034 - first check for Function ETIME and, if it fails, then check for subroutine
3035 ETIME and consistent output; use the appropriate version in timers.F
0e1fe683c9 Jean*3036 o model/src:
3037 - to check restart test, add option to apply EXCH to U,V earlier, just before
3038 integr_continuity; turned off by default.
3039 o pkg/dic:
3040 - remove CPP option USE_ATMOSCO2 (not needed)
3041 o tools/tst_2+2:
3042 - try to ignore difference between +0 and -0 in binary file, causing test
3043 to fail for no good reason.
3044 o eesupp & genmake2:
3045 - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
3046 but also check (in genmake2) that test runs and returns meaningful results.
a4406a661e Jean*3047 o coupler pkgs:
3048 Finish implementation of optionally-exchanged variable switches (started on
3049 Nov 12) with addition of few more exchanged fields, including 2-way exchange
3050 of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
3051 advection in OCN component; this requires sequential coupling.
3052 coupler (pkg/atm_ocn_coupler):
3053 - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
3054 routines (useful for debug).
3055 - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
3056 flux, DIC fields) if corresponding switch is ON.
3057 - add option to export RunOff to OCN (to use for DIC river input)
3058 - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
3059 components (pkg/atm_ & ocn_compon_interf):
3060 - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
3061 optionally exchanged fields; add a check & stop in cpl_readparms.F.
3062 ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
3063 OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
3064 - rename: fracIce -> sIceFrac_cpl (<- match coupler var name)
3065 + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
3066 - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
3067 - hold in common block coupler optionally-exchanged variable switch
3068 and set default "useImportXXX" accordingly; + check & stop if inconsistent.
3069 - add diagnostics for all imported fields from coupler (in both OCN & ATM);
3070 this is intended to replace the OCN cplFldtave.* output files (not updated
3071 to contain new additional exchanged fields).
826e3022ab Jean*3072 o pkg/dic:
3073 - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
3074 o pkg/thsice:
3075 - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
3076 and writing of thsice pickup files.
3077 o pkg/atm_compon_interf:
3078 - move all field individual export-call out of cpl_export_import_data.F
3079 into new S/R ATM_EXPORT_FIELDS
df3ba02ef4 Jean*3080 o pkg/atm_compon_interf:
3081 - store state variables (for now, only thSIce fields) just before beeing
3082 exported (in cpl_export_import_data.F, like on ocean side) instead of from
3083 atm_store_my_data.F like all exported fluxes.
3084 - new version of pickup_cpl: write field names into meta file and read meta
3085 file to find field postion in pickup. Also only write/read fields meeded for
3086 restart (same logic as main pickup file ; also using pickupStrictlyMatch)
cc55ade87f Jean*3087 o pkg/dic:
3088 - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
238b281666 Mart*3089 o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
cc55ade87f Jean*3090 pressure replacement method (=1., default) or original Hibler (1979) (=0.)
3091 value can be from domain [0,1] to average between the two methods
8f2cc0ef18 Jean*3092 o pkg/atm_phys:
3093 - allow to provide 2-d map of albedo and mixed-layer depth from files (but
3094 hold fixed in time).
3095
df5ab41a91 Jean*3096 checkpoint65r (2015/12/21)
3097 o pkg/seaice:
3098 fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
3099 solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
3100 o pkg/seaice:
3101 - fix a bug in computing areaS in (J-J -> J-1) that affects runs
d5321ae2f9 Mart*3102 when SEAICEscaleSurfStress=.TRUE.,
3103 - apply areaW and areaS in S/R seaice_calc_lhs
0b8d317bbe Jean*3104 o pkg/atm_phys:
3105 - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
3106 (shortwave & longwave, net & downward) and diagnostics of temp. tendency
3107 for individual contribution (convection, LSC cond, radiation)
8c8ba31314 Jean*3108 - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
0b8d317bbe Jean*3109 information); activated with: solar_exponent=0. and wv_exponent=-1.
3110 o pkg/ggl90:
e4d707b911 Mart*3111 - within IDEMIX add upper limit for horizontal group velocity to
3112 avoid instability problems in the explicit horizontal diffusion term for
3113 long time steps or high resolution
0602590031 Jean*3114 o pkg/diagnostics:
3115 - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
3116 (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
3117 o testreport:
3118 - remove "-v" (verbose option) in default mpirun command.
c162643754 Mart*3119 o pkg/seaice/seaice_growth:
0602590031 Jean*3120 - catch potential division by zero in ITD code, does not change
c162643754 Mart*3121 verification results
b8a0aa824d Gael*3122 o pkg/ecco:
0602590031 Jean*3123 - retire old codes to the Attic. The calls to retired functions are
3124 left in a commented form in case they ever need to be re-activated.
b8a0aa824d Gael*3125 - ecco_check.F: issue warning if any old CPP option is
3126 defined that corresponds to retired codes -- then stop.
4240d2d6ae Jean*3127 o pkg/atm_compon_interf:
3128 - change seaice fraction (use for OCN dic surf.flux) stored and sent to
3129 coupler: use last time-step value instead of average over cplSendFrq_iter
3130 time-step, similar to what is done for seaIceMass.
3131 This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
f439370875 Jean*3132 o eesupp & genmake2:
4240d2d6ae Jean*3133 - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
3134 <= remove until a fix is found for some ifort version on ia32 machine.
8e20d992b4 Mart*3135 o pkg/seaice/seaice_evp:
3136 - refine residual computation
3137
4d2bb60bd2 Jean*3138 checkpoint65q (2015/11/18)
3139 o pkg/seaice/seaice_evp:
acd0bab53d Mart*3140 - fix residual computations so that they no longer affect the actual
3141 simulation code
391b36ba77 Mart*3142 - fix seaice_readparams to be able to actually set new parameters
3143 SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
fbe544c5ad Jean*3144 o model/src:
3145 - fix wrong truncation (single prec) from "FLOAT" function in expressions
3146 like: deltaT*FLOAT(myIter) when myIter is large:
3147 a) replaced by DFLOAT (if not seen by TAF);
3148 b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
3149 o pkg/aim_v23:
3150 - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
3151 when pickupSuff is set ; do write rolling pickups + at the end of the run.
a90d2d6d41 Jean*3152 o pkg/atm_ocn_coupler + ocn_compon_interf:
3153 - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
3154 coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
3155 add corresponding call in DO_OCEANIC_PHYS.
728fbdfa55 Jean*3156 o coupler pkgs:
3157 Start a new way to set-up optionally-exchanged variables (previously, only
3158 there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
3159 data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
3160 send switch to ATM & OCN compon before reading their own "data.cpl" (so that
3161 compononent param default can be set accordingly).
3162 Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
3163 but rather applies to a group a fields (going both ways like for DIC)
3164 and corresponds to an option of coupling config.
3165 coupler (pkg/atm_ocn_coupler):
3166 - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
3167 and read namelist directly (without eessup S/R calls) instead of
3168 in the very un-flexible old way, 1 param per line, in fixed order;
3169 - add error-counter to track errors (e.g., missing "data.cpl") and to stop
3170 cleanly in CPL_CHECK_CPLCONFIG
3171 - add new coupling-exchange selectors (some not yet active) including
3172 cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
3173 and ocnCpl_exchange_DIC=T in OCNIDS.h);
3174 - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
3175 component ; called directly from coupler.F, after comp. registrations;
3176 - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
3177 atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
3178 -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
3179 components (pkg/atm_ & ocn_compon_interf):
3180 - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
3181 CPP header file in all pkg source files.
3182 - move checking of comp. configs out of cpl_exch_configs.F into new S/R
3183 ATM/OCN_CHECK_CPLCONFIG;
3184 - add error-counter to track errors (e.g., in "data.cpl") and to stop
3185 cleanly in ATM/OCN_CHECK_CPLCONFIG;
3186 - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
3187 from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
3188 before PACKAGES_READPARMS;
3189 verification/cpl_aim+ocn/:
3190 - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
3191 "data.cpl" for coupler (in input_cpl).
2f968f5f13 Jean*3192 o eesupp/inc:
3193 - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
3194 #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
3195 to always cumulate tile local-sum in the same order (still uses
3196 MPI_Allreduce like standard code).
3197 - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
3198 that are now identical to standard version (in eesupp/inc).
4014d9eb9b Dimi*3199 o pkg/shelfice:
3200 - add SHELFICETransCoeffTFile for initializing spatially varying
3201 heat and salt transfer coefficients
1f88340446 Jean*3202 o pkg/atm_compon_interf & ocn_compon_interf:
3203 - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
3204 S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
3205 - move bi,bj loops inside S/R OCN_STORE_MY_DATA
3206 o pkg/atm_ocn_coupler:
3207 - initialise to zero ATMVARS.h & OCNVARS.h arrays.
06e0575ae0 Jean*3208 o pkg/rbcs:
3209 - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
3210 to compile with maskLEN=1 when all tracers use the same RBCS-mask.
3211 - add a short report (to STDOUT) about RBCS-mask settings.
3212
87c2bed99f Jean*3213 checkpoint65p (2015/10/23)
53fe7f7443 Mart*3214 o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
87c2bed99f Jean*3215 there is no adjoint test for EVP, we don't know what it does to the adjoint
3216 solution, but at least there are no more recomputation warnings left
5790bd3152 Mart*3217 o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
87c2bed99f Jean*3218 a chance of giving the same results as a fully converged VP (JFNK) solver
8187002e7a Jean*3219 o tools/adjoint_options/adjoint_diva:
80f3898c9c Jean*3220 - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
4323a006ce Dani*3221 o pkg/streamice:
8187002e7a Jean*3222 - spotted bug in streamice_driving_stress using dyG where should have been dxG
fcf4f25c01 Jean*3223 o pkg/exf:
3224 - remove STOP statement that prevented to use wind or (wind-)stress
3225 interpolation for constant-in-time forcing fields (wind/stress period = 0).
3226 o pkg/seaice:
31d3f56edc Mart*3227 - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
3228 5 additionals 2D fields and 6 new store directives
3229 - change logic in seaice_readparms.F: EVP code can now be turned on in
fcf4f25c01 Jean*3230 various ways, setting SEAICE_deltaTev is no longer required,
3231 alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
31d3f56edc Mart*3232 or SEAICEaEVPcoeff
443b4c77b9 Dimi*3233 o pkg/shelfice/shelfice_thermodynamics.F
3234 - redefining uLoc/vLoc to u/v, instead of 2u/v
0a62312758 Mart*3235 o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
3236 - this is an intermediate state of a truely converging EVP that has
3237 the potential of outperforming implicit VP methods, I do not recommend
3238 using it yet.
3239 - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
3240 and all parameters are hardwired
3241 - for convergence it still requires very smooth regularisations, that means,
3242 if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
3243 different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
3244 specific averaging appears to be required, still subject to tuning
3245 - still needs cleaning and I need to turn parameter into runtime parameters
3246 - add code to compute and print residuals of iteration, compile with
3247 defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
912323e508 Mart*3248 o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
3249 that entered with r1.54 on Sep04, 2015, -> update results
3250
40fe6f59c8 Jean*3251 checkpoint65o (2015/09/14)
4c3e5a1532 Jean*3252 o pkg/mom_vecinv & mom_common:
3253 - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
3254 called from there.
3255 - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
3256 allows to use Vector-Invariant form in deep atmos and anelastic formulation
7d06cac49c Mart*3257 o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
3258 and Koenig-Beatty+Holland (2012)
3259 - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
3260 - global 2D field tensileStrength, computed in seaice_calc_ice_strength
3261 - requires an extra input argument for S/R seaice_calc_viscosities
3262 - tensileStrength's depth dependence is different from Itkin et al. (2015)
3263 (to be changed and played with, for now exponential)
22864ea3d8 Mart*3264 o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
3265 - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
3266 by AREA according to Connelly et al. (2004), JPO.
3267 - For EVP and the LSR solver, the implicit part of the drag term is
4c3e5a1532 Jean*3268 the only non-zero term in the denominator when there is no ice (which
22864ea3d8 Mart*3269 prevented running the model with zero ice-ocean drag). If
3270 SEAICEscaleSurfStress = .TRUE., this results in a division by zero
3271 (or zero main diagonals BU/BV) which need to be caught. A practical
3272 consequence is that for open water, the momentum equation reduce
4c3e5a1532 Jean*3273 to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
22864ea3d8 Mart*3274 they happen to be zero, often leading to a non-zero solution over
3275 open water.
4c3e5a1532 Jean*3276 o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
eac2f17d92 Mart*3277 efficient EVP method.
4c3e5a1532 Jean*3278 - introduce area-weighted averages for e12 (analogously to
eac2f17d92 Mart*3279 seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
3280 remain, but also changing the order of terms in the previous average
3281 changed the results as much) -> update experiment
3282 - add SEAICE_DELTA_SMOOTHREG code
4c3e5a1532 Jean*3283 - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
eac2f17d92 Mart*3284 TEM-code
3285 - adjust loop bounds so that only required fields are computed
4c3e5a1532 Jean*3286 - add new averaging code for zetaZ/deltaZ (again similar to
eac2f17d92 Mart*3287 seaice_calc_viscosities.F), inactive by default for now (will change
3288 results again), but will replace old code eventually
4b86bb6ef3 Jean*3289 o eesupp/src:
3290 - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
3291 to always cumulate tile local-sum in the same order
3292 (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
3293 Still uses MPI_Allreduce (like standard code) but on array of tiles
3294 and should be faster than GLOBAL_SUM_SEND_RECV code.
3295 - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
3296 (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
40fe6f59c8 Jean*3297 - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
4b86bb6ef3 Jean*3298 aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
40fe6f59c8 Jean*3299 fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
3300 natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
3301 tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
4b86bb6ef3 Jean*3302
1e127b2371 Jean*3303 checkpoint65n (2015/07/29)
3304 o pkg/thsice:
3305 - add a warning when used with pkg/aim but without updating SST
3306 (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
d167cbe4e6 Jean*3307 o pkg/offline:
65bcd0f1ad Jean*3308 - change where Offline-Fields are loaded, from load_fields_driver.F to
3309 directly within FORWARD_STEP, just after updating iter number and time;
3310 - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
3311 S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
3312 These changes allow:
3313 a) to recover exactly on-line results using deltaToffline=deltaTClock,
3314 tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
3315 both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
3316 time-step, both with GM & KPP files and with recomputing these fields;
3317 b) no needs to switch on staggerTimeStep anymore;
3318 c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
56d308cb5a Jean*3319 - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
65bcd0f1ad Jean*3320 o pkg/offline:
d167cbe4e6 Jean*3321 - change (rarely used) offset-iteration parameter to an offset time (in s):
3322 can easily recover previous offset-iter effect by setting offset-time
3323 (offlineTimeOffset) to offset-iter x deltaToffline;
3324 - do not turn-off Temp & Salinity surface relaxation when using KPP (used
3325 in KPP as part of surface buoyancy forcing) in offline run.
4a2e3073c9 Jean*3326 - fix ptracers KPP non-local term in the case where KPP is re-computed.
2a36d1b911 Patr*3327 o OpenAD
d167cbe4e6 Jean*3328 - Adding preliminary ggl90 test to OpenAD verification.
3329 Config. with ggl90 currently diverges after 64 time steps
3330 so will need more work to become more stable
3331 - Adding preliminary kpp test to OpenAD verification.
3332 required small tweakes in kpp_routines.F
3333 - Merge and update from Krishna Narayanan's contrib area:
3334 * Add one variable for preliminary OpenAD DIVA
3335 * Add replacement time-stepping for OpenAD DIVA
3336 * genmake2 flag -diva (but only for OpenAD; preliminary)
3337 * required modifs for OAD_support
3338 successful preliminary test for tutorial_global_oce_biogeo/
e81dec19cb Mart*3339 o pkg/seaice:
d167cbe4e6 Jean*3340 - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
3341 - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
3342 delta with a smooth function in s/r seaice_calc_viscosity
3343 (no effect on EVP)
3344 - rename local suffix "sqr" into "sq" for more consistent variable names
3345 o pkg/seaice:
3346 add new parameter SEAICE_deltaMin that is used ***only***
3347 for regularizing Delta (and nothing else, like the parameter
3348 which is also used for all sorts of things SEAICE_EPS).
3349 Defaults to SEAICE_EPS for backward compatibility only.
c9fe27f0ce Mart*3350 o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
d167cbe4e6 Jean*3351 the wrong key by inialising it before use -> fixes a recomputation
3352 problem but does not fix the gradient
abafc19a3b Jean*3353 o pkg/layers:
a3d5c99c9c Ryan*3354 - move resetting of flux arrays to outside the iLa loop
3355 (this caused layers_diapycnal to not work with more than one layer coord.)
3356 - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
3357 o pkg/layers:
abafc19a3b Jean*3358 - remove from common block 3D layers fields (used to diagnose transport
3359 in tracer coords) and declare them as local arrays in layers_calc.F
d0a27699e8 Mart*3360 o pkg/seaice:
3361 - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
3362 in lab_sea forward experiment (changes results -> updated)
229dc91f74 Mart*3363 - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
d167cbe4e6 Jean*3364 o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
3365 computations; for SEAICE_VECTORIZE_LSR
d0a27699e8 Mart*3366 - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
abafc19a3b Jean*3367 sweep to the outside,
d0a27699e8 Mart*3368 - remove store directives and add "CADJ loop sequential" directives
3369 in analogy to model/src/solve_tridiagonal.F
3370 - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
3371 boundaries to yield more readable code. This has also the charming side
abafc19a3b Jean*3372 effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
3373 SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
d0a27699e8 Mart*3374 seaice_lsr_tridiagu/v now requires either of these flags, vectorization
3375 still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
3376 an additional option)
abafc19a3b Jean*3377 The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
3378 but the adjoint gradients (which are affected by this change) still explode.
15da1f08b8 Jean*3379 o coupler (atm & ocn _compon_interf):
3380 - avoid using Exch2 IO mapping if not suitable.
3381
30863fa6ad Jean*3382 checkpoint65m (2015/06/15)
7139ed4ee5 Ryan*3383 o pkg/layers:
18e9f37a89 Jean*3384 - clean-up old parameters setting (from Sep 2012):
3385 + remove old parameters setting from common block (declared locally);
3386 + stop if any old parameter is mixed with new parameters;
3387 + check for valid or consistent parameter setting (e.g., layers_name)
3388 - check that layers_bounds for Pot.Density are in the right range;
3389 this is supposed to catch un-updated setting after recently shifting
3390 potential density field "prho" by -1000 (now in "sigma" scale).
3391 o pkg/layers:
edd113ba3f Ryan*3392 - Added missing call to layers_fill for keeping track of tottend in
3393 pkg/diagnostics/diagnostics_fill_state.F
3394 o pkg/layers:
cdcbace143 Ryan*3395 - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
3396 of diapycnal fluxes
3397 o pkg/layers:
f6012f0463 Ryan*3398 - reverted changes to interpolation to previous treatment; there
3399 was never actually a problem
3400 o pkg/layers:
7139ed4ee5 Ryan*3401 - fix interpolation of layers tracers in the presence of partial cells
3402 - add lots of new functionality to compute water mass transformation
3403 (enabled by CPP flag LAYERS_THERMODYNAMICS)
3404 - add new calls from main code (diags_oceanic_surf_flux.F,
3405 thermodynamics.F, impldiff.F) and gad to save the necessary fields
3406 for layers_thermodynamics calculations
152ce31913 Gael*3407 o pkg/ptracers:
18e9f37a89 Jean*3408 - add capability of stepping a passive tracer forward without advection
3409 by setting PTRACERS_advScheme to 0.
9152c0f425 Jean*3410 o pkg/diagnostics:
3411 - add few (threads) _BARRIER around any update of "diag_pkgStatus".
9cf13f2e40 Jean*3412 o pkg/layers:
eee4907c3b Jean*3413 - shift potential density field "prho" by -1000 for density layer averaging so
3414 that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
3415 Note that density bin boundaries (layers_bounds in data.layers) have
3416 to be set accordingly (i.e., shifted, in sigma scale).
3417 o pkg/layers:
9cf13f2e40 Jean*3418 - fix snap-shot output of layer thickness @ V.pt and output of pot.density
3419 - fix calculation of layer non-weighted velocity and layer probability
3420 - add diagnostics for pot.density used for layer averaging
3421 o pkg/seaice:
f81cc74571 Mart*3422 - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
9cf13f2e40 Jean*3423 positiveness, modify a few comments and improve variable names,
3424 - the changed computation of deltaC affects most seaice-related
3425 experiments at the truncation level.
f81cc74571 Mart*3426 seaice_itd.thermo is affected by far the most, with
3427 only 7 digits of agreement remaining; update experiments.
3428
adc564fd15 Jean*3429 checkpoint65l (2015/05/04)
b357f162e4 Dani*3430 o pkg/shelfice:
adc564fd15 Jean*3431 - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
3432 factor drKp1 to zero where it is negative (ie. do not use
b357f162e4 Dani*3433 SHELFICEBoundaryLayer if hFacC>1)
3434 - the same for factor drLoc in shelfice_forcing.F
307b498a12 Mart*3435 o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
adc564fd15 Jean*3436 with modules in ptracers, when using testreport option "-small_f"
36a331ccdf Mart*3437 o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
3438 - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
43f4321b67 Mart*3439 o verification/testreport
3440 - add new option -small_f
3441 with this option testreport first makes the target small_f (*.f files)
adc564fd15 Jean*3442 before running make (all). This is useful for explicit inlining when
43f4321b67 Mart*3443 all sources need to be full available.
adc564fd15 Jean*3444 o pkg/exf/exf_interp.F:
3445 remove previous changes related to reverse (decreasing) input grids latitude
43f4321b67 Mart*3446
d4262ce583 Jean*3447 checkpoint65k (2015/04/01)
3448 o pkg/ecco:
3449 fix missing cosphi initialization; use eccoiter in place of optimcycle;
3450 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
3451 instead of active read/write
3452 o pkg/ctrl:
3453 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
3454 instead of active read/write.
3455 o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
b905f133e5 Gael*3456 return if .NOT.useAUTODIFF
3457 o pkg/seaice: add CPP brackets (cost function related).
d4262ce583 Jean*3458 o model/src:
3459 add useAUTODIFF run time switch.
3460 o pkg/exf/exf_interp.F:
3461 add code to allow input grids with latitude starting in the north (i.e. when
3462 j=1 corresponds to northern edge of field); modify global_with_exf to test
3463 this feature.
0d0ef3b590 Mart*3464 o verification/testreport:
3465 - replace "grep -A3" with POSIX conformal sed command, because there are
3466 implementations of grep that cannot do contextual searches
3467 - replace "cat -n" by "nl" (two occurrences), because not all implementations
3468 of "cat" have the option "-n"
d4262ce583 Jean*3469 o model/src:
3470 add new file gsw_teos10.F that contains 3 functions, more or less a copy
3471 of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
3472 convert from conservative to potential temperature. For now they are not
3473 called anywhere.
8686b61ec1 Mart*3474 o pkg/ggl90: make "useIDEMIX" useful
3475 - re-organize code in s/r ggl90_calc a little to move computations that
d4262ce583 Jean*3476 are different for idemix into separate loops (changes verification
8686b61ec1 Mart*3477 experiment idemix at truncation level, 12 digits remain -> updated)
3478 - requires 2 new 2D fields KappaM, verticalShear
3479 - make hFacI and recip_hFacI local 3D variables that are passed to
3480 s/r ggl90_idemix
3481 - fix and improve some comments
3482
fec3c1643a Jean*3483 checkpoint65j (2015/02/25)
71e702ab4f Mart*3484 o pkg/openad
fec3c1643a Jean*3485 - synchronize seawater.F with version in model/src: replace routine
3486 body of sw_temp by calling sw_ptmp and fix/add a few comments.
2808e60b18 Jean*3487 o pkg/mnc:
3488 - change default value of pickup_read/write_mnc params to FALSE
3489 (since few features are missing in reading MNC pickup files).
3490 o model/src:
3491 - change default (background) vertical diffusivity for salt to be the
3492 temperature (background) vertical diffusivity.
3493 - change background vertical diffusivity in vertical mixing pkgs ggl90,
3494 kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
3495 This makes ptracers default diffusivity (that uses salt diffKr) more
3496 consistent with vertical mixing schemes.
0948a11536 Jean*3497 o verification/testreport:
3498 - fix typo in "-pcls" option ;
3499 - put temp files in /tmp (instead of in local dir)
3500 - add option "-ncad" to use genmake2 new option "-nocat4ad"
3501 - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
418827f27e Jean*3502 o pkg/ggl90 (idemix code):
3503 - apply few fixes ; add some missing "_d 0" ; update output of exp.
3504 global_ocean.90x40x15.idemix
c7c1da2019 Patr*3505 o OpenAD
3506 - enable active file I/O and begin removal of work-around code
3507 for OpenAD for handling control variables (memory vs. active files)
3508 - new CPP options file OPENAD_OPTIONS.h
ed1e2fbc34 Patr*3509 - revert to genarr2d gradient check for hs94.1x64x5
3510 - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
3511 - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
7da87823d7 Jean*3512 o tools/genmake2:
3513 - add option for an alternative Makefile (from Martin) where multiple
3514 source files are sent to TAF (instead of all in one file).
689aab8014 Mart*3515 o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
d4a41e9da2 Mart*3516 - code provided by Carsten Eden as an extension of ggl90
7da87823d7 Jean*3517 - so far the code is turned on within ggl90 by setting a CPP-flag at
d4a41e9da2 Mart*3518 compile time; a runtime flag implementation is not yet complete
3519 - tested in new verification experiment global_ocean.90x40x15.idemix
c9dca15fbe Jean*3520 o verification:
3521 - reduce length of the AD test run by half for experiments
3522 global_ocean.cs32x15 (std + thsice) and isomip
c7c1da2019 Patr*3523 - enable active file I/O for OpenAD, adjust verifications accordingly
3524 - halfpipe_streamice: change gradient check from genarr2d to gentim2d
58a2b24c42 Mart*3525 o verification/testreport:
3526 - fix two non-POSIX sed statements so that there are no error messages
c9dca15fbe Jean*3527 on Mac OS X
58a2b24c42 Mart*3528 - replace hostname -s with hostname | sed 's/\..*$//'
c9e57a3110 Mart*3529 o model/src/seawater.F:
3530 - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
3531 (following the matlab code), which would have avoided the bug caught
3532 by Matt (see below) in the first place
a208a455d6 Jean*3533 o pkg/shelfice:
3534 - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
3535 and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
3536 - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
3537 ice-shelf case (i.e., within surface level).
c9e57a3110 Mart*3538 - add config summary in shelfice_check.F
3539 - remove global variable recip_SHELFICElatentHeat and replace by a local
3540 variable recip_latentHeat
3541 - introduce diagnostics for friction velocity uStar (in case of
c9dca15fbe Jean*3542 SHELFICEuseGammaFrict)
c9e57a3110 Mart*3543 - change verification experiment isomip.htd:
3544 + start from pickup (as input_ad at nIter0=8640)
3545 + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
3546 + test SHELFICEuseGammaFrict = .TRUE.
3547 + test SHELFICEadvDiffHeatFlux = .TRUE.
93bf9c0d32 Jean*3548 o model/src:
3549 - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
3550 in-situ Temp) and in routine SW_TEMP (in pkg/openad);
3551 update output of experiments global_with_exf.yearly and isomip (all 6).
ad3ad8f6cb Jean*3552 o pkg/shelfice:
3553 - change setting of kTopC to also be zero where there is no ice-shelf.
93bf9c0d32 Jean*3554 - zero out surface forcing arrays (for now, for T & S + EmPmR) where
e2b17d5756 Jean*3555 ice-shelf is.
3556 - first attempt to get RealFreshWaterFlux effects: for now, only without
3557 SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
3d23c2b9e0 Mart*3558 o pkg/seaice: add the option to prescribe a fixed thickness PDF
3559 for thermodynamic calculations
ad3ad8f6cb Jean*3560 - because of divisions of the type 7/7 not exactly equal to 1, this change
3d23c2b9e0 Mart*3561 affects results of some verification experiments by up to 4 digits:
ad3ad8f6cb Jean*3562 global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
3d23c2b9e0 Mart*3563 seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
3564 adjoint: lab_sea, lab_sea.noseaicedyn
3565 -> updated
3566
982dd9a048 Jean*3567 checkpoint65i (2015/01/23)
f01a61ff96 Jean*3568 o model/src:
3569 - change units of frictionHeating field from W to W/m^2
3570 - fix bug in frictional heating from stratospheric drag in
3571 S/R ATM_PHYS_TENDENCY_APPLY_V
982dd9a048 Jean*3572 - with synchronous time-stepping: move resetting to zero of frictionHeating
01d0a60981 Jean*3573 field from load_fields_driver.F to thermodynamics.F ;
3574 - add diagnostics for frictional heating.
172fd5e8fd Jean*3575 o model/src & gmredi K3D:
3576 - add frictionHeating field to pickup-files (for synchronous time-stepping)
3577 - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
3578 - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
3579 and name in pickup file).
3580 - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
a55487f421 Jean*3581 o model/src:
3582 - move (from ini_forcing.F) initialisation of all arrays in header file
3583 FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
3584 (since Nov 2012) with option selectAddFluid=1.
376915f8ee Jean*3585 o pkg/shelfice:
3586 - change units (+ document) of newly added field "shelfIceMassDynTendency"
3587 - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
12e9160284 Mart*3588 o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
376915f8ee Jean*3589 o pkg/seaice: two new runtime parameters:
3590 - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
12e9160284 Mart*3591 long overdue
376915f8ee Jean*3592 - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
12e9160284 Mart*3593 parameterization of tensil stress for fast ice (does not do anything yet)
3594 o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
376915f8ee Jean*3595 for LSR: move checking overlaps out of JFNK-if-block
ff2a7562da Jean*3596 o pkg/atm_phys:
3597 - move copy of grid and dynamical fields out of atm_phys_driver.F into
3598 new S/R ATM_PHYS_DYN2PHYS.
3599 - fix level height for Linear Free-Surf case (to be consistent with
3600 fixed-in-time pressure levels).
5811c5042c Jean*3601 o pkg/mom_common (bottomdrag):
3602 - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
3603 to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
3604 update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
3605 o pkg/shelfice (u/v_drag):
3606 - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
3607 - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
3608 (now similar to shelfice_u_drag.F)
3609 - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
3610 from mom_vecinv.F (similar to mom_fluxform calls).
3611 o pkg/mom_common (bottomdrag):
3612 - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
3613 - add options for alternative discretisation of velocity norm in quadratic
3614 bottom drag: averaging of grid-cell-center KE to U.point and V.point
3615 (selectBotDragQuadr=0, original code) can produce noisy patterns; this
3616 improves when averaging only the other component (e.g. vVel for U bottom
3617 drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
3618 - add options (bottomVisc_pCell) to account for partial-cell in bottom
3619 friction (no-slip BC) thus getting the true distance from the bottom;
3620 off by default since this also reduces model stability (explicit bottom
3621 friction). Changes produce different machine truncation with linear-drag
3622 + no-slip BC: update output of experiments exp4.stevens (10 digits) and
3623 front_relax (bvp & mxl, 10 & 11 digits).
cda18d4551 Jean*3624 o model/src & mom pkgs:
3625 - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
3626 since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
3627 - for now and until vertical mixing scheme are updated to fill up level Nr+1,
3628 just copy level Nr value to level Nr+1.
3629 o doc:
3630 - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
c721362620 Jean*3631 o pkg/shelfice:
07201d0927 Dani*3632 - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
3633 SHELFICE.h: move array shelficemass to init_varia, initialise
3634 from array shelficemassinit, which is set in init_fixed and
3635 has option to be set from file; introduce array
3636 shelficeMassDynTend array, set thru file in init_fixed
3637 - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
cda18d4551 Jean*3638 shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
07201d0927 Dani*3639 pkg/streamice
cda18d4551 Jean*3640 - shelfice_thermodynamics.F: call shelfice_step_icemass if
07201d0927 Dani*3641 SHELFICEMassStepping = .true.
cda18d4551 Jean*3642 - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
07201d0927 Dani*3643
eabebaa9d2 Jean*3644 checkpoint65h (2014/12/17)
83c35e2265 Gael*3645 o verification/global_ocean.90x40x15, global_ocean_ebm:
3646 - update to generic controls.
3647 o pkg/ctrl:
3648 - ctrl_map_ini_genarr.F: test for igen>0
3649 - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
eabebaa9d2 Jean*3650 - move gentim2d part of ctrl_map_ini_genarr.F to
83c35e2265 Gael*3651 new separate routine : ctrl_map_ini_gentim2d.F
3652 - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
eabebaa9d2 Jean*3653 add time variable weights and cyclic controls (time mean,
83c35e2265 Gael*3654 seasonal cycle, etc) capabilities to gentim2d
3655 o pkg/ecco:
3656 - move reading of error, conversion to weights from
3657 ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
3658 o global_oce_llc90, cs32:
3659 - activte sbo.
3660 - CTRL_SIZE.h : add maxCtrlProc.
3661 - activate the new genctrl capabilities.
a435e833b1 Mart*3662 - update following reorganization of global_oce_input_fields.tar.gz
83c35e2265 Gael*3663 o pkg/ctrl/ctrl_ad_diff.list:
3664 - add missing ctrl_init_rec.f
3665 o tools/OAD_support/keepOriginal:
3666 - add ctrl_init_rec.F
3667 o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
3668 - avoid recomputations of xx_gentim2d_dummy.
a3e6888a7e Jean*3669 o momentum diagnostics:
3670 - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
3671 mom_vecinv.F to timestep.F (to include Smag-3D contribution).
3672 o pkg/seaice/seaice_lsr.F:
3673 - fix computation of BU/BV, make sure they are non-zero, only necessary
3674 for cubed sphere exchanges and SEAICE_OLx/y>0.
3675 This makes calling s/r fill_cs_corner_rl obsolete (removed).
07df50d3e2 Mart*3676 o verification/global_ocean.cs32x15/input.seaice
3677 - add test for strong implicit coupling and restricted addtive Schwarz
3678 methods for LSR
3679 - update results/output.seaice.txt
e0b9102457 Jean*3680 o verification/tutorial_global_oce_biogeo:
171611a792 Jean*3681 - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
3682 and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
3683 update output_adm,_oadm,_tlm.txt
3684 o pkg/dic:
3685 - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
3686 - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
3687 for tracer 1 & 2 is set (to avoid double counting of dilution effect).
3688 o verification/tutorial_global_oce_biogeo:
e0b9102457 Jean*3689 - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
3690 dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
3691 update output_adm,_oadm,_tlm.txt
171611a792 Jean*3692 o eesupp/src:
3693 - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
e0b9102457 Jean*3694 and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1a814ccfcd Mart*3695 o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
3696 LSR (following Hutchings et al. 2004)
3697 - introduce zetaZ as a global variable (requires adjustments in
3698 seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
e0b9102457 Jean*3699 in seaice_calc_viscosities.F
1a814ccfcd Mart*3700 - new flag SEAICEuseStrImpCpl (default off)
3701 - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
3702 momentum equations
3703 - JFNK-solver (preconditioner) adjusted to allow using this method
3704 (where it does not have any positive effect)
d6f9f4aeb9 Mart*3705 o pkg/seaice
3706 - add overlap for restrictive additive Schwartz method also to LSR, but
3707 turn it off by default (because it only seems to work for non-cubed
3708 sphere/llc topologies)
c8020f78c8 Mart*3709 o pkg/autodiff
3710 - add extra exchanges in addummy_in_steppging also for mnc output
3711 o pkg/seaice:
3712 - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
3713 to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
e87a86147c Jean*3714 o pkg/obcs:
3715 - add option to specify domain-connected piece Id along OB though files
3716 (for now, only used to diagnose PhiVel; default =1 -> global correction)
3717 - modify obcs_diag_balance.F to process each connected-part separately;
3718 exclude OB where Id = 0 but keep the full divergence there (-> constant
3719 Psi along this portion of OB and all inflow derived from grad(Phi))
3720 - add example of OB-conect files in verification/so_box_biogeo/input.
3721 o pkg/diagnostics:
88137b1de0 Jean*3722 - improve treatment of Open-Boundaries in Velocity-Potential calculation:
3723 a) use non zero matrix element across OB and solve for Phi 1 grid point
3724 outside OB (i.e, where tracer OBCS are applied).
3725 b) global imbalance of inFlow/outFlow across OB: instead of modifying
3726 velocity across OB, spread it uniformly along the OB in the RHS.
3727
790de314fc Jean*3728 checkpoint65g (2014/11/19)
3729 o pkg/diagnostcis:
3730 - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
075f468e41 Jean*3731 o pkg/my82,pp81,kl10:
3732 - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
3733 field diffKr as background diffusivity to set minimum diffusivity value.
3734 o pkg/seaice:
3735 - add new parameter SEAICEuseEVPrev (for revisited EVP by
d6ef696f9b Mart*3736 Bouillon et al 2013)
3737 - add SEAICE_evpAlpha/Beta to namelist
075f468e41 Jean*3738 - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
d6ef696f9b Mart*3739 involve trivial re-ordering of divisions/multiplications that should not
3740 have any effects, but ... they do change the results of lab_sea.hb87 so
075f468e41 Jean*3741 that only 2 digits of agreement remain, in line with the general
d6ef696f9b Mart*3742 instability/fragility of the evp-code. For now, I do not care and just
3743 update the verification experiment
ce66b4105d Gael*3744 o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
075f468e41 Jean*3745 - remove xx_genarr2d_numsmooth etc
ce66b4105d Gael*3746 - use xx_genarr2d_preproc etc instead
075f468e41 Jean*3747 - carry out smooth_correl2D at initialization stage rather than during
3748 time stepping.
ce66b4105d Gael*3749 - get smoothOpNb from xx_gentim2d_preproc
3750 o global_oce_cs32 :
3751 - add test of generic ecco capabilities.
3752 o pkg/exf/exf_getsurfacefluxes.F :
3753 - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
3754 o pkg/ctrl,ecco :
075f468e41 Jean*3755 - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
3756 is defined.
efb8db572a Mart*3757 o pkg/seaice: add diagnostics for Delta (deformation parameter)
c604292c00 Jean*3758 o model/src:
075f468e41 Jean*3759 - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
c604292c00 Jean*3760 diffusivity (background) is specified but ignored.
3761 o verification:
3762 - in testreport, convert hostname to lower case for default output dir name
bb3b849103 Gael*3763 o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
7c3a77b9ab Jean*3764 o pkg/dic: add modifications from Hajoon:
3765 - add iron sedimentation flux function of the flux of PO4 out of bottom layer
3766 - light attenuation: add self-shading effect by climatological Chlorophyll
3767 (read from file).
3768 o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
3769 compiles when SEAICE_ALLOW_DYNAMICS is undefined
3770 o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
3771 AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
3772 ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
3773 approach where CPP_OPTIONS.h includes an omnipotent
3774 ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
3775 o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
3776 ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
7c5e2c853b Gael*3777 o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
7c3a77b9ab Jean*3778 to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
3779 (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
7c5e2c853b Gael*3780 o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
3781 add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
3782 - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
3783 - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
3784 - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
7c3a77b9ab Jean*3785 o pkg/ctrl,ecco,exf :
3ae7845edf Gael*3786 - remove variables associated with NON-generic costs,
3787 unless ECCO_CTRL_DEPRECATED is defined.
7c3a77b9ab Jean*3788 - remove NON-generic NON-obcs controls,
3ae7845edf Gael*3789 unless ECCO_CTRL_DEPRECATED is defined.
3790 o pkg/ctrl : added ctrl_local_params.h
3791 o pkg/ecco : added ecco_local_params.h
7c3a77b9ab Jean*3792 o verification : added ECCO_CTRL_DEPRECATED to most as and oad
3793 experiments, which will progressively be removed once the
3794 experiments are revised to use only generic controls/costs.
3ae7845edf Gael*3795
f9e490a40b Jean*3796 checkpoint65f (2014/10/13)
e9cfc0e399 Gael*3797 o pkg/ctrl, ecco, seaice : minor changes in headers
edcd1bebe3 Gael*3798 o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
7c3a77b9ab Jean*3799 cost function and control capabilities added since checkpoint65c.
675cbb9806 Gael*3800 o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
f6a9bac81e Gael*3801 o pkg/ecco: increase modularity and improve logic
f0a41ddc00 Gael*3802 - ecco_toolbox.F (new) : basic operations that are often used,
3803 including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
3804 ecco_addcost, ecco_add, ecco_div, ecco_readbar.
f6a9bac81e Gael*3805 - cost_gencal.F (new) : determine filnames and records.
f0a41ddc00 Gael*3806 - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
f6a9bac81e Gael*3807 - cost_generic.F : use spzeroloc rather than hard-coded -9999,
3808 and exploit the above functions leading to more compact code.
f0a41ddc00 Gael*3809 - cost_genread.F : rm un-necessary arguments, re-arrange args order.
f6a9bac81e Gael*3810 - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
3811 using_ers, using_gfo, using_mdt is now only defined within gencost)
6a200487bb Gael*3812 o pkg/ecco: extend generic cost capabilities
3813 - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
f9e490a40b Jean*3814 capabilities via gencost_preproc (+ _c,_i,_r related params),
45a442938f Gael*3815 gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
3816 gencost_outputlevel arguments to cost_generic
6a200487bb Gael*3817 - pkg/ecco/cost_genread.F (new) : interface between cost_generic
3818 and active_read, making room for gencost_preproc to take effect.
45a442938f Gael*3819 Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
6a200487bb Gael*3820 - pkg/ecco/cost_generic.F :
3821 compute and store misfit maks*(model-data) in localdif that is
3822 then used in cost and for output, output misfit if outlev.GT.0
3823 - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
3824 rather gencost_barfile for deciding whether to write barfile
3825 - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
3826 - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
3827 ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
3828 - pkg/ecco/ecco_summary.F : report gencost variables
f6a9bac81e Gael*3829 - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
6a200487bb Gael*3830 o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
a883885bf1 Gael*3831 o pkg/ecco: internal re-organization
f9e490a40b Jean*3832 - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
a883885bf1 Gael*3833 (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
f9e490a40b Jean*3834 mv relevant variables definition from ecco_cost.h to ecco.h,
a883885bf1 Gael*3835 make sure gencost routines only include ecco.h)
3836 - throughout : add missing CCP switches, rm unused variables,
3837 and rm un-necessary CPP switches
f9e490a40b Jean*3838 - throughout gencost routines : replace modelstartdate with
a883885bf1 Gael*3839 gencost_startdate when needed
3840 - cost_bp_read.F : use arguments, instead of common blocs
f9e490a40b Jean*3841 so that it can be used also by (new) cost_gencost_bpv4.F
a883885bf1 Gael*3842 - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
3843 - ecco_phys.F : compute etanFull
3844 - ecco_readparms.F : rename using_topex as using_tpj, add
3845 bpv4-grace to gencost list, initialize added parameters
3846 - ecco_summary.F : include SIZE.h needed for augmented ecco.h
3847
82fee2871e Jean*3848 checkpoint65e (2014/09/28)
8d1168a02a Dimi*3849 o pkg/obcs:
432b2a4585 Dimi*3850 - replaced the just-added CPP options with run-time variables
3851 (see pkg/obcs/OBCS_PARAMS.h for details)
3852 o pkg/obcs:
3853 - add additional CPP options for sponge boundary layers
8d1168a02a Dimi*3854 (see pkg/obcs/OBCS_OPTIONS.h for details)
5de066abfb Jean*3855 o pkg/atm_phys:
3856 - implement simple (obliquity only, assuming circular planet orbit)
3857 seasonal cycle for incoming insolation ; used when run-time parameter
3858 "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
ba60baccdb Gael*3859 o pkg/exf, pkg/ecco, pkg/ctrl:
82fee2871e Jean*3860 - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
3861 - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
3862 - implement gentim2d for xx_tauu, xx_tauv
3863 o pkg/ctrl, pkg/ecco :
3864 - fix and complement the generic controls implementation
f673b530c1 Gael*3865 o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
5de066abfb Jean*3866 pkg/shelfice/shelfice_thermodynamics.F,
3867 verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
3868 verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
3869 - add weight in CTRL_GET_GEN calls
f673b530c1 Gael*3870 o pkg/ctrl :
5de066abfb Jean*3871 - ctrl_get_gen.F : add weight as input parameter, and apply
3872 it directly rather than using smooth_correl2Dw (to be retired).
3873 - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
f673b530c1 Gael*3874 o pkg/ctrl :
5de066abfb Jean*3875 - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
3876 ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
3877 - re-activate ctrl_summary (call in ctrl_init.F)
d797bbd6d6 Gael*3878 o pkg/ctrl/ctrl_cost_gen.F :
5de066abfb Jean*3879 - fix CCP brackets, remove un-necessary myiter, mytime
ba60baccdb Gael*3880 o pkg/ecco, pkg/ctrl :
5de066abfb Jean*3881 - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
3882 - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
3883 - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
3884 - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
5e10000fa1 Gael*3885
2334e86337 Jean*3886 checkpoint65d (2014/09/15)
139514ed64 Gael*3887 o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
2334e86337 Jean*3888 - add xx_genarr2d_bounds,xx_genarr3d_bounds,
3889 xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
139514ed64 Gael*3890 o pkg/ctrl/ctrl_map_ini_genarr.F :
2334e86337 Jean*3891 - remove compilation failure
3892 - replace hard coded example
3893 - use ctrl_map_ini_gen2D, 3D
139514ed64 Gael*3894 o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
2334e86337 Jean*3895 - on/off switch based upon xx_genarr2d_weight,3d
15e98114ad Gael*3896 o src/packages_init_variables.F :
3897 - regroup pkg/estimation calls
3898 - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
3899 (moved to ctrl_init_variables)
3900 o cost/cost_init_varia.F :
3901 - remove ecco_cost_init_varia
3902 (moved to ecco_init_varia)
3903 o ctrl/ctrl_init_variables.F :
3904 - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
3905 - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
3906 o ctrl/ctrl_map_ini.F :
3907 - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
3908 (moved to ctrl_init_variables)
3909 o ctrl/ctrl_map_ini_ecco.F :
3910 - remove ECCO_PHYS (mv to ecco_init_varia)
3911 - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
3912 o ecco/ecco_ad_diff.list :
3913 - add ecco_init_varia.f
3914 o ecco/ecco_init_varia.F
3915 - new routine
291ff6be85 Jean*3916 o pkg/streamice:
3917 - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
3918 to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
3919 - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
c4f4094732 Oliv*3920 o pkg/generic_advdiff:
3921 - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
291ff6be85 Jean*3922 o pkg/exf:
3923 - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
3924 xxg_precip capability
f3207a5bb2 Gael*3925 - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
291ff6be85 Jean*3926 o pkg/ctrl:
f3207a5bb2 Gael*3927 - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
291ff6be85 Jean*3928 o model/src/load_fields_driver.F :
f3207a5bb2 Gael*3929 - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
3930 so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
43187e68ca Jean*3931 o OpenAD verification experiments:
3932 - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
3933 in src files (to enable to skip the ECCO_CPPOPTIONS.h);
3934 for now, only in pkgs used in OpenAD verification experiments.
3935 - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
3936 specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
3937 instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
3938 This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
3939 o OpenAD verification tests:
3940 - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
3941 - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
3942 tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
3943 - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
3944 and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
781c4efe3e Jean*3945 o model/src & generic_advdiff:
3946 - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
3947 forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
3948 dynamics requires valid tracer forcing only over tile interior but, for
3949 some diagnostics, may need to extend it over 1 point in tile halo region.
3950 - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
3951 tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
3952 setting in temp/salt/ptracer_integrate.F
8b57565bf5 Jean*3953 o pkg/dic:
3954 - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
3955 gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
3956 in gchem_forcing_sep.F
3957 o pkg/autodiff & obcs:
3958 - add storage of current OB values for U & V (was already done for T & S).
3959
34ab325b96 Jean*3960 checkpoint65c (2014/08/30)
649425d785 Jean*3961 o pkg/dic:
3962 - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
3963 and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
3964 AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
4084975ddf Jean*3965 o verification:
649425d785 Jean*3966 - new experiment testing OBCS and DIC pkgs, using params & output from
3967 tutorial_global_oce_biogeo but limited to a sub-domain around Drake
3968 passage: take OBCS from the last year of a 2 yrs simulation and initial
4084975ddf Jean*3969 conditions from t=1.yr while keeping the same forcing.
e564aebabb Jean*3970 o model/src:
3971 - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
3972 (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
a14051dc1f Jean*3973 o pkg/diagnostics (Stats-Diags):
3974 - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
3975 a) refine region where stats are computed, excluding where arrhFac=0 ;
3976 b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
3977 c) extend regional stats over the region edges (for U or V pt location).
ec7eae4c86 Jean*3978 o pkg/gchem:
3979 - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
3980 pkg/dic is currently changing/updating ptracers values beyond the OB).
cd979ff82b Jean*3981 o verification (hs94):
3982 - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
3983 bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
3984 hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
3985 apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1097960fb8 Jean*3986 o pkg/ptracers:
3987 - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
3988 switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
3989 - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
3990 with AB-2 code (so that it get tested).
3991 o model/src:
3992 - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
3993 with AB-2 code (previously only available with AB-3 code).
3994 Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
3995 to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
3996 there, by calling CYCLE_AB_TRACER).
3997 o pkg/generic_advdiff:
3998 - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
3999 GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
4000 + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
4001 S/R temp/salt/ptracers_integrate.F
54809f081d Jean*4002 o model/src & pkg/ptracers:
1097960fb8 Jean*4003 - remove common block variables gT,gS (in DYNVARS.h), except when
4004 USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
54809f081d Jean*4005 - remove common block variable gPtr.
b613689ef8 Jean*4006 o model/src & pkgs:
4007 - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
4008 ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
4009 IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
4010 GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
4011 + change accordingly all calling S/R.
4012 - use local temperature/salinity/ptracer tendency array (without bi,bj)
4013 in S/R temp/salt/ptracers_integrate.F
da10b40ad9 Mart*4014 o pkg/seaice:
b613689ef8 Jean*4015 - move computation of stress contributions to rhsU/V in s/r seaice_lsr
da10b40ad9 Mart*4016 to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
4017 - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
b613689ef8 Jean*4018 in seaice_lsr
4019 - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
4020 in s/r seaice_lsr_calc_coeffs
4021 o pkg/mdsio:
4022 - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
4023 (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
4024 too long (e.g., > MAX_LEN_FNAM/2 )
da10b40ad9 Mart*4025
175cc7f2f5 Jean*4026 checkpoint65b (2014/08/12)
3a54eed890 Jean*4027 o pkg/matrix:
4028 - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
4029 o model/src:
4030 - fix initialisation of geothermalFile; compile geothermal-flux code in
4031 natl_box verification experiment.
09c3b72571 Jean*4032 o model/src & pkg/down_slope:
4033 - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
4034 - in dwnslp_apply.F, update tracer tendency instead of the future tracer
4035 field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
4036 results at machine truncation level: update output of experiments
4037 global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
4038 o pkg/diagnostics (Stats-Diags):
4039 - do not cumulate the full volume when DIAGNOSTICS_FILL is
4040 called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
4041 This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
4042 times (but Min,Max and StD are still wrong).
66f9b25d49 Jean*4043 o model/src:
597fa58847 Jean*4044 - add geothermal flux forcing: read in ini_forcing.F as time-constant
4045 field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
4046 o model/src:
4047 - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
4048 _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
4049 arrays are already updated while adjustments (filters, conv.adjustment) are
4050 still applied later, in S/R TRACERS_CORRECTION_STEP.
4051 o model/src:
66f9b25d49 Jean*4052 - store in common bloc array "rhoInSitu" the virtual potential temperature
4053 anomaly that is used to compute geopotential: this make the atmos code
4054 more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
549401e3a9 Mart*4055 o pkg/seaice/seaice_lsr.F
4056 - rename integer variable ilcall to ipass (that's what it is called
4057 in the residual diagnostics
4058 - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
66f9b25d49 Jean*4059 default) for improved non-linear convergence of the first few steps
2344d2d5a9 Mart*4060 - adjust a few comments and add new ones to explain some of the store
66f9b25d49 Jean*4061 directives
4062 o pkg/generic_advdiff (& ptracers):
4063 - re-work the code to check for valid advection scheme and for minimum
4064 size of overlap (now stored in local common bloc in gad_advscheme.F)
d192729d83 Mart*4065 o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
4066 - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
4067 - add an auxilliary variable "bet" and fix store directives and keys in
4068 seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
4069 less exact gradients in my tests); but there are still
4070 recomputation warning (although gradients are sort of OK), when
4071 SEAICE_LSR_VECTORIZE is not defined, so this flag and
4072 SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
66f9b25d49 Jean*4073 - update verification experiments lab_sea.
d192729d83 Mart*4074 - change some comments in S/R seaice_calc_viscosities
a25b59d486 Jean*4075 o model/src:
4076 - if staggerTimeStep=T, always apply exchange to velocity field in
4077 do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
4078 (independent of using multi-dim advection or not); no effect on FWD run
4079 but affects AD results (at machine truncation level): update output of
4080 experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
4081 and isomip (oad: 12.d).
4082 o pkg/generic_advdiff:
4083 - stop if doAB_onGtGs is set to FALSE but ignored
4084 - refine warning related to stability of tracer time-stepping
4085 regarding internal wave dynamics.
4086 - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
4087 on staggerTimeStep & implicitIntGravWave (will now get a warning
4088 if potentially unstable).
56bf0dc039 Jean*4089 o pkg/kl10:
4090 - add new pkg "kl10" for mixing due to internal wave breaking, from
4091 http://www.sciencedirect.com/science/article/pii/S1463500310000144
4092 (contribution from Jody Klymak), tested in verification experiment
4093 verification/internal_wave/input.kl10/
b4dd8aa52b Jean*4094 o isomip experiment:
4095 - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
4096 (input.htd) and update the output.
4097 o cd_code experiments:
4098 - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
4099 #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
4100 global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
4101 update the corresponding output.
4102 o pkg/seaice:
2a89c844fd Mart*4103 - reduce the number of include files and store directives in
4104 S/R seaice_lsr_tridiagu/v
4105 - change the order of loops in one case in S/R seaice_lsr_tridiagv
4106 (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
b4dd8aa52b Jean*4107 get rid off one store directive (a TAF bug?)
2a89c844fd Mart*4108 - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
4109 S/R seaice_lsr_tridiagv to change the loop range for consistency
b4dd8aa52b Jean*4110 - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
2a89c844fd Mart*4111 - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
4112 S/R seaice_lsr_tridiagu/v (requires update of
b4dd8aa52b Jean*4113 offline_exf_seaice/input.dyn_jfnk)
2a89c844fd Mart*4114
391aedad50 Jean*4115 checkpoint65a (2014/07/27)
262a665438 Jean*4116 o model/src:
90ac475d2f Jean*4117 - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
4118 surrounding hFacC=1 @ edge of a step with different kSurfC on either side
391aedad50 Jean*4119 (topo in p-coords, ice-shelf in z-coords); update output of experiments
4120 tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
90ac475d2f Jean*4121 o model/src:
262a665438 Jean*4122 - collect momentum forcing tendency into local 2-D array (passed as argument
4123 to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
4124 parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
4125 affects results at machine truncation level (e.g., if using OBCS_SPONGE).
4126 - collect T & S forcing tendency into local 2-D array (passed as argument to
4127 apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
4128 affects results at machine truncation level (e.g., ocean: if using
34ab325b96 Jean*4129 SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
4130 correction due to vertical advection).
262a665438 Jean*4131 - update output of experiments: fizhi-cs-32x32x40 (13 digits),
4132 global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
4133 seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
4134 obcs_ctrl (ad & fwd grd @ 12 & 7).
a991652077 Jean*4135 o pkg/ptracers & diagnostics:
4136 - use ptracers (short) name (instead of long one) to make ptracers diagnostics
4137 title (to avoid some unexpected truncation); sort out ptracers diags units.
262a665438 Jean*4138 - collect ptracer forcing tendency into local 2-D array (passed as argument
4139 to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
a991652077 Jean*4140
77d0805fa2 Jean*4141 checkpoint65 (2014/07/18)
09aa940b92 Jean*4142 o pkg/fizhi:
4143 - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
4144 affects results at machine truncation level. Update output of experiments
4145 fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
48bef89a30 Mart*4146 o pkg/seaice: more clean up
4147 - rename TAF common block tapes to be more consistent and remove
4148 unnecessary duplicates
09aa940b92 Jean*4149 - add store directives to remove more recomputations, but use smaller
4150 tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
4151 The idea behind this flag is to reduce the memory footprint when the
4152 adjoint of the LSR is not required. As of now, defining the flag
15c6e2792a Mart*4153 SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
09aa940b92 Jean*4154 a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
4155 For experiment offline_exf_seaice, this means on a linux box with gfortran
4156 nearly a factor of 10 (but keep in mind there is mostly seaice code in
77d0805fa2 Jean*4157 this experiment):
15c6e2792a Mart*4158 > size mitgcmuv_ad
790de314fc Jean*4159 text data bss dec hex
4160 5100659 1216 220458952 225560827 d71c8fb
48bef89a30 Mart*4161 5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
09aa940b92 Jean*4162 but only a moderate increase of 36% for global_ocean.cs32x15:
48bef89a30 Mart*4163 text data bss dec hex
4164 6695027 1648 1014578664 1021275339 3cdf6ccb
4165 6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
4166 - note: there are still recomputations in global_ocean.cs32x15 and
15c6e2792a Mart*4167 offline_exf_seaice and the gradient agreement changes (gets a
4168 little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
48bef89a30 Mart*4169 - in general, the AD gradients still are wrong
53bebe4a64 Patr*4170 o OpenAD
4171 - clean up code_oad/ directories somewhat by moving files
4172 dontCompile, dontTransform, keepOriginal to OAD_support/
f398288312 Jean*4173 o model/src:
930ff12251 Jean*4174 - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
4175 (not currently tested): add dissipation terms before NLFS rescaling of
4176 tendencies (previously done after).
4177 o pkg/diagnostics:
4178 - write stats-diags in ascii file with more digits (same as in monitor).
4179 o pkg/down_slope:
4180 - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
4181 NLFS (not tested), use new recip_hFac value in order to conserve tracer.
4182 o model/src:
f398288312 Jean*4183 - new file "apply_forcing.F" containing all the code previously in
4184 external_forcing.F, but with new argument list: pass, as new argument,
4185 the current level tendency array to update (instead of a direct update
4186 of the common bloc array). Change the corresponding calls.
4187 - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
4188 EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
5e1701d480 Mart*4189 o pkg/seaice/seaice_lsr, a little bit of clean up
4190 - rearrange some code blocks, so that now all calculations for
f398288312 Jean*4191 setting up the right-hand-sides done within one single block
5e1701d480 Mart*4192 (I find that easier to read and understand)
4193 - rearrange freedrift-code to reduce the number of ifdefs
4194 - adjust some indentations and comments
4195
6544591561 Jean*4196 checkpoint64z (2014/07/10)
c1d95c335c Jean*4197 o model/src and several pkgs:
4198 - change argument list of all S/R called from external_forcing.F and
4199 called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
4200 to pass, as argument, the current level tendency array to update
4201 (instead of a direct update of the common bloc array).
4202 - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
4203 - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
a122714692 Mart*4204 o pkg/seaice/seaice_lsr.F
4205 - always initialize local arrays in seaice_lsr_tridiagu/v
4206 - add more local tapes to seaice_lsr_tridiagu/v
c1d95c335c Jean*4207 - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
a122714692 Mart*4208 keep it in bi/bj loop; this seems to be essential
4209 - gradients are still wrong but only by 4-7 orders of magnitude
4210 instead of 15 orders of magnitude, lab_sea improves a little
822f9de729 Mart*4211 o pkg/seaice
4212 - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
4213 generates unnecessary code in seaice_lsr_ad
4214 - add more store directives in seaice_lsr to avoid unnecessary code
4215 in seaice_lsr_ad
4216 - exclude some residual computations in seaice_lsr when
4217 ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
c1d95c335c Jean*4218 in seaice_lsr_ad
822f9de729 Mart*4219 - add more storing, a new tape (model/src/the_main_loop.F) and
4220 another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
c1d95c335c Jean*4221 and klockey should be checked by a specialist)
822f9de729 Mart*4222 - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
4223 and update lab_sea after previous changes in pkg/seaice below
c1d95c335c Jean*4224 o pkg/autodiff:
4225 - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
d572335125 Gael*4226 viscFacInAd : run time parameters allowing for adjoint switches
4227 note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
c1d95c335c Jean*4228 o pkg/ecco:
4229 - introduce cost_gencost_boxmean.F that computes a box mean
d572335125 Gael*4230 temperature (for use in adjoint sensitivity studies).
4231 o model/src/set_defaults.F : initialize viscFacAdj to 1.
c1d95c335c Jean*4232 o pkg/mom_common/mom_calc_visc.F:
d572335125 Gael*4233 - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
c1d95c335c Jean*4234 o pkg/seaice/seaice_summary.F:
d572335125 Gael*4235 - statement for SEAICEadjMODE now in autodiff_readparms.F
c1d95c335c Jean*4236 o pkg/seaice:
1fa25402a0 Mart*4237 - remove some store directives and add new ones in an effort to get
4238 finally rid off the recomputation warnings. This is successful
1d0e5c687d Mart*4239 when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
4240 defined (i.e. no extensive recomputation warnings left), but there
4241 are still too many recomputations on the solver iteration level
0e792109e6 Mart*4242 - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
e06bd90b00 Mart*4243 - move definition of MPSEUDOTIMESTEPS into TAMC-block in
4244 SEAICE_SIZE.h
4245 - add a store directive in S/R seaice_calc_viscosities
fdfdc49113 Jean*4246 o pkg/seaice (ITD code):
4247 - fix definition of Hlimit for multi-threaded case
4248 - use double precision arithmetic to compute Hlimit: this affects results;
4249 update output of experiment seaice_itd.
7f033dc113 Mart*4250 o replace content of verification/seaice_itd
4251 - instead of a 1D column use the configuration of offline_exf_seaice
4252 to test the ice thickness distribution code with ridging
4253 - this is a first shot at this experiment
4254 - change of some defaults of ridging parameters SEAICEhStar (from
4255 100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
fdfdc49113 Jean*4256 and lot of new comments.
7f033dc113 Mart*4257
4fddc18258 Jean*4258 checkpoint64y (2014/06/20)
4259 o pkg/seaice/seaice_reg_ridge.F:
4260 - modify the regularization of very small volumes of ice; only check
4261 total volume HEFF, and do not apply correction to individual ice
4262 classes because that leads to funny patterns in the heat and fw-fluxes
c7c86ceb32 Mart*4263 into the ocean. Adjust seaice_itd/results/output.txt
4264 - replace nITD by SEAICE_multDim in loop-ranges
0a1362090f Jean*4265 o pkg/exf:
4266 - add code to process the case field period = -12. with UV interpolation.
4267 - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
4268 into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
f893122504 Jean*4269 o verification/global_with_exf:
4fddc18258 Jean*4270 - switch all fields period to -12. (was previously untested) in input/data.exf
f893122504 Jean*4271 (but keep secondary test ".yearly" unchanged); update the reference output.
4272 o pkg/cal:
4273 - new calendar type "noLeapYear" for 365 days calendar without any leap year.
4274 o pkg/exf:
4275 - new integer parameter "exf_debugLev" (default set to main model debugLevel)
4276 to replace logical switch "exf_verbose"
4fddc18258 Jean*4277 - report in STDOUT when loading a new record (if exf_debugLev >= 3)
3d5a62f3cd Jean*4278 o pkg/sbo:
4279 - update from Katherine Quinn: evaluate mass directly from density and SSH
4280 (budget using Finite Volume method) instead of from bottom pressure.
8471337f5d Jean*4281 - allow testreport to collect few selected SBO output ; tested in exp.
4282 global_ocean.90x40x15 (after updating the results, to include SBO output).
4283 - fix some multi-threading issues (in output part).
39a405bbb4 Jean*4284 o model/src & most packages:
4285 - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
4286 - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
4287 PACKAGES_UNUSED_MSG to print a weak warning when parameter file
4288 "data.{pkg}" exist ; and leave the S/R (return) just after.
f459cc48d3 Jean*4289 - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
4290 + call LAND_READPARMS from packages_readparms.F
39a405bbb4 Jean*4291 o pkg/seaice:
efc672bc35 Mart*4292 - remove code that resets useThSice in S/R seaice_readparms and
c7c86ceb32 Mart*4293 replace it by a warning in S/R seaice_check
efc672bc35 Mart*4294 - remove parameter MULTDIM, replace with nITD and runtime
4295 parameter SEAICE_multDim (still hard-wired to nITD if
4296 SEAICE_ITD is defined)
4297
32263cf74c Jean*4298 checkpoint64x (2014/05/24)
bb8f3ffecf Patr*4299 o verification/lab_sea:
32263cf74c Jean*4300 - update adjoint and TLM output following changes to pkg/salt_plume
4301 - un-do the update after putting back local recip_Cp in few places.
bb8f3ffecf Patr*4302 o pkg/salt_plume: modifications by An Nguyen:
32263cf74c Jean*4303 - add capability to do brine rejection (salt-plume) as function of
bb8f3ffecf Patr*4304 volume+tracers (instead of only salinity tracer).
32263cf74c Jean*4305 - conserve volume by exchanging volume from each kLev to above to
bb8f3ffecf Patr*4306 accommodate in-coming brine volume
4307 - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
32263cf74c Jean*4308 - switch KPP surf buoyancy due to brine forcing to 3-d
bb8f3ffecf Patr*4309 (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
4310 - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
32263cf74c Jean*4311 - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
bb8f3ffecf Patr*4312 in East/West Arctic.
751362a27d Jean*4313 o pkg/sbo:
32263cf74c Jean*4314 - incorporate modifications from Katherine Quinn to enable the use of sbo
751362a27d Jean*4315 pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
4316 output for future testreport verification (unfinished).
60958941f8 Jean*4317 o pkg/atm_phys:
4318 - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
4319 skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
4320 output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
0ad17fdd8c Mart*4321 o pkg/seaice
60958941f8 Jean*4322 seaice_calc_ice_strength.F: modify expression to avoid divisions
0ad17fdd8c Mart*4323 (affects truncation)
4324 seaice_do_ridging.F: clean up the insectarium
3fba0517c3 Mart*4325 - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
4326 - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
4327 - set closing/openingRate to zero where no extra iteration is need (3rd bug)
60958941f8 Jean*4328 - add some debugging information and error messages (warnings)
b062ea86d0 Jean*4329 o model/src: modifications relatd to atmosphere p*:
4330 - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
4331 - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
4332 of vertical profile tRef in geopotential background and anomaly.
4333 - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
4334 and pkg/atm_phys.
4335 - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
4336 fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
419c1f0b27 Mart*4337 o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1c0e70142a Oliv*4338 o pkg/ptracers: compute ptracer source/sink due to linear free surface.
4339 not used right now, but can be used in BGC packages to fix conservation.
4340 o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
4341 other packages too.
b062ea86d0 Jean*4342 o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
4343 SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
728a44199c Jean*4344 o model/src:
4345 - since we have several heat capacity (even in model/src), define "recip_Cp"
4346 as local variable (no longer in common block) to avoid any confusion.
4347 - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
7bb11c2f45 Jean*4348 o pkg/exf:
4349 - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
4350 air density as function of air Temp, Humidity and atm pressure.
4351
80e9662843 Jean*4352 checkpoint64w (2014/05/02)
4faee70d47 Jean*4353 o verification:
4354 - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
4355 seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
4356 code from seaice_growth.F & seaice_advdiff.F to new ridging routines
b062ea86d0 Jean*4357 seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
419c1f0b27 Mart*4358 (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
bcc533dbd4 Jean*4359 o model/src: for atmosphere in p* coords:
4360 - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
4361 - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
4362 but not yet activated.
cabb1e150c Mart*4363 o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
4364 - move computation of opnWtrFrac = 1-AREA to before computing ice strength
bcc533dbd4 Jean*4365 - this changes the results (but not for any verification experiment, because
4366 none tests this), but avoids having an extra field in the restart files
97d542e805 Mart*4367 o pkg/seaice: remove global variable TICE (not needed)
bcc533dbd4 Jean*4368 - replace by TICES or local variable where necessary (cost_seaice_test,
97d542e805 Mart*4369 seaice_diagnostics_state)
4370 - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
4371 - use specific read/write routines for reading and writing individual leves
4372 of a multilevel field
b1bf8777db Jean*4373 o pkg/ctrl & model/inc:
4374 - move additional anomaly fields of control vars (related to options:
4375 ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
4376 from DYNVARS.h into new header file: CTRL_FIELDS.h
cc5e1bc684 Mart*4377 o pkg/seaice: some small modifications to the ridging code
4378 - make fw2ObyRidge a global variable and add the freshwater flux to
4379 seaice_growth
b1bf8777db Jean*4380 - pass actual thickness from seaice_prepare_ridging, so that it is
cc5e1bc684 Mart*4381 computed only in one place and compute it in the same way as in
4382 seaice_growth
4383 - initialise more fields in seaice_do_ridging that where cause floating
4384 point exceptions over land
e990a77247 Mart*4385 o pkg/seaice: preparations for ridging code and first real ridging code
b1bf8777db Jean*4386 - move most of "PART 1" of S/R seaice_growth into a new and separate
e990a77247 Mart*4387 S/R seaice_reg_ridge that will both regularize the state variable after
4388 advection call the actual ridging routine;
b1bf8777db Jean*4389 - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
e990a77247 Mart*4390 d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
4391 - remove ridging code from seaice_advdiff
b1bf8777db Jean*4392 - clean up remaining part 1 of seaice_growth in an attempt to make it
e990a77247 Mart*4393 more readable (this is probably subjective)
4394 - call seaice_itd_redist once in the initialisation phase to have the initial
4395 conditions in the correct category
4396 - finally: add new ridging routine for ITD code
4397
e36f9ede36 Jean*4398 checkpoint64v (2014/04/11)
9994e4e8cb An T*4399 o pkg/ecco:
4400 - add runtime parameters mdt[start,end]date[1,2]
4401 - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
e36f9ede36 Jean*4402 o pkg/seaice:
4403 - make deltaC a global variable, so that it can be used in ridging code
67f02628d2 Mart*4404 - first step towards ridging: introduce new routines that compute
4405 ice strength based on ridging parameters
79793b3c13 Mart*4406 - add diagnostic for HSNOWITD
4407 - add opnWtrFrac as a global variable (required for ridging scheme)
9994e4e8cb An T*4408 o pkg/salt_plume + pkg/seaice/seaice_growth.F
4409 - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
4410 AREA exceeds a threshold (code contributed by I.Fenty in 2011)
684ea763ea Jean*4411 o verification/hs94.1x64x5:
4412 - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
4413 - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
4414 o autodiff:
4415 - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
4416 and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
4417 For now, only in pkgs used in verification/hs94.1x64x5.
4418 - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
4419 which are specific to TAF/TAMC).
4420 - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
4421 since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
4422 is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
4423 - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
4424 building mitgcmuv_ad (make adAll).
d85e4bb9df An T*4425 o pkg/ecco:
4426 - cost_gencost_seaicev4.F:
4427 reformulate proxy cost as function of sst and local param SEAICE_freeze
4428 change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
4429 - add stop statement if old names siv4-[sst,vol] are used
4430 - add snapshots + cost reports for atmospheric longwave
4431 - remove factor 0.1 in front of wtau[u,v]
4432 - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
4433 ALLOW_TMI_SST_COST_CONTRIBUTION
684ea763ea Jean*4434 o pkg/atm_phys:
d68eb785a9 Jean*4435 - add some diagnostics for Short-wave and for convection S/R.
684ea763ea Jean*4436 o pkg/seaice/seaice_growth:
ea66a54ac4 Mart*4437 - fix a bug in the lateral melt parameterization for SEAICE_ITD
4438 in seaice_growth; tempFrz needs to be computed inside the i/j-loop
4439 - rearrange loop order for better vector code in the same code block
4440 - rewrite the floeDiameter formula to have fewer divisions
4441 - (miraculously) none of this changes the results of seaice_itd
684ea763ea Jean*4442 o pkg/smooth:
4443 - move param smooth2Ddiffnbt to pkg/ecco
4444 o pkg/salt_plume:
4445 - salt_plume_frac.F:
4446 clean up local param names
4447 reformulate (1-frac) to frac; original 1-frac was based on swfrac code
6d2104f414 Jean*4448 o pkg/rw:
4449 - add RS version of S/R READ_MFLDS_LEV.
4450 o pkg/streamice:
4451 - fix the restart test by writing/reading pickup_streamice files.
4452 o pkg/seaice:
0e4bf54f91 Mart*4453 - refine checks for jfnk-related parameters
4454 - comment out if statement with SEAICEuseIMEX parameter as long as there
4455 is no IMEX code to avoid confusion and surprises
4456
1b217122f8 Jean*4457 checkpoint64u (2014/03/07)
85157af967 Jean*4458 o verification/MLAdjust:
4459 - rename secondary test suffix:
4460 1.leith -> A4FlxF + switch to flux-form & add side-drag
4461 0.leithD -> AhFlxF + switch to flux-form
4462 0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag
4463 0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag
f0b594ffe2 Jean*4464 o pkg/mom_vecinv:
4465 - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
4466 to be before mom_calc_visc.F)
4467 - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
4468 - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
4469 this is simpler for the adjoint and for diagnostics.
7ab8a42a9d Jean*4470 o model/src + pkg/momentum:
4471 - add input files for 2-D additional Western and Southern cell-edge wall
4472 (e.g., to add "thin-wall" where it is =1).
4473 - fix sideDrag option for thin-walls with Non-Lin Free-Surf
4474 using 2nd hFacZ that is computed from initial (fix domain) hFac
4475 - known limitations of thin wall implementation: not yet coded for sigma
4476 coords; not working with CD-scheme neither.
21cfbf5d41 Jean*4477 o pkg/seaice:
65555308b7 Mart*4478 - rename recently introduced parameters from (wrong name) AB to
4479 BDF (backward difference time discretisation)
4480 - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
21cfbf5d41 Jean*4481 o tools/adjoint_options:
4482 - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
65555308b7 Mart*4483
0819a3aef8 Jean*4484 checkpoint64t (2014/02/01)
d85e4bb9df An T*4485 o pkg/ecco
4486 - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
4487 runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
4488 - replace hard-coded record number and period which only work for monthly
4489 with read-in runtime param that works for other periods (month,day,year)
a4e96d71ae Patr*4490 o pkg/thsice
4491 - corrected store directive fixes thsice adjoint gradient checks
c610335cdc Jean*4492 o genmake2 & testreport:
4493 - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
4494 in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
4495 Update testreport accordingly. No need to set "export OPENAD=true"
4496 in adjoint_options/adjoint_oad anymore (will be removed later).
9a846a36d2 Jean*4497 o pkg/shelfice:
4498 - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
4499 only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
4500 so that surface forcing applies to k=kSurf if using pkg/shelfice.
62997f5aad Patr*4501 o pkg/ctrl, pkg/grdchk, pkg/ecco:
9a846a36d2 Jean*4502 - Changes to make GENARR more modular (i.e. invisible if not used)
cde67b4ce1 Gael*4503 o model/src/temp_integrate.F and salt_integrate.F
9a846a36d2 Jean*4504 - re-include store directives that were removed on Dec 27th.
3dbdd94ad6 Gael*4505 o model/src/external_forcing_surf.F
9a846a36d2 Jean*4506 - add storage directives for EmPmR and PmEpR to avoid recomputation of
4507 seaice_model in the adjoint that is problematic when seaice_model is
4508 turned off in the adjoint. The resolved issue dated back to July when
4509 EXTERNAL_FORCING_SURF call was moved.
4510 Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
20bd954105 Mart*4511 o pkg/exf/exf_check.F
9a846a36d2 Jean*4512 - fix a small bug again (originally found by Wentao Liu, now found again)
4513 - streamline error output
20bd954105 Mart*4514 o pkg/streamice and aim_v23:
9a846a36d2 Jean*4515 - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
4516 Apple's /usr/bin/cpp knows what to do:
4517 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
4518 Target: x86_64-apple-darwin13.0.0
20bd954105 Mart*4519
f23338cc5b Jean*4520 checkpoint64s (2014/01/05)
ce5f09424a Jean*4521 o tools/adjoint_options:
4522 - switch to fastopt.net TAF server (instead of default fastopt.de) for
4523 AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
4524 o model/src:
4525 - remove some unnecessary TAF storage directives in forward_step.F and
4526 in dynamics.F (note: not always removed by TAF, e.g., double storage
4527 of kappaRU,kappaRV in former version of dynamics.F).
f2a2ecef28 Jean*4528 o model/src & pkg/ptracers:
ce5f09424a Jean*4529 - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
f2a2ecef28 Jean*4530 salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
4531 and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
4532 - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
4533 - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
4534 - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
e71dbcdc66 Jean*4535 o useSingleCpuInput separates single-CPU input from single-CPU output;
4536 for now only implemented for in exf_interp_read.F
4537 o verification/advect_xy:
4538 - fix missing EXCH call in local version of ini_salt.F and update output.
4539 o momentum diagnostics:
4540 - fix which deltaT is used in Total-Tendency diagnostics.
4541 - fix typo in diagnostics for momentum tendency from AB.
4542 o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
4543 SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
05b3bcee70 Mart*4544
49ba07ded8 Jean*4545 checkpoint64r (2013/12/08)
21fae43a0a Jean*4546 o verification/*/results:
4547 - Update reference output of experiments that were passing with just 13 digits
4548 (make it easier to detect future changes in results)
4175fa5a6c Jean*4549 o model/src & pkg/ptracers:
4550 - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
4551 inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
4552 to inside ptracers_integrate.F ; remove ptracers_advection.F
13e111d31a Jean*4553 o coupling interface pkgs:
4554 [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
4555 - change the config check to test the agreement of Ocean Depth
4556 with ATM land/sea mask (instead of ATM orography);
4557 - send to coupler the number of coupler time-steps to do for this run:
4558 this allows to check for consistency and don't need anymore to be
4559 specified in parameter file "data";
4560 in coupler:
4561 - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
4562 - improve report to log-file of config setting (pass log-file unit to few S/R)
4563 o pkg/compon_communic:
4564 - add coupling send/receive for non-tiled integer vector;
4565 - add S/R to check and stop if any proc has an error (similar to
4566 eesupp/src/stop_if_error.F but single thread and across Comm_World).
b7f9d4a417 Jean*4567 o pkg/exch2:
4568 - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
4569 through list of all tiles my proc owns.
4570 o model/src:
4571 - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
4572 from rTrans) to simplify dependencies (no need to store rTrans anymore in
4573 calling S/R); this affects AD results at machine truncation level:
4574 update AD-output (TAF) of experiments: 1D_ocean_ice_column,
4575 bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
1088379d6a Jean*4576 o tools/build_options:
4577 - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
4578 o coupling interface pkgs:
4579 [compon_communic, atm_compon_interf & ocn_compon_interf]
4580 - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
4581 to each S/R that needs it; remove un-used variables.
4582 - change component tile registration (cpl_register.F in both compon_interf
4583 and mitcomponent_tile_register.F) to pass the full list of tiles
4584 information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
4585 - with pkg/exch2: adopt the same convention used for I/O to define mapping
4586 towards coupler global array (unless W2_useE2ioLayOut=F):
4587 a) can now use different tiling between atm & ocn comp.
4588 b) no needs to modify the run-Off map when changing tiling (was needed
4589 even if using the same tiling between atm & ocn).
4590 c) will allow to run with blank-tiles in 1 component (e.g., for ocean
4591 full land tiles); not yet tested.
4592 - check for valid mapping from comp. tile to coupler global array
4593 - improve report of tile registration results to log file.
4594 o pkg/exch2:
4595 - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
4596 tile-registration (CPL_REGISTER);
4597 - activate (un-comment) definition and setting of "W2_tileIndex" list to
4598 store the local bi,bj indices of each tile;
4599 - also print bi,bj in local report to log file;
4600 - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
4601 Jun 2009 modif of pkg/exch2).
4602 o testing on baudelaire:
4603 - run 2 tests at a time: no significant slow down (since enough cpu) and
4604 get the full set of test done earlier
4605 - switch the ifort test to "-devel" ; run the OpenAD test everyday.
a9265de95a Jean*4606 o model/src/thermodynamics.F and routines called from it:
4607 - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
4608 gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
4609 velocity (outp) by adding bolus velocity.
4610 - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
4611 mass transport from velocity + lateral grid cell area
4612 - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
4613 - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
4614 in thermodynamics.F
4615 - remove k from thermodynamics.F and move it to temp_integrate.F
4616 salt_integrate.F and ptracers_integrate.F (now done inside the tracer
4617 loop).
4618 - compute locally (in thermodynamics.F) 3-D velocity field that is used to
4619 advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
4620 PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
4621 GAD_IMPLICIT_R and PTRACERS_IMPLICIT
4622 - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
4623 global_ocean.90x40x15, tutorial_global_oce_biogeo and
4624 tutorial_tracer_adjsens (+ TLM output).
1088379d6a Jean*4625 o tools/OAD_support and (verification/*/) code_oad:
8f959368b3 Jean*4626 - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
4627 module conversion ; remove unneeded CPP_EEOPTIONS.h.
4628 - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
1088379d6a Jean*4629 version (closer to model/inc/CPP_OPTIONS.h).
8f959368b3 Jean*4630 o model/src:
4631 - remove parameter "useOldFreezing" from PARAMS.h and push it to the
4632 retired list of parameters (routine FREEZE has been replace by surface
4633 freezing (10.yrs ago) and by pkg/frazil (interior freezing).
4634 o pkg/gmredi:
4635 - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
4636 velocity (same scheme but affects machine truncation) for GM_AdvForm.
4637 - update output of FWD experiments: front_relax.bvp,
4638 global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
4639
ccabb03de3 Jean*4640 checkpoint64q (2013/11/17)
7669301999 Jean*4641 o verification:
4642 - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
4643 tutorial_global_oce_biogeo and global_ocean.90x40x15.
4644 - generate new output (growth & melt) for seaice_itd experiment after
4645 updating the input pickup_seaice files (previously wrong).
d498609aae Jean*4646 o pkg/cost:
4647 - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
4648 (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
c610335cdc Jean*4649 o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
d498609aae Jean*4650 cannot be applied to var in common block).
4651 o allows to get results independent of tile-per-proc setting (if using
4652 slower GLOBAL_SUM_SEND_RECV option).
4653 - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
4654 thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
4655 forward gradients: update output).
4656 - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
4657 S/R and, for most exp., also comment out GLOBAL_SUM_R8.
586c949ecf Jean*4658 o pkg/mom_common:
4659 - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
4660 code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
4661 viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
4662 ensure that all field value that are used are set.
4eccb07ab1 Jean*4663 o tutorial_deep_convection (smag3d):
4664 - add missing scaling in mom_calc_smag_3d.F;
4665 - set smag3D_coeff in input.smag3d such that results do not change.
4666 o pkg/dic:
4667 - change dic_cost.F to compute cost on each tile first and then apply
4668 GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
4669 tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
35050126c6 Oliv*4670 - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
a5d44ed107 Jean*4671 o eesupp/src & pkg/mdsio:
4672 - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
4673 (from pkg/mdsio) since they are no longer used for tape IO.
4674 - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
4675 (+ keep a copy in pkg/atm_ocn_coupler).
2e81182906 Jean*4676 o verification/isomip:
4677 - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
4678 o tools/build_options:
4679 - optfile linux_amd64_ifort11, fast (no ieee) case:
4680 to get a working restart for all experiments, add "-fp-model source"
4681 to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
4682
a01940b562 Jean*4683 checkpoint64p (2013/10/20)
5bfbd26026 Jean*4684 o pkg/autodiff:
4685 - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
4686 criteria, return to simple (default) tape IO format.
645a01b465 Jean*4687 o pkg/mdsio (+ eesupp/src):
4688 - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
4689 previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
4690 - fix globalFile and singleCpuIO options using simpler global mapping.
4691 - new pairs of scatter/gather vector S/R (one for each type, generated from
4692 template) corresponding to simpler global mapping.
4693 - adread_write.F: switch to new S/R (but leave old calls commented) and write
4694 to globalFile when parameter globalFiles is set to True.
4695 - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
b798a7d810 Jean*4696 o pkg/autodiff:
5bfbd26026 Jean*4697 - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
4698 with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
b798a7d810 Jean*4699 missing, just add a STOP if array type do not match.
dc136770de Jean*4700 o pkg/exf:
4701 - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
4702 rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
4703 and rename array obsSIce to exf_iceFraction.
94e0cca872 Jean*4704 o tutorial_deep_convection:
4705 - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
4706 for now all in this exp. code dir.
4707 - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
4708 testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
4709 o eesupp/src:
4710 - added SINGLE_DISK_IO option because reading of parameter files on
4711 very large number of processors did not work with existing set-up
4712
cc89d07104 Jean*4713 checkpoint64o (2013/09/25)
4714 o pkg/atm_phys & atm_compon_interf:
4715 - allows for coupling of gray-atmosphere (atm_phys) with ocean.
6bd6f7be12 Jean*4716 o tools/build_options:
4717 - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
4718 & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
4719 remove CPP setting (was identical to genmake2 default).
1115280ea7 Mich*4720 o pkg/gmredi & model/src: Some updating and work done on the residual model.
4721 - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
6bd6f7be12 Jean*4722 - fixed up the calculation of the eddy stress and how it is added to the
1115280ea7 Mich*4723 external forcing via taueddy_external_forcing.F
4724 - at the moment, it is very experimental and only works with the variable eddy
4725 diffusivity calculated in gmredi_k3d.F
6bd6f7be12 Jean*4726 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
4727 lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
4728 o testreport (& tools/do_tst_2+2):
4729 - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
addfa94074 Jean*4730 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
4731 - remove CPP='cpp -traditional -P' (this is genmake2 default)
4732 - add switch (for big setups) to use 'medium' memory-model (but leave it
4733 commented out for now). Note: needed with FC 19 to compile big setups.
3dca81485c Jean*4734 o pkg/atm_compon_interf:
4735 - regroup per field origin (model & pkgs) the coupling storage routines
4736 (which accumalate in time each coupling field)
addfa94074 Jean*4737 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
3dca81485c Jean*4738 update accordingly + simplify aim_do_physics.F
4739
8f1243bebb Jean*4740 checkpoint64n (2013/08/26)
5f5cc705f4 Dimi*4741 o pkg/bbl:
4742 - update formulation to reduce dispersion of tracer properties in bbl
4743 - replaced horizontal and vertical transport parameters with velocities
4744 - changes results for verification/global_with_exf.yearly
ffbb57e6f3 Dani*4745 o verification/halfpipe_streamice:
4746 - change to matrix construction; update both Fwd & AD output.
c91228a3b5 Jean*4747 o verification/tutorial_tracer_adjsens:
4748 - OpenAD test: switch to vector-invariant momentum since fluxform with
4749 rStar causes problems with OpenAD; update output.
983705b2af Jean*4750 o tools:
c91228a3b5 Jean*4751 - genmake2: define a common prefix for all temp-file names ; move them
4752 to local /tmp disk (but would be easy to move them back);
4753 - xmakedepend: apply the same switch for temp-files.
983705b2af Jean*4754 o pkg/offline:
c91228a3b5 Jean*4755 - changes for use with rStar (NLFS): assume that we continue to provide
983705b2af Jean*4756 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
4757 output files) and apply r* scaling at each time-step (function of the time
4758 varying Eta field); use normal pickup files (needed for restart with NLFS).
28e8749e94 Oliv*4759 o adjoint with OpenAD:
4760 - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
4761 package openad. This package has to be compiled for all runs with OpenAD
4762 instead of specifying code_oad_all as a modification directory.
4763 - link the fortran templates from tools/OAD_support to the build directory
4764 for preprocessing to avoid conflicts between different setups compiled
4765 simultaneously and simplify cleanup.
96b2fd29af Jean*4766 o pkg/exf:
4767 - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
4768 main model or other pkgs are exchanged in EXF_MAPFIELDS).
4769 o model/src:
4770 - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
4771 (similar to do_fields_blocking_exchanges.F).
4772 o tools/genmake2:
4773 - remove TAF output src code just before calling staf (when not doing a fresh
4774 built, will stop if things go wrong with staf).
4775 - fix target "adobj" (left from TAF version-2 transition)
2cbfd59e75 Jean*4776 o pkg/diagnostics:
4777 - add a parameter to track the status of pkg/diagnostics activation;
4778 this replace/extend the use of logical param "settingDiags" (to check
4779 when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
4780 New S/R to print error message and stop when pkgStatus is not right.
4781 - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
4782
45d3f75a8f Jean*4783 checkpoint64m (2013/08/13)
ee9d1fdd8f Jean*4784 o model/inc:
4785 - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
4786 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
4787 o pkg/kpp & aim_v23:
4788 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
19c1d5675e Jean*4789 o pkg/seaice:
4790 - restore (last time on 2011/12/24) ability to compile pkg/seaice with
4791 undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
ee9d1fdd8f Jean*4792 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
4793 o eesupp/src:
4794 - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
4795 in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
51fc369eef Jean*4796 o switch to TAF version-2:
4797 - add flow directives to "freeze" naming convention for ad-routines that
4798 are used in I/O routines of adjoint state and associated common blocks
4799 that are used in adcommon.h (backward compatible with version-1)
4800 - update all ad-optfiles (in tools/adjoint_options + few local to some
4801 verification exp) to switch to latest TAF version (currently 2.5.5);
4802 merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
4803 out except for diva).
4804 - the major change with TAF version-2 is that both the differentiated
4805 routines and the forward routines (new) are returned as part of the TAF
4806 output source code. Update genmake2 accordingly.
4807 - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
4808 with version-2 when compared to TLM or FWD gradient); other experiments
4809 output show minor changes (machine truncation level); update the few AD &
4810 TLM output with 12 matching digits only (some prior to version-2 switch).
4811
5ed109e8ff Jean*4812 checkpoint64l (2013/08/05)
f66939121e Jean*4813 o model/src:
4814 - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
ea7e42c5a8 Jean*4815 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
4816 when using TAF but only if using OpenAD.
c7389f7fae Jean*4817 o pkg/mom_common+fluxform+vecinv:
4818 - always set horiz. viscosity arrays to background value before calling
4819 MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
4820 only when using variable horiz. viscosity (useVariableVisc=T);
4821 - simplify mom_vecinv.F (only 1 block for momViscosity).
d9f9cc1105 Jean*4822 o pkg/mom_common: variable horiz. viscosity in NH code
4823 - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
4824 from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
4825 - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
4826 useBiharmonicVisc & useVariableVisc.
4827 - fix old bug (already in 1rst implementation of variable horizontal viscosity
4828 in calc_gw.F, version 1.27, 2006/06/20):
4829 horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
4830 even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
4831 - change background horiz viscosity in vertical momentum (gW) to always be
4832 viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
4833 any type of variable viscosity, e.g., viscAh/4Grid)
4834 - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
4835 viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
4836 horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
4837 default viscAh,viscA4 is zero).
e636cf27b8 Jean*4838 o model/src:
4839 - extend length of drC & recip_drC from Nr to Nr+1.
e8ed922ed3 Jean*4840 o Divided Adjoint (DIVA) with MPI:
4841 - genmake2: do not create local ./mpi_headers dir when no file to copy into.
4842 - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
4843 and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
4844
8dca956637 Jean*4845 checkpoint64k (2013/07/23)
dee062a69c Jean*4846 o tools/OAD_support:
8dca956637 Jean*4847 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
4848 and remove it from genmake2.
dee062a69c Jean*4849 o tools/build_options:
4850 - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
4851 MPI_HEADER_FILES list (let genmake2 find the missing headers)
4be02e3b08 Dani*4852 o verification/halfpipe_streamice:
dee062a69c Jean*4853 - change to driving stress formulation; update both Fwd & AD output.
4854 o tools/genmake2 and Divided Adjoint with MPI:
4855 - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
4856 - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
4857 - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
4858 Makefile, which is set by genmake2, and check which mpi-headers are needed.
4859 Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
4860 - update target "CLEAN" (to also remove ./mpi_headers/ dir).
bcf312c024 Jean*4861 o testreport:
4862 - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
4863 perform additional runs (number of additional runs is "add_DIVA_runs" taken
4864 from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
4865 o verification/lab_sea (AD test):
4866 - change to test Divided Adjoint Run in this set-up (both standard AD test
4867 and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
0f31045802 Jean*4868 o pkg atm_ & ocn_compon_interf:
4869 - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
4870 staggerTimeStep implementation) and disable (retired) corresponding
4871 parameter.
d761a6c43f Jean*4872 o pkg/offline:
4873 - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
4874 - add S/R OFFLINE_CHECK to print offline parameter summary
4875 and stop if loading a file that is not used;
4876 - enable to calculate GMRedi tensor, KPP mixing and convective index
4877 when the corresponding file(s) is/are not specified (but pkg is used).
2bbc535596 Jean*4878 - comment out resetting of monitorFreq (to endTime) since it still useful
4879 for monitoring CFL numbers and checking offline fields.
e44d40886c Jean*4880 o OpenAD:
4881 - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
4882 smaller standard output) and generate new (smaller) output (on baudelaire
4883 using gfortran with -ieee) for exp. tutorial_tracer_adjsens
5c3afaf8cf Jean*4884 o model/src:
4885 - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
4886 (where external_forcing_adjust was called) and change list of arguments;
4887 - merge external_forcing_adjust.F into external_forcing_surf.F
4888 - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
4889 which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
4890 previously in file "balance_relax.F", now removed); remove corresponding
4891 arrays in FFIELDS.h.
4892 - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
4893 a hack for getting back surfaceForcingS (loaded from file) when using
4894 ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
4895 - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
4896 (was getting only 11 digits for AD-grad, due to different truncation
4897 error in AD code).
4898
f15d0780a7 Jean*4899 checkpoint64j (2013/07/04)
b9ef6e0869 Jean*4900 o pkg/offline:
4901 - to enable the use of other features with pkg offline (e.g., obcs),
4902 also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
4903 - comment out "allowFreezing" (now active) in 2 offline testing exp.
27ebbc08f6 Dimi*4904 o pkg/exf ALLOW_RUNOFTEMP
4905 - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
5c3afaf8cf Jean*4906 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
684284fdda Dimi*4907 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
d2e18b684b Jean*4908 o pkg/atm_phys:
4909 - allows to add some damping on uVel,vVel (strength only function of k).
978ac82129 Jean*4910 o verification, ad-tests:
4911 - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
4912 global_ocean_ebm and offline_exf_seaice.thsice.
b8dffaf82f Dani*4913 o verification/halfpipe_streamice:
4914 - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
4915 flux input boundary conditions to be ignored; a fix for this bug changed
978ac82129 Jean*4916 verification results for forward test.
4917 - add adjoint test.
7ee27107e3 Jean*4918 o pkg/ptracers:
4919 - allow to restart without SOM pickup (resetting SOM to zero).
0d1e4b948d Mich*4920 o pkg/gmredi:
4921 - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
4922 - It uses mixing length theory and suppression by steering level effects to
4923 calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
4924 to JPO, for more details).
4925 - It also uses the diffusivity to calculate an eddy induced streamfunction
4926 based on a PV closure (rather than a buoyancy closure as in GM).
7ee27107e3 Jean*4927 - New files added to pkg/gmredi:
0d1e4b948d Mich*4928 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
4929 induced overturning streamfunction (called from gmredi_calc_tensor)
4930 gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
4931 for use in gmredi_k3d
4932 gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
4933 the eddy diffusivity
ffc1393533 Mich*4934
fe0ec941c0 Jean*4935 checkpoint64i (2013/06/18)
e68ed13a81 Jean*4936 o pkg/cheapaml:
4937 - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
4938 that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
4939 with pkg/cheapaml.
4940 o utils/python: add subpackage for cubed sphere function, first example is
4941 simple cs.pcol to plot 2D fields on a map
531678d622 Dani*4942 o pkg/streamice:
4943 - This is a new package in MITgcm, which solves dynamic equations for ice
4944 sheets and ice streams
e68ed13a81 Jean*4945 - At the moment it is independent of atmosphere/ocean dynamics, or any
531678d622 Dani*4946 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
4947 ed that this will change)
e68ed13a81 Jean*4948 - There is a new verification exercise that tests it, halfpipe_streamice,
531678d622 Dani*4949 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
4950 rectangular embayment
4951 - halfpipe_streamice is forward-only for now, will have TAF test soon
4952 - for questions, email dgoldber@mit.edu
04cb5dc10d Jean*4953 o pkg/thsice:
4954 - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
4955 of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
4956 - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
4957 call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
4958 - allow precip from pkg/cheapaml to make snow over seaice.
a5f3de150b Jean*4959 o pkg/cfc:
ac5b32ca4b Jean*4960 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
4961 - remove atmos CFC 2-D arrays from common bloc (now local variables)
4962 - change some hard-coded constant to run time parameter for reading and
4963 and interpolating atmospheric CFC ; keep same default as previously.
4964 - more flexible reading of Atmos CFC (number of records no longer hard-coded)
4965 - put arguments in standard order: myTime, myIter, myThid
4966 - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
4967 atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
4968 - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
4969 - new routine to print summary of CFC params and check for consistency.
7a8082e765 Mart*4970 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
4971 similar to thsice_advdiff.
4972 Note that for the B-grid case the routine parameters uc/vc are overwritten.
ac5b32ca4b Jean*4973 o pkg/cfc:
a5f3de150b Jean*4974 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
4975 update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
ac5b32ca4b Jean*4976 - fix interpolation of atmphspheric CFC between Sorthern and Northern
4977 hemisphere value.
5dd9cc40ef Jean*4978 o pkg/seaice:
4979 - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
a8ebf896c4 Mart*4980 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
4981 so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
4982 - requires an additional time level that is stored in the pickup
4983 - you can start with AB2 from a pickup without this time level with
4984 pickupStrictlyMatch = .false.
4985
2d517edcde Jean*4986 checkpoint64h (2013/05/26)
06294f69b9 Jean*4987 o pkg/cheapaml:
4988 - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
4989 affect machine truncation (but exp cheapAML_box still pass with 13 digits).
4990 - consistent treatment of uWind,vWind location: assume everywhere in
4991 pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
4992 (Note: was already the case for Tair,Qair advection);
4993 add option (INCONSISTENT_WIND_LOCATION) to recover old results.
4994 - compute diabatic forcing only in the interior (excluding overlap regions)
4995 - fill in array "Qsw" (for short-wave heating);
4996 - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
4997 before any update (consistent with MITgcm state var diagnostics);
4998 - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
4999 non periodic ; + adjusted for uWind,vWind (C-grid).
5000 o pkg/seaice:
5001 - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
5002 add explicitly pkg/exf in experiments that currently use pkg/seaice.
5003 - allows to compile pkg/seaice without pkg/exf.
142cc892c8 Jean*5004 o tools/OAD_support:
5005 - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
5006 of array "ourStepOf" in function rvNextAction (revolve.F90).
723a22990a Jean*5007 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
5008 - change pkg name (to be used with other atmospheric physics pkg)
5009 but by-pass CVS when making the new pkg so that we keep the CVS history.
a280c86ad5 Jean*5010 o pkg/offline:
5011 - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
5012 (previously called from pkg/dic_surfforcing_init.F)
5013 o model/src:
5014 - re-order sequence of calls within packages_init_variables.F, using
5015 standard order, except for:
5016 DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
5017 CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
ac0d2c71f0 Jean*5018 o new pkg: atm_phys
2edfb1b43c Jean*5019 - add entry point and source code (previously in contrib
5020 verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
5021 (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
ac0d2c71f0 Jean*5022 - re-order sequence of calls within packages_readparms.F,
5023 packages_init_fixed.F and packages_write_pickup.F
5024 (but skip packages_init_variables.F because of TAF issues).
2edfb1b43c Jean*5025 - update contrib/*/atm_gray/ experiment.
b7399a7436 Jean*5026 o pkg/seaice (ITD code):
76166139ef Jean*5027 - simplify and fix the writing of pickup-files for ITD case
5028 o pkg/seaice (ITD code):
b7399a7436 Jean*5029 - introduce floe size dependent lateral melt for ITD case;
5030 - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
5031 - update seaice_itd experiment main output.
ffa44e5be9 Jean*5032 o pkg/thsice:
5033 - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
5034 declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
5035 changed accordingly pkg/atm2d.
5036
134aa64c5b Jean*5037 checkpoint64g (2013/05/01)
8f8fcb55e3 Dimi*5038 o pkg/exf ALLOW_RUNOFTEMP
5039 - if defined, river and glacier runoff temperature can be read-in from
5040 runoftempfile; runoftempfile needs to have same format as runofffile
a665b019b3 Jean*5041 o pkg/thsice (& pkg/bulk_force):
5042 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
5043 for energy content of Precip + RunOff & Evap (like with pkg/exf).
5044 - change computation domain to always be the interior (without overlap).
5045 - fix bug (wrong overlap) when using EXF and stressReduction > 0.
690aeca19f Oliv*5046 o verification/tutorial_global_oce_biogeo:
5047 - add preliminary OpenAD setup (still has problems)
134aa64c5b Jean*5048 o pkg/seaice:
6c4c641ea1 Mart*5049 - turn some parameters for choosing the convergence criterion of
5050 the inexact Newton method (JFNK) into runtime parameters for convenience
134aa64c5b Jean*5051 - clean up seaice_calc_viscosities.F: remove/retire two options for
6c4c641ea1 Mart*5052 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
5053 the results of lab_sea/input because a division has been replaced by
5054 a multiplication with the reciprocal (sumNorm)
5055 - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
134aa64c5b Jean*5056 convergence of solver (changes results, of course), and to test some
6c4c641ea1 Mart*5057 new features
14111182a7 Jean*5058 o model/src:
5059 - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
5060 - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
5061 - move forcing adjustment (balancing surface forcing) in specific S/R
5062 where might also be applied exchanges (if needed) to forcing arrays.
f63796dcfc Jean*5063 o pkg/shelfice:
5064 - allow to specify the Ice-Shelf mass per unit area (instead of
5065 shelficeLoadAnomaly) and do the conversion from one to the other
5066 - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
5067 to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
5068 (b) will be loaded in time (before calling INI_PRESSURE) in case it is
5069 needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
5070 - update isomip experiment forward output (get machine truncation error
5071 from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
01fb631dba Jean*5072 o verification/offline_exf_seaice:
5073 revise data.seaice in input.thermo and input_ad and update results accordingly
b57d4b5259 Gael*5074 HO = 0.2, SEAICE_areaLossFormula = 2,
01fb631dba Jean*5075 SEAICE_growMeltByConv = .TRUE.,
b57d4b5259 Gael*5076 SEAICE_doOpenWaterMelt = .TRUE.,
01fb631dba Jean*5077 Improve consistency with input.thsice and fix the spurious 500m ice corners
5078 o verification/global_ocean.cs32x15:
5079 - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
5080 in icedyn (thsice+seaice-dyn) test and update output.
5081 o verification/offline_exf_seaice:
5082 - adjust list of tested variables (with testreport) and update
5083 standard test output with better slection of monitored fields.
8fe5c1e95b Jean*5084 o pkg/cd_code:
5085 - swtich off Adams-Bashforth on the 1rst iteration. Update output of
5086 experiment lab_sea.hb87
9f4f698356 Jean*5087 o tools/genmake2:
5088 - change default makedepend from the system default to tools/xmakedepend:
5089 When no makedepend is specified, select tools/xmakedepend it the test pass,
5090 otherwise select the system default (if exist and pass the test) or
5091 try to build cyrus-makedepend ; stop if none of the 3 works.
329d560e65 Jean*5092 o pkg/exf & pkg/thsice:
5093 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
9f4f698356 Jean*5094 for energy content of Precip + RunOff & Evap. Assumes:
329d560e65 Jean*5095 1) Rain has same temp as Air.
5096 2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
5097 3) Run-Off comes at the temp of surface water (with same Cp)
5098 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
5099 put directly into Latent Heat flux & should use water-vapor heat capacity.
5100 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
5101 with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
f21dfbc609 Mart*5102 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
5103 (compile when SEAICE_ALLOW_JFNK is defined)
47259ecf74 Jean*5104 o pkg/thsice:
5105 - fix oceanic flux diagnostics & timeave (left from new sequence of calls
5106 implementation): move THSICE_AVE call after the advection (called directly
5107 from thsice_do_advect.F).
0005dc42e3 Patr*5108 o verification/global_ocean.90x40x15 and OpenAD:
5109 New experiment for OpenAD is identical to the one in input_ad except that
5110 multiDimAdvection=.FALSE.,
5111 There is still an issue with this.
b105fb69b1 Jean*5112 o pkg/thsice:
5113 - account for ice velocity (ocean relative velocity) in turbulent heat flux
5114 at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
5115 and offline_exf_seaice (main test).
5116
490ead03b8 Jean*5117 checkpoint64f (2013/03/31)
5118 o verification/OpenAD:
5119 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
5120 o verification/isomip, pkg/shelfice and OpenAD:
789efdf83c Patr*5121 - add OpenAD setup to this exp and make shelfice package work with OpenAD
490ead03b8 Jean*5122 o verification/tutorial_global_oce_biogeo:
5123 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
5124 o verification/offline_exf_seaice:
5125 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
ee82888721 Oliv*5126 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
5127 - add OpenAD setup to this exp and make ptracers package work with OpenAD
490ead03b8 Jean*5128 o pkg/seaice/seaice_evp.F:
5129 mask the asymmetric contribution of the ice-ocean stress (when
5130 the turningAngle is non-zero) over open water to avoid stripes
5131 in the EVP-solutions after many EVP-substeps. This does not change
5132 the verification experiment (because turningAngle=0 in that experiment),
5133 but will affect other EVP solutions with turningAngle.ne.0
d38c2a4135 Jean*5134 o verification, AD & TLM output:
5135 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
5136 additions and multiplications which affect results at machine truncation
5137 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
5138 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
5139 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
5140 digits of matching.
b3668e95f2 Mart*5141 o pkg/seaice:
d38c2a4135 Jean*5142 modify lsr-algorithm so that it vectorizes AND converges by using a
5143 "zebra" method: split vector loop into two with step size 2; this
5144 solves a general convergence problem for the JFNK solver on a vector
5145 computer. It has the potential to even improve convergence for
5146 non-vector machines, but it does change the results so it is turned
5147 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
5148 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
b3668e95f2 Mart*5149
06b25f9a40 Jean*5150 checkpoint64e (2013/03/05)
59b6bd98c8 Patr*5151 o pkg/ecco and several verification experiments:
06b25f9a40 Jean*5152 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
5153 from ecco package, and revert to unified routine in model/src/
5154 Adjust verification experiments accordingly, especially gloal_oce_llc90
5155 Should conclude long-standing work by Gael to reconsile the_main_loop with
5156 ECCO and will enable OpenAD's revolve loop in ECCO setup.
7c6b6a09d0 Jean*5157 o pkg/generic_advdiff:
ccf9e62cda Jean*5158 - implement compressible flow method for multi-dim advection (similar to
5159 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
5160 TAF generates many recomputations) to use it; no yet coded with implicit
5161 vertical advection.
5162 - change experiment advect_cs (new output) and advect_xy (same output)
5163 to test compressible flow multi-dim advection.
5164 o pkg/generic_advdiff:
7c6b6a09d0 Jean*5165 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
5166 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
5167 o pkg/seaice:
cfab924fcb Mart*5168 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
7c6b6a09d0 Jean*5169 bug affects two verification experiments (lab_sea and lab_sea.hb87),
5170 recover old (wrong) results by setting noSlipFac = 2. in
cfab924fcb Mart*5171 seaice_calc_strainrates.F;
8c657eb247 Mart*5172 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
7c6b6a09d0 Jean*5173 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
8c657eb247 Mart*5174 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
5175 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
c59d410006 Mart*5176 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
5177 - new subroutines seaice_lsr_tridiagu/v
5178 - introduce loop bounds i/jmin/max to be able to use a restricted
5179 additive Schwarz method, but not used for now.
5180 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
5181 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
9743b80f75 Patr*5182 o OpenAD support
06b25f9a40 Jean*5183 Reorganize S/R call for overall time-stepping loop to facilitate
5184 OpenAD revolve loop replacement
5185 (new S/R main_do_loop.F)
6dd77b4354 Jean*5186 o model/src:
5187 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
5188 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
5189 ADAMS_BASHFORTH2.
7bfbef8b82 Jean*5190 o pkg/cheapaml:
5191 - add new parameter (default=F, same as before) to disable full domain
5192 (including land) periodicity in X & Y dir.
5193 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
5194 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
5195 into single S/R CHEAPAML_TIMESTEP.
5196
544247e9eb Jean*5197 checkpoint64d (2013/02/17)
11fe9ae9a2 Jean*5198 o pkg/monitor (angular momentum):
5199 - do not add Eta contribution to the total AM if using rigid-lid;
5200 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
5201 - horizontal discretisation: compute Zonal wind contribution separately for
5202 each component (instead of from cell centered averaged) and use the 4
5203 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
5204 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
5205 FreeSurf) if using vectorInvariant momentum.
5206 o model/src (horizontal grid):
5207 - move initialisation of all horizontal grid arrays to null value
5208 from specific horizontal grid S/R to main S/R INI_GRID;
5209 - add 2 new arrays to project model C-grid velocity on to zonal direction
5210 (similar to AngleCosC & -AngleSinC but at U and V point location) and
5211 compute them in S/R CALC_GRID_ANGLES.
48a47574f9 Mart*5212 o pkg/seaice: replace a hard coded parameter by a runtime parameter
11fe9ae9a2 Jean*5213 SEAICE_JFNK_tolIter
a1321f078e Mart*5214 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
5215 preconditioner for JFNK (run LSR into the overlaps as far as possible,
5216 i.e OLx/y-2, but overwrite the solution in the overlaps)
5217 - extend loop range in seaice_calc_viscosity
5218 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
5219 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
5220 - slightly modify loops in tridiagonal solver lsr-preconditioner
5221 - by default remove the extra exchange in seaice_preconditioner with a
5222 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
5223 - modify offline_exf_seaice so that old results without RAS are reproduced
5224 for output.dyn_jfnk.txt
5225 in seaice_fgmres.F (unrelated to RAS)
5226 - add a cpp-flag option for a re-ordered mapping (potentially more
5227 efficient), but because this changes the results, turn it off by
5228 default
5229 - replace the save statement by local common blocks
4a6b51e826 Jean*5230 o utils/matlab:
5231 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
5232 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
5233 instead of local script "load_cs.m".
0d86f34c41 Mart*5234 o pkg/seaice:
5235 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
5236 to the scalarProductMetric and the unrolling. By chance this does not
4a6b51e826 Jean*5237 change the verification experiment, because of the particular domain
0d86f34c41 Mart*5238 decomposition
4956a0134a Jean*5239 o pkg/diagnostics:
5240 - change default missing_value from UNSET_RL to -999.
b24144b856 Mart*5241 o pkg/layers: improve vectorization of layers_fluxcalc.F
4a6b51e826 Jean*5242 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
b24144b856 Mart*5243 time spent in this routine by more than a factor of 3 on an NEC-SX8
5244 - step 2: replace search algorithm by a bisection algorithm found in
4a6b51e826 Jean*5245 Press et al. Numerical Recipes in Fortran. This algorithm can be
b24144b856 Mart*5246 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
5247 For now, use this algorithm only for TARGET_NEC_SX defined.
5248 - moved the search algorithm into a separate subroutine, that is kept
5249 within the same file for automatic inlining.
5250 - modified catching potential errors
4956a0134a Jean*5251 o pkg/ecco:
27b515a5c9 Gael*5252 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
4956a0134a Jean*5253 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
27b515a5c9 Gael*5254 - modifications for ALLOW_GENTIM2D_CONTROL
5255 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
5256 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
5257 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
5258 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
f193ea8b76 Jean*5259 o model/src:
5260 - account for moist thermodynamics in (dry) potential temperature equation;
5261 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
5262 and cpl_aim+ocn.
25fdd6d933 Jean*5263 - also switch to standard compiler (gfortran, was using ifort previously)
5264 for fizhi-cs experiments reference output.
f193ea8b76 Jean*5265 o pkg/ctrl:
93e42e1e05 Patr*5266 - 1st step toward generic time-varying control variable (2D) via CPP option
5267 ALLOW_GENTIM2D_CONTROL
5268 - note new namelist ctrl_nml_genarr in data.ctrl
df3d2037ba Jean*5269 o verification/global_ocean.cs32x15:
5270 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
5271 thsice calling sequence and update "output.icedyn.txt" output file.
a618488a45 Jean*5272 o pkg/ptracers:
5273 - from Ryan A.: code to allow to restart a tracer at regular time interval
5274 specifying a reset frequency and a reset-phase (for each tracers).
8d7c0d8037 Jean*5275 o pkg/thsice:
b8ed299f9d Jean*5276 - implement new sequence of calls for thsice+seaice:
5277 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
5278 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
5279 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
5280 in CPP_OPTIONS.h) to recover old sequence;
5281 - update diagnostics for Intermediate State thsice diagnostics: now filled
5282 just before advection (instead of just after advection in old sequence);
5283 - update output of experiment offline_exf_seaice (standard test);
5284 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
5285 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
5286 o pkg/aim_v23:
5287 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
5288 - use standard pkg/mdsio routines to read & write CO2 pickup file;
5289 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
5290 - Implement new sequence of calls for seaice advection (with thsice and
5291 seaice diffusion): do ice advection after ice-Thermodynamic (previously
5292 was done before); change aim_do_physics.F (split the bi,bj loops block);
5293 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
5294 o pkg/thsice:
8d7c0d8037 Jean*5295 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
5296 where just seaice diffusion is used without seaice-dynamics.
5297
9f6899b968 Jean*5298 checkpoint64c (2013/01/18)
5299 o pkg/seaice:
5300 - add a parameter JFNKres_tFac that can replace JFNKres_t
9ebe58d4fa Mart*5301 (= JFNKres_tFac*JFNKresidual before JFNK solver)
5302 - add a line search option to the JFNK solver
9f6899b968 Jean*5303 - move update of u/vIce and computation of initial residual into a separate
c937d257c3 Mart*5304 routine (same file); makes the code a little easier to read (?)
5305 - the line search requires computation of the residual and for some reason
9f6899b968 Jean*5306 I cannot do the update of u/vIce at the beginning of the Newton loop
c937d257c3 Mart*5307 without changing the results, so we move computation of the new residual
5308 also to the end of the Newton loop, even without the line search
3b4e62adf7 Jean*5309 o pkg/mdsio:
5310 - write missing value (corresponding to undefined array value) to meta files;
9f6899b968 Jean*5311 skip this if missing value is one (UNSET_RL would be a better value for the
3b4e62adf7 Jean*5312 case of undefined missing value but it's current the default missing-value);
5313 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
93ace0b1be Jean*5314 o pkg/exf & thsice:
9f6899b968 Jean*5315 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
9ebe58d4fa Mart*5316 diagnostics) even when SHORTWAVE_HEATING is #undef;
93ace0b1be Jean*5317 o verification/cfc_example:
9f6899b968 Jean*5318 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
9ebe58d4fa Mart*5319 illustrate how to use it).
7f496449e0 Jean*5320 o verification/offline_exf_seaice:
5321 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
5322 files to only one time-record.
5323 in input.thermo: narrow the 2 bands of low initial ice-concentration near
5324 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
9f6899b968 Jean*5325 snapshot output; same mcPheePiston value as in thsice with
9ebe58d4fa Mart*5326 surf-current=0.2m/s.
7f496449e0 Jean*5327 in input.thsice: similar set-up as in input.thermo (channel with same seaice
5328 initial conditions).
a504296e19 Jean*5329 o verification/cfc_example:
5330 - update file "data" with more standard choice (default rotationPeriod,
5331 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
5332 set deltaTFreeSurf to deltaTtracer) and update the output.
5333 o pkg/layers:
5334 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
5335 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
5336 o verification/offline_exf_seaice:
5337 - set all {field}period to zero for constant-in-time forcing (not tested
5338 anywhere else).
bde2cd981d Jean*5339 o verification/offline_exf_seaice:
5340 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
5341 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
a4ef5db77d Jean*5342 o model/src:
5343 - implement Finite-Volume method for (hydrostatic) presure gradient
5344 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
5345 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
5346 - In order to be compatible with the default EVP code, this requires changing
5347 the EVP code around a little; and because any small change immediately
5348 breaks the lab_sea.hb87 verification experiment, the reference output is
5349 updated two times (each time the remaining aggrement was only 2 digits):
5350 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
5351 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
5352 The adjoint test lab_sea.evp also needed to be updated.
5353 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
5354 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
5355 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
5356 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
5357 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
5358 kept obscure, because I need to test it a little more.
9902b68429 Jean*5359 o pkg/cheapaml:
5360 - fix few incorrect type (_RL/_RS) in subroutine calls.
5361 o pkg/seaice:
5362 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
5363 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
8ecbb13ed3 Jean*5364 o model/src:
5365 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
5366 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
5367 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
01e3fdb926 Jean*5368 o pkg/cheapaml:
5369 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
5370 update output of experiment cheapAML_box.
d9f9739596 Jean*5371 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
5372 and set them only in one place (cheapaml_readparms.F).
5373 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
5374 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
5375 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
69e136acfe Gael*5376 o model/src/the_main_loop.F:
5377 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
5378 o pkg/seaice:
5379 - remove legacy branch code.
5380 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
5381 o verification/*/code*/SEAICE_OPTIONS.h:
d9f9739596 Jean*5382 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
01e3fdb926 Jean*5383 SEAICE_CAP_HEFF).
b4639cc807 Jean*5384 o pkg/cheapaml:
5385 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
5386 to load new forcing fields.
5387 - add missing "_d 0" where it's needed; + some editing (improve indentation).
5388 - remove switch to "-r8" compiler option (no longer needed) in verification
5389 cheapAML_box, keep same output (small trucation error differences).
692e8490be Jean*5390 o verification/offline_exf_seaice:
54b88f0722 Gael*5391 - add thermodynamics only test.
692e8490be Jean*5392 o verification/cheapAML_box:
5393 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
5394 keep same output (same 14 digits for cg2d).
5395 - switch on "-r8" compiler option (some numerical values are missing
5396 the "_d 0") and update output (only 6 digits for cg2d were preserved).
54b88f0722 Gael*5397
026a4385c5 Jean*5398 checkpoint64b (2012/12/24)
51ad14de13 Jean*5399 o pkg/cheapaml:
5400 - remove un-used variables (Qnet,EmPmR) from pickup files.
5401 - store tendency of advected variables into cheapaml pickup file
5402 and fix the AB-2 restart.
0ef659ed72 Gael*5403 o verification/offline_exf_seaice and lab_sea adjoint:
51ad14de13 Jean*5404 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
5405 - switch to 4 time steps in offline, consistent with lab_sea.
026a4385c5 Jean*5406 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
51ad14de13 Jean*5407 - update results after change of experiment seaice.
026a4385c5 Jean*5408 o pkg/seaice:
5409 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
5410 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
5411 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
5412 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
7755429b93 Jean*5413 o model/src:
5414 - add run-time parameter to select CG2D solver minimum-residual solution
5415 (in case of a poor convergence).
262f1a37c5 Mart*5416 o pkg/seaice/seaice_lsr.F
7755429b93 Jean*5417 - move calculation of matrix coefficients into new
ed8217d1df Mart*5418 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
5419 file; the main purpose of this change is to be able to reuse the code
5420 in S/R SEAICE_PRECONDITIONER
262f1a37c5 Mart*5421 - modify the computation of the residual so that the mass of sea-ice
026a4385c5 Jean*5422 is not used twice; this simplifies the calculations, but since
262f1a37c5 Mart*5423 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
5424 not tested in testreport---this does not affect the testreport results.
adb13907c3 Dimi*5425 o verification/seaice_obcs:
5426 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
5427 verification/lab_sea/input.salt_plume; changes results/output.txt*
c178b9393a Jean*5428 o model/src:
5429 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
7e9893ac33 Mart*5430 o pkg/seaice:
5431 - improve description of parameters in seaice_fgmres.F and start
5432 cleaning up the code
c178b9393a Jean*5433 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
7e9893ac33 Mart*5434 second argument
5435 - add a metric based on grid cell area to SEAICE_SCALPROD; update
5436 results of offline_exf_seaice.dyn_jfnk
5437 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
e4684a75d6 Jean*5438 o pkg/aim_v23:
5439 - fix an other bug in dissipation heating (grid-cell area was missing).
2dc84f624e Jean*5440 o model/src + pkg/seaice:
5441 - add global (multi-tile) linear solver for pair of tri-diagonal system
5442 along X and Y lines, respectively for U and V component.
5443 Note: 1) MPI and cube-exchange not yet coded.
5444 2) probably not accurate for poorly conditioned / large size problem.
5445 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
5446 default: not compiled and not used.
88a8f1f812 Mart*5447 o pkg/seaice:
5448 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
2dc84f624e Jean*5449 introduce bi/bj loops and use global_sum_tile_rl instead of
88a8f1f812 Mart*5450 mpi_allreduce in seaice_fgmres.F
5451 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
5452 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
5453 - add a verification experiment for JFNK in offline_exf_seaice
d5a9a292e9 Jean*5454 o verification:
6531f48833 Jean*5455 - change (for now, only fwd test) offline_exf_seaice experiment:
026a4385c5 Jean*5456 use a re-entrant channel with idealized coastline (trapezoidal shape)
6531f48833 Jean*5457 at southern boundary to explore seaice dynamics and thermodynamics
5458 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
5459 secondary test (input.thsice) use thermodynamics only with SST relaxation.
5460 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
5461 o pkg/exf:
5462 - disable "sstExtrapol" when Nr=1
5463 o verification:
d5a9a292e9 Jean*5464 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
5465 to test pkg/cheapaml.
46af042642 Jean*5466 o pkg/aim_v23 & pkg/shap_filt:
5467 - fix dissipation heating (erroneous gravity multiplication factor).
5468 o pkg/seaice:
7729ab9475 Mart*5469 - remove unused field pressPre from jfnk solver
5470 - rename two subroutines in seaice_preconditioner.F
e5a4e727cd Jean*5471 o eesupp/src:
5472 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
6ac4f1544e Mart*5473 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
5474 - remove wrong parts of the rhs and the lhs (were in there
5475 because I did not understand the concept of this preconditioner)
5476 - add an exchange between u- and v-sweep. This increases communication
5477 by a factor of two but improves the convergence of jfnk. Ideally,
5478 one would like the u- and v-sweep to be independent. So far within
5479 undocumented ifdefs
5480 - reorganize the extra computations for printing the residuals
24fc5488c9 Jean*5481 o tools/genmake2:
5482 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
5483 since it's not necessary (and was preventing to use MNC in some cases).
5484
3b68c5ef24 Jean*5485 checkpoint64a (2012/11/16)
0e1d0943d5 Jean*5486 o pkg/autodiff:
5487 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
5488 autodiff_readparms.F no longer depends on calling order (within
5489 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
5490 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
5491 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
ed6db82373 Dimi*5492 o pkg/obcs:
5493 - adding tidal velocity forcing capability to obcs
5494 for usage example, see verification/seaice_obcs/input.tides
7972e6de33 Mart*5495 o pkg/seaice:
0e1d0943d5 Jean*5496 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
7972e6de33 Mart*5497 SEAICE_LSRrelaxU/V
356e5485d1 Mart*5498 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
be55e6379a Jean*5499 o pkg/aim_v23:
5500 - implement heating from friction (bottom friction and stratospheric drag).
5501 o pkg/shap_filt:
5502 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
5503 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
0c723af82e Jean*5504 o model/src:
5505 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
5506 time-constant addMass field from file (addMassFile);
5507 - support for heating due to friction (and Kinetic Energy dissipation):
5508 add option, run-time switch and 3-D field array + support code ; each pkg
5509 or S/R can add heating contribution (if there is a sink of KE); the sum is
5510 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
93029454d2 Mart*5511 o pkg/seaice:
96c8307cd6 Patr*5512 - complete merge of ITD code into seaice_growth.F
5513 from MITgcm_contrib/torge/itd/code/
5514 no verification so far, but Torge Martin tested
5515 "1-D test case and Beaufort set up;
5516 deliver okay results after 1 model year."
5517 - complete merge of SEAICE_SIZE.h into all relevant routines
db6b283965 Mart*5518 - move computation of eta at Z-points into calc_viscosities
5519 + introduce global field etaZ
5520 + add different methods for computing etaZ, for now the old
5521 method (simple averages of eta to Z-points) is hardwired
0c723af82e Jean*5522 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
db6b283965 Mart*5523 seaice_preconditioner
5524 - simplify computations for SEAICE_ZETA_SMOOTHREG
0c723af82e Jean*5525 - seaice_preconditioner:
773a0cee43 Mart*5526 + replace one remaining press by pressLoc (mistake)
5527 + adjust printing of residuals
54dc59c155 Mart*5528 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
0c723af82e Jean*5529 + add (SEAICE.h) and rename some counters (initiliased in
54dc59c155 Mart*5530 seaice_init_fixed.F)
5531 + add _BEGIN/END_MASTER (myThid) around print statements
5532 + print total number of iterations and failures over SEAICE_monFreq
5533 interval to STDOUT
5534 - move control over output-messages by fgmres to seaice_jfnk to save
5535 some operations
93029454d2 Mart*5536 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
5537 in order to make restarts with sol .ne. zero (fgmres with restarts)
5538 (seaice_jfnk.F, seaice_fgmres.F)
5539 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
5540 a serious convergence problem when open boundaries are involved
0c723af82e Jean*5541 o pkg/ggl90: fix computation of control volumes for the case of
58e6249dd7 Mart*5542 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
5543 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
8e17d76640 Mart*5544 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
48ffb9e808 Patr*5545 o pkg/autodiff
5546 - Add inAdMode switch for SEAICEuseDYNAMICS:
0c723af82e Jean*5547 SEAICEuseDYNAMICSinAdMode
48ffb9e808 Patr*5548 (extend logic in ADAUTODIFF_INADMODE_SET)
17353ce854 Patr*5549 o pkg/seaice
5550 - Step 1 of merging ice-thickness distribution (ITD) code from
5551 MITgcm_contrib/torge/itd/ (author: Torge Martin)
5552 The code implements concept laid out in Thorndike et al. (1975);
5553 code is enabled via CPP flag SEAICE_ITD
5554 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
5555 code is not complete yet!!
48ffb9e808 Patr*5556 - SEAICE_SIZE.h now included in almost all seaice routines
d28bbf0830 Jean*5557 o verification (using seaice):
5558 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
5559 global_ocean.cs32x15.seaice ; update results.
5560 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
5561 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
5562 offline_exf_seaice (previously compiling B-grid).
b3a1d973db Jean*5563 o pkg/exf:
5564 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
5565 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
5566 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
c6bd7aced7 Jean*5567 o pkg/layers (adjust changes from Sept 19):
dfcf827164 Jean*5568 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
5569 this allows to remove "layers_maxNum" dimension from all layers arrays.
5570 o pkg/layers (adjust changes from Sept 19):
c6bd7aced7 Jean*5571 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
5572 - snap-shot extended to all type of layers (not just the 1rst type);
5573 - remove layers variables when corresponding CPP option is undef.
5574 o pkg/layers:
5575 - rename pkg/layers variable and add new output (layer exist & un-weighted
5576 velocity in layer)
5577 o pkg/seaice:
2c43bfffcf Mart*5578 - simplify (?) ocean-drag coefficent computations by using
5579 the same routine in all three solvers (saves some code lines)
5580 - remove global fields DRAGA and DRAGS from C-grid code and
5581 declare them locally in lsr.F (the only place where they are
5582 still used)
0db5f1068d Jean*5583 - update AD output of lab_sea.evp (very sensitive anyway).
8c62e844bf Mart*5584 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
5585 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
5586 and SEAICEuseJFNK=.true. A few things to note:
5587 - involves a FGMRES, that is parallel but very inefficient,
5588 because of many scalar products (global sums) in the Gram-Schmidt
5589 orthogonalization method. Needs to be replaced. Original code
5590 from J.-F. Lemieux
5591 - preconditioner for FGMRES is a stripped down version of LSOR
c6bd7aced7 Jean*5592 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
8c62e844bf Mart*5593 preconditioner. For the preconditioner, the default is set to 10.
5594 - Jacobian times vector is computed with finite differences
5595 - marginally related to JFNK-solver: add a smooth regularization for
5596 zeta with tanh that will improve convergence (Lemieux and Tremblay,
5597 2009) for any implicit solver (not implemented for EVP because EVP
5598 does not need this regularization in the first place). Define
5599 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
8e5804ab61 Jean*5600 o eesupp/src:
5601 - check in genmake2 that intrinsic S/R flush is available.
5602 - add S/R to flush IO unit (if intrinsic S/R flush is available)
5603 - flush standard & error msg unit before MPI termination
5604 - if debugMode, flush IO unit after printing msg
5605 o pkg/ctrl:
5606 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
5607 to ctrl_set_unpack_xyz.
5608
f9281bf7f3 Jean*5609 checkpoint64 (2012/10/09)
6ae30b06da Patr*5610 o pkg/shelfice
f9281bf7f3 Jean*5611 - in mom_fluxform.F, mom_vecinv.F:
5612 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
5613 Bug fix KappaRU -> KappaRV
5614 does not change verification/isomip but may change other setups
5615 (presumably constant KappaRU=KappaRV)
9574f2afeb Mart*5616 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
5e26aed318 Dimi*5617 o pkg/obcs:
5618 - fixed some indexing bugs in obcs_seaice_sponge.F
5619 - added obcs relaxation subroutines for HSALT and HSNOW
5620 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
78e0c35225 Mart*5621 o pkg/seaice:
5622 - add "multicategory" parameterization for snow in analogy to ice,
5623 default is off for now.
fd94cbb100 Jean*5624 o pkg/obcs:
c7c4b57180 Dimi*5625 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
5626 see verification/seaice_obcs/input.seaiceSponge for example application.
fd94cbb100 Jean*5627 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
5628 index setting by master-thread. This fix multi-threads Pb in previous modifs.
4d8bc9f16f Gael*5629 o pkg/layers :
fd94cbb100 Jean*5630 - add diagnostics to pkg/layers
5631 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
5632 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
4d8bc9f16f Gael*5633 o pkg/generic_advdiff/gad_implicit_r.F :
fd94cbb100 Jean*5634 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
5635 o pkg/seaice/seaice_growth.F:
4d8bc9f16f Gael*5636 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
9bb13a83a0 Jean*5637 o pkg/obcs:
f9543ec2af Jean*5638 - change default setting of OBCS_UVICE_OLD from defined to undef;
5639 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
5640 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
5641 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
5642 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
5643 with Southern & Western OB at a tile edge (at least in a simple set-up).
5644 o pkg/obcs:
9bb13a83a0 Jean*5645 - change settings of OB index in case OB coincides with tile edge (shared by
5646 2 tiles), so that common OB location is registered by both tiles (instead of
5647 only 1). However, for Southern and Western OB, index value = 0 is not
5648 recognized as valid OB index (=default null value) and needs to be fixed.
5649 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
f9543ec2af Jean*5650 - new parameter "OB_indexNone" for null index value (for now, still zero)
9bb13a83a0 Jean*5651 to replace hard-coded null index value of zero.
c783d09169 Jean*5652 o pkg/exch2:
5653 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
5654 always check buffer-size (but outside the loop); move checking for valid
5655 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
5656 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
307cef9ba4 Jean*5657 o pkg/ctrl (pack & unpack):
5658 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
5659 (locally defined) for different variables (+ remove the variable-specific
5660 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
5661 (to be extended to other local file names in ctrl.h).
5662 o pkg/flt:
5663 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
31ef3766a3 Jean*5664 o pkg/mdsio:
5665 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
4308379183 Jean*5666 o tools/genmake2:
5667 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
5668 (added by Alistair in version 1.51 for building without make depend);
5669 - remove Header files list (H_SRC_FILES) from the dependence of targets
5670 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
5671 place in version 1.23): this save going through staf when unrelated header
5672 file has been modified.
5673 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
5674 "make depend" step, still need to do "make links" before "make adtaf".
e4daa51e76 Jean*5675 o eesupp/src (+ few pkg src files) & genmake2:
5676 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
5677 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
4308379183 Jean*5678 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
e4daa51e76 Jean*5679 upper/lower case ; account for space between "#" and undef/define)
5680 o pkg/flt (with exch2):
5681 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
4308379183 Jean*5682 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
e4daa51e76 Jean*5683
441c88984f Jean*5684 checkpoint63s (2012/09/05)
8de17d15ea Gael*5685 o pkg/ecco:
f1085458a2 Jean*5686 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
5687 - add more relevant #ifdef ALLOW_SMOOTH ones.
5688 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
8de17d15ea Gael*5689 o pkg/ctrl:
5690 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
5691 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
f1085458a2 Jean*5692 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
5693 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
5694 ctrlSmoothCorrel3D (new).
8de17d15ea Gael*5695 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
5696 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
f1085458a2 Jean*5697 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
8de17d15ea Gael*5698 controls when useAtmWind, and vice versa.
5699 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
5700 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
f1085458a2 Jean*5701 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
5702 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
5703 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
5704 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
5705 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
8de17d15ea Gael*5706 o pkg/smooth:
f1085458a2 Jean*5707 - remove un-necessary includes.
5708 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
5709 Those CPP options were never defined, and not necessary.
8de17d15ea Gael*5710 o model/src:
5711 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
5712 - standard treatment of useSMOOTH.
5713 o pkg/autodiff:
f1085458a2 Jean*5714 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
5715 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
dace8652ae Jean*5716 o pkg/exch2:
5717 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
8de17d15ea Gael*5718 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
dace8652ae Jean*5719 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
5720 and tiles to process mapping.
5721 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
5722 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
5723 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
5724 from w2_eeboot.F to w2_readparms.F.
5725 o eesupp/src:
5726 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
5727 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
5728 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
5729 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
5730 is defined (remove condition on usingMPI) to match cases where MPI_INIT
5731 has been called.
5732 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
5733 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
5734 (so that on 1 proc, get same myPid independently of usingMPI)
5735 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
5736 useCubedSphereExchange with EXCH-1 (safer).
5737 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
e2a9470322 Jean*5738 o pkg/ggl90:
5739 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
5740 used in ALLOW_GGL90_SMOOTH code.
5741 o pkg/flt:
5742 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
5743 floats at the Southern end of the domain).
5744 o eesupp/inc:
5745 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
5746 but not used (and not to be used) anywhere, just for documentation.
c7b36da2b3 Jean*5747 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
5748 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
5749 a) can damage previously written records in any other multi-record files.
5750 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
32c6b8e3e2 Jean*5751 o tools/genmake2:
5752 - define variable MAKE within Makefile and use it in place of 'make';
5753 - update AD_CONFIG.h (if needed) before building any of the executable
5754 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
5755 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
5756 - always print usual warning comment 'this file is automatically generated'
5757 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
c7b36da2b3 Jean*5758 o pkg/cheapaml:
5759 - updated to correspond to the code used in accepted paper (Nico Wienders).
32c6b8e3e2 Jean*5760 o pkg/exf:
5761 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
5762 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
5763 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
5764 o pkg/exf, autodiff, ctrl, ecco and seaice:
5765 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
5766 o pkg/ctrl, ecco:
5767 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
5768 Depending on useAtmWind, one is inactive, and the other is active (see
5769 exf_getffields.F/exf_getsurfacefluxes.F).
4681beea4a Jean*5770 o tools/genmake2:
5771 - improve error msg when failing in 2nd test of check_for_broken_Ff
5772 - fix option '-makefile' short-name (-mf according to genmake2 -help)
5773 - source local config file "genmake_local" just after processing the genmake2
5774 command arguments (previously done before processing arg).
07c8ca60a9 Jean*5775 o pkg/grdchk:
5776 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
5777 to this routine from cost_final has been dropped in g_cost_final)
5778 - improve printed information (more explicit msg, no longer using "print *,"
5779 fix fcpertminus printed value).
0c39183c54 Jean*5780 o model/src:
5781 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
5782 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
5783 this prevents getting cost-funct reset in adinitialise_varia recomputations.
2b983d7243 Jean*5784 o pkg/dic:
5785 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
5786 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
5787 o pkg/grdchk:
c78fad8e88 Gael*5788 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
2b983d7243 Jean*5789 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
5be1b702e4 Gael*5790 o pkg/autodiff/ctrl/grdchk :
2b983d7243 Jean*5791 - attempt to sort out what works and what does not,
5be1b702e4 Gael*5792 with regard to I/O, and to warn/stop accordingly.
2b983d7243 Jean*5793 o pkg/grdchk:
5be1b702e4 Gael*5794 - attempt to fix grdchk in the case of useSingleCpuIO.
5795 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
5796 statements were moved from grdchk_main.F and into
5797 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
5798 - a global sum is applied to record numbers icvrec/layer
5799 out of grdchk_loc so that they be passed to I/O routines.
2b983d7243 Jean*5800 o pkg/smooth:
5801 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
5be1b702e4 Gael*5802 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
97ed0955b8 Jean*5803 o verification/testreport:
5804 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
5805 - can also use compressed (gzip) reference output file;
5806 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
5807 to be easier to collect by testreport.
5808 - update existing TLM output (half out-of-date by more than 3 yrs).
090e7aded7 Jean*5809 - report NETCDF & LAPACK settings (from genmake2) in output dir.
5810 - report run-time in each individual summary (previously only for AD test);
5811 for TLM test, add also TAF version.
5812 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
97ed0955b8 Jean*5813
5ea440c02d Jean*5814 checkpoint63r (2012/08/15)
5815 o tools/genmake2:
5816 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
a7fab58b1c Gael*5817 o pkg/ecco/ecco_cost_final.F :
5ea440c02d Jean*5818 - fix fc print statements (to stdout and costfunction0000) so
a7fab58b1c Gael*5819 that the printed value is always after the global sum.
5820 o pkg/seaice/seaice_dynsolver.F :
5821 - fix ice strength assymptote at SEAICE_area_max<1
5822 (no change for the standard case of SEAICE_area_max=1)
f0c312b070 Jean*5823 o some cleaning:
5ea440c02d Jean*5824 - pkg source files: ensure that all *.F files from each pkg included the
f0c312b070 Jean*5825 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
5ea440c02d Jean*5826 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
f0c312b070 Jean*5827 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
5ea440c02d Jean*5828 includes;
f0c312b070 Jean*5829 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
5ea440c02d Jean*5830 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
5831 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
f0c312b070 Jean*5832 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
5833 - update option-file CPP_OPTIONS.h of all AD experiments:
5ea440c02d Jean*5834 * no longer include PACKAGES_CONFIG.h ;
5835 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
5836 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
f0c312b070 Jean*5837 including ECCO_CPPOPTIONS.h).
0185f8e796 Jean*5838 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
5839 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
5840 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
5841 not necessary accurate).
5842 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
5843 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
5844 deliberately break compilation (a remainder that it needs to be customized)
5845 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
5846 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
5847 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
5848 o tools/genamke2:
5849 - check for lapack.
53ea01923d Gael*5850 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
0185f8e796 Jean*5851 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
5852 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
5853 from both packages.
53ea01923d Gael*5854 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
5855 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
0185f8e796 Jean*5856 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
5857 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
53ea01923d Gael*5858 o pkg/cost : add comments to explain special and/or untested setups.
6e25847946 Jean*5859 o pkg/exf:
5860 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
5861 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
5862 o verification/*/code_ad:
5863 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
5864 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
5865 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
5866 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
c67a77c8bb Gael*5867 o pkg/seaice :
6e25847946 Jean*5868 - added possibility to change ice strength/PRESS0 relationship to
5869 HEFF, according to the following run time parameters
5870 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
5871 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
5872 SEAICEpresH0 :: HEFF threshold for ice strength (m)
c67a77c8bb Gael*5873 o pkg/ggl90 :
6e25847946 Jean*5874 - added run time flag mxlSurfFlag to include the code that ensure
c67a77c8bb Gael*5875 mixing between first and second level (previously included as a comment)
135650b823 Gael*5876 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
6e25847946 Jean*5877 - add test of newly added dumpAdByRec=T option where
135650b823 Gael*5878 we write all records to one file per variable.
5879 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
5880 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
5881 to check that this code is ok with taf and compiles in adjoint.
5882 o pkg/autodiff :
5883 - added run time param dumpAdByRec : ad dump format switch.
6e25847946 Jean*5884 If true then write all records to one file per variable.
5885 Else write one file per record (remains the default).
135650b823 Gael*5886 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
e9b3a4dec3 Gael*5887 o pkg/seaice:
5888 - Added SEAICEuseTILT run time switch : if set to
6e25847946 Jean*5889 false then omit the tilt term in seaice dynamics.
e9b3a4dec3 Gael*5890 - Fix free drift calculation.
a8eec7f730 Patr*5891 o pkg/shelfice:
6e25847946 Jean*5892 When initializing SHELFICEDragQuadratic, set default to be
5893 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
a8eec7f730 Patr*5894 but retain option to set it independently
5895 (inconsistenty spotted by Veronique Dansereau)
fe9611ab7a Jean*5896 o eesupp/inc:
5897 - in EEPARAMS.h, add real-type constant for some frequently used simple number
5898 (0,1,2,1/2), with name explicitly referring to RS/RL type.
5899 o model/src:
5900 - move balancing of relaxation terms to new S/R balance_relax.F.
9eb8003f99 Jean*5901 o pkg/autodiff:
5902 re-write active I/O high-level (control) S/R:
5903 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
5904 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
5905 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
5906 MDS_READ/WRITE_FIELD); change loops to multi-threads.
5907 - update and merge active_file_control_slice.flow into active_file_control.flow
5908 - update the calls in lower level S/R (active_file.F, active_file_g.F and
5909 active_file_ad.F) keeping the argument list and function unchanged.
ee91acaaf9 Jean*5910 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
5911 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
75bd0a9954 Jean*5912 - new low-level active I/O routines, one for each type (RL/RS), for active var
5913 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
5914 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
5915 right type.
9eb8003f99 Jean*5916 o autodiff and RS=real*4:
5917 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
5918 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
5919 - change argument type of 3-D mask argument to _RS to match type in the call
5920 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
4cdea015c1 Jean*5921 o pkg/thsice:
5922 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
5923 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
5924 fresh-water flux: uniform correction or proportional to local precip.
10741bb907 Patr*5925 o pkg/ctrl:
5926 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
5927 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
5928 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
5929 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
4cdea015c1 Jean*5930
5ba9855446 Jean*5931 checkpoint63q (2012/07/30)
09b7b7656d Jean*5932 o pkg/autodiff:
5933 note about monitor and snap-shot of ad-variables:
5934 a) need to apply ADEXCH before monitor or output of ad-vars to include
5935 overlap contributions (was done for adjDump but missing for monitor).
5936 b) since ADEXCH implies adding overlap values to interior array, machine
5937 truncation error is expected when adding an ADEXCH call in the middle of
5938 the time-stepping (although mathematically identical).
5939 modifs:
4d079479ad Jean*5940 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
5941 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
09b7b7656d Jean*5942 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
5943 apply ADEXCH before monitor or snap-shot of ad-variables:
5944 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
5945 - implement new method (copy+adexch) for snap-shot and monitor of main model
4d079479ad Jean*5946 ad-vars (initially not used by default -> output unchanged).
5947 - change default (set to 2) to use new method and update few output_adm.txt
5948 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
5949 and both tutorial_tracer_adjsens tests).
5950 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
5951 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
01d011442e Patr*5952 o pkg/ctrl:
5953 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
5954 generic control variables via
5955 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
5956 Only required customization should be S/R ctrl_map_ini_genarr.F
5957 (routine in repository contains example)
7f14c670e9 Jean*5958 o pkg/exf:
5959 - fix and refine checking of surface-relaxation setting when using EXF
cda8c5ef00 Jean*5960 o verification (adjoint exp):
5961 - reduce length of simulation by half for experiment global_ocean.cs32x15
5962 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
a2b6ec31fa Mart*5963 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
cda8c5ef00 Jean*5964 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
a2b6ec31fa Mart*5965 of KE that can occur with aggressive optimization
cda8c5ef00 Jean*5966 + put quadratic bottom drag calculation in separated loops (only done if
5967 using bottomDragQuadratic)
fb5ebe7993 Jean*5968 o model/src: CG2D_NSA
5969 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
5970 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
5971 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
5972 change cg2d residual target to be expressed in Wunits (=> do not normalise
5973 RHS ; this fix global_max Pb with TAF); update output.
04c0091821 Jean*5974 o verification/tutorial_tracer_adjsens:
fb5ebe7993 Jean*5975 improve parameter consistency (and get rid of warnings):
04c0091821 Jean*5976 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
5977 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
5978 - use staggerTimeStep (for stability) in som81; use default rotation period.
0288336348 Jean*5979 o pkg/exch2:
5980 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
5981 reset to 0 = 1 long line in X)
5982 o pkg/mdsio:
5983 - fix reading of dimensions from meta file for large-size domain
02de2b8dd0 Jean*5984 o model/src:
5985 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
5986 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
5987 Cubed-Sphere Exch with CS-corners inside the domain;
5988 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
5989 globalArea and to set hasWetCSCorners.
5990 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
5991 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
5992 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
5993 useCDscheme and useCubedSphereExchange).
b1b02f4641 Gael*5994 o pkg/seaice/seaice_growth.F :
02de2b8dd0 Jean*5995 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
5996 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
5997 when the previous code was not correct.
5998 - in all cases diagnoze the boundary condition mismatch to SIaaflux
5999 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
6000 that term to QNET (essentially to set the melt/freeze water to 0degC).
6001 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
82e953e38c Gael*6002 o verification/global_ocean.cs32x15/input.seaice :
02de2b8dd0 Jean*6003 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
6004 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
6005 - update results (output.seaice.txt) accordingly.
82e953e38c Gael*6006 o verification/lab_sea/input/data.seaice :
02de2b8dd0 Jean*6007 - remove SEAICEheatConsFix, which is now be tested
6008 in global_ocean.cs32x15. The presently coded fix
6009 is only consistent with real fresh water + nlfs.
6010 - update results (output.txt) accordingly.
b0139591bd Gael*6011 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
81055d8424 Jean*6012 o AD_CONFIG.h file:
02de2b8dd0 Jean*6013 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
6014 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
6015 add it explicitly in each fortran src file where it is needed.
6016 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
6017 thus introducing potentially wrong dependency; therefore, better to include
6018 it only where it's really needed, and after any other included OPTIONS file
6019 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
6020 or ALLOW_TANGENTLINEAR_RUN).
81055d8424 Jean*6021
361210b820 Jean*6022 checkpoint63p (2012/07/06)
94af53ae23 Jean*6023 o pkg/autodiff:
6024 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
6025 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
6026 which are now read from new parameter file "data.autodiff" (inAdExact
6027 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
6028 - add file "data.autodiff" in all verification/*/input_ad/ directories.
6101a96b98 Jean*6029 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
6030 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
aa94224112 Patr*6031 o verification/tutorial_tracer_adjsens/
6032 - add extra sub-verification which uses "SOM" advection scheme
6033 (2nd Order-Moment Advection Scheme, Prather Limiter) with
94af53ae23 Jean*6034 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
aa94224112 Patr*6035 and in data:
94af53ae23 Jean*6036 multiDimAdvection=.TRUE.,
6037 tempAdvScheme=81,
6038 saltAdvScheme=81,
d3350d435b Gael*6039 o model/src:
6040 - introduce ALLOW_BALANCE_RELAX which allow the removal
6041 of the global mean of relaxation terms by setting
6042 balanceThetaClimRelax and balanceSaltClimRelax
361210b820 Jean*6043 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
d3350d435b Gael*6044 This case is now treated appropriately in seaice_growth.F
6045 o pkg/seaice:
361210b820 Jean*6046 - do balanceEmPmR and balanceQnet based on the net fluxes
6047 (SItflux) that enter the ocean+ice system rather than QNET
6048 and EMPMR. Works best in real fresh water.
6049 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
6050 out of the diagnotics bloc, and stored in global arrays.
aa94224112 Patr*6051
e03d424aa5 Jean*6052 checkpoint63o (2012/06/29)
7ea3641d7d Jean*6053 o vertical mixing schemes:
6054 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
6055 - replace computation of density (in Function STATE1, opps_calc.F) by a call
6056 to S/R FIND_RHO_SCALAR
6057 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
6058 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
6059 affects output (vermix.ggl90) at truncation level.
de24565c3d Jean*6060 o testreport:
6061 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
6062 (nSx,nSy) for the number of threads (from eedata.mth)
11491399e8 Jean*6063 o model/src:
6064 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
6065 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
f7139038cb Patr*6066 o verification/tutorial_tracer_adjsens/
6067 - compile with ALLOW_CG2D_NSA
6068 - run with nonlinFreeSurf=3
6069 - update reference output_adm.txt
69c15f0fc5 Jean*6070 o tools/genmake2:
6071 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
6072 refine usePROFILES switching off (only when NetCDF is not available).
781a2dcf80 Jean*6073 o verification (atmospheric set-up):
6074 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
89f2ec68ea Gael*6075 o pkg/profiles : refine profiles and files handling.
6076 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
c8b7080413 Gael*6077 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
6078 - changes to use model/src/the_main_loop.F rather than the ecco version
6079 in ecco type adjoint runs.
18d45ae82f Jean*6080 o model/src:
781a2dcf80 Jean*6081 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
6082 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
6083 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
6084 o model/src:
6085 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
18d45ae82f Jean*6086 update output of test experiment bottom_ctrl_5x5.
d8428293bd Jean*6087 o pkg/generic_advdiff:
6088 - implement vertical bi-harmonic diffusion (for now, only for T & S and
6089 only explicitly).
1beab3301f Patr*6090 o verification/bottom_ctrl_5x5/
6091 update reference output (results changed quite some time ago,
6092 not sure when; but new reference results look ok in terms of grdchk)
2478d50aeb Patr*6093 o verification/1D_ocean_ice_column/
6094 For verification purposes, the exact adjoint rather than an approx.
6095 should be used (e.g., to comare against F.D. or TLM).
6096 removed autodiff_inadmode*_ad.F routines in code_ad/
6097 Update results/ accordingly.
2889362499 Jean*6098 o pkg/cal:
6099 - change cal_getdate.F so that output date is function of input time only
6100 (less ambiguous, not mixed up with input iteration number).
6101 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3078ffbadd Jean*6102 o pkg/diagnostics:
6103 - implement calendarDumps also for stats-diags
6104 - implement calendarDumps also for snap-shot output (negative freq)
6105 - for now, ignores calendarDumps if non-zero phase-lag.
6106
fb29d0ce0b Jean*6107 checkpoint63n (2012/06/04)
e2c4129169 Jean*6108 o model/src:
6109 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
6110 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
95205589aa Jean*6111 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
6112 similar to calc_r_star.F); update results of experiment internal_wave and
e2c4129169 Jean*6113 tutorial_global_oce_in_p (affected @ truncation level).
6114 o pkg/shelfice:
6115 - add parameterisation of advective-diffusive flux into the ice shelf
c1ef53a9f3 Mart*6116 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
6117 - simply eps3/3a computation
83625f7fb2 Jean*6118 o eesupp:
6119 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
6120 between tiles, just fill-in edges assuming locally periodic subdomain) and
6121 add corresponding exchange subroutines (EXCH0);
6122 - new CG-solver version (_EX0) for disconnected-tiles special case.
30e5f8e0a0 Jean*6123 o model/src (CG-solvers):
6124 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
6125 (similar final residual output and max-Iter number as with standard version);
6126 - allows to store and use lowest-residual solution (standard & _SR versions);
6127 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
6128 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
6129 o eesup/src:
6130 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
6131 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
0f5e9791d2 Patr*6132 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
6133
b4f2dc2460 Jean*6134 checkpoint63m (2012/04/27)
fa1b72b057 Jean*6135 o pkg/shelfice:
6136 - account for partical cells in surface level below ice-shelf for hydrostatic
6137 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
f74931b354 Jean*6138 o ad test experiments:
6139 - update and rename to "ad_optfile.local" local AD-optfile specific to a
6140 particular adjoint verification experiment (in verification/*/code_ad/)
fb5f9f12be Patr*6141 o pkg/seaice & pkg/exf:
f74931b354 Jean*6142 - Part two of ECCO-CLIVAR code merges.
fb5f9f12be Patr*6143 Completes merge of seaice area relax. code.
6144 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
6145 to be set in EXF_OPTIONS.h since this pkg controls its I/O
6146 (and avoids second CPP option in SEAICE_OPTIONS.h)
f74931b354 Jean*6147 - change default value of costIceStart & costIceEnd to a valid date.
f053446eb2 Dimi*6148 - add snowPrecip to HSNOW in seaice_growth
2db9a89c59 Jean*6149 o pkg/ptracers:
6150 - move ptracers summary and setup check into separated S/R ; add a check for
6151 valid PTRACERS_Iter0 value (error+stop or just warning).
9afd0876bd Jean*6152 o pkg/cal (+ pkg/ecco):
6153 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
6154 as input; and for AD, unless both are not differentiable (e.g., k index)).
546970fc27 Jean*6155 o model/src:
6156 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
6157 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
6158 temporary set to usingZCoords value (to be changed to F when using shelfice).
6159 - hydrostatic pressure: implement partial cell near the surface also for
6160 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
6161 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
6162 o pkg/ctrl/ctrl_init.F:
6163 - add a formal parameter to s/r ctrl_init_rec to print
d993cf017d Mart*6164 xx_$(ctrl_valiable)_file for easier debugging
6165 - move call of cal_* routines into the if-block where they are really
546970fc27 Jean*6166 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
d993cf017d Mart*6167 to specify a startdate
5b4194ac9e Jean*6168 o pkg/seaice:
6169 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
6170 global_ocean.cs32x15/code versions).
6171 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
6172 verification experiment global_ocean.cs32x15.seaice and update results.
0c1f58d8ac Jean*6173 o pkg/exf:
6174 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
6175 (according to useExfYearlyFields).
e876af632a Jean*6176 o pkg/cal:
6177 - move calendar setting & summary (previously in cal_readparams.F) into new
6178 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
6179 length of the simulation is set (after SET_PARMS call); This is an attempt
6180 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
6181 - For safety: keep a record of pkg/cal parameter settings status
6182 to allow to STOP if one pkg/cal S/R is called too early.
0c1f58d8ac Jean*6183 - add a stop in all basic pkg/cal subroutines if called before setting is done.
6184 - modify cal_getdate.F: stop when nothing was returned;
6185 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
6186 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
e876af632a Jean*6187
c0d26944d6 Jean*6188 checkpoint63l (2012/04/04)
39e65f8d9e Jean*6189 o pkg/bbl:
6190 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
6191 update global_with_exf output.yearly.txt file.
ceea6e3706 Jean*6192 o pkg/cal:
6193 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
6194 - remove 2 unsused and very short (1 line only) functions ;
6195 - remove unsused subroutines from AD-Diff list.
e8bf169f85 Jean*6196 o model/src:
6197 - start to implement clean wait to stop in initialization S/R (config_check.F,
c0d26944d6 Jean*6198 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
e8bf169f85 Jean*6199 o folowing PRINT_MESSAGE changes:
6200 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
28ed837189 Dimi*6201 o pkg/bbl:
6202 - modification so it can work with z*
6203 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
6204 - global_with_exf/input.yearly verification; changes output.yearly.txt
c064649ac0 Jean*6205 o eesupp/src:
6206 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
6207 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
6208 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
6209 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
6210 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
6211 - when using MPI, always set usingMPI=T ; set default accordingly and stop
6212 if not consistent.
6213 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
6214 argument is zero (in case called within single-thread section).
45e37a1efd Jean*6215 o pkg/fizhi:
6216 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
6217 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
12a35945df Jean*6218 o pkg/exch2:
6219 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
6220 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
6221 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
6222 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
6223 with bad ones coming from a not-yet-updated halo.
6224 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
bb86b07795 Dimi*6225 o pkg/frazil:
12a35945df Jean*6226 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
6227 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
16e5bb3e87 Mart*6228 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
709f986fa5 Patr*6229 o verification/lab_sea
6230 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
6231 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
6232 * nTimeSteps 3 -> 4
6233 * changed reference output accordingly
6234 o pkg/ctrl:
6235 * fix ctrl_get_gen for xx_sst, xx_sss
0a88b6db42 Jean*6236 o pkg/fizhi:
6237 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
6238 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
6a018349c4 Jean*6239 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
6240 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
6241 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
4afb828a3b Jean*6242 o pkg/gmredi:
6243 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
e39d8c1644 Jean*6244 o pkg/fizhi:
6245 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
6246 (old)aces open64 tuv test.
fe82383027 Dimi*6247 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
55118a358d Jean*6248 o pkg/mom_vecinv:
6249 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
6250 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
6251 with non-lin free-surf).
6252 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
6253 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
a826ffe6b9 Mart*6254 some compilers (gfortran 4.6.0 on MacOS)
71f40693ee Jean*6255 o momentum:
6256 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
6257 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
6258 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
6259
104669e183 Jean*6260 checkpoint63k (2012/03/17)
ecdd0492fa Jean*6261 o model/src:
6262 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
6263 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
6264 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
6265 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
20e7fd8d99 Jean*6266 o model/src: solve_*diagonal.F
6267 - replace division with multiplication by inverse (similar to original version)
de7acf9ff6 Jean*6268 update output of AD exp. global_ocean.90x40x15.
20e7fd8d99 Jean*6269 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
6270 to enable the use of the vectorized & differentiable solve_tridiagonal.F
de7acf9ff6 Jean*6271 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
6272 vertical advection (to get solve_tridiagonal tested in AD mode).
20e7fd8d99 Jean*6273 o pkg/seaice: ECCO-CLIVAR merge:
6274 1. seaice AREA relaxation
65e93cc4f0 Patr*6275 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
6276 * runtime flag: SEAICE_tauAreaObsRelax
20e7fd8d99 Jean*6277 2. modified global mean cost imbalance code: CPP option
6278 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
b0f7f403cf Patr*6279 o another iteration on solve_*diagonal.F
20e7fd8d99 Jean*6280 Make choices independent of AUTODIFF
6281 Default will be the adjoinable vectorized version.
6282 Alternative choices are:
6283 * non-adjoinable original version with low memory footprint:
6284 #define SOLVE_DIAGONAL_LOWMEMORY
6285 * still adjoinable but does not vectorize (k as inner-most loop):
6286 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
49c840e1d0 Jean*6287 o testreport
6288 - add option to use a home made wrapper around "make"
6289 - remove MITGCM_IEEE env. variable (no longer active)
fa18eab287 Mart*6290 o pkg/shelfice
6291 - improve computation of friction velocity for velocity dependent
6292 exchange coefficients: include velocities into SHELFICEBoundaryLayer
6293 block to average velocities vertically
6294 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
ac52667c1a Patr*6295 o Modify diagonal solvers, now three versions (upon request):
6296 #ifndef SOLVE_DIAGONAL_AUTODIFF
6297 1. default version (dating back a while ago)
6298 #else /* def SOLVE_DIAGONAL_AUTODIFF */
6299 # ifdef SOLVE_DIAGONAL_KINNER
6300 2. adjoinable version with k-innermost loop (G. Forget)
6301 # else
6302 3. adjoinable vectorized version of 2.
6303 # endif
6304 #endif /* SOLVE_DIAGONAL_AUTODIFF */
6305 All flags are currently set within routines, but could/should be moved to CPP-options.
6306 Array bounds for 1. are as before, for 2.,3. cover the entire domain
6307 (could be changed for 1. too).
cc29266a93 Jean*6308 o verification/lab_sea (fwd):
6309 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
6310 use 7 categories (except hb87), new solve4temp params (except salt_plume),
6311 constant salinity (=4) or variable salinity (salt_plume) done through
6312 SItracer.
05513da3da Jean*6313 o pkg/seaice:
6314 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
6315 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
6316 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
6317 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
6318 SEAICE_freeze got retired) but already better than previously with
6319 SEAICE_freeze=123456.7 deg.C;
6320 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
6321 (safer multi-threaded setting); always set SEAICEuseEVP;
6322 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
6323 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
6324 stop if multiple specifications for the same coeff; make sure default
6325 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
e6a9f2bf3c Jean*6326 o pkg/obcs:
6327 - allow to switch to upwind 1rst order advection scheme for the advective
6328 flux computation at the open-boundary; disabled for adjoint built.
e5a3138db8 Jean*6329 o pkg/ptracers:
6330 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
6331 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
6332 - add parameter to decide when to start a tracer; use internal flag to
6333 know which tracer to step-forward; switch this internal flag at the top
6334 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
6335 for adjoint built.
3e983913d2 Jean*6336 o pkg/seaice:
6337 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
6338 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
6339 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
ecde946d49 Jean*6340 o pkg/ecco:
6341 - fix writing of output file DiagnosCost_ClimSalt/Theta
6342 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3e983913d2 Jean*6343 o pkg/seaice:
e8787c77e2 Jean*6344 - add missing initialisation of COR_ICE array in dynsolver.F
6345 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
6346 compiled either way, and is tested in all exps (multidim was only tested
6347 in lab_sea ad before).
6348 - cosmetic change to prepare for future addition of ITD. no change to results.
6349 no defaults change.
4ed98c0a60 Gael*6350 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
e8787c77e2 Jean*6351 - by lack of adequate verification experiments, I further used custom versions
6352 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
6353 should be correct.
4ed98c0a60 Gael*6354 - avoid recomputations in ad.
7c31770a0d Jean*6355 o array initialisation in adjoint mode:
6356 1) pkg/mom_common/mom_calc_ke.F:
6357 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
6358 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
6359 part this initialisation is gone, resulting in Floating Point Exception
6360 (caught by open64 compiler with debug option).
6361 2) model/src/convective_weights.F
6362 set output convectCount over the full array range (instead of doing
6363 an update): this fix a similar issue when called within recomputation (adjoint)
6364 which could by-pass the initialisation (normally done in the caller S/R).
6365 o pkg/seaice:
c5b170d8ca Gael*6366 - final version of turbulent flux params, as agreed at MIT ice meet:
6367 SEAICE_mcPheePiston (default is ~ 0.000875)
6368 SEAICE_mcPheeTaper (default is 0.)
6369 SEAICE_frazilFrac (defualt is 1.)
6370 SEAICE_mcPheeStepFunc (default is false)
610e3cd50d Dimi*6371 - changes results at trunction error level
6372 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
7c31770a0d Jean*6373 o added pkg/frazil:
6374 - see frazil_description.tex for details
a7657da9ef Dimi*6375 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
bc661abca1 Mart*6376 o pkg/shelfice/shelfice_thermodynamics.F
7c31770a0d Jean*6377 - fix exponents for velocity dependent exchange coefficients: change
bc661abca1 Mart*6378 from 2/3(=0) to 0.66666666666666667
7c31770a0d Jean*6379 - move computation of velocity dependent exchange coefficients into
bc661abca1 Mart*6380 separate loop, so that it applies to both thermodynamics
6381 - move some divisions by constants out of loops
6382
3d1eabb9e3 Jean*6383 checkpoint63j (2012/02/16)
6384 o pkg/seaice:
6385 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
6386 - SItracer: added run time params, and allow coupling to ocn salinity.
df0f758af6 Jean*6387 o pkg/seaice: remove (almost) all divisions by constants within loops
6388 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
a54a2ad240 Mart*6389 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
df0f758af6 Jean*6390 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
6391 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
6392 o pkg/seaice :
3d1eabb9e3 Jean*6393 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
6394 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
84662a0e96 Gael*6395 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
df0f758af6 Jean*6396 - add permanent SItflux diag that corresponds to TFLUX but includes
3d1eabb9e3 Jean*6397 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
df0f758af6 Jean*6398 - allow activation/testing of a fix for suspected missing term in
3d1eabb9e3 Jean*6399 ocn-ice heat budget (to be confirmed). To test this, you want to
6400 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
6401 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
84662a0e96 Gael*6402 - no change in results, fwd or ad.
3d1eabb9e3 Jean*6403 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
df0f758af6 Jean*6404 - switch to variable freezing point.
dbf649edf9 Gael*6405 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
6406 - bug fix : the sublimation term that was missing is now activated.
6407 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
df0f758af6 Jean*6408 - bug fix : flooding sign term for SIsal0.NE.0.
dbf649edf9 Gael*6409 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
6410 o pkg/seaice:
6411 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3d1eabb9e3 Jean*6412 is now the default, and the old default constant freezing point is recovered
6413 with SEAICE_tempFrz0 = -1.96,
6414 SEAICE_dTempFrz_dS = 0.,
6415 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
dbf649edf9 Gael*6416 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
df0f758af6 Jean*6417 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
3d1eabb9e3 Jean*6418 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
df0f758af6 Jean*6419 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
3d1eabb9e3 Jean*6420 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
df0f758af6 Jean*6421 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
3d1eabb9e3 Jean*6422 seaice_growth r149 for legacy branch (no results change).
6423 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
6424 from I. Fenty).
6425 - results did not change except for global_ocean.cs32x15, mostly due to the
6426 switch to variable freezing point (see above item for detail).
74dd18420e Jean*6427 o pkg/thsice:
6428 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
6429 seawater freezing in thsice_calc_thickn (not used).
c2dec35684 Gael*6430 o pkg/seaice: turbulent flux term specification via run time params.
6431 - replace CPP switches with run time switches to facilitate testing
3d1eabb9e3 Jean*6432 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
6433 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
c2dec35684 Gael*6434 - added runtime parameter : SEAICEturbFluxFormula
6435 - move Mcphee constants to SEAICE_PARAMS.h
6436 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
3d1eabb9e3 Jean*6437 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
6438 remove seaice_summary call (moved to seaice_init_fixed)
74dd18420e Jean*6439 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
6440 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
3d1eabb9e3 Jean*6441 - seaice_summary.F : add missing report of read turbulent flux term set up
6442 and SITRACER.
6443 - seaice_check.F : check range; inform and stop if retired CPPs are used
6444 (incl. SEAICE_AGE).
74dd18420e Jean*6445 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
3d1eabb9e3 Jean*6446 CPP switch, same computation as before for the different options.
c2dec35684 Gael*6447 - change results at the truncation level.
1a36f96c43 Jean*6448 o pkg/seaice:
6449 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
6450 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
6451 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
6452 - update verification/*/input*/data.seaice:
6453 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
6454 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
6455 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
6456 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
5355c2bbd8 Jean*6457 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
6458 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
6459 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
6460 difference in results only due to machine truncation.
6461 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
6462 MaykutPolySatVap; keep MIN_LWDOWN.
6463 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
6464 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
6465 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
f1369fd6d4 Jean*6466 o pkg/salt_plume:
5355c2bbd8 Jean*6467 - isolate saltPlumeFlux array exch into a specific S/R called from
6468 do_oceanic_phys.F
6469 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
f1369fd6d4 Jean*6470 o verification:
5355c2bbd8 Jean*6471 - move untested set-up to MITgcm_contrib/verification_other.
4a20d767d7 Jean*6472 o pkg/seaice:
ba96883e1a Gael*6473 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
6474 o pkg/seaice:
4a20d767d7 Jean*6475 - seaice_solve4temp.F (keeping results unchanged):
6476 * add 2 future run-time params to select which saturation vapor pressure
6477 formula is used and how post-iteration fluxes are set.
6478 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
6479 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
6480 the linearized expression to stay consistent with tsurf finding.
6481 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
6482 can be < 0.
2953de52a5 Jean*6483 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
6484 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
6485 conductive heat flux F_c , and add it explicitly when updating tsurf as
6486 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
6487 so that now F_ia has a consistent meaning through the entire routine.
6488 This causes differences at truncation level: update output of fwd exp.
6489 global_ocean.cs32x15.seaice.
0c26ee70ab Jean*6490 o pkg/seaice:
c714f5b2dc Jean*6491 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
6492 of arrays, sign/direction of fluxes; no effect on results.
6493 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
6494 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
6495 note: this should have been done before changing celsius2K default.
6496 - to keep results unchanged, add back old value of celsius2K in verification
6497 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
6498 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
6499 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
6500 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
6501 freezing temp is consistent with value in seaice_growth.F ; this causes
6502 differences at machine truncation level: update lab_sea AD output (3/4).
6503 o pkg/seaice:
0c26ee70ab Jean*6504 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
6505 and climsst/sss even when using seaice (to prevent calculation that might
6506 use SST on land); does not affect any verification exp.
6507 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
6508 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
4091800f77 Mart*6509 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
6510 over land (non-legacy code)
0c26ee70ab Jean*6511 o vectorize salt_plume package:
d797683660 Mart*6512 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
6513 - this code computes plumebk everywhere (also over land), thus requires
6514 code to avoid divisions by zero and catch the case of kLev=Nr.
6515 - efficiency of salt_plume_frac is still sub-optimal
a355e8fb2b Jean*6516 o tools (genmake2):
6517 - fix makefile NAME specification (option: -makefile NAME) by adding
6518 "-f $MAKEFILE" in few places where it was missing including makedepend
6519 command (contribution from Paul).
6520
6b11434b7a Jean*6521 checkpoint63i (2012/01/24)
fcc1645548 Jean*6522 o model/src:
6b11434b7a Jean*6523 - add factorized versions of some EOS code to find_rho.F,
23bdfc896d Mart*6524 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
6b11434b7a Jean*6525 o model/src:
fcc1645548 Jean*6526 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
6527 - change default celsius2K from 273.16 to 273.15
6528 - to keep results unchanged, add back old value of celsius2K in verification
6b11434b7a Jean*6529 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
6530 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
b730078f53 Mart*6531 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
6532 to make TAF generate vectorizable code
6533 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
6534 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
6535 have flags that do this more efficiently.
70ade2cedc Mart*6536 o pkg/diagnostics/diagstats_calc.F
6537 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
bd19520b1a Jean*6538 o pkg/obcs (with exch2):
6539 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
6540 and remove code (in obcs_readparms.F) which was based on EXCH of indices
6541 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
5759772599 Jean*6542 o pkg/exf and seaice exp:
6543 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
6544 so that switching off area & heff advection flags does not affect results.
6545 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
19182668ca Jean*6546 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
6547 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
6548 results of verification experiments: 1D_ocean_ice_column(fwd),
6549 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
6550 and offline_exf_seaice (all 4).
fac86b0a61 Jean*6551 o pkg/seaice:
6552 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
6553 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
6554 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
6555 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
6556 not multi-dim advection;
6557 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
6558 SHORTWAVE_HEATING #undef.
89b3de8a81 Mart*6559 o optim: make Makefile more robust (?)
7e9d85ac6b Patr*6560 o pkg/obcs:
6561 * fix treatment of obcs_read_pickup for TAF
fac86b0a61 Jean*6562 o pkg/shelfice:
7e9d85ac6b Patr*6563 * add missing initialisation of num_shifwflx
6564 * new adjoint verification exp. for isomip
6565 * change Prandtl and Schmidt numbers from generic formulations
fac86b0a61 Jean*6566 (in terms of model diffus. and visc.) to separate runtime
7e9d85ac6b Patr*6567 parameters, with Holland and Jenkins (1999) default values.
85fbbba158 Jean*6568 o pkg/exf (interpolation):
6569 - extended input field (2 rows) near the N & S poles:
6570 * fill in with the symetric value (when even Nb of data in longitude)
6571 * add average value at the poles only for scalar quantities ; for vector
6572 component interpolation, skip the averaging and keep duplicated values,
6573 unless the 2 components have same location (uvInterp=T) in which case
6574 interpolate the 2 components together using S/R EXF_INTERP_UV.
6575 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
6576 together: this allows to account properly for local orientation when
6577 averaging at N & S pole.
6578 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
6579 exf-interpolation near N & S poles. Undef by default.
6580 - add debug check/print on 1rst iter if debugLevel >=2.
45bd772f0f Jean*6581 o pkg/exf:
6582 - change masking flags definition (no longer "parameter"), put them in
6583 common block and set them in S/R EXF_INIT_FIXED.
6584 - change recognized masking flag from s,u,v to c,w,s since the mask
6585 to use (maskC,W,S) depends on position on model grid and has little to
6586 do with scalar/vector difference; fix masking if using P-coordinates.
6587 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
6588 and update results of exp. global_with_exf (x2).
6589 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
dd08a0bdad Mart*6590 o pkg/obcs
6591 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
473f3cfaa4 Jean*6592 o pkg/exf (interpolation):
6593 - assume periodicity in X only if input field cover full longitude range.
6594 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
6595 and should vectorise).
6596 - fix input lat of the 2 added row (in case we provide N.pole data).
6597
afd13745c6 Jean*6598 checkpoint63h (2011/12/30)
d0a750d46b Jean*6599 o pkg/seaice:
6600 - change declaration of UVM from _RL to _RS in order to get B-grid
6601 uIce,vIce monitor when _RS = real*4
35af42145b Jean*6602 o pkg/offline:
6603 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
6604 - compute vertical velocity if not read from file (switch on exactConserv
6605 & staggerTimeStep);
6606 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
02149d96ab Jean*6607 o verification:
6608 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
6609 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
6610 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
6611 - update output of exp. global_ocean.cs32x15.viscA4 after changing
6612 grid-file angles (used here for coriolis-3d);
6613 - remove (or gzip) few files not needed to run fizhi-cs experiments.
473f3cfaa4 Jean*6614 o pkg/exf (vector interpolation):
4ee3919357 Jean*6615 - rotate vector component toward local grid-axis orientation using grid-angles
6616 (stored in GRID.h) instead of locally computed rotation angle; keep old code
6617 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
6618 o pkg/seaice:
6619 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
6620 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
5803321947 Jean*6621 o pkg/PKG_OPTIONS.h files:
6622 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
6623 outside of the #ifdef ALLOW_THISPKG / #endif block.
6624 - update verification/*/code/PKG_OPTIONS.h files.
dd0bbd259d Mart*6625 o add a verification experiment (offline_exf_seaice/input.seaice) that test
6626 the B-grid LSOR solver
5d7b3caf45 Mart*6627 o pkg/seaice: sort out emissivity and long wave radiation step 2:
5803321947 Jean*6628 - add emissivity for snow and ice as new run-time parameters
6629 (unfortunately) that default to the corresponding exf values; this
5d7b3caf45 Mart*6630 changes results in most verification experiments so that for backward
6631 compatibility these parameter have to be set explicitly to inconsistent
5803321947 Jean*6632 values (ugly);
5d7b3caf45 Mart*6633 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
6634 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
6635 until we agree how to handle this bug properly
a2895221f1 Jean*6636 o pkg/exf (interpolation):
6637 - add a set of run-time param ({inputfield}_interpMethod), one for
6638 each interpolated input field, to select the interpolation method
6639 with a value of zero switching off the interpolation;
6640 - print interpolation parameters to standard output;
6641 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
6642 (to use instead runoff_interpMethod=0 in data.exf).
f156ca0fb7 Jean*6643 - simplify default setting of interpolation parameters (for all fields,
6644 set position to match model grid cell-center position, leading to trivial
6645 interpolation in case of regular Lat-Lon grid) and fix for the case of
6646 non-uniform delY.
a2895221f1 Jean*6647 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1ca970e947 Mart*6648 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
a2895221f1 Jean*6649 this factor is absolutely required, because the lw exitance (= out-going
6650 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1ca970e947 Mart*6651 where the reflectivity rho = 1-emissivity for conservation reasons. Once
6652 this is established, we can remove the CPP-Flag (if we want to).
a2895221f1 Jean*6653 o pkg/seaice:
31c8334354 Mart*6654 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
6655 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
3fa95d7893 Mart*6656 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
6657 what the name implies (and not emissivity*BoltzmannConstant), this means
a2895221f1 Jean*6658 the old default value of 5.5e-8 now means
6659 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
3fa95d7893 Mart*6660 S/R exf_readparms
6661 - FV-discretization of the B-grid LSOR solver, turn on with
1ca970e947 Mart*6662 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
6663 of the calling routine dynsolver, so that B and C-grid code look a
6664 little more alike.
31c8334354 Mart*6665 - fix index bugs in ostres.F (B-grid code)
03e90c79ad Mart*6666 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
b7727eb6f8 Mart*6667 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
6668 default for SEAICE_emissivity, if useEXF; requires setting a wrong
6669 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
6670 backward compatiblity
6671 o model/src: use sigmaR in calc_ivdc
6672
b1b3dce3a2 Jean*6673 checkpoint63g (2011/12/16)
abaf70634e Gael*6674 o pkg/seaice/seaice_growth.F:
6675 fix heat conservation of the coupled ocean-seaice system.
6676 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
6677 solid vs liquid water treatment is resolved via QNET.
6678 o pkg/seaice/seaice_growth.F:
6679 add missing term for sublimation in saltFlux, which was breaking conservation.
6680 o pkg/seaice/seaice_model.F:
6681 Remove this patholigical case treatment in evolution branch,
6682 where it is un-necessary and breaks conservation.
a2895221f1 Jean*6683 Update global_ocean.cs32x15/results accordingly for
6684 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
bf53796fe2 Jean*6685 o model/src:
6686 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
6687 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
6688 o pkg/obcs:
6689 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
6690 tendency for temperature and salinity that is then applied to update
6691 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
6692 horizontal advection and diffusion contributions on the boundary (in
6693 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
6694 removing the mask in S/R timestep_tracer. The advantage of this approach is
6695 that the updated tracer values include contributions from the surface
6696 forcing and vertical diffusion.
c0f0db71ad Mart*6697 This modification changes exp4.stevens because of vertical diffusion.
c947c6ddc4 Jean*6698 o model/src:
c79ab16fdf Jean*6699 change non-curvilinear grid setting to also work with exch2 + blank tiles:
6700 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
6701 face dimensions.
6702 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
6703 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
6704 and INI_SPHERICAL_POLAR_GRID.
6705 change test-experiment global_ocean.90x40x15:
6706 - split the domain in many more tiles (9x4 tiles of 10x10 each);
6707 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
6708 - update results of both test (std & dwnslp).
bf53796fe2 Jean*6709 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
c0f0db71ad Mart*6710 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
c79ab16fdf Jean*6711 o model/src:
f9a1d5f8b7 Jean*6712 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
6713 and fix initialisation when using sigma-coords.
6714 o model/src:
6715 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
6716 to their current value at the beginning of forward_step.F": add a new run-time
c947c6ddc4 Jean*6717 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
6718 - set doResetHFactors=T in the following test exp:
6719 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
6720 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
6721 and tutorial_global_oce_in_p (nonLinFS in p)
64ea3e84ce Matt*6722 o pkg/ecco
6723 - added IES cost term
be6cb3adad Jean*6724 o verification/advect_xz
6725 - scale down the depth by 1/100 (from 200 km to just 2.km)
6726 - add secondary test using divergent flow, r-star and implicit vertical advection.
1bf7a90a0b Jean*6727 - add note (check_conserve_TS.txt) and matlab script to check global
6728 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
be6cb3adad Jean*6729 o pkg/rbcs:
6730 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
212c574d0b Mart*6731 o pkg/obcs (Stevens BCs):
be6cb3adad Jean*6732 - fix various problems in the phase speed computations of the Stevens
212c574d0b Mart*6733 boundary conditions:
6734 - sign error for western and southern boundaries,
be6cb3adad Jean*6735 - time tendencies were underestimated by factor of dTracerLev and some just
212c574d0b Mart*6736 zero (for multidim advection schemes) -> now estimate time tendencies
6737 from difference between previous (n) time level and the one before (n-1);
be6cb3adad Jean*6738 this requires storing a field per tracer per boundary, also in the pickup
212c574d0b Mart*6739 files.
6740 - replace deltaTmom in cflMer/Zon computation with dTracerLev
6741 - set default phase velocity to cflMer/Zon
6742 - update verification experiment exp4.stevens
2232bea0cd Jean*6743 o pkg/generic_advdiff (implicit_r):
6744 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
6745 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
6746 - fix implicit vertical diffusion or advection with NonLin FreeSurf
6747 (was using current recip_hFacC instead of future recip_hFacC): set future
6748 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
6749 solver S/R ;
6750 - fill diagnostics of vertical advective fluxes (computed from tendency)
6751 when using implicit vert. advection;
6752 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
6753 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
6754 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
6755 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
6756 o pkg/diagnostics:
6757 - add diags for T & S tendency which goes through Adams-Bashforth.
6758
3cb41ba0ef Jean*6759 checkpoint63f (2011/11/30)
764028acbf Mart*6760 o pkg/obcs/obcs_calc_stevens.F:
5bef8326ad Mart*6761 - join some loops to reduce number of if-statements
764028acbf Mart*6762 - fix a bug in code for northern and southern boundaries.
564b34aefd Mart*6763 o pkg/seaice/seaice_init_varia.F
3cb41ba0ef Jean*6764 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
564b34aefd Mart*6765 caused zero ice-velocities for the B-grid code
2876330f22 Mart*6766 o pkg/seaice/seaice_init_fixed.F
3cb41ba0ef Jean*6767 - fix a bug in the initialisation of the second metric terms
2876330f22 Mart*6768 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
6769 - this affects all seaice configurations with useCurviLinearGrid = .true.
6770 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
6771 = .true. (default)
6772 - the only verification experiment affected is global_ocean.cs32x15:
6773 icedyn, seaice, and seaice_dynmix (AD)
6774 o pkg/thsice/thsice_diagnostics_state.F
6775 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
6776 not contain garbage that can lead to surprises in diagstats_calc.F
431cbbbe2d Jean*6777 o model/src:
6778 - move bi,bj loops inside INTEGR_CONTINUITY ;
6779 - call INTEGR_CONTINUITY directly from forward_step.F
6780 (previously called from momentum_correction_step.F)
6781 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
6782 forward_step.F and pkg/ecco/the_main_loop.F
fbc9c53f7c Jean*6783 o model/src/do_oceanic_phys.F:
6784 - reset addMass to zero only if useICEFRONT ;
6785 - separated k-loop for rhoInSitu calculation ;
6786 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
6787 and at constant T,S (= WdRHOdP);
6788 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
6789 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
6790 transport of locally-referenced potential density);
6791 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
f2d1e2a4fc Mart*6792 o gluemnc:
6793 - replace ncrcat with ncks when adding variables to *.glob.nc
6794 - change the way variables without record dimensions are handled so that
6795 files that have variables with and without record variables can be glued:
6796 add a record dimension with a new unique name to be able to differentiate
6797 between variable with and without a-prior record dimensions. Remove
6798 this record dimension before adding the variable to the *.glob.nc file.
6799 This procedure automatically works also for grid.*.nc files that do not
6800 have any record dimension.
7f71bb5257 Jean*6801 o verification/cpl_aim+ocn:
6802 - generate new reference output on baudelaire (gfortran, mpich2) (previously
6803 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
6804 o pkg/obcs/obcs_calc_stevens.F:
b81f64aee3 Mart*6805 - add code for northern and southern boundaries.
6806 - reorder some loops to save some operations and so that drFBar can be scalar
12d8e73fbb Jean*6807 o model/src:
6808 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
6809 truncation) and add diagnostics for Adams-Bashforth tendency increment.
6810 - update test-exp. AD output:
6811 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
6812 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
6813 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
6814 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
6815 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
6816 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
6817 tutorial_plume_on_slope.
b06a6ce7ab Mart*6818 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
6819 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
6820 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
6821 does not even come with an F77 compiler anymore, this should not be
6822 a limitation
6823
34f1dd7af6 Jean*6824 checkpoint63e (2011/11/06)
16b186ab26 Patr*6825 o pkg/seaice adjoint of LSR:
6826 - substantially rework STORE dirs.
6827 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
6828 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
6829 and only perform SOLV_MAX_FIXED adjoint iters.
37e94e8cfb Patr*6830 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
6831 always goes to same record, meaning that the last forward field will be
6832 the one used in the adjoint - an approximation.
16b186ab26 Patr*6833 - now produces non-zero LSR-related gradients, and acceptable gradients for
6834 An's zonal (x-z) test case (to be checked in)
6835 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
6836 (but these are screwed up by the thermodynamics in the first place);
6837 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
6838 output_adm.txt also reflects changes to seaice_lsr
34f1dd7af6 Jean*6839 - global_ocean.cs32x15:
16b186ab26 Patr*6840 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
6841 (output_adm.seaice.txt was updated)
6842 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
6843 (output_adm.seaice_dynmix.txt)
ca66b179c0 Jean*6844 o test-exp. exp4+stevens:
6845 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
de0cda9935 Jean*6846 o pkg/seaice (lsr solver):
6847 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
6848 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
6849 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
6850 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
6851 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
6852 - compute (with new S/R) and print initial (+ free-driff sol. if available)
6853 and final residual of linearised system.
8a3a83c787 Mart*6854 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
6855 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
383735f3ce Mart*6856 o pkg/obcs: Stevens BCs (still only for east and west)
6857 - fix Stevens BCs by using intermediate velocities of previous
6858 time step as "baroclinic" contribution rather velocity of one grid cell
6859 inside the boundaries; more consistent but makes the entire treatment
de0cda9935 Jean*6860 more complicated, requires new pickup files and two new S/Rs:
383735f3ce Mart*6861 obcs_copy_uv_n and obcs_save_uv_n
de0cda9935 Jean*6862 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
383735f3ce Mart*6863 (undefined by default)
de0cda9935 Jean*6864 - silently move computation of some grid factors into separate loops to
383735f3ce Mart*6865 save some recomputations
6866 - add a hack for non-linear free surface
6867 - add a verification experiment to exp4 that tests this code
14398673cd Mart*6868 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
6869
77e57aaf77 Jean*6870 checkpoint63d (2011/10/25)
ffb3679b95 Jean*6871 o pkg/obcs + seaice-dynamics:
6872 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
6873 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
6874 values (consistent with an implicit method).
6875 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
6876 return to older implementation (same results as before); note that none of
6877 the "experimental" OBCS_SEAICE options are implemented in the new version.
2d58d55cc0 Jean*6878 - switch test exp. seaice_obcs to use new version (update output).
6b9597f12c Jean*6879 o pkg/seaice:
ffb3679b95 Jean*6880 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
6881 - add parenthesis in Water-Ice drag calculations (evp & lsr);
6882 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
6b9597f12c Jean*6883 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
6884 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
6885 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
026da5ed8a Davi*6886 o pkg/layers:
6887 - Include potential density as new coordinate (Thanks to David Munday)
6888 o pkg/dic:
6889 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
6890 carbonate computation/output to CALC_PCO2_APPROX
d1527a124d Mart*6891 o pkg/generic_advdiff
77e57aaf77 Jean*6892 - make TAF generate code that vectorizes:
d1527a124d Mart*6893 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
77e57aaf77 Jean*6894 o model/src:
6895 - improve vectorization also for adjoint code of
713532b2ce Mart*6896 solve_tridiagonal and solve_pentadiagonal. As this requires up to
6897 5 new 3D-fields, this code is only turned on for the combination of
d1527a124d Mart*6898 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
6899 for singular matrix check (only for TARGET_NEC_SX).
713532b2ce Mart*6900 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
ffb3679b95 Jean*6901 ALLOW_AUTODIFF. This flag now needs to be set outside of
713532b2ce Mart*6902 solve_tri/pentadiagonal.F
6857319532 Jean*6903 o pkg/exf:
6904 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
6905 optional namelist EXF_NML_OBCS).
6906 - add many debug-print (to trace down where pkg/cal error msg comes from)
71df2e2fe0 Mart*6907 o pkg/mom_vecinv/mom_vi_hdissip.F
6908 - rearrange loops so that vectorization is improved and in particular
6857319532 Jean*6909 the adjoint routine vectorizes. The code is a little longer now, but I
6910 think easier to read.
71df2e2fe0 Mart*6911 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
69771f84cc Jean*6912 o pkg/seaice:
6913 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
69238317a2 Jean*6914 o pkg/exch2:
6915 - alternative code (without tile x tile matrix) for cumulated (global) sum;
6916 used as default; keep using matrix version in adjustment.cs-32x32x1.
5f3dfa25b7 Jean*6917 o tools/build_options:
6918 - after merging some MPI and/or multi-threads specific optfiles so that
6919 the modified default optfile support both built (using genmake2 -mpi
6920 for the MPI built, using genmake2 -omp for OpenMP built),
6921 move now obsolete optfiles to tools/build_options/unsupported/
6922 (add copy of email sent to support list in doc/optfiles_changes.txt)
6923
348beac9cc Jean*6924 checkpoint63c (2011/09/28)
b0522d7987 Jean*6925 o pkg/ebm:
348beac9cc Jean*6926 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
b0522d7987 Jean*6927 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
f2b8a2f2ef Patr*6928 o pkg/seaice (SItracer pickup)
6929 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
6930 To be done:
6931 - thorough testing of missing fields in S/R seaice_read_pickup
6932 - thorough matching between generic tracers and specific fields used
6933 (e.g. volume-weighted age, area-weighted age, salinity, ...)
2475d1c482 Jean*6934 o pkg/grdchk:
6935 - all procs calculate and print finite-difference gradient (for testreport)
6936 - change description output used by testreport;
6937 - AD testing: also compare and report Finite-difference gradient;
6938 => update all output_adm*.txt
6939 o test exp. global_ocean_ebm:
6940 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
6941 and turn on exactConserve; update (fwd) output.
22a5e4b7f8 Jean*6942 o pkg/seaice (LSR):
6943 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
6944 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
6945 * identical results with non-CS topology (but save up to half of EXCH calls)
6946 * no much changes in cs-32 verification tests since no ice at face edges
6947 (differences due to convergence criteria, since nb of iterations changed)
6948 * expect some differences on lat-lon-cap grid.
6949 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
21773ac32d Jean*6950 o pkg/exch2:
6951 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
6952 many tiles); until alternative coding is added, just add a stop.
7c74433c3f Jean*6953 o pkg/kpp:
6954 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
6955 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
6956 o optfiles:
6957 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
6958 into corresponding standard one, which now support different build:
6959 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
6960 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
a9fbe2edc0 Jean*6961 o pkg/obcs (seaice):
6962 - add missing EXCH for uIce,vIce after applying OBCS;
6963 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
6964 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
6965 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
6966 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
6967 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
6968 and eedata.mth for MPI and mutlti-threaded testing.
ecd451586c Jean*6969 o pkg/flt:
6970 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
6971 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
6972 - fix pickup and trajectories + profiles output with multi-threads;
6973 - add parameter to select group of fields to write along trajectory and
6974 profile (default unchanged);
6975 - only call PORT_RAND* function when flt_noise <> 0;
6976 - add multi-threaded test for verification exp. flt_example.
6977 o eesupp/src:
6978 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
6979 - USE_OMP_THREADING: check that number of threads (from eedata) matches
6980 actual number (from env.var. setting).
2e701c809e Jean*6981 o pkg/ebm:
6982 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
6983 - add multi-threaded test for verification exp. global_ocean_ebm
6984
a51afa12b8 Jean*6985 checkpoint63b (2011/08/29)
1554b54595 Jean*6986 o pkg/ebm:
6987 - fix sign of runoff;
6988 - update directly forcing fields (Qnet,EmPmR) to use standard
6989 external_forcing_surf.F (remove ebm_forcing_surf.F);
6990 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
6991 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
6992 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
6993 - update global_ocean_ebm parameters file data and update output (fwd+ad).
753be3d4e2 Jean*6994 o verification/matrix_example:
fcfc72a991 Jean*6995 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
6996 MPI and mutlti-threaded testing.
6997 o pkg/matrix:
6998 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
6999 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
7000 - fix for multi-threaded (remove DATA statement);
7001 - use standard DIFFERENT_MULTIPLE function;
7002 - add MATRIX_OPTIONS.h
7003 o verification/matrix_example:
753be3d4e2 Jean*7004 To allow to split the domain in several tiles, change the domain size
7005 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
7006 Western side) of land points.
7007 o (*_)write_pickup:
7008 - fix few bugs in mypackage_read/write_pickup.F
7009 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
7010 array of length 1 (was caught by compiler syntax-check).
6768a51e8b Jean*7011 o pkg/diagnostics (velocity potential solver):
7012 - fix initialisation of main diagonal matrix (for overlap values)
02665fe70b Jean*7013 o tools/build_options:
7014 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
7015 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
7016 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
7017 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
7018 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
7019 and use "-devel" testreport option for standard testing on baudelaire.
b6649ac208 Jean*7020 o pkg/grdchk:
7021 - Assume that all gradient-check position are within the same tile
7022 corresponding to global indices (iGloTile,jGloTile) and that
7023 positions (i,j indices or nbeg) are local to this tile;
7024 - set tile local-indices and proc. number according to tile global-indices;
7025 - remove grdchkwhichproc from namelist (retired param);
7026 - send adjoint gradient to all procs so that all procs print it to STDOUT;
7027 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
15338fa568 Dimi*7028 o adding package bbl (Bottom Boundary Layer)
7029 description in MITgcm/pkg/bbl/bbl_description.tex
7030 example/test experiment in MITgcm_contrib/bbl
50d533af19 Patr*7031 o adjoint verifications
1c8f7d3c14 Jean*7032 - changed 5 experiments to multi-tiles
50d533af19 Patr*7033 * global_ocean.90x40x15
7034 * obcs_ctrl
7035 * offline_exf_seaice
7036 * tutorial_dic_adjoffline
7037 * tutorial_tracer_adjsens
7038 changed reference output for those that crossed tile boundaries
7039 (changed choices of gradient check positions)
1c8f7d3c14 Jean*7040 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
50d533af19 Patr*7041 - temporary bug fix in grdchk_loc.F for obcs
d5826a2b12 Jean*7042 o genmake2 & testreport
7043 - add target "obj" (just for OBJFILES files) to Makefile;
7044 - add option to specify FEXTRAFLAGS on command line.
ea9625adec Jean*7045 o pkg/mypackage:
7046 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
7047
975e02919b Jean*7048 checkpoint63a (2011/08/02)
ff219d41cf Jean*7049 o pkg/diagnostics (velocity potential):
7050 - fix velocity-potential calculation when using OBCS: balance net inflow
7051 at each level (new S/R OBCS_DIAG_BALANCE).
7052 - fix some of the problems with OBCS in stream-function calculation.
773313b0d2 Mart*7053 o pkg/exf/exf_readparms.F
ff219d41cf Jean*7054 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
773313b0d2 Mart*7055 EXF_NML_OBCS) more consistent, so that you need not have these lists
7056 in data.exf when they are not used.
45b245ccf5 Mart*7057 o optim/optim_readdata.F:
7058 - add some output about obcs variables that might help debugging
daab778156 Mart*7059 - add a check about nvarlength
d602d84af0 Mart*7060 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
4750cf8833 Jean*7061 o pkg/diagnostics (velocity potential):
7062 - fix mask for OBCS (still problems in stream-function with OBCS);
7063 - add specific parameter (default = main code CG2D params) for solver;
7064 - in case of poor convergence, use solution corresponding to lowest residual.
a045c08a46 Mart*7065 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
7066 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
7067 and should be avoided where possible.
40639c975a Jean*7068 o model/src (rStar):
7069 - include r* effect on reference-state (PhiRef) in totPhiHyd
7070 (so that it's really the potential anomaly at the cell center);
7071 affect solution only if z* with full pressure in EOS.
7072 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
7073 update output (because of z* in totPhiHyd and viscA4 changes);
7074 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
7075 @ constant r) until interpolation at constant r is implemented.
7076 o pkg/diagnostics
7077 - fix RCENTER diagnostics in case cell center is not at interface middle
6a4d8594a7 Mart*7078 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
7079 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
7080 that THETA and SALT are "conservative temperature" and "absolute
7081 salinity"
7082 o pkg/ctrl
7083 - fix computation of endrec in s/r ctrl_init_rec
7084 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
aa222beea6 Mart*7085 o pkg/seaice/seaice_growth.F
7086 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
7087 remove then obsolete STORE directives
7088 - fix STORE directives for tice and tices, so that only the
7089 appropriate part of the fields are stored (and not the entire
40639c975a Jean*7090 field); update global_ocean.cs32x15.seaice AD output.
aa222beea6 Mart*7091 - cosmetic changes: adjust CPP flags and indentation for better
7092 legibilty
7093 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
7094 Chris Wilson)
5c5b0c67fc Jean*7095 o pkg/gmredi:
7096 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
7097 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
7098
975e02919b Jean*7099 checkpoint63 (2011/07/11)
0efa36856a Jean*7100 o pkg/exch2:
7101 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
7102 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
7103 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
7104 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
9ec7daa021 Jean*7105 o pkg/diagnostics:
7106 - deal with pairs of post-processed diags which are computed together; in
7107 particular, re-order list of diags within 1 file to save 2nd computation.
7108 - add S/R to compute velocity stream-function (called after velocity-potential
7109 calculation) from divergence free transport -> new diagnostics "PsiVEL".
32f824cd14 Jean*7110 - add parameter to select grid-point location where PsiVEL == 0.
9ec7daa021 Jean*7111 o eesupp/src:
7112 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
7113 (specific S/R needed with exch2 topology - for now, just print an error msg)
f3cfd88687 Patr*7114 o pkg/shelfice
7115 - Implement friction velocity-dependent transfer coefficients following
7116 Holland and Jenkins, JPO, 1999
7117 Original code by M. Losch with small modifs.
7118 Enable with CPP option SHI_ALLOW_GAMMAFRICT
7119 and runtime flag SHELFICEuseGammaFrict
a8b943f1d9 Jean*7120 o verification lab_sea & global_ocean.cs32x15:
7121 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
7122 does not miss some dependencies (but is slower) and also works with many files
7123 (default makedepend limitation for AD built).
7124 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
c5e360349a Jean*7125 o pkg/diagnostics:
7126 - add run-time parameter "useMissingValue" (def=False) to fill land-point
7127 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
7128 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
7129 - Extend the use of "missing_value" setting from data.diagnostics for the case
7130 of counter-diagnostics (where fraction-weight is zero). This applies both to
7131 MNC and MDS output files.
f3bb97e385 Gael*7132 o pkg/seaice/seaice_growth.F:
b7df5ca569 Ian *7133 - add 'a priori' cap of latent heat flux based on actual mass considerations
7134 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
7135 non-legacy seaice_solve4temp.
7136 - add diagnostic of the residual sublimation freshwater flux (the freshwater
9ec7daa021 Jean*7137 flux taken from the ocean if the total actual latent heat fluxes exceed
b7df5ca569 Ian *7138 the maximum)
f3bb97e385 Gael*7139 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
7140 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
7141 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
7142 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
7143 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
7144 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
12f262973b Ian *7145 o verification 1D_ocean_ice_column:
7146 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
7147 update results
43043edca4 Jean*7148 o pkg/diagnostics:
7149 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
7150 which are not filled-up but computed from other diags ; In this case, the mate
7151 diag points to the primary (filled-up) diag to used for post processing.
7152 - Update Velocity-potential computation using post-processed diag framework.
234bdec1fe Jean*7153 ==> Change the ordering of fields and time-periods in MDS output file
9b34d3ce48 Jean*7154 when using periodic averaging: now writes one time record with the full set
7155 of fields for this time period, then the next time reccord (it used to be
7156 one field with the full set of time records then the next field).
234bdec1fe Jean*7157 Note: this is now similar to NetCDF (MNC) output file. <==
43043edca4 Jean*7158
19985267f5 Jean*7159 checkpoint62z (2011/06/21)
fb247706a7 Patr*7160 o adjoint monitor:
7161 - Add adjoint monitor output for packages exf, seaice
a18fc746e5 Patr*7162 and update relevant testreport output
6de796d755 Gael*7163 o pkg/seaice:
7164 - re-order diags inits so that they appear in order in available_diagnostics.log
7165 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
7166 area/heff/hsnow preceeding thermodynamic growth/melt.
7167 - modified diag: SIdA; output actual effect, as the description states.
7168 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
7169 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
3897a97e38 Jean*7170 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
6de796d755 Gael*7171 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
7172 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
3897a97e38 Jean*7173 - added diagnostics for seaice generic tracers (SItr*).
6de796d755 Gael*7174 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
7175 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
d7d0e261c7 Patr*7176 I. Fenty: 18-Jun-2011:
7177 Minor changes to seaice package:
7178 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
7179 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
3897a97e38 Jean*7180 - Differentiated "regularization variables" from "floor variables"
d7d0e261c7 Patr*7181 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
7182 * hiceMin became SEAICE_hice_reg (old hiceMin)
7183 (with _reg meaning regularization variable)
7184 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
7185 so as to ensure energy conservation when going between phases
3897a97e38 Jean*7186 - A22 was not used anywhere
d7d0e261c7 Patr*7187 2) Changed regularization procedure for heffActual and hsnowActual to ensure
7188 well-boundedness and smooth adjoint in seaice_growth.F
7189 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
7190 because the old regularization always set heffActual >= 0.05 cm
7191 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
3897a97e38 Jean*7192 on AREA when HEFF > 0.
7193 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
7194 requiring that DISABLE_AREA_FLOOR *not* be defined
d7d0e261c7 Patr*7195 Affected verifications:
7196 - 1D_ocean_ice_column (output.txt output_adm.txt)
7197 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
4c5a4fb4d7 Jean*7198 o pkg/diagnostics:
7199 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
7200 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
7201 (was _RL, now integer) with option = 0 to retrieve all levels.
2d3c84b138 Jean*7202 - add pieces of code to compute velocity potential at each level (new diagnostics
7203 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
7204 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
3897a97e38 Jean*7205 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
7206 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
7207 and in diagnostics_fract_fill.F (do not need a valid pointer for the
7208 diagnostics counter-mate); check that definition of counter-diagnostic
7209 includes a valid counter-mate (in diagnostics_set_levels.F).
d2ffb46800 Jean*7210 o model/src (rStar):
7211 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
7212 affect solution only if z* with full pressure in EOS;
7213 update output of test-exp global_ocean.90x40x15.
7214 o pkg/seaice:
3b6fc6245d Gael*7215 - introduce siEps=1e-5 parameter
7216 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
7217 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
d2ffb46800 Jean*7218 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
3b6fc6245d Gael*7219 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
7220 as well as ice cover age and ridging index (attached to AREA).
d2ffb46800 Jean*7221 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
7222 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
3b6fc6245d Gael*7223 Up to SItrMaxNum=3 tracers can be used simultaneously.
7224 o pkg/salt_plume:
d2ffb46800 Jean*7225 -introduce SPsalFRAC run time parameter that sets the fraction of the
7226 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
7227 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
43306f4baa Jean*7228 o model debug options:
7229 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
7230 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
7231 - Refine debug-msg printing selection (3 new levels):
7232 debugMode : controls printing of debug messages (sequence of S/R calls).
7233 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
7234 debLevZero = 0 ; /* level of disabled aux. msg printing */
7235 debLevA = 1 ; /* level of minimum aux. msg printing */
7236 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
7237 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
7238 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
7239 debLevE = 5 ; /* level of extensive debug printing */
7240 New debugLevel default: with default debugMode value (=F),
7241 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
7242 and if debugMode=T, default debugLevel = 4 (debLevD).
7243 Relation with previous settings:
7244 debLevB (=2) corresponds to former debLevA (=1)
7245 debLevD (=4) corresponds to former debLevB (=2)
7246 Note:
7247 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
7248 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
7249 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
7250 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
7251 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
8a9e9a473a Jean*7252 o pkg/obcs:
7253 - change OBCSfixTopo default from True to False (should not change the results);
7254 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
cc3bbdb6bb Jean*7255 o pkg/thsice:
7256 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
7257 2nd layer seaice sublimation (unlikely to happen)
7258 - use Interior mask for OBCS in thsice_advection.F (similar to what is
7259 done in gad_advection & seaice_advection).
bd46b07a96 Patr*7260 o adjoint:
7261 bug fix spotted by Gael Forget:
7262 seaice_advection and thsice_advection still had
7263 legacy CPP options to avoid CS corner updates for adjoint
0c22b81a88 Jean*7264 o pkg/seaice:
7265 => Change some of the defaults (2011/05/29):
7266 - change SEAICEuseFluxForm default (from False to True)
7267 - change DIFF1 default (from 0.004 m/s to 0. m/s)
7268 And print warnings if DIFF1 is not set in data.seaice and centered
7269 avection scheme is used without any diffusion.
7270 also:
7271 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
7272 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
7273 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
7274 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
7275 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
7276 update results of test exp.:
7277 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
7278 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
7279 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
7280 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
7281 seaice_obcs: output (SEAICEuseFluxForm=T)
7282 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
7283 for standard fwd & AD lab_sea tests (to keep the same output).
fc3b49c003 Gael*7284 o pkg/seaice/seaice_growth.F:
0c22b81a88 Jean*7285 - use Ian Fenty's capping formulas for actual ice
fc3b49c003 Gael*7286 thickness thoughout EVOLUTION branch.
7287 - put treatment pathological case #2) in CPP brackets
7288 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
0c22b81a88 Jean*7289 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
fc3b49c003 Gael*7290 o pkg/seaice:
7291 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
0c22b81a88 Jean*7292 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
7293 also pass fac as a param, which can be 1. (to update the tendency
fc3b49c003 Gael*7294 field) or the time step (to update the field itself).
0c22b81a88 Jean*7295 - seaice_advdiff.F: for multidim, call seaice_diffusion with
fc3b49c003 Gael*7296 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
7297 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
0c22b81a88 Jean*7298 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
fc3b49c003 Gael*7299 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
a6e3308c72 Jean*7300 o pkg/seaice:
7301 diffusion with centered advection scheme (diffus.F & advect.F):
7302 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
7303 to just compute the laplacian of input-field.
7304 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
7305 - fix flux-form version in diffus.F to conserve tracer.
7306 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
7307 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
7308
f23903c179 Jean*7309 checkpoint62y (2011/05/26)
b9ea5855ae Gael*7310 o pkg/seaice:
f23903c179 Jean*7311 - seaice_growth.F : in EVOLUTION branch, always include
b9ea5855ae Gael*7312 a_QSWbyATM_cover in qnet (as it should be).
7313 - verification/global_ocean.cs32x15 : update results accordingly
f23903c179 Jean*7314 (output.seaice.txt output_adm.seaice.txt).
665e1cc782 Jean*7315 o pkg/seaice + obcs:
7316 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
7317 equivalent of assuming no tracer gradient outside the OB region.
7318 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
7319 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
7320 after changes above);
7321 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
7322 only at OB location (instead of over a band of OLx width).
7323 o pkg/seaice:
7324 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
7325 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
ae7ba49648 Jean*7326 o pkg/obcs:
ae802b970e Jean*7327 - split header file "OBCS.h" into 4 separated files:
7328 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
7329 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
435c8dd190 Jean*7330 (contain no conditional statement which depends on OBCS options).
7331 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
7332 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
ae802b970e Jean*7333 o ctrl, cost, grdchk & autodiff pkgs:
7334 - make options file more standard (like other {PKG}_OPTIONS.h file but
7335 with AD_CONFIG.h); clean-up some of the included header files.
7336 o pkg/obcs:
ae7ba49648 Jean*7337 - do not mask tracer when applying OB (tracer == 0 could generate problems)
7338 - apply tracer OB values to tracer field only at OB location (instead of
7339 over a band of OLx width)
7340 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
7341 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
7342 obcs_apply_tloc.F & obcs_apply_sloc.F
7343 o obcs in model/src:
7344 - call OBCS_APPLY_W only if NonHydrostatic.
7345 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
7346 - reset dEtaHdt and wVel to zero outside OB interior region ;
7347 - leave tracer unchanged outside OB interior region: This has no effect
7348 on the solution but just to prevent unrealistic tracer value outside OB.
7349 - zero out velocity outside OB interior region: This has no effect on
7350 the solution but just to prevent unrealistic velocity outside OB.
1228ad56fc Jean*7351 o obcs and non-lin free-surf:
7352 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
7353 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
7354 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
7355 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
7356 update results of test-exp. exp4(nlfs).
b642a711f1 Jean*7357 o exp4 (nlfs) test-exp:
7358 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
7359 with NonLin-FreeSurf); update output.nlfs.txt
691f44a031 Jean*7360 o obcs and 2d/3d solver norm:
b642a711f1 Jean*7361 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
7362 and outside OB interior region (will allow to place OB further inside the
7363 domain). Depending on the domain, can affects cg2d-Norm (previous
ae7ba49648 Jean*7364 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
691f44a031 Jean*7365 and cg3d-Norm (previous Norm was computed before canceling OB terms),
7366 e.g. in tutorial_plume_on_slope.
7367 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
6202f959ce Jean*7368 o pkg rbcs:
7369 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
7370 - add capability to apply relaxation to horizontal velocity uVel & vVel.
5f47d9d3a7 Mart*7371 o pkg/grdchk: add gradient check for control variable xx_shifwflx
7372 o pkg/shelfice/shelfice_init_fixed.F
7373 fix CPP-flag combinations
2706e7ceae Patr*7374 o pkg/seaice: Merge iceage code of Pierre Rampal
7375 * update/change/correct ice age calculations
b642a711f1 Jean*7376 * add age updates for pathological cases
2706e7ceae Patr*7377 Probably needs more testing...
5f47d9d3a7 Mart*7378
fb01456aea Jean*7379 checkpoint62x (2011/05/13)
7380 o pkg/mom_vecinv:
6202f959ce Jean*7381 high-order vorticity scheme: use interior masks (maskInW & S)
fb01456aea Jean*7382 to zero-out (outside OB) gradient of vorticity.
94a41b18e5 Jean*7383 o verification exp.:
7384 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
7385 hs94.128x64x5 and seaice_obcs ; update results.
abb2d742f7 Oliv*7386 o pkg/obcs:
7387 fix bug in OBeta for YZ sections in obcs_exf_load.F
94a41b18e5 Jean*7388 o pkg/ctrl, pkg/shelfice, and optim:
7389 - add new control variable xx_shifwflx (fresh water flux underneath ice
7390 shelves). This is almost as tedious as obcs-ctrl, because the
c39d626e4c Mart*7391 variables needs its own mask.
94a41b18e5 Jean*7392 - add a cost function term that penalizes the deviation of xx_shifwflx
c39d626e4c Mart*7393 from the first guess (zero) in analogy to other control variables
40171df3a2 Patr*7394 o pkg/shelfice:
7395 - start basic adjoint
94a41b18e5 Jean*7396 o pkg/ctrl:
a14e708176 Mart*7397 - remove extra 2D field "for good measure" when initializing in
7398 ctrl_set_globfld_[xy/xz/yz].F
00525899b2 Mart*7399 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
7400 - improve error messages in ctrl_set_unpack_*
cb8d4055f8 Jean*7401 o OBC implementation in momentum:
7402 use interior masks (maskInC,W & S) in momentum S/R:
7403 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
7404 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
7405 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
7406 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
7407 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
7408 (and also with Leith/Smagorinsky harmonic-viscosity).
7409 Update output of experiment dome and exp4 (+nlfs).
19fda1148c Jean*7410 o exp4 test-exp:
ce8a4681c6 Jean*7411 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
7412 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
7413 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
7414 time-varying OB at Western-side for wVel (NonHyd); update output.
19fda1148c Jean*7415 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
ce8a4681c6 Jean*7416 and biharmonic-viscosity ; also use prescribed time varying OB.
19fda1148c Jean*7417 o pkg/obcs:
7418 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
cd0d82611c Jean*7419 o model/src:
7420 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
7421 - initialise startTime & nIter0 with unlikely values: allows to set one
7422 from the other without ambiguity.
e27288cd7f Jean*7423 o seaice_obcs test-exp.:
7424 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
575d4c6487 Jean*7425 o pkg/obcs:
7426 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
7427 no longer needed with maskInC,W,S in pkg/generic_advdiff.
81db1d5414 Ian *7428 o pkg/seaice:
575d4c6487 Jean*7429 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
81db1d5414 Ian *7430 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
575d4c6487 Jean*7431 - fixed bug in the initialization of sea ice salinity variable HSALT
81db1d5414 Ian *7432 in seaice_init_varia.F (removed dependence on ICE2WATR)
3fb96de6bc Jean*7433 o fizhi-cs test exp.:
7434 switch reference output convention for these 2 non-standard test-exp,
575d4c6487 Jean*7435 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
3fb96de6bc Jean*7436 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
7437 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
38710791cb Jean*7438 o model/inc:
7439 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
7440 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
c5deacd5a8 Ian *7441 o pkg/seaice:
7442 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
7443 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
81db1d5414 Ian *7444 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
7445 and initial HSALT
c5deacd5a8 Ian *7446
1c58c84abe Jean*7447 checkpoint62w (2011/04/26)
0585a400b7 Jean*7448 o pkg/mom_fluxform:
7449 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
7450 - use parameter "sideDragFactor" in no-slip BC side-drag part.
7451 - update output of exp. global_ocean.90x40x15
f79fbf5b9f Jean*7452 o pkg/mom_vecinv:
7453 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1c58c84abe Jean*7454 o update seaice exp.:
7455 use more consistent parameter values (remove "backward compatability only":
7456 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
7457 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
7458 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
f79fbf5b9f Jean*7459 o update test-exp global_ocean.90x40x15:
7460 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
7461 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
7462 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
7463 o turn on zStar & viscA4 in standard set-up (dir input/)
7464 and update output files: output.txt & output.dwnslp.txt
37df334812 Jean*7465 o new AD-test experiment: obcs_ctrl
7466 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
7467 o pkg/dic:
7468 fix two bugs in handling water vapour pressure in carbonate chemistry
7469 and air-sea fluxes. Found by Val Bennington and Galen McKinley
7470 (add DIC Option = WATERVAP_BUG to recover old results)
7471 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
7c642b2a2b Dimi*7472 o adding allowInteriorFreezing option to check for water below freezing point
7473 at depth and bring the negative heat anomaly to the surface level
37df334812 Jean*7474 o pkgs _fields_load:
7475 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
7476 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
62852f670d Jean*7477 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
7478 rbcs to get interpolation weights and time reccord number.
37df334812 Jean*7479 - fix multi-threading in aim_fields_load.F
7480 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
83f3340abe Jean*7481 o external_fields_load:
7482 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
7483 interpolation weights) to use in a periodic time-series ; do not divide by
7484 time-step to convert to integer:
7485 - this fixes case where externForcingPeriod is not multiple of time-step
7486 (Thanks to Christopher L. Wolfe)
7487 - this fixes case where externForcingPeriod is an odd multiple of time-step
7488 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
7489 store index of time-record which is currently loaded:
7490 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
7491 - needed for the adjoint but not yet used because of extensive recomputations;
7492 (to be fixed soon)
7493
aea6723cc0 Jean*7494 checkpoint62v (2011/04/02)
d0b6c8f47c Ian *7495 o verification/1D_ocean_ice_column added to test Ian Fenty's
7496 pkg/seaice_growth.F modifications for improving sea ice code differentiability
aea6723cc0 Jean*7497 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
7498 (new velocity statistics after changing maskInW & maskInS definition)
75620d6d39 Jean*7499 o pkg/generic_advdiff with OBCS:
7500 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
7501 equivalent to assumption of no tracer gradient outside the OB region.
7502 This will affect the results if using obcs+biharmonic diffusion.
7503 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1634337404 Jean*7504 o pkg/obcs:
7505 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
7506 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
7507 in Interior region. No impact on solution but affects Velocity monitor stats.
5933dabdc8 Patr*7508 o pkg/ptracers (adjoint)
1634337404 Jean*7509 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
5933dabdc8 Patr*7510 tape file for each tracer
1634337404 Jean*7511 o model/inc/src and pkg/autodiff: add parameters that allow to turn
7512 of parts of the adjoint code at run time. For now, there are only
7513 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
7514 parameters are set in data.pkg.
7515 This is the lazy coward's version of doing this, but still useful for
7516 debugging. In order to do it right, everything needs to be moved to
d6ce1e6c67 Mart*7517 pkg/autodiff.
1634337404 Jean*7518 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
d6ce1e6c67 Mart*7519 the end; this fixes the adjoint balancing code for open boundaries.
ae6e7b0b9d Mart*7520 o pkg/ctrl:
7521 - change behavior of xx_${varname}period to be analogous to exf-conventions:
7522 xx_${varname}period = 0., means time-independent control part
1634337404 Jean*7523 xx_${varname}period = -12., means one-year-periodic monthly control part
ae6e7b0b9d Mart*7524 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
7525 clean up ctrl_init a little, remove unused variables
e7fdbcdd62 Mart*7526 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
ae6e7b0b9d Mart*7527 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
7528
61d23e1802 Mart*7529 checkpoint62u (2011/03/15)
4866a81958 Jean*7530 o model/src:
7531 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
7532 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
7533 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
7534 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
7535 o pkg/ctrl/obcs/ecco:
633dbf7240 Mart*7536 - remove obsolete, unused, and partially broken code:
4866a81958 Jean*7537 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
633dbf7240 Mart*7538 ALLOW_CTRL_OBCS_BALANCE
4866a81958 Jean*7539 - put a stop statement into ecco/cost_obcsvol.F, but also add
633dbf7240 Mart*7540 cost_obcsvol to ecco_ad_diff.list
d9c90338d2 Mart*7541 o pkg/ecco: fix counting cost function contributions for obcs (code
7542 by Matt M.) and diffkr for diagnostics
a5506f4305 Patr*7543 o pkg/ecco, pkg/ctrl, pkg/grdchk:
7544 add cost penalty terms for initial uvel, vvel, eta controls
7545 and I/O for prior error files
a2fd64e7bb Jean*7546 o pkg/mdsio:
7547 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
7548 (new argument) to check for tiled file in mdsioLocalDir : this fix the
7549 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
fbadcb8ae6 Mart*7550 o pkg/ctrl:
7551 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
7552 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
7553 unused and superfluous variables
7554 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
8bc4946ad4 Mart*7555 o pkg/ecco
7556 - enable adjoint of Stevens OB
a2fd64e7bb Jean*7557 o pkg/ctrl/ecco/grdchk:
ac86e3d04f Mart*7558 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
8bc4946ad4 Mart*7559 Fortunately, we do not have any tests for the numerous cpp-flagged
ac86e3d04f Mart*7560 option of "obcs as control parameters" so we will never know
7561 if this is an improvement (but at least now things compile).
7562 - remove an obsolete initialization from ecco_cost_init_barfiles.F
a2fd64e7bb Jean*7563 - fix some problems within never used ifdefs to make the code compile
7ee9bd2cad Jean*7564 o pkg/obcs:
7565 - Refine Interior mask definition to work with more complex OB (e.g.
7566 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
7567 read in Interior mask from file. Check if Interior mask is consistent
7568 with OB list of indices.
19ebde807c Patr*7569 o pkg/seaice
7570 - beginning code for a seaice tracer package,
7571 but currently only used for seaice age: SEAICE_AGE
7572 SEAICE_num = 4
7573 iTracer = 1: area-weighted ice age
7574 = 2: volume-weighted ice age
7575 = 3, 4: template for one-year vs. multi-year ice
7576 data.seaice has new namelist SEAICE_PARM03 for arrays related to
7577 SEAICE_num
7578
954840cffd Patr*7579 checkpoint62t (2011/03/05)
686e612f13 Jean*7580 o pkg/obcs:
289f5415be Jean*7581 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
7582 then normal component. This ensures that the normal component is set
7583 correctly even when it conficts with tangential setting from an other OB.
7584 Affects results of test-experiment seaice_obcs: update the output.txt
7585 o pkg/obcs:
686e612f13 Jean*7586 - add code to monitor statistics of dynamical fields at OB.
7587 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
7588 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
7589 - change default: balance the Net inflow through all OB (instead of balancing
7590 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
7591 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
7592 to match Nortern OB inflow (OBCS_balanceFacN=0).
7f2854329f Dimi*7593 o pkg/seaice:
7594 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2afe30fba0 Dimi*7595 o pkg/seaice (seaice_growth v 1.113):
7596 - reverting seaice_growth to v 1.111 in order to have code with exact bit
7597 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
7598 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
7599 runtime flag SEAICEareaFormula is kept but is inactive
fa83c0daea Jean*7600 o model/src:
7601 - add new param to scale curvilinear grid distance and area when using
7602 a different sphere radius from the grid-files.
7603 - test/check multi-threads EXCH applied to local variable (cg2d_x)
878ab8c79d Patr*7604 o adjoint:
7605 - enable adjoint of Stevens OB
7606 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
7607 (a bit delicate because of potentially modified adj. common block structure;
7608 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
fa83c0daea Jean*7609
d6110c5749 Jean*7610 checkpoint62s (2011/02/15)
2afe30fba0 Dimi*7611 o pkg/seaice (seaice_growth v 1.112):
83f1d2d932 Gael*7612 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
d6110c5749 Jean*7613 computing the ice cover tendency from effective thickness tendencies. Include
7614 Ian Fenty's formula.
7615 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
7616 SEAICEareaFormula.
83f1d2d932 Gael*7617 - simplify notations for the various d_HEFF/d_AREA terms.
6555d1e696 Jean*7618 o pkg/gmredi:
7619 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
7620 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
7621 add a verification test-run (front_relax.bvp) to test GM_useBVP.
2afe30fba0 Dimi*7622 o pkg/seaice (seaice_growth v 1.111):
dbc3f8d6b1 Gael*7623 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
d6110c5749 Jean*7624 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
7625 also melt ice.
6555d1e696 Jean*7626 o pkg/seaice:
13127f64f6 Gael*7627 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
7628 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
6d3c37bddc Jean*7629 o pkg/cheapaml:
7630 - from Nico Wienders: New version of this package.
ffaad0659f Jean*7631 o pkg/flt:
7632 - add CPP options to prevent floats to re-enter the opposite side of
7633 a periodic domain (default: keep periodicity)
520f9effa6 Jean*7634 o pkg/gmredi:
7635 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
7636 (needed for multi-dim advection).
20e9cc15d6 Jean*7637 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
520f9effa6 Jean*7638 o model/src:
7639 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
f40e476a49 Patr*7640 o tutorial_tracer_adjsens
7641 - extend to NLFS and replace maskC by hFacC
7642 (change reference output accordingly)
520f9effa6 Jean*7643
24aac58d71 Jean*7644 checkpoint62r (2011/01/24)
b8c827cb68 Jean*7645 o testreport:
7646 - add option -deloutp (-do) to remove output file after successful run
7647 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
7648 extract exact list of procs from this file ; adjust COMMAND by
7649 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
ab3c25e729 Mart*7650 o pkg/ecco: replace old ineffective way of penalizing deviations from
7651 first guess (of obcs) with code by Matt Mazloff
b8c827cb68 Jean*7652 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
aad046c5da Mart*7653 exf/cal
7654 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
7655 and handle case of obcs?period == 0
7656 Not affected by these changes: There is still an inconsistency in
b8c827cb68 Jean*7657 the computation of start/endrec for the obcs variables for ALLOW_CAL
aad046c5da Mart*7658 defined (see comment by Menemenlis, 7-Mar-2003)
7659 - make S/R ctrl_get_gen_rec return something meaningful even if
7660 ALLOW_CAL is not defined
b8c827cb68 Jean*7661 - ctrl_getobcs?: simplify code so that it does not need to use
aad046c5da Mart*7662 S/R exf_swapfields
28266d9344 Jean*7663 o testreport:
7664 allow to test MPI with different number of processors for each experiment:
7665 create file "SIZE.h.mpi" in each build dir.
7666 Note: update of "-command" argument not yet implemented.
96bd925d69 Gael*7667 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
7668 alleviate the need for additional 3D tapes when using
7669 the non-inear free surface in the adjoint. This is done
b8c827cb68 Jean*7670 by adding an 'update' of hfacc etc. to their current
7671 value at the beginning of forward_step.F.
484f2586c6 Mart*7672 o pkg/seaice
7673 seaice_lsr: move stress-divergence computations out of outer pseudo-
3d83c2ccc1 Jean*7674 timestepping loop
484f2586c6 Mart*7675 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
7676 up, so that the calls of the ctrl_* subroutines are really at the end
7677 of the routine.
3d83c2ccc1 Jean*7678 o pkg/gmredi:
7679 allow to specify a 2-D horizontal map and a 1-D vertical profil
7680 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
96bd925d69 Gael*7681 o pkg/seaice:
7682 move lsr iterations from seaice_dynsolver to seaice_lsr.
7683 o pkg/seaice:
7684 reduce memory footprint of seaice mutldim advection tapes,
7685 by using a 2D tape independent of the generic_advdiff ones,
7686 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
484f2586c6 Mart*7687
aaf4b7889a Jean*7688 checkpoint62q (2010/12/29)
56906110dd Jean*7689 o model/src:
7690 - check horizontal grid-spacing for unset or zero/negative values.
7691 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
9827e6a18a Jean*7692 o pkg/flt:
7693 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
7694 - precision of input and output files set according to readBinaryPrec
7695 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
7696 - initial float position from tiled file was not converted to index space
7697 (looks like a bug): fixed to make it similar to initial pos. global file.
7688b175d1 Jean*7698 o global_ocean.cs32x15:
7699 change SIZE.h of AD set-up to get same tiling as with MPI.
7700 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
7701 o model/src:
7702 add flag to control printing of domain fields (bathymetry, hFac ...) in
7703 ini_mask_etc (call to plot_fieds_xy*).
7704 o pkg/thsice:
7705 if useEXF, some forcing fields are not valid in overlap: fixed by computing
7706 over the interior only + apply EXCH at the end (like with SEAICE advection).
71e006c2cc Jean*7707 o pkg/mdsio:
7708 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
7709 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
7710 - change barrier call for safe multi-threads access to 3-D shared buffer.
7711 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
7712 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
7713 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1d0c7afaa8 Oliv*7714 o pkg/flt:
7715 - add fourth-order Runge-Kutta integration
7716 - add basic exch2 support (only 1 facet supported so far!)
824747e6ac Jean*7717 o pkg/mdsio+rw:
7718 new S/R to read local (or tile independent) vector (read counterpart of
7719 mds_writevec_loc, and front-end write_glvec_rl/rs).
1196ad766d Gael*7720 o global_ocean.cs32x15: additional input_ad.seaice experiment
7721 that uses pkg/seaice rather than pkg/thsice.
7722 (using multidim advection for seaice)
bba939b996 Jean*7723 o towards more F95 syntax for array specification in namelist:
7724 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
7725 of all verification experiments.
7726 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
7727 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
7728 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
a913ac327f Gael*7729 o global_ocean.cs32x15: additional input.seaice experiment
7730 that uses pkg/seaice rather than pkg/thsice.
bba939b996 Jean*7731
38e5b192c3 Jean*7732 checkpoint62p (2010/12/17)
b8373d841d Gael*7733 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
7734 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
7735 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
7736 allow for use of multim. advection in seaice adjoint.
a71dccbd8b Mart*7737 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
7738 - first attempt to close budgets by taking into account the freshwater
38e5b192c3 Jean*7739 flux implied by the sublimation of snow and ice. So far only the
a71dccbd8b Mart*7740 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
7741 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
0e4cbd8946 Jean*7742 o eesupp/src:
7743 new S/R with new option (NML_EXTENDED_F77) to change array specification
7744 from F95 standard to commonly accepted extended F77 form.
7745 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
7746 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
7747 for less tolerant f77 compiler (e.g., pgf77, g77).
8da37cabce Jean*7748 o globalFiles:
7749 commented out in parameter file "data" since it's not safe with MPI
7750 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
7751 in this case); no longer commented out in restart test (tst_2+2).
7752 o add adTapeDir to specify a special directory where adjoint tapes are
7753 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
0e71fc82ff Mart*7754 and cannot be used together with mdsioLocalDir.
372ecbd193 Jean*7755 o nesting pkgs:
7756 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
7757 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
7758 - add parameter files + utils dir + output from short run on beagle.
99f78b5547 Gael*7759 o pkg/seaice:
7760 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
372ecbd193 Jean*7761 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
b3992b16ea Mart*7762 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
7763
810405d6e0 Jean*7764 checkpoint62o (2010/11/25)
b2aaf537fd Jean*7765 o pkg/exf:
7766 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
810405d6e0 Jean*7767 o pkg/seaice:
7768 - seaice_ocean_stress: split a loop for better vectorization of the
7769 adjoint code
bb0aaa13c1 Mart*7770 - seaice_growth.F: fix bug in conservation of freshwater connected to
475a61469a Mart*7771 capping of heff, put contribution into d_HEFFbyNEG
bb0aaa13c1 Mart*7772 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
7773 by something more sensible (parameters that are what their name implies)
7774 - change some defaults, so that by default exf-parameters are used for
7775 things like rhoAir, cpAir,latent/sensible heat parameters, in order
7776 to reproduce the old results, many data.seaice now contain funny values
7777 for cpAir and latent heat of sublimation
810405d6e0 Jean*7778 o packages_readparms.F: move exf_readparms up in line so that
bb0aaa13c1 Mart*7779 exf-parameters are visible for other packages (e.g. seaice)
a7e5ab30a6 Jean*7780 o debugMode & debugLevel=2:
7781 - differentiate between debugMode & debugLevel=2:
7782 debugMode: controls printing of debug messages (sequence of S/R calls).
7783 debugLevel: controls printing of algorithm intermediate results and stats.
7784 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
7785 => allows to print debug-stats without all sequence of call messages.
7786 - switch control of debug print from debugLevel to debugMode in many S/R.
7787 o pkg/obcs (obcs-sponge):
7788 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
7789 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
db3f21a7ea Jean*7790 o pkg/generic_advdiff:
7791 - record overlap minimum size for each advection scheme;
7792 - refine criteria on overlap minimum size;
7793 - check and stop (in gad_check) if overlap size is too small.
7794 o pkg/obcs:
7795 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
7796 once, in ptracers_implicit.F)
7797 - with seaice: remove test on empty file name in obcs_apply_seaice (always
7798 apply OB values when tile has OB)
c4900f4204 Jean*7799 o model/src, coriolis setting:
7800 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
7801 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
7802 files (selectCoriMap=3) with any grid.
7803 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
7804 o pkg/seaice/seaice_growth.F:
7805 a few cosmetic changes that reduce the number of lines of code
36f4ad1be7 Mart*7806 o pkg/obcs: add boundary conditions following Stevens (1990)
7807 - the code follows old MOM/NAOSIM code
7808 - so far it is only implemented for the eastern and western boundaries
7809 and NOT for pTracers
3710b30939 Oliv*7810 o pkg/rbcs:
7811 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
7812 beginning of the first rbcs forcing period.
7813 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
7814 offline package, i.e., one file per time, labeled by iteration number;
7815 deltaTrbcs sets the timestep with which the data was generated;
7816 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
7817 - rbcsForcingCycle=0 makes forcing non-cyclic.
7818 - make arithmetic safe for negative times and odd forcing periods.
7819
19b92f2fb3 Jean*7820 checkpoint62n (2010/11/09)
501625885e Mart*7821 o pkg/seaice:
2a7b0e3fd3 Jean*7822 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
7823 o pkg/obcs:
7824 New S/R to copy tracer value from the OB location to narrow band region
7825 (width = same as overlap) beyond the OB: preserve OB value (needed for
7826 high-order scheme) which were overwritten by EXCH call if in overlap
7827 region. Applied to theta, salt, ptracer and advected seaice variables.
7828 With seaice: use maskInC in similar way as in gad_advection.F,
7829 in seaice_advection.F and advect.F.
7830 Update output of experiment seaice_obcs and change exp4 to test OBCS with
7831 4th order Adv.Scheme. for pasive salt and ptracer.
7832 o tools/genmake2:
7833 - when looking for an optfile (not specified), only search for Fortran compiler
7834 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
7835 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
7836 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
7837 - set default for CPP to "cpp -traditional -P" (was the case without specifying
7838 an optfile, but otherwise default was just "cpp".
7839 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
7840 - when "CC" is not set in the optfile, look for possible C compiler
7841 (instead of just setting CC=cc)
7842 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
7843 => add a ".F" to ".o" rule for source files with no "#include" (such as
7844 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
7845 - move gfortran before g77 in list of possible Fortran compiler (consistent
7846 with reference compiler switch from g77 to gfortran)
7847 o pkg/seaice:
7848 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
501625885e Mart*7849 seaice_check that stops the model, when the CPP flag is used.
7850 o seaice_growth.F: make capping of ice volume conserving by returning the
7851 capped ice as freshwater to EmPmR. This does not change the verification
7852 experiments but will change runs where the capping is acutally active
b25aab9f85 Jean*7853 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
7854 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
7855 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
7856 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
7857 o tools/genmake2:
7858 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
7859 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
7860 - clean previous genmake log files before anything else.
7861 - change Makefile to remove testreport log files (*.tr_log) and genmake log
7862 files only with "CLEAN" target (instead of "Clean");
8488313509 Jean*7863 o pkg/generic_advdiff:
7864 Change OBCS in multiDim advection (gad_advection.F):
7865 Use maskInC to prevent intermediate update of tracer-field in OB regions,
7866 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
7867 which were applying future time-step OB values.
7868 This way, all explicit calculations use current-time-step OB values
7869 (simpler and more consistent).
7870 Affects results when set-up uses time-varying OBC and multi-dim advection;
7871 update output of experiment seaice_obcs.
7b24ec4b62 Jean*7872 o pkg/seaice:
7873 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
7874 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
7875 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
7876 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
7877 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
7878 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
cc732d4fb4 Davi*7879 o pkg aim (2010/10/26):
7880 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
7881 formulation with obliquity, eccentricity, ... as run-time parameters,
7882 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
7883 upward shortwave radition at the surface (all-sky and clear-sky).
f84aaa453a Jean*7884 o pkg/obcs:
11aa53a8c7 Dimi*7885 - writing sections with globalFiles=T does not work: switch to tiled-files
7886 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
7887 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
7888 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
f84aaa453a Jean*7889
dfe4303922 Jean*7890 checkpoint62m (2010/10/21)
f4c40b0961 Mart*7891 o pkg/seaice: vectorize seaice_solve4temp.F
7892 - move iterations loops outside of i/j-loops
7893 - requires 2D arrays for TB and effConduct
dfe4303922 Jean*7894 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
f4c40b0961 Mart*7895 modified in this routine
7896 - a little bit of clean up, adjusting indentation, etc.
dfe4303922 Jean*7897 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
7898 performance and '**TWO' by '**2' (because TWO is a float),
f4c40b0961 Mart*7899 replaced ONE, ZERO
2708f6625c Jean*7900 o eesupp/src:
7901 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
473a1d0f79 Gael*7902 o pkg/seaice/seaice_growth.F
2708f6625c Jean*7903 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
7904 merging process. The merged routine has two branches, and one activates the 'evolution'
473a1d0f79 Gael*7905 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
7906 In summary, here is what the '10/10 revision' did consist of
2708f6625c Jean*7907 part 1: seaice_growth.F revisions 1.71 to 1.75
473a1d0f79 Gael*7908 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2708f6625c Jean*7909 The emphasis here was on improving readability (e.g. by trying to use meaningful
473a1d0f79 Gael*7910 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2708f6625c Jean*7911 part 1.5:
7912 - revising the lab_sea experiment to make it a more useful (i.e. stable
7913 and representative of an actual model run). This was done by generating a
7914 (winter) pickup to start from, switching back the main experiment dynamic
473a1d0f79 Gael*7915 solver from evp to lsr, having one of the experiments use the free drift solution.
2708f6625c Jean*7916 part 2: seaice_growth.F revisions 1.76 to 1.85
473a1d0f79 Gael*7917 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2708f6625c Jean*7918 - Sorting out the various fields units and sign (set early on and reset at the end)
7919 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
7920 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
7921 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
473a1d0f79 Gael*7922 and simplifying logical expressions to further improve readibility.
7923 part 3: seaice_growth.F revisions 1.86 to 1.89
7924 - Re-organize the blocks of code more logically.
7925 - Merging the '_if.F' pieces that add something new.
2708f6625c Jean*7926 o pkg/thsice:
7927 - vectorize thsice_solve4temp and thsice_get_exf.
65de7ad9cd Mart*7928 Problem: thsice_solve4temp has an unvectorizable statement that
7929 might also be problematic for TAF
2708f6625c Jean*7930 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
7931 does not change the verifcation experiment, but will change all
65de7ad9cd Mart*7932 experiments that have this flag undefined (not tested in verification);
7933 a little reorganization to save a few 2D fields and recomputations
0d66e9256f Patr*7934 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
07a36c38a7 Patr*7935 - 2nd step: fix some store dirs
7936 o seems to work somewhat, i.e. using ifort but not g77
7937 o likely cause are incomplete init. or recomputation
7938 o start verification/global_ocean.cs32x15/input_ad.thsice
cce7f684db Oliv*7939 o pkg/obcs: add support for exch2
7940 - the position of the boundary and prescribed values are specified using
7941 a global domain with exch2 facets stacked
7942 - in x for N,S boundaries (like W2_mapIO=-1)
7943 - in y for E,W boundaries (so E,W boundaries do not overlap)
7944 o pkg/mdsio: add support for writing global sections with exch2
7945 file layout is as for obcs described above:
7946 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
7947 - for y-z sections, facets are stacked in y
8f33527490 Jean*7948 o pkg/thsice:
033392cf3f Mart*7949 - change a few routines for better vectorization: thsice_albedo.F,
7950 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
7951 not affected, but in particular the latter routine has changed
7952 dramatically (not necessarily easier to read now).
7953 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
8f33527490 Jean*7954 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
7117852a81 Gael*7955 o verification/lab_sea:
7956 - overhaul of the forward model experiments. The main motivation
2708f6625c Jean*7957 for this revision is that lab_sea has proven quite fragile (when
7117852a81 Gael*7958 changing the sea-ice code, and switching platforms) to a point
7959 when failures were very hard to attribute to specific code problems.
2708f6625c Jean*7960 - the suspected reason for this fragility is noise amplification by evp so,
7117852a81 Gael*7961 to start with, we decided to replace evp with lsr in the main experiment.
7962 - the input.lsr experiment thus became obsolete and was removed.
2708f6625c Jean*7963 - it was replaced with the input.fd experiment that uses an
7117852a81 Gael*7964 analytical "free drift" solution as the ice velocity field.
7965 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
7966 will hopefully allow us to discriminate problems due to dynamic solvers
7967 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
7968 us to test additional options, along with the salt plume package.
2708f6625c Jean*7969 - Finally a pickup was generated (at the end of a one year run) to
7117852a81 Gael*7970 make the tests more representative of an actual model run. Previously
7971 the tests starting point was a 1m thickness of ice everywhere.
2708f6625c Jean*7972 o pkg/seaice:
7117852a81 Gael*7973 - introducing S\R seaice_freedrift.F that compute the
2708f6625c Jean*7974 analytical solution to an approximate ice momentum
7117852a81 Gael*7975 equation (i.e. the simple stress/coriolis balance).
7976 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2708f6625c Jean*7977 of the free drift velocity field, and enable its use.
7978 To actually use the free drift solution as the model ice
7979 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
9aa451bbe6 Mart*7980 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
7981
512c5638c7 Jean*7982 checkpoint62l (2010/10/04)
6915e96d9b Jean*7983 o pkg/seaice:
7984 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
7985 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
7986 version (with USE_ORIGINAL_SBI undef);
ddb00487db Mart*7987 o add hooks for new packages OASIS, the package will follow
7988 (hooks exclude the seaice pkg for now)
63712fce08 Gael*7989 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
6915e96d9b Jean*7990 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
63712fce08 Gael*7991 rather than mdsio_readvector.F/mdsio_writevector.F, within
7992 adread_adwrite.F to read/write adjoint-related tapes to disk.
6915e96d9b Jean*7993 o eesupp and pkg/mdsio: ALLOW_WHIO
7994 Option to write/read 2D fields to files including tiles halos.
7995 The main purpose is for adjoint related "tape I/O".
b7f33b42e8 Gael*7996 The secondary purpose is for debugging phases.
7997 A word on those rather specifically intended purposes.
7998 The code was meant to be stripped down to the bare minimum.
6915e96d9b Jean*7999 Typically, there is a unique and basic mapping to the global
b7f33b42e8 Gael*8000 buffer (tile by tile, then proc by proc, then level by level), and
8001 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
6915e96d9b Jean*8002 meant to generate user friendly outputs of various shapes and forms.
b7f33b42e8 Gael*8003 Rather it is intended, for the knowledgeabale developers,
8004 to be largely independent of the many mdsio options, to allow
6915e96d9b Jean*8005 outputs of tiles+halos in debugging phases and in adjoint runs,
b7f33b42e8 Gael*8006 and to allow some flexibility in tuning (adoint) I/O depending on each
6915e96d9b Jean*8007 file system behavior. With regard to tuning, most of the potential knobs
b7f33b42e8 Gael*8008 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
8009 to specify directories, to specify the typical size of I/O calls, etc.)
8010 are not yet included, and will be added if they prove useful.
2ec921609d Jean*8011 o pkg/seaice:
65c3c27d2c Jean*8012 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
8013 o pkg/seaice:
2ec921609d Jean*8014 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
8015 code (seaice_budget_ice_if.F) which enable to recover old standard
8016 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
8017 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
8018 o model/src (rStar):
8019 use simple average (not area weighted) of rStarFac at U,V point when using
8020 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
8021 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
813dd65ac9 Jean*8022
e356351660 Jean*8023 checkpoint62k (2010/09/17)
05855df642 Patr*8024 o adjoint
8025 * changed verification/global_ocean.cs32x15 ; adjoint now tests
8026 Adams-Bashforth 3 + NLFS + RSTAR
8027 * some more modifs required for ECCO-GODAE v4
54f6436301 Dimi*8028 o pkg/seaice
8029 add SEAICE_AGE_VOL option to use volume instead of area for
8030 integrating SEAICE_AGE
a89a34c510 Jean*8031 o model/src:
8032 first check-in of sigma & hybrid-sigma coordinate code ; also includes
8033 non-linear free-surface parts ; but pressure-gradient not yet coded.
96a7eb29e8 Jean*8034 o pkg/ptracers:
8035 option for ptracer to convert Salt Relax into additional EmP.
8036 tested in exp. global_ocean.90x40x15.dwnslp (update output)
8037
3eaaf3fa4e Jean*8038 checkpoint62j (2010/08/25)
4d3d3c392f Jean*8039 o pkg/ggl90:
8040 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
deff84d11b Mart*8041 o pkg/dic: car_flux.F, phos_flux.F
8042 - reduce number of exp-calls in order to improve performance
4d3d3c392f Jean*8043 - clean up a little (replace fields by their macros, etc., fix
deff84d11b Mart*8044 typo in CPP-flag)
fa4ac57b5c Gael*8045 o pkg/ggl90: minor changes
8046 - GGL90diffKrS was removed --> always use GGL90diffKr
8047 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
4d3d3c392f Jean*8048 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
8049 (commented out for now)
fa4ac57b5c Gael*8050 - change in max/min operations to ensure that smoothing is ok
8051 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
8052 - always use diffKrNrT as background profile (i.e. never use diffKr field)
3983b1167c Mart*8053 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
c3c9befee2 Mart*8054 o pkg/dic:
1cfcce3655 Mart*8055 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
8056 vectorization
33b1baef56 Mart*8057 - small bug fix in insol for the unlikely case of a cartesian grid
8058 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
8059 + now vectorize, which also removes adjoint recomputations;
8060 + replace integer maksp1 by _RL maskp1
1cfcce3655 Mart*8061 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
c3c9befee2 Mart*8062
ee1e0f95df Jean*8063 checkpoint62i (2010/07/21)
1e3aeb8ba1 Jean*8064 o pkg/flt:
8065 - with OBCS: stop floats which enter the OB region
8066 o model/src:
8067 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
8068 for implicit vertical advection.
ac416c45e2 Jean*8069 o pkg/seaice:
8070 - account for melting in seaice age evolution.
1e3aeb8ba1 Jean*8071 - remove double counting of seaice ridging effect on seaice age.
ac416c45e2 Jean*8072
283e101b7e Jean*8073 checkpoint62h (2010/06/18)
ad5bd052a0 Jean*8074 o pkg/exch2:
8075 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
8076 o tools/genmake2
8077 - remove "-pdefault" option: redundant with the use of "packages.conf";
8078 - remove file pkg/pkg_default : set the default as a pkg group
8079 ("default_pkg_list") defined in pkg/pkg_groups;
8080 - fix for case pkg/pkg_depend is missing (was hanging before);
8081 - add option "-pgroups" to specify a different pkg_groups than the default.
82644c0ee5 Jean*8082 o verification/adjustment.cs-32x32x1:
8083 add a "minimal" set-up test (code_min & input_min) which only compiles
8084 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
f30b73b1e2 Jean*8085 o tools/genmake2
8086 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
8087 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
c5f3ee7c60 Mart*8088 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
8089 files are nearly the same anyway.
8090 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
8091 - redefinition of tau(i,i) (by a factor of ustar)
8092 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
8093 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
8094 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
6f9d992eff Jean*8095 - replace
c5f3ee7c60 Mart*8096 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
8097 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
8098 by
8099 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
8100 (changes results)
6f9d992eff Jean*8101 -> exf_bulkformulae v1.22,
c5f3ee7c60 Mart*8102 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
8103 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
6f9d992eff Jean*8104 output.txt 1.63
c5f3ee7c60 Mart*8105 offline_exf_seaice: output.seaicetd.txt 1.7
8106 seaice_obcs: output.txt 1.10)
8107 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
8108 -> exf_bulkformulae v1.23,
8109 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
8110 and global_ocean.cs32x15.icedyn (only 11 matching digits)
6f9d992eff Jean*8111 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
48a7bf5f11 Jean*8112 o adjoint of exch-1:
8113 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
8114 (note: was already like this when using EXCH-2) and remove flow dir
8115 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
8116 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
8117 - update pkg/exch2 diff list.
8118
1431f62bbf Jean*8119 checkpoint62g (2010/05/19)
0bb3693507 Jean*8120 o eesupp/src (exch-1):
8121 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
8122 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
8123 (renamed to exch1_*rx_cube.F).
8124 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
8125 to call new exch1 S/R ; update Makefile and .cvsignore.
8126 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
8127 exch2_xy_rx later)
8128 Note: after updating your code, need to run "make clean" in eesupp/src
71519bb137 Jean*8129 o test experiment bottom_ctrl_5x5:
0bb3693507 Jean*8130 new output_adm.txt with fewer grdchk & less monitor output.
71519bb137 Jean*8131 o model/src:
8132 remove the call to ini_cori in initialise_varia.F (just keep the usual one
0bb3693507 Jean*8133 in initialise_fixed.F). More consistent with coriolis & horizontal grid
71519bb137 Jean*8134 beeing treated in the same way (ini_grid is not called a 2nd time).
0bb3693507 Jean*8135 o pkg/exf:
1c4c64c172 Mart*8136 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
ba8369cbfe Mart*8137 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1c4c64c172 Mart*8138 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
a435e833b1 Mart*8139 - cosmetic changes to exf_bulkformulae.F to make it look more like
8140 exf_bulk_largeyeager04.F
f286872c74 Jean*8141 o eesupp/src (exch-1):
8142 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
8143 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
8144 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
8145 (even without using MPI).
8146 - Message mode: move RecvAck setting (indicator of buffer being ready)
8147 from send_put to recv_get S/R (was useless before, but not sure if
8148 it's much more useful now);
71519bb137 Jean*8149 - Switch the order of sync: MPI-proc 1rst and then threads;
f286872c74 Jean*8150 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
71519bb137 Jean*8151 - fix AD code for communication mode ='get' (but not used).
b74efa0efe Jean*8152 o model/src:
8153 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
8154 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
b42ffdc64e Mart*8155 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
46e98d66db Mart*8156 o pkg/ctrl: require a specific set of control variables and exf-flags for
8157 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
c3aa58ac7a Gael*8158 o model/src:
4caeefbbc4 Jean*8159 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
8160 1rst forward sweep, to avoid over-writing output files during recomputations
8161 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
8162 b) 2nd version:
8163 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
8164 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
8165 writePickupAtEnd) + seaice & ptracers output;
8166 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
958aba4d71 Jean*8167 o model/src:
c3aa58ac7a Gael*8168 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
7b55f0c147 Jean*8169 o pkg/exch2:
958aba4d71 Jean*8170 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
7b55f0c147 Jean*8171 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
6f7f051ae5 Jean*8172 o pkg/autodiff & exch2:
8173 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
8174 (for now, only if ALLOW_EXCH2 is defined).
72ca7aff83 Jean*8175 o pkg/autodiff:
958aba4d71 Jean*8176 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
72ca7aff83 Jean*8177 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
8178 + clean-up comments (_RS is not always real*4)
8179 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
8180 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
8181 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
e4c55a32ae Jean*8182 o testreport (AD-tests):
8183 no longer link files from dir "../input" (1rst link files from
8184 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
8185
39ab2f324f Jean*8186 checkpoint62f (2010/04/29)
dd69ba5157 Mart*8187 o model/src/the_main_loop.F:
8188 adjust store directives for seaice evp and multicategory according to
8189 pkg/ecco/the_main_loop.F
ec74c4ec27 Patr*8190 o adjoint:
e4c55a32ae Jean*8191 global_sum_ad was incomplete (noted many times by many people ;)
ec74c4ec27 Patr*8192 nice description by Jean U. as follows:
e4c55a32ae Jean*8193 * allreduce(var) in global_sum.F can be interpreted as
8194 reduce(sum) followed by broadcast of sum.
8195 * The adjoint of that is
8196 sum(adjoint) followed by broadcast(summed adjoint value)
ec74c4ec27 Patr*8197 or in other words, allreduce(sum, adjoint vars)
8198 We were missing the sum(adjoint)!
8199 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
8200 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
8201 The fix should produce 16-digit accuracy between
8202 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
8203 multi-CPU single-tile (e.g. nSx=1, nPx-2)
8204 We'll probably change this yet again shortly
3b017f85c7 Jean*8205 o eesupp/src:
8206 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
94ec5b807d Dimi*8207 o pkg/icefront
8208 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
8209 specification of addmass array based on a 2D field, which is added
8210 at bottommost wet level at each horizontal location.
c99b00e28d Jean*8211 o model/src:
8212 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
8213 layout; (not always compatible with delX,delY setting; commented out for now).
062357823a Jean*8214 o pkg/exch2:
8215 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
8216 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
8217
e98d34196c Jean*8218 checkpoint62e (2010/04/15)
a175514333 Jean*8219 o pkg/obcs:
8220 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
6526bf38ab Jean*8221 o pkg/dic:
8222 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
8223 (note: not presently tested in any forward verification exp.)
8224 update tutorial_global_oce_biogeo AD output file.
8225 o pkg/exf:
a294fb3ca0 Gael*8226 - account for the variation of albedo as a function of zenith angle
6526bf38ab Jean*8227 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
e8d83fb93d Jean*8228 o build_options:
8229 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
8230 o pkg/dic:
8231 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
8232 - use binary pickup file for restart;
8233 - initialise atmos-CO2 box from dic_pCO2 parameter;
8234 - fix multi-threaded.
186276afbe Jean*8235 o pkg/rbcs:
8236 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
8237 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
8238 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
8239 and update output.txt
faaf90f2c5 Jean*8240 o pkg/kpp:
8241 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
8242 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
e8d83fb93d Jean*8243 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
faaf90f2c5 Jean*8244 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
8245 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
8246 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1a6563ae72 Davi*8247 o pkg/offline:
4daea5a88d Jean*8248 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
8249 (bug was added in version 1.10 on 2007-08-23).
8250 o pkg/offline:
1a6563ae72 Davi*8251 - no need to specify periodicExternalForcing, etc ... to use offline pack
8252 - offline input files no longer just single prec --> parameter offlineLoadPrec
3d5d3248cf Patr*8253 o verification/lab_sea:
4daea5a88d Jean*8254 change AD test to multi-tile setup and update all 4 AD output.
3d5d3248cf Patr*8255 NOTE: while cost function values remain very similar,
8256 gradients are very different, although gradient checks are self-consistent
8257 Should try to get to the bottom of this (cost function summation order?)
0978c8a77f Jean*8258 o pkg/dic:
8259 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
8260 a weakness of TAF that drops part of double precision in log10 derivative.
d7e064ff4e Jean*8261 <= changes removed since problem has been fixed in current TAF version 1.9.71
0978c8a77f Jean*8262 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
5fd4ec8263 Jean*8263 o pkg/ecco:
8264 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
8265 update all 4 lab_sea AD output.
8266
9f4cf29369 Jean*8267 checkpoint62d (2010/03/22)
8268 o build_options:
8269 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
b9024a78e5 Jean*8270 o remove unbalanced quote (single or double) in commented line of source code
8271 (may cause some warning with some preprocessor/makedepend versions).
8272 o pkg/seaice:
87ed893815 Jean*8273 fix seaice_model.F for adjoint (gael) and update AD results of experiments
8274 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3b0f45b28f Jean*8275 o testreport:
8276 add option '-runonly' (short: '-ro') to just do the run part (without make).
2956a926ec Jean*8277 o eesupp: remove JAM communication code (obsolete).
8194302c25 Jean*8278 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
a435e833b1 Mart*8279 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
8194302c25 Jean*8280 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
8281 (update also the output).
8282
f916330b2a Jean*8283 checkpoint62c (2010/03/02)
c805d90c6c Jean*8284 o tools/build_options :
8285 move (some) old optfiles from build_options/ to build_options/unsupported/
74230ba5cf Gael*8286 o model/src and pkg/exf
8287 surface relaxation -- separating data and data.exf options
8288 The point is to ensure that we specify the surface relaxation
a435e833b1 Mart*8289 either in data or in data.exf (but not half and half) and to
8290 avoid an accidental relaxation to 0 (which happened if a time
74230ba5cf Gael*8291 scale was specified but the file name was left empty)
4b97e458f0 Gael*8292 o model/src model/inc and pkg/mom_common
8293 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
8294 => addition to the viscosity field as computed by others schemes
a435e833b1 Mart*8295 o tools/build_options:
076c0d73b3 Jean*8296 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
8297 but keep the former optfile for few weeks for smooth transition
01d7251472 Gael*8298 o pkg/ecco
8299 - allow user defined cost function contributions
cc732d4fb4 Davi*8300 CPP: ALLOW_USERCOST_CONTRIBUTION
8301 USAGE: compute contributions in cost_usercost_all.F
01d7251472 Gael*8302 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
8303 the two options are complementary.
5939a6479f Gael*8304 o pkg/smooth
8305 - migration from contrib to the main repository
076c0d73b3 Jean*8306
e7a2735eaf Jean*8307 checkpoint62b (2010/01/26)
075e0d2187 Jean*8308 o pkg/monitor:
a435e833b1 Mart*8309 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
075e0d2187 Jean*8310 (in case someone forgot to update customized pieces of code)
8311 o nonHydrostatic:
af06fd5b92 Jean*8312 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
8313 - add a simple 2-D experiment (short_surf_wave) to test it.
8314 o pkg/icefront:
8315 adding the shell of, and the hooks to, a new package that
5da8ce63fa Dimi*8316 will model melting and freezing of vertical glacier ice fronts
af06fd5b92 Jean*8317 o momentum:
451e002b6f Jean*8318 add diagnostics of momentum tendency from Hydrostatic pressure gradient
8319 (without surf.pressure term: would need a 2nd filling since implicit term).
af06fd5b92 Jean*8320 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
8321 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
8322 cannot deal with the former
884840d195 Jean*8323 o cleaning:
451e002b6f Jean*8324 - remove all (except OpenAD) old TLM output from results_ad dirs.
884840d195 Jean*8325 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
8326 - comment out maskH definition (replaced by maskInC)
8327 o pkg/monitor:
8328 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
075e0d2187 Jean*8329 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
884840d195 Jean*8330
0be9783367 Jean*8331 checkpoint62a (2010/01/15)
e95eb1d512 Jean*8332 o model/src:
8333 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
987f6e1ae3 Jean*8334 o pkg/diagnostics:
8335 - add optional level number diagnostics (i.e., level number to be define
8336 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
8337 - strictly check for valid parser-code(10) ;
8338 - check if adding diag to the list from the right place.
09d7c96a8d Oliv*8339 o pkg/longstep:
8340 - change parameters and fix tracer conservation with rstar/nonlinear free surface
f8b182d288 Jean*8341 o diagnostics:
8342 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
8343 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
75ecb6f722 Jean*8344 o pkg/diagnostics:
8345 - Add option for writing vertical integral (sum of selected levels) of an output
8346 field instead of writing output field levels. Activate this option on a per
8347 output-file basis, by setting the 2nd character of fileflag to 'I'.
8348 - Add field-specific information relative to level integral in 3rd postion
8349 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
8350 vertically (x level-thickness x hFac), "r"=same but without hFac.
281db5ef19 Jean*8351 o do_the_model_io:
8352 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
8353 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
8354 writing pickups and stopping.
8355 o pkg/diagnostics (for now, only with mdsio):
8356 - write time information to meta file (and modify accordingly rdmds.m) :
8357 time-averaged diagnostics output: write starting and ending time of the
8358 time-averaging interval ; snap-shot diagnostics output remains unchanged;
e9ac57b72c Jean*8359 o pkg/timeave:
8360 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
8361 always Nr), now assumed to be equal to number of levels of averaged field;
8362 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
8363 o pkg/sbo:
8364 - fix ocean bottom pressure global-average & 2-D time-ave output (was
8365 neither initialised nor filled).
8366 - add starting iteration in suffix of global-average output file
8367 (to avoid over-writing the file after a restart)
8368 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
8369 o time-average:
8370 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
8371 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
8372 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
8373 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
8374 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
8375 - fix missing accumulation for pkg/opps.
8376 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
8377 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
8378 - fix initialisation of time-ave vars and do only full time-step increment
8379 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
580b2d0e2d Jean*8380 o pkg/layers:
8381 - use standard RW pkg S/R to write the output
8382 and remove local write_fld version (which had a problem).
8383 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
8384 - fix LAYERS_CALC argument list.
8385 o pkg/timeave:
8386 - store cumulative-time in a simple tiled array (drop the level index)
8387 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
b59b551857 Jean*8388 o pkg/ocn,aim_compon_interf
8389 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
8390
6a7fcc88c2 Jean*8391 checkpoint62 (2009/12/23)
c32120bcda Jean*8392 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
8393 (was not previously tested in any other exp.)
262f5d9bf0 Jean*8394 o pkg/monitor:
8395 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
6a7fcc88c2 Jean*8396 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
262f5d9bf0 Jean*8397 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
8398 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
8399 - change del2 calculation.
8400 - use interior masks (instead of maskH, <- to be remove).
8401 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
8402 o mask & obcs:
8403 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
6a7fcc88c2 Jean*8404 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
262f5d9bf0 Jean*8405 (called after packages_init_fixed)
3a86c9b47d Oliv*8406 o pkg/obcs:
8407 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
8408 Fixes bug in obcs+exf with nSx*nSy.GT.1
8409 - fix multi-tile handling in obcs balance code
c93c5f4bd8 Jean*8410 o nonHydrostatic:
8411 - Implement AB-3 for non-hydrostatic vertical momentum ;
8412 (change ordering of var. stored in pickup file when using NH)
8413 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
8414 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
8415 (in prep. for new NH free surface form).
4d27a257dc Jean*8416 o pkg/obcs:
8417 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
6a7fcc88c2 Jean*8418 o model/src:
4d27a257dc Jean*8419 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
8420
0e6056cd20 Jean*8421 checkpoint61z (2009/12/01)
4848a3791a Jean*8422 o nonHydrostatic:
8423 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
8424 a spurious source of energy in simple baroclinic adjusment test case.
8425 Update all non-hydrostatic exp output.
8426 o model/src (3-d solver):
8427 Change again 3-D solver free-surface RHS term when exactConserv=T:
8428 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
8429 (which was not the case with previous formulation).
8430 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
8431 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
8432 o nonHydrostatic:
8433 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
8434 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
8435 - change 3-D solver to work with r* (for now, only with linear free-surf.)
8436 - add few debug diagnostics (cg3d_x, residual)
85d256894a Jean*8437 o model/src:
8438 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
8439 update output of exp. global_ocean.cs32x15.viscA4
f470880b96 Jean*8440 o update output of exp. global_ocean.cs32x15.icedyn after removing
8441 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
8442 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
a435e833b1 Mart*8443 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2a44bd20e3 Mart*8444 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
043540edbe Mart*8445 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
f470880b96 Jean*8446 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
a435e833b1 Mart*8447 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
f470880b96 Jean*8448 to test this code
eb4cdc75fa Jean*8449 o pkg/cd_code:
8450 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
8451 C-grid momentum. D-grid velocity used to be stepped forward in time with
8452 Adams-Bashforth only on surface pressure term. Tests show that using AB on
8453 D-grid coriolis term improves stability (as expected from CD-scheme paper).
8454 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
8455 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
8456 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
8457 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
8458 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
4d27a257dc Jean*8459 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
4a2ef1ee39 Jean*8460 o pkg/obcs:
eb4cdc75fa Jean*8461 - fix bug in initialisation (broken since Oct 1rst modification)
4a2ef1ee39 Jean*8462 for useOBCSprescribe without useEXF.
8463
0e6056cd20 Jean*8464 checkpoint61y (2009/11/15)
10b70e5d9c Mart*8465 o pkg/seaice
8466 - change (once again) the discretization for the evp solver: rather than
8467 squaring the averages of strain rates, average the squares to give
8468 a better approximation to VP behavior (in simple test); this breaks
8469 verification experiments that use EVP (lab_sea and lab_sea.hb87)
8470 --> update outputs
dde99557d4 Jean*8471 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
b2a741ef12 Mart*8472 to improve vectorization of adjoint code on TARGET_NEC_SX
29d62326d0 Davi*8473 o verification/vermix:
a435e833b1 Mart*8474 - change vermix to a more "classical" 1d column with high vertical
8475 resolution, seasonal heat flux forcing and constant wind forcing
10b70e5d9c Mart*8476 --> update outputs
6636ec7a94 Mart*8477 o pkg/seaice
8478 - fix diagnostics of principal stress components for EVP
8479 - add optional diagnostics of non-linear convergence for LSOR solver
8eb548676f Mart*8480 - make maximum zeta a runtime parameter
d7bdbe3409 Jean*8481 o model/src (3-d solver):
8482 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
8483 which consisted in removing the Surf. Non-Hydrostatic pressure from the
8484 whole column and adding it to Eta (inspired from Casualli, 1999):
8485 Only affects 3-D solver initial guess and only if using ExactConserv,
8486 but tests did show a degradation of solver convergence. For this reason,
8487 decide to disable this piece of code.
8488 to recover previous version, just set zeroPsNH = exactConserv (line 78).
8489 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
a435e833b1 Mart*8490 o pkg/ggl90:
8f048929ff Jean*8491 - fix previous modif (unfortunatly has not been documented here).
ef30cce719 Mart*8492 o pkg/seaice/autodiff:
e69eb16cf6 Mart*8493 - add CPP flag to include clipping of zeta in EVP code;
8494 although clipping of zeta is not necessary for EVP and not recommended
8495 it was done by default, now clipping is disabled by default
d68173436e Mart*8496 - modify computation and store zetaC/Z in seaice_evp for TAF
043891c656 Mart*8497 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
6636ec7a94 Mart*8498 - change seaice_calc_viscosities/strainrates for better
043891c656 Mart*8499 vectorization after AD by TAF
9fb8a4afa4 Jean*8500 - rearrange common blocks in SEAICE.h once again for easier dumps of
ef30cce719 Mart*8501 adjoint output, adjust adcommon.h and g_common.h
8502 - change flux form of default advection scheme for better vectorization
8503 of adjoint code
a435e833b1 Mart*8504 - modify lab_sea/input.lsr to test the flux form of default advection
ef30cce719 Mart*8505 scheme
8c04a08a06 Mart*8506 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
8507 transition in checkpoint61r)
8508
0e6056cd20 Jean*8509 checkpoint61x (2009/10/19)
3ccf557bdf Patr*8510 o adjoint: adding two new verification experiments
a435e833b1 Mart*8511 * tutorial_global_biogeo: an online dic sensitivity experiment
3ccf557bdf Patr*8512 (work with G. Forget)
8513 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
8514 (an update of the Dutkiewicz et al., 2006 paper)
8515 Both use the same CO2FLUX cost function, but different controls
8516 Gradient checks look good, but some recomp. could still be traightened out
8517 Should add xx_dic control variable to test at some point
51b66c683d Jean*8518 o model/src:
8519 add run-time parameters to check and/or mask initial Temp & Salt
7744ec9132 Jean*8520 o pkg/ptracers:
8521 apply zonal filter (if used) to all passive tracers
8522
0e6056cd20 Jean*8523 checkpoint61w (2009/10/12)
d5930766d9 Patr*8524 o adjoint:
8525 * update and finish work on adjoint of dic package (G. Forget)
8526 * start adjoint of offline package
8527 * bug fix for cube-sphere TLM code (active_file_g.F)
5ff9d8d8a4 Jean*8528 o tutorial_global_oce_optim:
8529 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
7784d9f62a Jean*8530 and add SIZE.h_mpi for MPI testing
442ec6ef47 Mart*8531 o pkg autodiff
8532 - fix bug in autodiff_restore
a435e833b1 Mart*8533 - make genmake2 remove comments and empty lines from ad_input_code.f in
442ec6ef47 Mart*8534 order to reduce file size (new script file remove_comments_sed)
54e442a4cf Jean*8535 o allows to specify vertical profile of vertical viscosity (viscArNr)
38d9d89a2d Mart*8536 o pkg autodiff
a435e833b1 Mart*8537 autodiff_ini_model_io: comment out writing of grid information to netcdf
8538 files, because at this time the grid fields are a bunch of zeros
8539 (this is analogous to ini_mnc_vars.F)
74b7cbac64 Mart*8540 o pkg seaice/autodiff:
a435e833b1 Mart*8541 left-over from removing the 3-time-level fields:
74b7cbac64 Mart*8542 - small rearrangement of common blocks (SEAICE.h)
a435e833b1 Mart*8543 - fix field declaration in order to get meaningful output in
8544 adseaice.*.nc (adcommon.h)
7532a9f33f Jean*8545 o pkg obcs:
8546 - go through NH code only if nonHydrostatic=T
8547 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
7784d9f62a Jean*8548 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
53056a14f9 Jean*8549 => Update output of experiment seaice_obcs
8550 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
8546425e3d Jean*8551 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
6463eff00c Jean*8552 - fix restart for useOBCSprescribe + useEXF
793e0bf23c Mart*8553 o pkg ctrl
8554 - make obcs as control parameter work also with useSingleCPUio
8555 - replace a few sny and snx by Ny and Nx to be consistent with
8556 ctrl_set_globfld_x/yz.F
cffcf702d2 Mart*8557 o pkg seaice
a435e833b1 Mart*8558 - re-introduce global field frWtrAtm for the case of
cffcf702d2 Mart*8559 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
8560 - catch the case of an empty filename in seaice_cost_init_fixed.F
8561 o pkg ecco:
8562 - small bug fixes in the_main_loop
8563 . fix order of monitor arguments
8564 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
8565 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
8566 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
a435e833b1 Mart*8567 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
8568 imbalance diagnostics for wmean_h/sflux = 0
cffcf702d2 Mart*8569 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
a435e833b1 Mart*8570 - catch the case of empty filenames in ecco_cost_init_fixed.F
cffcf702d2 Mart*8571 and ecco_readparms.F
8572 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
793e0bf23c Mart*8573 to make this statement meaningfull in ecco_cost_weights.F
339ad6c3b5 Jean*8574 o pkg zonal_filt:
8575 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
8576 - when using rStar, filter uVel*hFacW instead of uVel
8577 (tested without topography: fix a Pb of growing instability with NLFS)
9fba1b3510 Davi*8578 o pkg/aim/thsice:
8579 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
8580 (works as SST restoring)
55b32f1302 Davi*8581 o pkg/thsice:
8582 -add specific parameter for salt restoring in slab mixed-layer
8583 (by default equal to the temperature restoring)
8584
0e6056cd20 Jean*8585 checkpoint61v (2009/09/21)
e5d361f9aa Mart*8586 o pkg/kpp:
a435e833b1 Mart*8587 -add double diffusive contributions as a hack, turned off by default
8588 for now, and the code can be excluded with a CPP-flag
e5d361f9aa Mart*8589 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
8590 -add a verification experiments to "vermix" to test this code
f81982db08 Davi*8591 o pkg/mom_common:
8592 Move computation of length scales to mom_init_fixed.F (avoid recomputation
8593 at each time-steps*levels).
0dd6d0e826 Ryan*8594 o pkg/layers:
8595 Created a new package for computing volume fluxes in temperature or
8596 [not yet implemented] density layers, e.g. for calculating residual
a435e833b1 Mart*8597 overturning circulations.
8598 o pkg/diagnostics:
f4e6557763 Jean*8599 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
8600 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
f88b29d124 Jean*8601 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
8602 To avoid mixing type (RS/RL) of input/output array argument,
8603 replace single mixed-type array with a pair from each type (RS/RL).
03e0cc6d31 Jean*8604 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
a435e833b1 Mart*8605 is now implemented for all pkgs (previously only done for the main pickup)
03e0cc6d31 Jean*8606
0e6056cd20 Jean*8607 checkpoint61u (2009/08/25)
7b5bc55348 Mart*8608 o pkg/obcs:
23ff66f209 Mart*8609 - change OB?eta from _RS to _RL and put them into a separate commen block
8610 - add code to read OB?eta from a file via obcs_prescribe_read: the code
8611 compiles and does not destroy any other experiments, the data is read
8612 properly, but the code is not tested in actual applications
a435e833b1 Mart*8613 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
8614 create a meaningful unit attribute for the time coordinate variable
b6045d9739 Jean*8615 o pkg/ebm: add plenty of missing "_d 0" ;
a435e833b1 Mart*8616 update results of experiment global_ocean_ebm (fwd + adjoint tests)
b6045d9739 Jean*8617 Notes: several pieces of code only works for (very) specific set up
a435e833b1 Mart*8618 (domain size, lat range, etc ...); should be documented & stop if one
b6045d9739 Jean*8619 of those assumptions is not meet.
6b1574ad60 Jean*8620 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
a435e833b1 Mart*8621 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
6b1574ad60 Jean*8622 and offline_exf_seaice (seaicetd + adjoint).
70d7fbc59b Jean*8623 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
a435e833b1 Mart*8624 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
70d7fbc59b Jean*8625 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
a435e833b1 Mart*8626 o few changes to pass when compiling with strick checking of arguments
70d7fbc59b Jean*8627 across S/R (allow to find few bugs in S/R calls).
d5724f98ed Mart*8628 o pkg/seaice:
a435e833b1 Mart*8629 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
d5724f98ed Mart*8630 2d-fields, for slightly better performance
70d7fbc59b Jean*8631
0e6056cd20 Jean*8632 checkpoint61t (2009/07/22)
a435e833b1 Mart*8633 o pkg/seaice:
f503466573 Mart*8634 - remove unused variables in seaice_evp
8635 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
570ee1ae01 Jean*8636 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
8637 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
5a08ea66a4 Jean*8638 each processor opens a different file (a fix from Matt).
78e9a5d276 Jean*8639 o cg2d:
8640 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
8641 this reduces number of EXCH calls by 2 when using exch2.
a435e833b1 Mart*8642 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
78e9a5d276 Jean*8643 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
a435e833b1 Mart*8644 o pkg/thsice:
78e9a5d276 Jean*8645 add code for Near Infra-Red albedo (from Jeff)
f3e78cec2b Jean*8646 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
78e9a5d276 Jean*8647 o ini_model_io:
8648 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
8649 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
8650 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
f3e78cec2b Jean*8651
0e6056cd20 Jean*8652 checkpoint61s (2009/06/30)
2afd155f68 Jean*8653 o pkg/exch2 (exch2_rxN_cube*):
8654 remove last BARRIER (no need to synchronise after getting data from shared
8655 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
78c0da63a8 Jean*8656 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
8657 and generate new output (for the 2 tests) using default rotationPeriod.
e33637256c Jean*8658 o pkg/exch2:
8659 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
8660 (was already the case with AUTODIFF_EXCH2 defined)
8661 - add bj in exch2 arrays and S/R.
78c0da63a8 Jean*8662 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
8663 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
e8488bfd93 Oliv*8664 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
8665 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
8666 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
8667 - verification experiment natl_box.longstep
02bc4aeec0 Jean*8668 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
8669 allow different versions of ifort (8 or 9) and different versions
8670 of mpi (mpich or mpich2) to be used with the same optfile.
8671 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
8672 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
a435e833b1 Mart*8673 o pkg/seaice:
8674 fix previous modif (3-level field removed) for old-pickup reading
02bc4aeec0 Jean*8675
0e6056cd20 Jean*8676 checkpoint61r (2009/06/25)
a435e833b1 Mart*8677 o pkg/seaice:
88ddcec046 Mart*8678 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
64469ab2ce Mart*8679 1. introduce fields for time step (N-1)
88ddcec046 Mart*8680 2. do not use levels 2 and 3 anymore (but keep them)
a435e833b1 Mart*8681 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
8682 includes changes to pkg/thsice/thsice_get_velocity.F,
88ddcec046 Mart*8683 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
8684 pkg/obcs/obcs_apply_uvice.F.
8685 - completely remove code for leap-frog time stepping for second order
8686 advection
2e0a6baf06 Patr*8687 - adjusted adjoint accordingly;
8688 gradient checks have improved by an order of magnitude!
a435e833b1 Mart*8689
0e6056cd20 Jean*8690 checkpoint61q (2009/06/22)
bfa01eb1b6 Mart*8691 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
8692 - the boundary conditions along open boundaries are unclear, because the
8693 associated masks are set to zero and are thus treated as closed when
8694 applying the slip-boundary conditions.
8695 - move initialisation of grid variables from seaice_init_varia to _fixed
14ff2fe9e4 Dimi*8696 o adding doc/diags_changes.txt
a435e833b1 Mart*8697 o model/src:
8698 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
dddd7d8ee5 Jean*8699 to avoid "_diags" naming if no relation to pkg/diagnostics.
a435e833b1 Mart*8700 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
dddd7d8ee5 Jean*8701 file and only call PLOT_FIELD_XYZ if debugMode=T.
8702 remove few PLOT_FIELD_XY calls outside initialisation.
8703 remove few unnecessary BARRIER.
1aca59cbdd Dimi*8704 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
a435e833b1 Mart*8705 of salt_plume package in Southern Ocean
8706 o pkg/thsice:
8707 - fix hOceMxL in overlap (needed for sea-ice advection);
a870da40f8 Jean*8708 update output of experiment global_ocean.cs32x15.icedyn.
a435e833b1 Mart*8709 o pkg/seaice:
2fe56e7563 Mart*8710 - make the (placeholder-)tracer IceAge a little more meaningful
0ccf00deac Mart*8711 by avoiding ridging of age due to convergent ice flow
14ff2fe9e4 Dimi*8712 - add diagnostics for surface temperature, atmospheric and oceanic
8713 heat flux, and atmospheric and oceanic ice growth
0ccf00deac Mart*8714
0e6056cd20 Jean*8715 checkpoint61p (2009/06/10)
7b728547f6 Jean*8716 o eesupp (global_max & global_sum):
8717 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
8718 - remove starting & endding barrier (no longer needed)
4877fb20d9 Jean*8719 o pkg/mdsio, writelocal:
8720 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
8721 (remove the STOP): uses shared buffer IO to store data from all threads
8722 and then let master-thread write nThreads tiles.
1f0f779d4b Jean*8723 o pkg/mdsio (read/write field):
8724 - tiled IO done in 1 piece (all levels at a time);
4877fb20d9 Jean*8725 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1f0f779d4b Jean*8726 - multi-threaded: allow to read/write local (non-shared) array
8727 (was already working with singleCpuIO ; now works also without);
8728 => no longer needs barrier call after reading a file (added inside
4877fb20d9 Jean*8729 mds_read/write field).
1f0f779d4b Jean*8730 - move barrier calls outside gather/scatter_2d to mds_read/write_field
b54505b067 Mart*8731 o pkg/obcs/exf
a435e833b1 Mart*8732 - exf_getffieldrec.F: add a few ". _d 0" and
8733 add code to catch the case fldperiod = 0.
8734 - obcs_precribe_read.F: change if statements so that they match
b54505b067 Mart*8735 the variable type (_RL)
a435e833b1 Mart*8736 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
b54505b067 Mart*8737 exf_iprec) as part of namelist EXF_NML_01
70cbc60ad4 Jean*8738 o pkg/mdsio:
8739 - read/write tiled (local) files: read/write 1-level tile chunk at a time
8740 (instead of segment of length sNx); expected to speed up tiled IO.
8741 o pkg/exch2:
c53c960d6f Jean*8742 - take buffer copy from/to array out of S/R exch2_send/recv into new
8743 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
8744 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
8745 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
70cbc60ad4 Jean*8746 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
c53c960d6f Jean*8747 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
8748 including Topology header file (and common blocks).
8749 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
8750 remove 2nd exch call in exch2_s3d_rx (no longer needed).
8751 - document S/R arg. list (+ update some comments)
1ce2a5cdfd Dimi*8752 o pkg/seaice:
8753 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
8754 temperature and humidity over sea ice based on climatological values.
3827b3ff39 Mart*8755 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
a435e833b1 Mart*8756 of LSR (this change is expected to change the results slightly because now
3827b3ff39 Mart*8757 it uses slightly difference moduli from the second last LSR solution, but
a435e833b1 Mart*8758 that is more consistent with the stress computations; this part of the code
3827b3ff39 Mart*8759 is not tested in the verification experiments)
7beac62984 Mart*8760 - fix diagnostics for flux of ice in case of B-grid
a435e833b1 Mart*8761 - turn strain rates eij and press into global fields within global
7beac62984 Mart*8762 common block in SEAICE.h for more straighforward diagnostics
8763 - fix diagnostics for principal stress components, press, zeta, eta
8764 to give something meaning full
607aea417f Jean*8765 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
8766 new output (all 4 tests) using default rotationPeriod.
37512d714c Davi*8767 o pkg KPP:
8768 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
8769 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
8770 and normal grid from 1 to Nr)
6a8a92ceb1 Davi*8771 o Fix computations of L4rdt in mom_calc_visc.F
4444d50a00 Jean*8772 o eesupp:
8773 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
8774 should be called before a "stop" if we know that all process are going
8775 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
8776
0e6056cd20 Jean*8777 checkpoint61o (2009/05/26)
52b3903673 Jean*8778 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
8779 o model/src/ini_curvilinear_grid.F:
680765c772 Mart*8780 compute angleSin/CosC when they are not read from a file
52b3903673 Jean*8781 o pkg/seaice:
680765c772 Mart*8782 add pseudo time stepping for LSOR
cfdf8f6dc3 Jean*8783 o pkg/exch2:
8784 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
f834b21bef Dimi*8785 o pkg/seaice:
f81e0cd482 Dimi*8786 Adding separate sea ice albedo, drag coefficients, and HO in Southern
8787 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
39f815874d Jean*8788 o SingleCpuIO:
8789 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
8790 o pkg/seaice:
affccff0e4 Jean*8791 put exchanged variable in (local) common block for MPI+Multi-Threads
8792 to work (necessary with exch1, and for now with exch2 too).
8d614a5ef7 Jean*8793 o verification: to get more experiments tested with mpi, mth and mpi+mth,
8794 change tiling of:
8795 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
8796 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
8797 update output of exp:
8798 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
8799 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
8800 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
8801 (note: output.txt generated on faulks using only 1 tile)
505fa6b5f0 Jean*8802 o eesupp & mdsio (SingleCpuIO):
8803 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
8804 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
8805 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
8806 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
8807 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
8808 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
8dd64871a3 Jean*8809 o pkg/exch2:
8810 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
8811 read parameter file "data.exch2" if it exists; otherwise try default regular
8812 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
8813 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
8814 with new code (not to be used, just as a backup solution).
a435e833b1 Mart*8815 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
505fa6b5f0 Jean*8816 in utils/exch2/input.
8dd64871a3 Jean*8817
0e6056cd20 Jean*8818 checkpoint61n (2009/05/12)
6805d023a2 Jean*8819 o eesupp & mdsio (SingleCpuIO):
8820 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
8821 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
8822 receive real*4 array (instead of real*8) to read/write 32.bit files.
8823 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
8824 and remove new mapping S/R)
b983b0a9f3 Jean*8825 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
8826 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
8827 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
8828 when using exch2. Add S/R to map global io-buffer to global model array.
8829 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
8830
0e6056cd20 Jean*8831 checkpoint61m (2009/04/29)
b983b0a9f3 Jean*8832 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
8833 and add 3 other S/R for other types (R4,R8,RS).
5ae9fbe2f9 Jean*8834 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
8835 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
8836 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
8837 - reduce number of macro definitions (keep only those which are used);
8838 can always call directly the corrresponding S/R if needed.
b983b0a9f3 Jean*8839 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
5ae9fbe2f9 Jean*8840 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
8841 Fixed wrong type of arg in:
b983b0a9f3 Jean*8842 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
5ae9fbe2f9 Jean*8843 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
8844 To fix: global_sum of var in common block is wrong (multi-threaded) in:
8845 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
8846 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
b983b0a9f3 Jean*8847 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
8848 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
52af3a32f7 Jean*8849 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
8850 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
8851 edges are closed (zero depth); might happen with "blank tiles";
b983b0a9f3 Jean*8852 for now, disabled if using OBCS.
52af3a32f7 Jean*8853 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
855948c4e0 Jean*8854 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
52af3a32f7 Jean*8855 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
6e7414edd7 Jean*8856 to reduce length of 1.D array print in STDOUT.
71c716cb9b Jean*8857 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
8858 + use 48 tiles (16x8): this will allow to test "blank tiles".
8859 o start to test MPI + multi-threaded (change testreport to skip tests
8860 where number of tiles do not match).
8861 o genmake2: add option "-omp" to turn on Open-MP ;
8862 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
0ab0cf443f Jean*8863 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
8864 and keep the original tile numbering. Note: compatible with old
8865 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
8866
0e6056cd20 Jean*8867 checkpoint61l (2009/04/07)
5a8046a779 Jean*8868 o Overlaps had been forgotten in calculating ijk keys : fixed
8869 o fix cyrus makedepend for gcc 4.4
54b0077775 Jean*8870 o experiment fizhi-cs-aqualev20:
8871 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
71c716cb9b Jean*8872 and generate new output. Note: new output is much closer to the old
8873 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
54b0077775 Jean*8874 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
8875 o pkg/fizhi:
8876 - change to avoid indices going deliberately over array-bounds
8877 - remove unnecessary MPI stuff
8878 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
8879 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
8880 does not go over array-bounds and therefore returns reliable output.
8881 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
8882 this S/R has 4 output arguments, which are used inside "get_alarm";
8883 when it is called with the same variable "ndum" in place of several
8884 output arguments, this produces weird side effect inside "get_alarm"
8885 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
8886 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
8887 address) and produces error.
855948c4e0 Jean*8888 o tools/gemake2: (March 27-29 2009)
a435e833b1 Mart*8889 with option "-mpi": link *_mpi files from "MODS" dir (this is what
855948c4e0 Jean*8890 testreport does).
405ae5a3ac Jean*8891 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
54b0077775 Jean*8892 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
405ae5a3ac Jean*8893 update lab_sea.lsr & lab_sea.salt_plume results
a435e833b1 Mart*8894 o pkg/seaice:
90652fd079 Mart*8895 Major overhaul of the LSOR solver: change discretization from original
8896 finite differences to finite volume. The old routine is still in the
8897 file seaice_lsr.F and can be turned on with the CPP-flag
8898 SEAICE_OLD_AND_BAD_DISCRETIZATION
8899 Along with this change, the discretization of the strain rates is changed.
8900 The same flag turns on the old discretization in seaice_calc_strainrates.F
a435e833b1 Mart*8901 All verification experiments with seaice are affected (except for
90652fd079 Mart*8902 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
8903 results by setting the above flag.
8904 Further changes involve changes in defaults:
8905 - ALLOW_FLOODING is defined and turned on by default
f6450d3114 Patr*8906 - SEAICEadvSnow = .true. is now the default
8907 - SEAICEadvSalt = .true. is now the default
8908 - SEAICEadvAge = .true. is now the default
a435e833b1 Mart*8909 - SEAICE_clipVelocities = .false. is now the default
5d15d4162f Mart*8910 (as per J. Zhang's recommendation)
90652fd079 Mart*8911 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
8912 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
8913 - seaice_growth: replace computation of UG by a simple copy from wspeed
8914
0e6056cd20 Jean*8915 checkpoint61k (2009/03/18)
4acbf6fef8 Mart*8916 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
8917 seaice_lsr: fixed a few metric terms,
8918 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
8919 add more debugging diagnostics
8920 seaice_evp: removed superfluous many metric terms of FV discretization
8921 of stress divergence
8922 affects lab_sea, lab_sea.hb87
8923 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
a435e833b1 Mart*8924 of stress divergence for non-evp solver
4acbf6fef8 Mart*8925 (this part is not tested anywhere)
8926 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
8927 they were effectively only half slip
8928 affects lab_sea.hb87
71a18d0f38 Jean*8929 updated all relevant verification experiments (except lab_sea//output_adm.txt
8930 which was left over, but fails at level 7 & 6)
4acbf6fef8 Mart*8931
0e6056cd20 Jean*8932 checkpoint61j (2009/03/17)
78416b4f31 Mart*8933 o pkg/seaice: turn a few hard wired parameters into run time parameters
a435e833b1 Mart*8934 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3393e77079 Mart*8935 time in seconds as promised by the usints in seaice_monitor and exf_monitor
a32626876a Mart*8936 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
8937 that are not cubed-sphere grids
f577077207 Mart*8938 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2db8cfe50f Jean*8939 o pkg/ctrl:
8940 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
0ad8ad6f0c Jean*8941 o non-hydrostatic (calc_gw.F):
8942 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
8943 update output of exp. global_ocean.cs32x15.viscA4
8944 o remove backward compatibility for thetaMin,phiMin
ece53aa93e Jean*8945 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
a435e833b1 Mart*8946 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
8947 interpolated wind field not only for curvilineargrid=.true., but also
514437540a Mart*8948 for a rotated grid (rotateGrid=.true.)
58378fc26e Mart*8949 o pkg/exf: add capability to bypass interpolation for runoff
8950 by setting yet another CPP-flag
ece53aa93e Jean*8951 o eesupp/src, B-grid exchange:
8952 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
bb9388b6fb Patr*8953 o autodiff
8954 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
8955 allows to switch to single-prec common blocks;
8956 corresponding switch occurs in tamc.h, integer isbyte
8957 TAF store directivs "byte" and "kind" seem equivalent;
8958 Most tamc.h have been updated correspondingly.
8959
0e6056cd20 Jean*8960 checkpoint61i (2009/02/13)
05fc4302e4 Patr*8961 o autodiff:
8962 fix autodiff_sore/_restore indices for obcs
8963 (spotted by I. Hoteit, M. Mazloff)
685514cedc Patr*8964 o pkg/autodiff, pkg/ctrl:
a435e833b1 Mart*8965 Add flag to reduce all tapelev I/O to single-prec.
685514cedc Patr*8966 In data.ctrl set
8967 doSinglePrecTapelev = .TRUE.
ece53aa93e Jean*8968 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
8969 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
a435e833b1 Mart*8970 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
6870c5ed6c Mart*8971 real fresh water flux (not yet)
a94d876c45 Jean*8972 o pkg/mdsio & rw:
8973 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
8974 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
6be08e3e5c Jean*8975 o pkg/flt:
8976 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
8977 init_fixed & ini_varia.
71a5d709a0 Jean*8978 - clean-up & simplify linear interpolation S/R:
8979 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
8980 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
a94d876c45 Jean*8981 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
b57550bbcf Jean*8982 - add vert. coordinate & horiz. indices to output files.
8983 - change vertical position in initial condition, from index to depth [m].
1cae6a1a9f Jean*8984 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
8985 (easier to get to a curvilinear grid) ; delX,delY no longer used.
97caae06d7 Davi*8986 o pkg/ggl90: a few modifications:
8987 - fix bottom boundary condition, and interpolation of KappaE
8988 near top and bottom
a435e833b1 Mart*8989 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
97caae06d7 Davi*8990 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
a435e833b1 Mart*8991 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
d236014eb6 Jean*8992 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
8993 (maintain temporary backward compatibility, until next checkpoint)
8994
0e6056cd20 Jean*8995 checkpoint61h (2009/01/27)
021d69ec69 Jean*8996 o pkg/diagnostics with "periodic averaging diagnostics":
a435e833b1 Mart*8997 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
794d630b5b Jean*8998 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
de15b00af7 Mart*8999 o pkg/obcs: fix loop ranges for balancing code
de52daaeea Jean*9000 o pkg/flt:
9001 - improve criteria for finding which tile owns a float.
9002 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
d7a6322cee Davi*9003 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
9004 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
9005 with ocean biogeo)
5de0afb7f6 Jean*9006 o pkg/flt:
9007 - do some cleaning and fix the restart ;
9008 - add output.txt in flt_example/results to get this pkg tested.
9009 o genmake2: add an EXTENDED_SRC option and flag.
9010 for now, cannot be turned on on command line (only through genmake_local)
b5cd61a537 Jean*9011 o pkg/mdsio: read/write vector:
9012 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
5de0afb7f6 Jean*9013 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
b5cd61a537 Jean*9014 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
9015 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
9016 (drop to 4 digits matching for grad). But this test does not look very
9017 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
9018
0e6056cd20 Jean*9019 checkpoint61g (2008/12/29)
ca04df591d Jean*9020 o pkg/flt:
9021 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
9022 + make OPTIONS file more standard.
9023 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
9024 - fix _BYTESWAPIO CPP-Flag
9025 - standard reading of file-parameter "data.flt"
b95b67d7aa Jean*9026 - fix argument list of S/R FLT_RESTART
ca04df591d Jean*9027 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
d67bffc17c Mart*9028 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
46b3c62480 Mart*9029 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
9030 a still unfixed compiler/optimization bug
9031
0e6056cd20 Jean*9032 checkpoint61f (2008/11/21)
a435e833b1 Mart*9033 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
45b6388240 Jean*9034 update results of global_ocean.cs32x15.icedyn test.
aa713d5dbf Jean*9035 o move getcon.F from model/src to pkg/fizhi.
a435e833b1 Mart*9036 o pkg/exf: add parameter for extrapolation of temp up to the surface
df444da92e Jean*9037 and option to prevent negative evap (in bulk_largeyeager04 only).
a78ca545b5 Jean*9038 o Prather Advection scheme: fix tracer conservation for divergent flow
9039 (e.g., when using NonLin Free-Surface).
e18a7f3164 Davi*9040 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
db624d91db Jean*9041 o gmredi (Visbeck-variable-K):
9042 - add more parameters to Visbeck-variable-K.
9043 - use a 5 points average for dSigmaR in Visbeck-K calculation
9044 (more "homogenous": same stencil and same weights as in dSigmaH)
9045 - update output of ideal_2D_oce experiment.
a435e833b1 Mart*9046 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
8d0c7e204b Mart*9047 (#undef REAL4_IS_SLOW)
a435e833b1 Mart*9048 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
8d0c7e204b Mart*9049 coordinate variable
a435e833b1 Mart*9050 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
8d0c7e204b Mart*9051 (surface forcing fields), removes some of the functionality
a435e833b1 Mart*9052 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
9053 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
9054 probably not all: copy _RS surface flux fields to RL field before
8d0c7e204b Mart*9055 calling DIAGNOSTICS_FILL
a435e833b1 Mart*9056 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
c983541b6d Mart*9057 real*4 (CALL EXCH_*_RS) versions.
04c02cca57 Jean*9058 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
9059 (generate new output).
8d0c7e204b Mart*9060
0e6056cd20 Jean*9061 checkpoint61e (2008/10/23)
c01397a2cf Jean*9062 o gmredi (Visbeck-variable-K):
9063 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
a435e833b1 Mart*9064 - change computation of Visbeck-K where Slope > Smax :
c01397a2cf Jean*9065 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
9066 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
bd21fff799 Jean*9067 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
9068 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
9069 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
c3fe1ef4e7 Jean*9070 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
c01397a2cf Jean*9071 does not become too large (to avoid precision problems in implicit-diffusion
c3fe1ef4e7 Jean*9072 solver); update ideal_2D_oce output.
9b7442ecc8 Davi*9073 o pkg ggl90:
9074 - in ggl90_cal.F: compute only one set of visc/diff, used to
9075 step forward TKE/T/S/momentum
9076 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
9077 have Prandlt =1)
c01397a2cf Jean*9078 o gmredi (fm07):
284c68fd43 Jean*9079 - add lower limit on Transition layer thickness + lower limit on 1/lambda
883da68718 Jean*9080 - allow to set few more params from data.gmredi
5c4169b4ba Davi*9081 o pkg ggl90:
a435e833b1 Mart*9082 - add missing sqrt(2) factor in computation of mixing length
5c4169b4ba Davi*9083 scale in ggl90_calc.F
9084 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
9085
0e6056cd20 Jean*9086 checkpoint61d (2008/09/25)
900e7deb27 Patr*9087 o adjoint modifs
9088 - adapt to new field rhoInSitu
9089 - allow to revert from StoreDynVars2D, StoreDynVars3D
9090 to individual fields
9091 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
9021e26bd9 Jean*9092 o store 3-D (in-situ) density in commom block (DYNVARS.h)
9093 - save 1 rho computation.
9094 - no longer modify T & S inland when using down_slope pkg.
a435e833b1 Mart*9095 o gad_som : allow to switch to SOM advection for T & S without corresponding
b3d25f406d Jean*9096 pickup files (using new S/R: MDS_CHECK4FILE).
9097 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
9098 (for useSingleCpuIO to work in multi-threaded)
30b946f21e Mart*9099 o pkg/shelfice:
9100 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
9101 with SHELFICEtopoFile in data.shelfice
9102 - move code for reading ice shelf topography and modifying hFacC into separate
9103 subroutines of the shelfice package
9104 - separate initialisation of "fixed" and "variable" variables
9105 - kTopC is not (yet) replaced by kSurfC, although this is possible
b3d25f406d Jean*9106 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1c7cf036e1 Jean*9107 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
9108 and rename:
9109 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
9110 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
9111 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
9112
0e6056cd20 Jean*9113 checkpoint61c (2008/08/30)
a435e833b1 Mart*9114 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
9115 to add mass source/sink of fluid in the interior (3-D generalisation
f035afc50f Jean*9116 of oceanic real-fresh water flux).
9117 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
aa106dc1b1 Jean*9118 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4d4605f96d Jean*9119 o new pkg: down_slope
9120 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
9121 - presently, modify T & S inland (dwnslp_calc_rho.F).
9122 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
9123 - implementation for ocean in P-coords not tested.
9124 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
9125 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
50f1c7ab80 Jean*9126 (to facilitate conversion of oceanic pkg to p-coordinate).
a435e833b1 Mart*9127 o change FIND_RHO to FIND_RHO_2D :
f257f8b0f6 Jean*9128 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
9129 o new pkg: cheapaml
9130
0e6056cd20 Jean*9131 checkpoint61b (2008/08/05)
a435e833b1 Mart*9132 o exch2:
37ee8575fd Jean*9133 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
9134 - no longer depend on the order sequence (N,S,E,W).
9135 - 3rd exchange no longer needed (tested with 24 tiles).
9136 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
9137 - exch_UV_A-grid readily available (but not yet tested).
a435e833b1 Mart*9138 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
9139 (both are no longer needed) in exch_uv: no effect in forward run; but
37ee8575fd Jean*9140 get truncation error differences with adjoint exch.
a435e833b1 Mart*9141 o exch2:
0e9f2e49ad Jean*9142 - change index-bounds storage (moved from target to local tile,
9143 more intuitive this way) ; rename/remove some variables.
37ee8575fd Jean*9144 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
0e9f2e49ad Jean*9145
0e6056cd20 Jean*9146 checkpoint61a (2008/07/29)
a435e833b1 Mart*9147 o exch2/matlab-topology-generator:
9d45a8c11b Jean*9148 fix bug in index bounds for N-S internal exchange (hard to tell if this
9149 had any effect on the solution).
677d07a6b5 Mart*9150 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
9151 is exceeded
a435e833b1 Mart*9152 o testreport: modify syntax of awk, so that it works also with
0d1768695f Mart*9153 awk, and not only with nawk and gawk
9154
0e6056cd20 Jean*9155 checkpoint61 (2008/06/24)
0a92c8c20d Patr*9156 o autodiff
9157 Change default for TAF usage by removing argument '-nonew_arg'
9158 This changes TAF subroutine argument list (ordering of active var.)
9159 Omission of this flag leads to incompatibility w.r.t. TAMC
9160 To restore TAMC-compatibility, need following modifs:
9161 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
9162 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
9163 Tested TAF version is 1.9.22
9164 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
9165
0e6056cd20 Jean*9166 checkpoint60 (2008/06/19)
f8c2a15654 Patr*9167 --->>> This is the last checkpoint for which generating the adjoint
9168 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
9169 --->>> by default.
9170 --->>> Future checkpoints will ommit this flag by default.
40cd24c888 Jean*9171 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
1b63dc87ac Gael*9172 o pkg/grdchk: Add gradient check to etan0 perturbations.
a435e833b1 Mart*9173 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
9174 o pkg/autodiff: more flexibility in zeroadj.
9175 model/src: modifying do_oceanic_phys.F accordingly.
fa59c87170 Gael*9176 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
9177 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
a435e833b1 Mart*9178 special setup of gmredi for which the adjoint is stable
fa59c87170 Gael*9179 enough for parameter optimization.
e67ddf28f4 Gael*9180 o bridging the gap between eddy stress and GM.
9181 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
9182 along with a change in CPP option (now ALLOW_EDDYPSI).
a435e833b1 Mart*9183 -> when using GM w/ GM_AdvForm:
e67ddf28f4 Gael*9184 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
9185 is applied either in the tracer Eq. or in momentum Eq.
9186 depending on data.gmredi (intro. GM_InMomAsStress).
9187 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
9188 The key modifications are in model/src/taueddy_external_forcing.F
9189 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
40cd24c888 Jean*9190
0e6056cd20 Jean*9191 checkpoint59r (2008/05/29)
0d306f558f Jean*9192 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
9193 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
9194 fix option to read coriolis(@ cell-corner) from files with CS-grid.
aa539d5971 Mart*9195 o pkg/mnc: add some attributes to standard 1D-coordinate variables
79e37afef0 Mart*9196 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
9197 mass points, when using mnc for output
a435e833b1 Mart*9198 - add runtime parameter (missing_value, missing_value_int) to override
79e37afef0 Mart*9199 default (which is the value of getcon('UNDEF'))
9200 o pkg/mnc: prepare mnc for the actual use of missing values with the
9201 diagnostics package: small fix in mnc_cw_readwrite.template and more
9202 initialisation of never used fields
cebfffcf05 Mart*9203 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
9204 versions
a435e833b1 Mart*9205 o pkg/thsice/thsice_ini_vars.F added default initial values so that
9206 thermodynamics sea ice solver does not blow up when some initial fields
cebfffcf05 Mart*9207 are missing.
87838921ba Jean*9208 o move from external_forcing_surf.F to ini_forcing.F
9209 the p-coord. hack consisting in using pLoad to set phi0surf ;
9210 update output of tutorial_global_oce_in_p (affected @ truncation level).
a435e833b1 Mart*9211 o Freshen up a bit hs94.1x64x5, notably:
9212 remove rotationPeriod and tRef=5*0. (adjoint only), and add
cebfffcf05 Mart*9213 exactConserv=.TRUE.
34e240c0d3 Jean*9214 o pkg/generic_advdiff:
9215 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
9216 applies to files where Temperature & Salinity 2nd Order moments are used.
bc2cda07c1 Oliv*9217 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
9218 this uses a dynamically allocated internal state data structure
a435e833b1 Mart*9219 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
bc2cda07c1 Oliv*9220 and requires a fortran 90 compiler
9221
0e6056cd20 Jean*9222 checkpoint59q (2008/05/06)
934822fb62 Jean*9223 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
9224 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
bb5c940526 Davi*9225 o Refresh tutorial_global_oce_biogeo, notably:
9226 - change bathymetry (put back seamounts in ACC, use hFacs)
9227 - change EOS (POLY3 --> JMD95Z)
9228 - use Bryan-Lewis vertical diffusivity
9229 - use multidimensional advection
9230 - remove old virtual virtual in dic pkg, now done through ptracer pkg
9231 - change a couple of parameters in dic pkg
b488248973 Gael*9232 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
a435e833b1 Mart*9233 o pkg/obcs: change default to OBCSfixTopo = .true.,
37d6577e8a Mart*9234 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
9235 - replace "debugMode" with "debugLevel .GE. debLevB"
a435e833b1 Mart*9236 o implementation of TAF directives for gchem,cfc,dic
c668f876bd Jean*9237 o remove "exp5" (replaced by tutorial_deep_convection).
ba199509e7 Mart*9238 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
9239 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
9240 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
68dbdb7bfc Mart*9241 --> changes results in exp4, seaice_obcs
c668f876bd Jean*9242 o tutorial_deep_convection :
4c59896cb2 Jean*9243 update the set-up and increase resolution and domain size ; start
9244 from pseudo initial conditions = output at t=120mn in order to see
9245 something happening when running testreport.
e3f6e77e00 Mart*9246 o pkg/seaice: add os7mp as an advection scheme
9247 add check for advection schemes
f414077a87 Mart*9248 add a flag for restoring T and S underneath sea ice
a435e833b1 Mart*9249 o pkg/my82: add netcdf-support and diagnostics
ea0ee0d61a Davi*9250 o thsice pkg:
ba199509e7 Mart*9251 - Now hsMax limits snow height by turning it into ice following
ea0ee0d61a Davi*9252 flooding scheme (and now conserving energy)
9253 - Slight rewriting of the formula in thsice_calc_thick.F
9254 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
a435e833b1 Mart*9255 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
ea0ee0d61a Davi*9256
0e6056cd20 Jean*9257 checkpoint59p (2008/04/10)
2fbf89db82 Jean*9258 o gchem / dic / cfc :
9259 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
9260 - add new parameter files: "data.dic" & "data.cfc" ;
9261 - various re-arrangement in initialisation & header file ;
9262 - fix tutorial_global_oce_biogeo for multi-threaded test.
9263 o pkg/dic: test for "pickup_dic" file when restarting ;
9264 if no pickup-file, can restart with a re-initialised pH (same as it did
b3b930c218 Jean*9265 before) providing pickupStrictlyMatch is set to False.
eec9c6a066 Jean*9266 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
9267 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
9bfbe2231e Jean*9268 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
9269 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
9270 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
9271 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
9272 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2f4da9d91b Jean*9273 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
9274 scheme to use for vorticty-term ;
a435e833b1 Mart*9275 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2f4da9d91b Jean*9276 (with default selectVortScheme, return to original discretisation)
9277 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
0b784ff841 Mart*9278 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
81ea2c715a Jean*9279 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
9280 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
9281 also fix diagnostics VISCAHW & VISCA4W.
9282
0e6056cd20 Jean*9283 checkpoint59o (2008/03/07)
92268978d1 Jean*9284 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
360ad14abb Mart*9285 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
9286 move a few statemens out the main loop into separate loops
a435e833b1 Mart*9287 o pkg/shelfice:
9288 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
674cb80ca8 Mart*9289 (kg/m^2/s), does not break tests, because in verification/isomip,
9290 rhoConstFresh=rhoConst (by accident)
e3465203db Mart*9291 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
9292 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
9293 new file model/src/seawater.F, so that they are available for all pkgs.
9294 - convert potential temperature into in-situ temperature. This changes the
9295 isomip tests => update tests
a435e833b1 Mart*9296 o add a flag writePickupAtEnd (default=true) to be able to suppress
97a8c939f6 Mart*9297 writing a pickup at the last timestep
a435e833b1 Mart*9298 o tools/mpack-1.6 :
7739cd8f78 Jean*9299 - disable automake (not working) and autoconf (not needed).
9300 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
9301 also cleaner with much less compilation warnings.
a435e833b1 Mart*9302 o pkg/profiles:
9e1d042ca2 Gael*9303 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
9304 (for "less than 32 characters name" compiler requirement)
212017a383 Dimi*9305 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
9306 conditions that have a different sampling frequency than S/T/U/V obcs
a435e833b1 Mart*9307 o pkg/diagnostics (stats-diags):
cae4654411 Jean*9308 - fix global Min/Max in case 1 processor get only empty tiles
e89c0084d6 Mart*9309 o genmake2: replace (4 times)
9310 make genmake_tc_1.o >> genmake_warnings 2>&1
9311 with
9312 COMM="$CC $CFLAGS -c genmake_tc_1.c"
9313 echo $COMM >> genmake_warnings
9314 $COMM >> genmake_warnings 2>&1
9315 to make genmake2 always see the value of CC as specified in the optfile.
2c62398d5b Jean*9316 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
9317 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
9318 - modify verification advect_cs test to test SOM-advection on CS-grid.
239c38208f Gael*9319 o pkg/ctrl:
a435e833b1 Mart*9320 - Rewrite of ctrl_map_ini_ecco.F,
239c38208f Gael*9321 introducing a generic routine (ctrl_map_ini_gen.F).
9322 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2c62398d5b Jean*9323
0e6056cd20 Jean*9324 checkpoint59n (2008/02/09)
a435e833b1 Mart*9325 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
ae37e502a3 Jean*9326 number in dedicate array "hdiag":
9327 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
9328 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
9329 - many small changes (integer format) for large number of diagnostics
9330 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
9331 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
7514c1bd55 Mart*9332 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
9333 usingSphericalGrid, this allows to define the rotated grid coordinates
9334 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
9335 geographical coordinates according to the inverse of the rotation defined
a435e833b1 Mart*9336 by the Euler angles, so that Coriolis parameter and online-interpolation by
7514c1bd55 Mart*9337 exf works with the geographical coordinates on XC/YC/XG/YG.
a435e833b1 Mart*9338 Naturally, this feature does not work with all packages, so some
9339 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
9340 profiles), because there the coordinates are assumed to be regular
9341 spherical grid coordinates.
c9e4a2e67d Gael*9342 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
9343 - introduce isopycnal diffusion coefficient control.
a435e833b1 Mart*9344 o tools/adjoint_options:
c9e4a2e67d Gael*9345 - additional control vector components.
8b4eff4f81 Mart*9346 o pkg/mnc: have mnc create marginally meaning full coordinate variables
a435e833b1 Mart*9347 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
9348 o pkg/mypackage:
9349 - add example of read/write pickup for state-var ;
1c85ab9892 Jean*9350 - add entry points to the main code for state-vars diags & write-pickup.
659d0ae881 Dimi*9351 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
9352 transitions for useExfYearlyFields
a435e833b1 Mart*9353 - add new subroutine that determines the file to read from for
510778fc01 Mart*9354 use*YearlyFields = .TRUE. and .FALSE.
a435e833b1 Mart*9355 - add a verification experiment to global_with_exf that tests
23f0d70669 Mart*9356 useExfYearlyFields with USE_EXF_INTERPOLATION defined
a435e833b1 Mart*9357 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
9358 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
9359 subroutines (which could be generated from a template, because they are
7c7f4c7f71 Mart*9360 almost identical), for now they are included in obcs_prescribe_read.F for
9361 simplicity
e189b52423 Mart*9362 o pkg/exf:
a435e833b1 Mart*9363 - add a little more diagnostic to exf_interp_read (in analogy to
e189b52423 Mart*9364 mds_read_field, can be turned off with debugLevel < debugLevA=1)
9365 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
a435e833b1 Mart*9366 ugly but fast by unrolling short inner loops, inserting a unroll=8
4f5a52ae80 Mart*9367 directive in routine lagran, and splitting a loop and making do while the
9368 outermost loop (the latter requires the intoduction of index arrays)
0f64a7d6fb Dimi*9369 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
02aabb8fe5 Dimi*9370 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
9371 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3b88786c4e Dimi*9372 o verification/seaice_obcs: updated for restart test and latest options
dadd13178c Mart*9373 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
9374 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
9375 for now this is only available for the C-grid code and also within
9376 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
9377
0e6056cd20 Jean*9378 checkpoint59m (2008/01/14)
b1bf47d3b3 Dimi*9379 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
9380 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
a435e833b1 Mart*9381 o gad_som : fix flux output (& diagnostics) to have same units as other
9382 advection scheme fluxes (was previously multiplied by deltaT).
41fb919ba6 Dimi*9383 o added verification/seaice_obcs both to test seaice open boundaries
9384 and to provide an example matlab scrpt for generating them
9385 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
5968a91b01 An T*9386 o pkg/salt_plume: clean up salt_plume_frac.F to
9387 remove redundancy in PlumeMethod 1 and 4
30c6f5b1cd An T*9388 o pkg/kpp: added saltplume diagnostics
49834856da Dimi*9389 o pkg/obcs and pkg/seaice:
9390 - do not set uice and vice to zero when OB*icefile are unspecified
9391 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
9392 - moved seaice tracer obcs after call to seaice_growth
824966555a Dimi*9393 o pkg/salt_plume: added various options for salt plume depth
9394 criterion and for vertical distribution of the salt
c98c324ec7 Jean*9395
0e6056cd20 Jean*9396 checkpoint59l (2007/12/18)
94059a384d Jean*9397 o pkg/ptracers: new version of ptracers pickup:
9398 read meta file and write only fields which are needed to restart.
9399 ( same logic as main pickup file ; also using pickupStrictlyMatch )
e6b0d1006c Dimi*9400 o pkg/seaice:
f2446b8a43 Mart*9401 - add timescale for melting due to warm mixed layer as a means of
9402 setting SEAICE_availHeatFrac more conveniently
9403 - add a CPP-flag/runtime parameter check for flooding algorithm
e6b0d1006c Dimi*9404 - reformulated availHeat in seaice_growth.F to be independent of AREA
f2446b8a43 Mart*9405 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
9406 unit changes
00127a5872 Dimi*9407 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
ef5afff8c1 Mart*9408 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
9409 SX vector computer.
6eb23881b9 Dimi*9410 o pkg/seaice:
9411 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
9412 seaice forcing fields can now be read only through pkg/exf
9413 - removed some unused halos
21234f54a9 Jean*9414 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
0b49ffce6f Dimi*9415 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
9416 or U/VICE from U/VWIND before computing U/VSTRESS
cd7677e357 Dimi*9417
0e6056cd20 Jean*9418 checkpoint59k (2007/11/30)
409b09eb42 Dimi*9419 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
9420 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
62e148683f Jean*9421 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
94059a384d Jean*9422 all experiments pass when compile with un-initialised var. checking option.
e4775240e5 Dimi*9423 o added pkg/salt_plume
c28f57ed2e Jean*9424 o script to test restart (for now, in MITgcm_contrib/jmc_script)
a435e833b1 Mart*9425 o pkg/seaice: new read/write pickup version.
c28f57ed2e Jean*9426 read meta file and write only fields which are needed to restart.
9427 ( same logic as main pickup file ; also using pickupStrictlyMatch )
df45546054 Mart*9428 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
b030fd2059 Jean*9429 o lab_sea.hb87: modify the domain & update output.hb87.txt :
9430 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
9431 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
9432 process. Fixed here by closing the domain at the Northern boundary.
9433 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
9434 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
9435 a set of consecutive levels in/from a 3-D array.
a435e833b1 Mart*9436 o pkg/ptracers:
b030fd2059 Jean*9437 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
74f73e83d7 Jean*9438 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
9439
0e6056cd20 Jean*9440 checkpoint59j (2007/11/09)
054a6ca04b Jean*9441 o in pkgs: dic, obcs, offline, rbcs:
9442 standard way to compute coeff. for time interpolation between 2 time reccords
9443 which retains full precision (& make results less dependent on compiler).
9444 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
f82f0d1e3a Mart*9445 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
9446 packages instead of reading ice cover and wind speed separately
dee09995de Jean*9447 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
9448 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
9449 to allow to compile customized code before the update)
a435e833b1 Mart*9450 o cleaning-up:
1330311b36 Jean*9451 - fix CPP instruction syntax in pkg/obcs
9452 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
9453 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
9454 - fix some threads issue in IO parts.
7f2d5ae7b4 Davi*9455 o pkg/dic:
9456 - add tons of "_d 0" (--> much better testreports !)
9457 and then update outputs of tutorial_global_oce_biogeo
7d697fe457 Jean*9458 o pkg/mom_fluxform:
9459 add a special version of momentum advection intended to conserve momentum
9460 next to a bathymetry step or a coastline edge. (default = off = #undef)
715883b931 Jean*9461 o new read/write pickup version:
9462 - for now, only implemented for main (mdsio) pickup file.
9463 - write out only what is needed to restart; merge pickup_nh , pickup_ph
9464 and main pickup together.
9465 - read meta file; read only what is needed to restart; stop if a field
9466 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
9467 if it make sense (even if the restart is not perfect).
9468 - if no meta file, assume that pickup to read corresponds exactly to
9469 a pickup that would currently be written.
9470 - read pickup written in the old format (until checkpoint59i) if it
9471 recognizes an old meta file (no field-list).
9472 - add a meta file in exp. which starts from a pickup: 2 cases:
9473 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
9474 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
9475 b) a meta file describing the content of the associated pickup file
9476 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
9477 o pkg/mdsio & pkg/rw:
9478 - new routine to read a meta file ; new set of routine to read
9479 Multiple-fields file (with meta file).
5459643feb Dimi*9480 o added open boundary conditions capability for seaice
9481 HSNOW, HSALT, UICE, and VICE
fa757486b0 Dimi*9482
0e6056cd20 Jean*9483 checkpoint59i (2007/10/21)
3420897bc6 Patr*9484 o adjoint:
a435e833b1 Mart*9485 * fix multiDimAdvection adjoint
3420897bc6 Patr*9486 (partial recomputation problem by TAF for fVerT(:,:,kDown)
9487 and comlev1 size definition (maxpass vs. max. number of tracers)
9488 * verification/global_ocean.90x45x15 adjoint now tests
9489 NLFS and multiDimAdvection using DST3 (=30)
9490 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
a435e833b1 Mart*9491 o pkg/kpp: add "_d 0" to real constant (if missing);
846ec3a65a Jean*9492 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
9493 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
97b9193f01 Jean*9494 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
9495 for internal parameters related to restart process (formerly from PARAMS.h)
9496 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
9497 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
9498 as argument. (only atm2d & obcs write_pickup have not yet been updated)
fc36747b80 Jean*9499 o pkg/monitor:
9500 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
9501 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
9502 - account for deep Atmosphere factor and density factor (anelastic)
b48f786726 Dimi*9503 o added open boundary conditions capability for seaice HEFF and AREA
11b7991b31 Mart*9504 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
9505 thermodynamics
a435e833b1 Mart*9506 - requires a little reorganization, which affects the testreport results
11b7991b31 Mart*9507 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
9508 so that now the conservative form is tested
9509 - add a few comments
fc36747b80 Jean*9510 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
5cc78a2bb0 Mart*9511 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
37de51ebf5 Mart*9512 o add new diagnostics to seaice: advective, diffusive fluxes (only for
a435e833b1 Mart*9513 multidim-advection, for scheme 2 they are not filled) and transports,
37de51ebf5 Mart*9514 thermodynamic growth rates
5c9e11f575 Jean*9515 o change units of EmPmR (inside the code, + within coupling interface)
9516 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
a435e833b1 Mart*9517 Affects results @ truncation level (cg2d match) and update output of
5c9e11f575 Jean*9518 experiments: lab_sea(6), global_ocean.90x40x15(10),
8106187dda Jean*9519 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
9520 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
5c9e11f575 Jean*9521 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
8106187dda Jean*9522 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
9523
0e6056cd20 Jean*9524 checkpoint59h (2007/09/29)
a435e833b1 Mart*9525 o pkg/exf:
97f0a6ab4c Mart*9526 - improve vectorization by moving if-statement out of loops in
9527 exf_mapfields, exf_radiation
9528 - exf_bulkformulae.F: introduce 2D fields and vectorize code
63ceaaa79c Dimi*9529 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
a435e833b1 Mart*9530 o testreport:
9531 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
b60e6e79c3 Jean*9532 monitor & update offline_exf_seaice exp. output.
9533 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
f09197aee0 Mart*9534 o pkg/seaice:
9535 - bug fix in the evp solver: boundary conditions were affected be
9536 masking of zMax/zMin (changes results)
a435e833b1 Mart*9537 - minor bug fix in boundary conditions in seaice_calc_strainrates
f09197aee0 Mart*9538 (changes results for no_slip)
9539 - seaice_lsr.F: make interpolation of eta dependent on boundaries
9540 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
9541 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
9542 stress formulation and no-slip boundary conditions
453b5521e5 Jean*9543 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
9544 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
e06023d8a7 Dimi*9545 o pkg/seaice: a first HSALT time stepping equation has been checked in
6aebec07e1 Dimi*9546 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
9547 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
9548 without requiring DO-IF statements
acdf6745c2 Jean*9549 o pkg/thsice:
9550 use continuous power-law function for partition of energy between lateral
9551 melting/freezing and thinning/thickening ; old code using step function
9552 still available with #undef THSICE_FRACEN_POWERLAW
9553 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
9554 o testreport: change AD testing : check against results/output_adm.txt
9555 using same scripts as for forward test.
6aebec07e1 Dimi*9556
0e6056cd20 Jean*9557 checkpoint59g (2007/09/17)
6d61a12d79 Jean*9558 o adjoint testing: in preparation for changing testreport:
9559 - output format: cost and grad written on separated lines
9560 - ad output results in directory "results" (instead of "results_ad")
fdfa8e151f Dimi*9561 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
06687b5615 Dimi*9562 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
a435e833b1 Mart*9563 o pkg/ecco: allow user defined cost function contributions
a3953b5266 Jean*9564 o testreport:
9565 Allow to choose (per experiment) the list of tested output variables
9566 and the main variable (used to issue a pass/FAIL ) ;
9567 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
6d61a12d79 Jean*9568 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
a3953b5266 Jean*9569 Also modify printing of summary:
9570 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
9571 b) echo the list of tested variables in the individual summary.txt of
9572 each experiment.
768f1a0767 Jean*9573 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
9574 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
9575 (but still depend on the tile decompostion of the domain).
a435e833b1 Mart*9576 o pkg/seaice: change a discretization detail to make the B-grid code
9577 "more symmetric". This change is likely to remove all "ridges/leads" that
9578 where quasi-aligned with the grid in B-grid solutions. It may also be
9890ce5b02 Mart*9579 the solution to the stress coupling issues with the B-grid.
746e4b22c8 Jean*9580 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
9581 remove .cvsignore from input dir. (since testreport no longer run here).
00f1a01b56 Jean*9582 o pkg/thsice:
746e4b22c8 Jean*9583 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
00f1a01b56 Jean*9584 - fix reshaping of sea-ice just after advection:
9585 melt all the ice only if ice-volume is too small.
9586 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
9587 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
9588 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
be8537d9a0 Jean*9589 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
9590 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
a435e833b1 Mart*9591 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
de702e22c7 Jean*9592 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
9593 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
9594 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
9595 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
9596 -> update output.txt
9597 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
9598 this affects truncation error: -> update output.txt of exp:
9599 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
9600 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
9601
0e6056cd20 Jean*9602 checkpoint59f (2007/08/21)
a435e833b1 Mart*9603 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
9604 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
5e4d837505 Gael*9605 a bounded range (in forward mode)
59227d8f71 Gael*9606 o pkg/ecco, ctrl, autodiff and mom_common:
9607 internal parameter controls, completements of implementations
7cb9ec3ac0 Jean*9608 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
9e6f983930 Jean*9609 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
9610 (not seem any difference in testing results).
a435e833b1 Mart*9611 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
7cb9ec3ac0 Jean*9612 at face corners.
a435e833b1 Mart*9613 o pkg/generic_advdiff:
c3947d579e Jean*9614 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
9615 loop range indices for computing vertical advection tendency
9616 and do the calculation in the interior only (no overlap) ;
9617 for now, only implemented for SOM advection (to save CPU time).
9618 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
ffa5f4b126 Patr*9619 o exch2 adjoint
9620 First set of changes:
9621 - add exch2 hand-written adjoint templates
9622 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
9623 This will require cleanup in pkg/autodiff/*.F
9624 (changed routines currently kept separate in verif. code/)
9625 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
9626 that used to hide exch2 or cubed-sphere specific code
9627 (commented via 'cph-exch2')
eb0337bb06 Dimi*9628 o pkg/seaice
9629 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
a435e833b1 Mart*9630 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
142f944c15 Jean*9631 output of global_ocean.cs32x15.thsice .
ffa5f4b126 Patr*9632
0e6056cd20 Jean*9633 checkpoint59e (2007/07/26)
eed8e492b5 Jean*9634 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
9635 for B-grid vector (not yet tested) and C-grid vector (<- only used
9636 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
8c3259a14c Dimi*9637 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
9638 (#ifdef ALLOW_SALT_PLUME)
713e6ff2ab Dimi*9639 o gather_2d/scatter_2d: removed halo regions
ca76150054 Jean*9640 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
9641 scheme and the corresponding test case (under front_relax dir). For now,
9642 only available with Skew-flux form and not yet tested in realistic set-up.
a614482486 Patr*9643 adjoint: store directives updated, but gradient checks deteriorated,
9644 so maybe GM/Redi adjoint is now broken.
7dadb0325c Patr*9645 o seaice adjoint
9646 * add AREA, HEFF, HSNOW as control variable
9647 (should not change lab_sea results)
9648 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
09379e5080 Dimi*9649 o pkg/seaice:
9650 * added computation of saltFlux in seaice_growth;
9651 For time being, sea ice salinity is assumed constant
9652 contribution of snow flooding to freshening of sea ice is neglected.
9653 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
9654 defaults to 0.0 in order to maintain backward compatibility.
9655 Typical values for SEAICE_salinity are 4 to 10 g/kg.
9656 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
9657 * added SEAICE_availHeatFrac, which specifies fraction of surface level
9658 heat content used to melt or grow ice
c7cb92a732 Dimi*9659 * commented out cap of HICE: it helps keep ice thinner
9660 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
a6d2313c04 Dimi*9661 * applied OBCS T/S mask to HEFFM sea ice mask
7dadb0325c Patr*9662
0e6056cd20 Jean*9663 checkpoint59d (2007/06/21)
d2b8341951 Jean*9664 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
9665 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
9666 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
9667 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
9668 and change default value of parameter "GM_Small_Number";
9669 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
a435e833b1 Mart*9670 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
d2b8341951 Jean*9671 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
f79922cd31 Gael*9672 o pkg/ecco: cost function when applying pkg/smooth to controls
9673 o pkg/ctrl: add forcingPrecond run time parameter
6ac96a67e3 Mart*9674 o pkg/seaice:
9675 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
a435e833b1 Mart*9676 - fix bug in metric terms of u-equation in LSR solver (implicit part),
6ac96a67e3 Mart*9677 changes verification/lab_sea
9678 - rearrange implicit part of u-equation in LSR solver to make it easier to
9679 read, understand, and debug. This causes changes at the truncation level.
a435e833b1 Mart*9680 - fix (serious) bug in the boundary conditions (sign error in the implicit
6ac96a67e3 Mart*9681 part) of the LSR solver. Changes all LSR results.
de31ea8481 Dimi*9682 - fixed problem with HSNOW initialization to avoid thick snow when AREA
9683 is initilized with small values - does not change lab_sea results.
9684 - added HsnowFile initialization capability
a435e833b1 Mart*9685 o pkg/smooth: addition to model/src and pkg/ctrl so allow
bf0c19d334 Gael*9686 initialization of pkg/smooth and application to control vector
19ab789a27 Mart*9687 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
249fe8e752 Gael*9688 o dependencies: pkg/profiles requires pkg/cal
8d3088d3d7 Gael*9689 o pkg/profiles:
9690 - added option ALLOW_PROFILES_GENERICGRID
9691 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
a435e833b1 Mart*9692 that interpolation information (grid points and coefficients) is provided
8d3088d3d7 Gael*9693 within the netcdf input files.
9694 -> sample matlab scripts can be found in MITgcm_contrib/gael
9695 that allow you to prepare netcdf input files.
a435e833b1 Mart*9696 - also modified: cleaner include statements, cleaner error print statements,
8d3088d3d7 Gael*9697 cleaner stops when error, and more tests of the netcdf input files consistency.
a0c93d7fd2 Jean*9698 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
04b45d6d21 Mart*9699 o pkg/seaice:
583c1cf330 Mart*9700 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
9701 requires a new routine: seaice_diagnostics_fill.F
acaec430f5 Mart*9702 - make sure that seaice does not move if not forced (pressure replacement
9703 method, Hibler and Ip, 1995), changes results
04b45d6d21 Mart*9704 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
a435e833b1 Mart*9705 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
04b45d6d21 Mart*9706 It is turned off by default (=-1.), because it changes the results.
b1e9686d05 Mart*9707 - make it possible to read AREA from a file, too.
04b45d6d21 Mart*9708
0e6056cd20 Jean*9709 checkpoint59c (2007/06/04)
93133b7df9 Jean*9710 o add S/R and diagnostics for oceanic mixed-layer depth
9711 o move GMRedi call after all vertical mixing schemes (including KPP)
a435e833b1 Mart*9712 o pkg/thsice:
93133b7df9 Jean*9713 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
9714 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
de3611c1c1 Mart*9715 o pkg/obcs:
9716 - bug fix for balance code
2d85697240 Mart*9717 o pkg/seaice:
6bfbbed422 Mart*9718 - allow values of SEAICE_elasticParm > 1
a435e833b1 Mart*9719 - add new parameter SEAICE_evpTauRelax as an alternative
b559ca9c5c Mart*9720 to SEAICE_elasticParm
6bfbbed422 Mart*9721 - make lsr boundary conditions free slip (by default), changes result
887a79a904 Mart*9722 - add code for no slip boundary conditions for lsr
2d85697240 Mart*9723 - set minimum of zeta to zero (and not 4e8) (changes results)
b559ca9c5c Mart*9724 - add a cap on AREA after advecting AREA if seaice_growth is not called
04010225bf Jean*9725 o change calculation of Visbeck K:
a435e833b1 Mart*9726 - no longer depend on tapering scheme; instead, compute slope (limited
04010225bf Jean*9727 by GM_maxSlope). this is equivalent to what was comuted before with
9728 clipping or linear tappering.
93133b7df9 Jean*9729 - fix vertical averaging (wrong by 1/2 level)
04010225bf Jean*9730 - leave the old version (but will not be maintained) within
9731 #ifdef OLD_VISBECK_CALC / #endif
93133b7df9 Jean*9732 - update output of exp. ideal_2D_oce
ae6dbd4886 Mart*9733 o change error catch in calc_r_star to improve vectorization
fc0ec0c7ea Jean*9734 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
9735 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
5728d4a98b Patr*9736 o adjoint:
9737 Re-organized adjoint checkpointing according to Matt Mazloff
9738 (but with modifs/completions/cleanups)
9739 Storing is now bundled into large arrays to optimized I/O
9740 (and second step in cleanup of the_main_loop)
fc0ec0c7ea Jean*9741
0e6056cd20 Jean*9742 checkpoint59b (2007/05/16)
59d7b34837 Jean*9743 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
9744 - export/import (between ocean & coupler) fields needed for ocean DIC.
a435e833b1 Mart*9745 o pkg/seaice:
9746 - get rid of three more exchanges seaice_calc_viscosities (required
17cb3b1135 Mart*9747 different loop boundaries in seaice_lsr and seaice_ocean_stress)
9748 - bug fix in seaice_ocean_stress (update of lab_sea required)
9749 - reduce loop boundaries to necessary minimum also in seaice_evp
a435e833b1 Mart*9750 - go back to the old way of computing deltaC/Z as the adjoint likes that
17cb3b1135 Mart*9751 better
ec0736eb1a Davi*9752 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
9753 passive tracer to an Age Tracer) + update output.txt
93f8102905 Jean*9754 o pkg/exf:
7bb7cdd467 Jean*9755 - implement A-grid / C-grid selection for wind-stress input files.
9756 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
9757 for now, in exf_bulk_largeyeager04.F only :
9758 - change implementation for case where windspeed + 2. components wind-stress
9759 are read-in. AND use rhoConstFresh to convert evap.
9760 o pkg/seaice:
9761 - use correct EXCH_UV for wind-forcing (on A-grid).
9762 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
9763 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
9764 o pkg/exf:
93f8102905 Jean*9765 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
a435e833b1 Mart*9766 EXF_INTERPOLATION:
93f8102905 Jean*9767 - merge global_with_exf/code version of exf_interp_read.F
a435e833b1 Mart*9768 to the main code ;
9769 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
9770 reading the file ; Important: This options needs to be defined to recover
93f8102905 Jean*9771 previous code.
9772 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
9773 - no longer loose real*8 precision along the way when using exf_iprec=64.
2f88b60189 Mart*9774 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
b3e6145587 Mart*9775 - change discretisation of evp-solver in order to avoid another exchange
9776 (changes lab_sea) and clean up a little
a435e833b1 Mart*9777 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
b3e6145587 Mart*9778 help the adjoint (this also changes the results slightly)
9779 - add a few "_d 0" where they had been missing in seaice_evp.F
9780 - cleaning up: remove unused seaice_calc_rhs.F
35a74aa2c2 Jean*9781 o pkg/exf: some cleaning-up:
9782 - change various "constants" into runtime parameters
9783 - cleaned-up Large&Yeager04 routine which should eventually
9784 replace exf_bulkformulae.F (changed names of S/R and CPP)
9785 and merged various ALLOW_ATM_WIND options
9786 only used with thsice pkg (in thsice_get_exf.F):
9787 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
9788 which are used when useStabilityFct_overIce=TRUE (= the default)
9789 - change default values of ice & snow emissivity and scale downward LW
9790 by ice & snow emissivity.
9791 o pkg/thsice:
0a9955b282 Jean*9792 fix few little problems, in thsice_calc_thickn.F:
9793 - growth vertically (and not laterally) if iceFrac == iceMaskMax
93133b7df9 Jean*9794 - melt only laterally if hIce < hThinIce (as the comments say)
0a9955b282 Jean*9795 and in thsice_extend.F:
9796 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
9797 - start to form ice as soon as the minimum ice-volume is reachable.
a435e833b1 Mart*9798 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
0a9955b282 Jean*9799 and cpl_aim+ocn
66b38c4c51 Mart*9800 o pkg/kpp
9801 - move computation of surface related input fields to KPP into a new
9802 subroutine kpp_forcing_surf.F
0a9955b282 Jean*9803 - remove wrong (within bi,bj loops) EXCH calls.
9804 - little cleaning (add argument myThid in last position, cvs header ...)
a435e833b1 Mart*9805 - for now, fix conservation problem by exchanging KPPviscAz (may not
0a9955b282 Jean*9806 be the best fix)
f83c00719e Mart*9807 o pkg/seaice
9808 - check for inconsistent evp parameter/cpp-flag combination
9809 - remove leftover errIO flat for obsolete name list error handling
4b058176c1 Patr*9810 o OpenAD
9811 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
f83c00719e Mart*9812
0e6056cd20 Jean*9813 checkpoint59a (2007/05/01)
09e3b53265 Mart*9814 o pkg/seaice: some parameter clarifications and a little bit of clean up
f8fa27d193 Jean*9815 o pkg/thsice: rename run-time parameters:
9816 himin -> hIceMin
9817 himin0 -> hThinIce
9818 hihig -> hThickIce
9819 i0 -> i0swFrac
9820 transCoef -> bMeltCoef
9821 frac_energy -> fracMelting
9822 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
9823 with default values (for now) that do not change the results.
9824 remove old version of thsice vars advection in pkg/seaice.
a435e833b1 Mart*9825 o in FFIELDS.h:
18ca872a92 Jean*9826 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
9827 - make pLoad & sIceLoad always available (but still only used if
9828 ATMOSPHERIC_LOADING is #define).
fe66051ebd Dimi*9829 o pkg/kpp: replaced _KPP_RL with _RL
059d9fc14f Dimi*9830 o bug fixes for vertical diffusivity computations when both KPP and
a3b5d49db3 Dimi*9831 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
9832 are no longer updating the vertical diffusivity array
9833 (passed as argument) but are (re-) setting those arrays.
2e88c0564a Mart*9834 o pkg/seaice: fix bug in evp solver, while doing that
9835 - change (improve?) discretization of stress computations for both
9836 cgrid-lsr and evp solver
9837 - add a new routine to compute strain rates
ed84a09795 Mart*9838 - the above changes lab_sea results
9839 - add no slip conditions for evp solver (off by default), lsr-version
9840 may follow
9841 - fix exchange for shear at Z-points (does not change lab_sea)
9842 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
9843 (to force the user to pick a time step since there is not "safe" way
9844 of choosing it)
4686684434 Mart*9845 - add principal stress diagnostics
a435e833b1 Mart*9846 - rearrange fields for evp a little to avoid having to call a: too many
9847 exchanges and b: exchanges for stress trensor components which we do
fe367969c0 Mart*9848 not have.
9849 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
9850 of evp, complete rewrite for lsr case (latter is does not yet work
9851 in all cases)
efab83c021 Mart*9852 o pkg/kpp: add code to have mixing in shelf ice caverns
cb6682d07b Mart*9853 - add myThid to all kpp routines (long overdue)
efab83c021 Mart*9854
0e6056cd20 Jean*9855 checkpoint59 (2007/04/19)
a435e833b1 Mart*9856 o pkg/exf:
62cf11cfe0 Patr*9857 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
9858 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
a435e833b1 Mart*9859 - move exf header files from lower_case.h to UPPER_CASE.h ;
62cf11cfe0 Patr*9860 add missing cvs Header & Name
9861 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
d9a285b784 Patr*9862 - add namelist param. selectStressGridPosition, exf_monFreq
a435e833b1 Mart*9863 - retire many _CLIM routines, and remove data.exf_clim
d9a285b784 Patr*9864 + params moved to data.exf
9865 + climsst, climsss now handled by exf_set_gen, i.e.
9866 climss?period=0 refers to constant field,
9867 climss?period=-12 to monthly forcing
9868 - split up namelists in data.exf
e1d22dfae3 Mart*9869 o pkg/seaice:
9870 - remove seaice_exch and seaice_exch_uv
9871 - remove superfluous exchange of theta
9872 - add myThid to seaice_budget_ocean/ice
039e537654 Mart*9873 - add new interface for atmospheric wind forcing (C-grid only)
9874 + new routine
9875 + two new field (taux, tauy for stress over ice)
9876 + removed one global field (DAIRN) for C-grid case only
62cf11cfe0 Patr*9877 o pkg/thsise
9878 - 2nd set of modifs for thsice adjoint in conjunction with exf
d9a285b784 Patr*9879 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
e1d22dfae3 Mart*9880
0e6056cd20 Jean*9881 checkpoint58y_post (2007/04/15)
0aefc24df1 Dimi*9882 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
e40c34e398 Dimi*9883 vertical diffusivity, similar to that in MOM4; turned on using
9884 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
9885 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
a7c5f770ff Dimi*9886 o Added capability for 3D specification of background vertical diffusion
9887 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
9888 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
9889 "data" file that contains the 3D vertical diffusivity coefficients.
a10167ebd7 Jean*9890 o ice dynamics (pkg/seaice) with thsice thermodynamics:
9891 - add code within pkg thsice to advect & diffuse sea-ice fields
9892 similar to (and will replace) what has been added in seaice_advdiff.F,
9893 but: - conserving Mass, Heat & Salt.
9894 - better when using non-linear advection scheme (not yet fully tested)
9895 - can also be used in atmospheric set-up (for now, only the diffusion).
bf363e629f Dimi*9896
0e6056cd20 Jean*9897 checkpoint58x_post (2007/04/04)
fa535b8213 Jean*9898 o IO option for global-file compact format:
9899 - add options when generating topology (utils/exch2/matlab-topology-generator)
9900 - add I/O capability (pkg/mdsio).
9901 - adapt utils/matlab/rdmds.m to read this format.
9902 for now long-line format not yet supported by pkg/mdsio (& exch2).
4c0efb30d8 Mart*9903 o shelfice: add a few diagnostics
9904
0e6056cd20 Jean*9905 checkpoint58w_post (2007/03/13)
db8fa666e0 Jean*9906 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
9907 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
9908 (and replace horiVertRatio in NH code).
a435e833b1 Mart*9909 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
db8fa666e0 Jean*9910 and tutorial_plume_on_slope (sensitive to truncation)
2496f367f4 Mart*9911 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
9912 directly to drive seaice model (C-grid only)
9913 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
a435e833b1 Mart*9914 - reintroduce computation of wind from stress,
9915 - compute tau (in exf_bulkformulae.F) from windstress averaged to
2496f367f4 Mart*9916 mass points to avoid tau = 0
b3d6cfe67b Mart*9917 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
2496f367f4 Mart*9918 o rdmnc.m: make it work with "global" files created with gluemnc
fedb0baa62 Jean*9919 o rdmnc.m : some improvements in dealing with singleton dimension
9920 (tested on all testreport mnc output files).
9921 o genmake2: disable pkg/profiles if netcdf test fails.
108c7eb2d4 Jean*9922 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
462fd48b6a Mart*9923 o move call to cal_readparms up to make calendar parameters/variable available
9924 to all packages
9925
0e6056cd20 Jean*9926 checkpoint58v_post (2007/02/08)
bafc84b6a4 Jean*9927 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
9928 useDynP_inEos_Zc tested.
5d2261ac89 Dimi*9929 o pkg/exf: changes to properly interpolate/mask/scale initial fields
7c705f78f8 Dimi*9930 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
9931 and portions thereof. See read_cs.txt for description and examples.
c4b9b1e3e9 Jean*9932 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
9933 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
9934 following the great-circle arc between those 2 points.
9935 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
9936 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
95c3249206 Jean*9937 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
9938 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
9939 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
9940 - still needs work (not working with some options ; efficiency to improve)
9941 and serious testing.
9942 - use this scheme for temperature & salinity in 2 advection test exp.:
9943 advect_xy & advect_xz, respectively.
9944
0e6056cd20 Jean*9945 checkpoint58u_post (2007/01/12)
42a486092f Jean*9946 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
31fd7701e4 Jean*9947 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
9948 o testreport: add option "-skipdir" to skip some test.
a435e833b1 Mart*9949 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
31fd7701e4 Jean*9950 momentum calculation.
9951 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
9952 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
9953 remove checkpoint.F and the_correction_step.F (no longer used);
9954 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
a435e833b1 Mart*9955 o add option (linFSConserveTr) to correct for tracer source/sink due to
31fd7701e4 Jean*9956 Linear Free surface
0e1f0a567f Mart*9957 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
9958 o pkg/thsice: fix reading mnc-pickups
9959
0e6056cd20 Jean*9960 checkpoint58t_post (2006/12/30)
62990a23c1 Jean*9961 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
9962 o pkg/mdsio:
9963 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
9964 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
9965 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
9966 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
9967 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
9968 either MDS_READ_FIELD or MDS_WRITE_FIELD )
9969 - new S/R (to replace MDSWRITEMETA), which allows to write more
9970 informations (variable names, time ...) to meta files.
9971 - modify rdmds.m to give back the meta file content.
f0676079d6 Jean*9972 o pkg/diagnostics: change vertical interpolation to be safer, and more
9973 flexible (define p-levels to interpolate to in data.diagnostics);
a435e833b1 Mart*9974 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
f0676079d6 Jean*9975 diagnostic pointer.
494a260c71 Mart*9976 o pkg/seaice: more cleaning up of seaice_growth, added many comments
0e1f0a567f Mart*9977 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
72f428a311 Mart*9978 o fix multi-category seaice:
a435e833b1 Mart*9979 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
72f428a311 Mart*9980 SEAICE_MULTICATEGORY
9981 - fix short wave heat flux
ac10466ef6 Jean*9982 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
a435e833b1 Mart*9983 and allow to use EVP solver. Change forward lab_sea: test both EVP
ac10466ef6 Jean*9984 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
13ac555e3c Patr*9985 o Initial check-in of lab_sea adjoint
9986 (very similar to natl_box_adjoint/code_seaice)
9987 * used C-grid and EVP solver
9988 * used KPP, GM/Redi
9989 * uses inAdExact=.TRUE.
9990 * gradient checks fail for both ADM and TLM
9991 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
9992 f.d. gradients actually seem more problematic than ADM, TLM gradients;
9993 issue is related to forward mismatch between g77 an ifort
66cb0aa2f6 Mart*9994 o pkg/seaice: overhaul of thermodynamics
9995 - growth.F and groatb.F are replaced by new routine seaice_growth.F
9996 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
9997 - move a few global fields out of SEAICE.h into seaice_growth.F and
9998 make them 2D (FICE/QNETO/ ...)
9999 - remove FO (it is the same as QNETO)
10000 - introduce a few local fields to avoid modifying external fields such
10001 as atemp, etc.
10002
0e6056cd20 Jean*10003 checkpoint58s_post (2006/12/11)
58d34f56b6 Dimi*10004 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
10005 changed exf_set_gen.F so that
10006 genperiod=0 means input file is one time-constant field and
10007 genperiod=-12 means input file contains 12 monthly means
475943d866 Jean*10008 o CG2D: use pre-computed solver main-diagonal (stored in common block);
10009 this affects truncation error ; generate new output file for exp. which
10010 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
10011 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
10012 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
10013 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
10014 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
10015 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
c5d33297c7 Jean*10016 o start implementation of deep-atmosphere and anelastic formulation
d83c991b0e Jean*10017 o verification: remove 2nd copy of input files and use script "prepare_run"
10018 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1c10df8cad Mart*10019 o mom_common/vecinv/fluxform: fix a few initialisation isssues
544c96562c Gael*10020 o profiles: fix for multithreaded case
10021
43ae10a9d8 Jean*10022 o diagnostics: rename few diags:
10023 s/'PRESSURE'/'RCENTER '/g
10024 s/'TICE '/'oceFreez'/g
10025 s/'TAUX '/'oceTAUX '/g
10026 s/'TAUY '/'oceTAUY '/g
10027 s/'SWFLUX '/'oceQsw '/g
10028 s/DIFx/DFxE/g
10029 s/DIFy/DFyE/g
10030 and add few ocean-forcing diagnostics:
10031 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
ab48336167 Dimi*10032 o modifications to pkg/seaice/growth.F and budget.F, which change results of
10033 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
10034 as actual snow thickness. It now refers everywhere to effective snow
10035 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
43ae10a9d8 Jean*10036
0e6056cd20 Jean*10037 checkpoint58r_post (2006/11/17)
8307959141 Dimi*10038 o modifications to pkg/seaice/growth.F, which change results of
10039 lab_sea experiment: fixes pertain to melting snow over open water, to
10040 masking EVAP under sea ice, and to using the correct AREA variable for
10041 computations of EVAP, PRECIP, HSNOW, and GHEFF
5f4df5533c Ed H*10042 o add ability to read bathy, salt, and theta using MNC (off by def)
eefc792916 Mart*10043 o add flooding algorithm and advection of HSNOW for pkg/seaice;
10044 both are turned off by default and do no change any results
a435e833b1 Mart*10045 o seaice advection with pkg/thsice: a step toward the use of non-linear
cc4235ab79 Jean*10046 advection scheme, but #ifdef or commented out for now (requires more EXCH).
23209571d0 Jean*10047 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
10048 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
10049 in natl_box (affects results @ truncation level: update output.txt)
10050 o multi-threading and IO:
ba51931058 Jean*10051 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
10052 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
10053 (needed to work with SingleCpuIO): tested in all verif. exp.
874c68b9c9 Jean*10054 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
10055 affects the results (but none of the verification test uses this scheme).
9913de8fec Patr*10056 o Adding some pkg/diagnostics capability to pkg/seaice
10057 (will certainly be subject to changes)
983e72444d Patr*10058 o ctrl: adding new control variables:
10059 lwflux, lwdown, evap, snowprecip, apressure, runoff
9913de8fec Patr*10060
0e6056cd20 Jean*10061 checkpoint58q_post (2006/10/20)
f5cbf7b96d Dimi*10062 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
10063 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
10064 high_res_cube configuration by 4% on Columbia.
a615280822 Jean*10065 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
10066 add (in global_with_exf/code) a version of EXF_INTERP_READ without
10067 dynamical allocation (seems to work in multi-threaded).
10068 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
10069 single CPU io) so that TAF does not have to see EESUPPORT.h
725982e0dd Jean*10070 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
10071
0e6056cd20 Jean*10072 checkpoint58p_post (2006/09/08)
fc187b9c6d Mart*10073 o obcs: stop if obcs is used with useCDscheme = .true.
a435e833b1 Mart*10074 o shelfice:
4fd1c14d86 Mart*10075 - fix a sign error so that no slip at shelfice interface works
a435e833b1 Mart*10076 - remove stop for combination non-hydrostatic code and shelfice. That does
4fd1c14d86 Mart*10077 not mean, that the results are correct, but at least they are numerically
10078 stable
bd91f7dab7 Davi*10079 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
9dd22fcf15 Patr*10080 o added adjoint exch routined for all exch*3d* routines
10081 and updated flow directives
bd91f7dab7 Davi*10082
0e6056cd20 Jean*10083 checkpoint58o_post (2006/08/28)
acd22c6e91 Jean*10084 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
10085 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
d0ebb46870 Jean*10086 o change controling S/R for writing pickup file (new S/R do_write_pickup)
10087 and clean-up reading/writing of pickup files.
10088 o fix local version of read/write pickup (NH part) in rotating_tank/code
49423ca970 Jean*10089 o simplify EXCH interface:
10090 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
10091 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
134f469a8d Ed H*10092 o added the regrid package
a435e833b1 Mart*10093 o shelfice:
29ffe622cd Mart*10094 - add a simple boundary layer scheme to reduce noise
10095 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
49423ca970 Jean*10096
0e6056cd20 Jean*10097 checkpoint58n_post (2006/08/14)
a435e833b1 Mart*10098 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
bbc1d9f1e8 Jean*10099 local variable (not in common block).
a435e833b1 Mart*10100 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
10101 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
da8bc3fbe0 Jean*10102 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
10103 to work with SingleCpuIO.
a435e833b1 Mart*10104 o add "_d 0" to real constant of pkg/cfc subroutines ;
d77b191e54 Jean*10105 update exp. cfc_exemple & tutorial_cfc_offline output files.
15d8704b4b Jean*10106 o multi-threading and IO:
a435e833b1 Mart*10107 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
15d8704b4b Jean*10108 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
10109 - barrier before and after reading.
10110 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
10111 - avoid using MDS_WRITELOCAL for LAND pkg output.
10112 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
10113 common-block variables ; Allows multi-threading with master-thread IO.
a435e833b1 Mart*10114 o change default MAX_NO_THREADS from 32 to 4 ;
10115 and stop cleanly when MAX_NO_THREADS is too small.
e20ba03425 Jean*10116 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
10117
0e6056cd20 Jean*10118 checkpoint58m_post (2006/07/17)
ade0862df3 Jean*10119 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
10120 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4641b6f2a1 Jean*10121 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
a435e833b1 Mart*10122 keep global_ocean.90x40x15 (for AD testing) with former secondary test
4641b6f2a1 Jean*10123 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
10124 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
10125 add MITgcm_tutorials (= code + all the tutorials)
61b89af843 Gael*10126 o ecco, option to compute cost for total ssh (mean+anom)
fe8bfd2a85 Gael*10127 o consistent with addition of ptracer and ssh in pkg/profiles
021f06a8d1 Gael*10128 o profiles: adding ptracer and ssh
a435e833b1 Mart*10129 o testreport: change multi-test output-file name
a91df43a18 Jean*10130 (from output.txt.{name} to output.{name}.txt)
da8bc3fbe0 Jean*10131 o profiles: now ok for mutli-tiles case
a435e833b1 Mart*10132 o seaice: add 4 parameters for different advection schemes for area,
1633c22cfc Mart*10133 (effective) seaice thickness, enthalphy, and snow height. Their default
10134 is the standard parameter SEAICEadvScheme
a435e833b1 Mart*10135 o calc_gw:
78de812e24 Jean*10136 - add cosFacU in zonal viscous flux (harmonic.visc.).
10137 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
10138 of tutorial_plume_on_slope.
10139 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1fa758ce8e Jean*10140 o calc_gw: true flux-form, account for horizontal grid spacing.
a435e833b1 Mart*10141 update rotating_tank results, but not plume_on_slope (affected at
1fa758ce8e Jean*10142 truncation level, 11 digits).
10143
0e6056cd20 Jean*10144 checkpoint58l_post (2006/07/12)
a435e833b1 Mart*10145 o calc_gw:
1fa758ce8e Jean*10146 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
10147 - remove side-drag for now (need to fix it); update plume_on_slope results.
10148 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
066de0bcd6 Patr*10149 o commit code to make SST/SSS weights spatially variable
10150 (based on either variable in-situ or variable initial T/S weights)
9c7011b92a Patr*10151 o pkg/ecco:
10152 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
10153 now based on horizontally varying weights wthetaLev, wsaltLev
10154 * cost_averagesflags now returns year indices in addition to day, month
a435e833b1 Mart*10155 * sflux balance is performed on annual basis
9c7011b92a Patr*10156 (sflxumm, sfluxmm2, bal_sfluxmm)
10157 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
10158 including separate counting and multipliers
11d329f17a Patr*10159 o pkg/rbcs
10160 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
926e82ae0e Jean*10161
0e6056cd20 Jean*10162 checkpoint58k_post (2006/07/06)
a75fd4a3a0 Jean*10163 o testreport:
a435e833b1 Mart*10164 - always build in dir. "build" (if not there, mkdir build instead of building
a75fd4a3a0 Jean*10165 & running in input)
10166 - run in dir run (if it exists), in build otherwise.
10167 - call prepare_run (if input/prepare_run exists)
10168 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
6519624399 Dimi*10169 o pkg/exf modifications to interpolation and rotation routines for more
10170 reasonable treatment of North Pole singularity: for tracers North Pole
10171 value is set to northernmost zonal-mean value, for zonal velocity it is
10172 set to zero, and for meridional velocity it is set to northernmost value.
35141c3376 Mart*10173 o pkg/exf/exf_check_range.F
a435e833b1 Mart*10174 - add tile index to diagnostics and move stop statement to the very
10175 end of the routine.
05aa25be39 Jean*10176 o pkg/diagnostics: (diagnostics_main_init.F)
10177 define title of isomorphic variables according to the current config.
842bb5f1d9 Jean*10178 o pkg/thsice with pkg/seaice dynamics:
6789e1f33d Jean*10179 - fix domain of computation (interior only, required for exf) and do exchanges
10180 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
ae35500ca3 Jean*10181 o towards a standard way of dealing with multi-threading in MONITOR
10182 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
a435e833b1 Mart*10183 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
10184 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
6f6b52a4f5 Jean*10185 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
e03f83af3c Jean*10186 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
10187 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
10188 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
a435e833b1 Mart*10189 o tracer advection:
d8d36aa8bb Jean*10190 - clean-up and simplify calc_common_factors.F
a435e833b1 Mart*10191 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
d8d36aa8bb Jean*10192 advection subroutine (but still not used within DST advection S/R)
2baa3a4f30 Jean*10193 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
10194
0e6056cd20 Jean*10195 checkpoint58j_post (2006/06/15)
95f2c2ae3f Patr*10196 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
10197 from file (collects calls previously in FORWARD_STEP)
10198 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
a0d26c252a Patr*10199 o adjoint store dir. adjusted accordingly
95f2c2ae3f Patr*10200 o genmake2
10201 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
a0d26c252a Patr*10202
0e6056cd20 Jean*10203 checkpoint58i_post (2006/06/14)
a435e833b1 Mart*10204 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
c9058eda34 Mart*10205 on wind stress (SEAICEstressFactor defaults to 1.)
4a7f47048d Jean*10206 o Total number of Timers is finite (<=40): comment out 2 non-essential one
10207 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
a435e833b1 Mart*10208 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
b161d628fb Jean*10209 on CS-grid: no longer loosing mass.
6be7d7dc38 Jean*10210 o exf & curvilinear-grid: no longer modify longitude xC & xG.
5ea0c8294d Mart*10211 o pkg/ggl90: fix sloppy output and fix a bug
d558d05cf5 Dimi*10212 o pkg/seaice: added SEAICEuseEVPpickup parameter
10213 - Set to false in order to start EVP solver with
10214 non-EVP pickup files when using SEAICEuseEVP
b53f333527 Mart*10215 - fix sign error in diffusion in seaice_calc_rhs
5ea0c8294d Mart*10216
0e6056cd20 Jean*10217 checkpoint58h_post (2006/06/07)
4a4ac2b6f4 Patr*10218 * Modifications for bottom topography control
10219 o replace hFacC by _hFacC at various places
10220 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
10221 o add non-self-adjoint cg2d_nsa
10222 o update autodiff support routines
10223 o re-initialise hfac after ctrl_depth_ini
10224 o works for 5x5 box, doesnt work for global_ocean.90x40x15
10225 * Adding verification for 5x5 box (4-layer) bottom topography control
10226
0e6056cd20 Jean*10227 checkpoint58g_post (2006/06/07)
6f0ec9a199 Jean*10228 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
10229 used for mean seasonal cycle, mean diurnal cycle); add an example
10230 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
a435e833b1 Mart*10231 o pkg/ggl90:
2539abbd59 Mart*10232 - add parameter (minimum surface kinetic energy)
10233 - fix bug (avoiding division by zero)
a5d3c9e070 Mart*10234 o couple pkg/thsice to pkg/seaice:
10235 - modify advection in seaice to accomodate new scalar fields to be advected
10236 - only muliDimAdection scheme work with seaice/thsice
10237 - mapping of thsice-variables to seaice-variables, back and forth
10238 - does not break the verification experiments, but does not give the
10239 desired results either
10240 o pkg/seaice
10241 - make (default) second order advection a bit less confusing?
10242
0e6056cd20 Jean*10243 checkpoint58f_post (2006/06/05)
a435e833b1 Mart*10244 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
10245 to pkg/seaice):
25f8242518 Mart*10246 - new routines thsice_map_exf and thsice_get_exf provide the interface
a435e833b1 Mart*10247 - add an additional formal parameter to thsice_solve4temp
558a6f8862 Patr*10248 o pkg/exf:
10249 - add new fields wspeed, snowprecip (to be able to couple to thsice)
10250 - correct Stefan-Boltzmann constant
10251 - new parameter for longwave surface emittance
a435e833b1 Mart*10252 - separate some stuff from exf_bulkformulae into new routines
558a6f8862 Patr*10253 exf_radiation, exf_wind
a435e833b1 Mart*10254 - add new parameters and constants: longwave emissivity for ocean, ice
25f8242518 Mart*10255 and snow, evaporation parameters over ice
51cdae4cbe Mart*10256 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
10257 either wind from stress or stress from wind
766e50be03 Jean*10258 o pkg/thSIce:
10259 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
10260 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
10261 and THSICE_CALC_THICKN
10262 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
10263 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
10264 to make debugging easier.
10265 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
a435e833b1 Mart*10266 o pkg/bulk_force:
10267 - clean-up comments and parameters ;
766e50be03 Jean*10268 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
086faee439 Jean*10269 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
10270 generate new output for test-experiment: aim.5l_cs.thSI
de56cb35d0 Jean*10271 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
558a6f8862 Patr*10272 testreport accordingly
de56cb35d0 Jean*10273
0e6056cd20 Jean*10274 checkpoint58e_post (2006/05/17)
23424617f8 Patr*10275 o SEAICE_CGRID adjoint done
f66b450460 Patr*10276 o R_STAR adjoint implemented.
10277 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
10278 * need to sort out init. of h0facc, etc.
5ff8d4a5cf Patr*10279 o Make pkg/profile fully independent of ecco,cost, etc. stuff
10280 to be able to use it in pure forward.
2619b6fb59 Patr*10281
0e6056cd20 Jean*10282 checkpoint58d_post (2006/04/21)
3112405dc7 Jean*10283 o upgrade simple test-experiment to tutorial example:
10284 step.1: duplicate the experiment and (step.2) will remove the old copy.
10285 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
10286 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
10287 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
10288 tutorial_global_oce_biogeo <- copy of dic_example
10289 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
10290 tutorial_plume_on_slope <- copy of plume_on_slope
10291 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
10292 tutorial_global_oce_optim <- empty for now (David ?)
10293 tutorial_global_oce_in_p <- copy of global_ocean_pressure
10294 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4c5f492b95 Gael*10295 o correct a sign problem in cost_scat.F
a435e833b1 Mart*10296 o obcs and ptracers: fix boundary conditions for advections schemes
10297 with larger stencil
2057f5cbae Patr*10298 o thsice adjoint: start
a435e833b1 Mart*10299 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
9108661f3b Mart*10300 completeness
a435e833b1 Mart*10301 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
562e0a15fe Mart*10302 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
a4d028af27 Patr*10303 o ptracers adjoint:
10304 * avoid extensive recomputatations
10305 * fix missing re-init. of gptr (missed by TAF)
a435e833b1 Mart*10306 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
8ef23b4c75 Mart*10307 me to turn off the excessive output to STDOUT that this package produces
b030b75637 Jean*10308 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
10309 and add those terms in Vector-Invariant formulation.
a435e833b1 Mart*10310 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
d4f53c1fd3 Gael*10311 if the control period (xx_hfluxperiod etc) is 0
10312 o in profiles pkg, clean routines and fix details
a435e833b1 Mart*10313 o in ecco pkg, reading ssh data:
d4f53c1fd3 Gael*10314 fix problem in case the model does not start at iter0=0
587564817e Mart*10315 o fix mnc-pickup/restart for ptracers
b970da0492 Patr*10316 o new package prifiles:
10317 code to compute profile-based cost by Gael Forget
01c71301a9 Patr*10318 (modifs in ecco, ctrl, autodiff)
b970da0492 Patr*10319 o Benign bug fix in initialization (spotted by M. Mazloff) of
10320 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
01c71301a9 Patr*10321
0e6056cd20 Jean*10322 checkpoint58c_post (2006/03/23)
5f86d55b22 Patr*10323 o adjoint: finish NLFS adjoint and provide reference output in
10324 verification/global_ocean.90x40x15/results_ad_nlfs
a435e833b1 Mart*10325 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
c401c03915 Mart*10326 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
a435e833b1 Mart*10327 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
c401c03915 Mart*10328 with SEAICE_CGRID defined.
eaf6816ef6 Jean*10329 o move calendarDumps from "data" to "data.cal" and clean-up the code
10330 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
10331 o add useEXF & useCAL flags (for now, set in hard-coded way)
8f72ee0f86 Jean*10332 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
10333 (were missing in NH mode, and wrong in quasihydrostatic mode).
10334 waiting for Chris updated version of calc_gw to add those CALLs.
10335 o fix bug in quasihydrostatic S/R ;
10336 add a test for this option: global_ocean.90x40x15.qshyd
808cde9ea6 Jean*10337 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
10338 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
10339 o add on/off flag useOffLine for package OFFLINE
a435e833b1 Mart*10340 o seaice:
ed94531ee9 Mart*10341 - modify advection so that it works also on the C-grid
a435e833b1 Mart*10342 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
ed94531ee9 Mart*10343 problem in multi-tile runs with C-grid
362dbfa680 Mart*10344 - add flags for clipping ice velocities and/or masking solver forcing
8582a6e33f Mart*10345 - fix drag (ocean on ice) formulation and a bug that caused noise in the
10346 C-grid solver
3dce9279c3 Mart*10347 - added a few comments to seaice_diffusion.F
10348 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
10349 are now exclusive)
a435e833b1 Mart*10350 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3dce9279c3 Mart*10351 required re-ordering the code a little:
10352 + make DAIRN global variable (defined in SEAICE)
10353 + move computation of the viscosities eta and zeta into a new separate
10354 routine (because I need to recompute them in seaice_ocean_stress.F)
0946cb6a20 Mart*10355
0e6056cd20 Jean*10356 checkpoint58b_post (2006/03/13)
a435e833b1 Mart*10357 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
12cf6f073b Jean*10358 update output.txt of exp. aim.5l_cs.thSI
9705a0d5c6 Ed H*10359 o various mnc cleanups and improvements:
10360 + shrink lookup tables by factor of ~4
10361 + better error reporting when running out of lookup space
10362 + able to handle longer path/file names (up to 500 chars)
07c24e37c2 Patr*10363 o adjoint:
10364 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
10365 - TBD: "hidden" mom_vecinv recomp. in dynamics
3975cf6076 Jean*10366 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
10367 (allow to differentiate between forcing components using new integer flags:
10368 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
10369 and add new flag to put Dissipation tendency out of Adams-Bashforth.
d7e0df64ad Patr*10370 o ecco
10371 - enable trend removal from SSH anomaly obs.
10372 o adjoint
10373 - a fix for PmEpR when #undef EXACT_CONSERV
10374 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
10375 - try to fix "hidden" recomp. in forward_step for NLFS
10376 (NLFS seems broken sometimes after I checked it in)
a435e833b1 Mart*10377 o seaice:
73792e16df Mart*10378 - add c-grid version of the dynamic solver:
10379 + three new routines that are the c-grid substitute lsr, dynsolver
10380 and ostres
10381 + put a few fields that were local to dynsolver into global common
10382 blocks, so that I can move the computation of stresses etc into
10383 seaice_lsr (saves coding but may break the adjoint).
10384 - replace more hardwired parameters by runtime parameters
10385 - add ice masks that mask the rhs of the implicit solvers where there
10386 is no ice (commented out in seaice_dynsolver, because i am not sure
10387 if this works properly), eventually this should replace the clipping
10388 of ice velocities in seaice_dynsolver to +/-40cm/s.
a435e833b1 Mart*10389 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
2f7dcdd863 Ed H*10390 include it only where its needed
a69f02f073 Mart*10391 o move balancing of fluxes before the call of external_forcing_surf
6ed81927e7 Mart*10392 o seaice:
10393 - correct units of turning angles (now they are really in degrees)
10394 - move computation of GWATX/Y out of main routine into dynsolver
10395 - initialize GWATX/Y in seaice_init
6f005fadde Jean*10396 o Apply mask on Fresh-Water flux (needed for SSH forcing).
a435e833b1 Mart*10397 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
03a9a80809 Mart*10398 o seaice: add runtime flags for turning angles (default to zero)
a435e833b1 Mart*10399 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4bf6063982 Patr*10400 and trend from exf forcing and ctrl control adjustments
10401 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
10402 (since checkpoint57x_post)
f5e99809b0 Jean*10403 o change the default rotation period to 86164.s = the Earth rotation
6fdf842d4f Jean*10404 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
10405 and based on a reference stratification. Tested within hs94.cs-32x32x5.
009bbbd3aa Mart*10406 o seaice advection: add code for choosing between the default (2nd order
10407 central differences) and multiDim advection schemes provided by
10408 pkg/generic_advdiff
7d6367e3db Mart*10409 o seaice:
a435e833b1 Mart*10410 - removed all references to SEAICE_GRID.h fields from
7d6367e3db Mart*10411 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
10412 (cubed-sphere configuration will change a little)
10413 - grid computations in seaice_init are obsolete now.
10414 - cleaned up code a little so that is easier to read (hopefully).
009bbbd3aa Mart*10415 - added new (better?) discretizations of default advection and diffusion
10416 (turn on with SEAICEuseFluxForm)
10417 - replace 1 in 3d global fields by kSurface in growth.F
a435e833b1 Mart*10418
0e6056cd20 Jean*10419 checkpoint58a_post (2006/02/13)
14e9b6a754 Mart*10420 o seaice:
10421 - bug fix in advect.F
a435e833b1 Mart*10422 o shelfice:
10423 - separate shelfice load anomaly from pload (breaks with time
70b0991389 Mart*10424 dependent forcing), => introduce constant field shelficeLoadAnomaly.
10425 Its default is 0., but it may be computed more cleverly from (unknown)
10426 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
10427 done offline. A good approximation of the pressure load anomaly is
a435e833b1 Mart*10428 necessary to avoid large initial adjustment processes underneath
70b0991389 Mart*10429 deep-reaching shelfice.
e5cc225f5e Mart*10430 - small fix in ISOMIP shelfice_thermodynamics
a435e833b1 Mart*10431 - add more sophisticated thermodynamics of Hellmer (1989), this is
e5cc225f5e Mart*10432 now the default
10433 - give a few constants more intuitive names
d5413e2490 Mart*10434 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
10435 if bulk formulae are used in long integration (especially EmPmR). Turn
10436 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
10437 if balancePrintMean, the imbalance that is substracted is printed to
10438 STDOUT.
48ddec2149 Jean*10439 o fix bug (typo) in obcs_apply_eta.F
506298a7d9 Mart*10440 o add a new package shelfice which enables us to model the circulation
10441 underneath shelf-ice with draughts of hundreds of meters.
10442 - works
10443 - to do: + include improved thermodynamics
10444 + check whether kSurfC (from model/inc/SURFACE.h) can be used
10445 instead of new field kTopC
a435e833b1 Mart*10446 + can we use topoFile, Ro_surf and existing code in ini_depth.F
506298a7d9 Mart*10447 instead of new field R_shelfIce and new code in ini_depth.F
10448 and ini_mask_etc.F?
70b0991389 Mart*10449 + adjust vertical mixing schemes?
a435e833b1 Mart*10450 o seaice pkg:
10451 - add a cpp-flag to include a simple formula for a salinity dependent
f2368faea9 Mart*10452 freezing point of sea water at the surface
10453 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
10454 meridional stresses are now different (and hopefully correct)
da87ea6f08 Jean*10455 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
10456 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
10457 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
a435e833b1 Mart*10458 o pkg/diagnostics: add options and parameters for regional-statistics
10459 diagnostics ; define regions by reading a region-mask from a file
575f9a835c Jean*10460 (might add other options later)
bae467ec49 Jean*10461 o pkg/bulk_force:
10462 - add option and parameters to use AIM surface-flux formulae.
10463 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
a435e833b1 Mart*10464 others forcing fields (defined in PARM05, parameter file "data") are loaded
bae467ec49 Jean*10465 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
a435e833b1 Mart*10466 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
bae467ec49 Jean*10467 - use the right EXCH call for uwind,vwind (to work on CS-grid).
10468 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
10469 and parameters (note: calcWindStress replaces .NOT.readwindstress).
10470 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
10471
0e6056cd20 Jean*10472 checkpoint58 (2006/01/12)
a435e833b1 Mart*10473 o add "--embed-source" option to genmake2 which, when the supporting
10474 tools can be compiled (as determined by genmake2) will turn on the
10475 embed_files package which then embeds the entire MITgcm source code
d79bbe5ed9 Ed H*10476 (*.[fFhc] + Makefile) used for the build within the executable
10477 - requested by CNH but off by default
10478 - adds a paltry <9MB to the mitgcmuv executable in most cases
10479 - only writes the output when useEMBEDSRC in eedata is true
f4ab189f71 Patr*10480 o clean up 3-dim. relaxation codes:
10481 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
10482 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
10483 * Thanks to Tom Haine for testing!
10484
0e6056cd20 Jean*10485 checkpoint57z_post (2005/12/31)
b83f88edb2 Jean*10486 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
10487 affects output (@ truncation level) of exp. plume_on_slope ; updated.
b00d0b5f70 Mart*10488 o fix the pickup behavior for obcs in combination with ptracers
10489 o fix a bug in ptracers_external_fields_load
10490 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
10491 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
10492 o transfered surface NH pressure to eta field (if exactConserv).
0330ceca59 Jean*10493 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
10494 and update lab_sea output.txt file.
7276a6414c Patr*10495 o completing 3-dim. relaxation code: additional term
10496 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
10497 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
10498 * At compile time, in "EXF_OPTIONS.h" set
10499 #define ALLOW_CLIMTEMP_RELAXATION
10500 #define ALLOW_CLIMSALT_RELAXATION
10501 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
10502 tauThetaClimRelax3Dim = 15552000.0,
10503 tauSaltClimRelax3Dim = 15552000.0,
10504 * 3 cases:
10505 1) Use a constant-in-time 3-dim. field
10506 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
10507 3) Real-time relax. to time-evolving prescribed field
a435e833b1 Mart*10508 o Adding Laplacian-type smoothness constraint on
3ed7687b4d Patr*10509 initial and boundary (forcing) controls (ic, bc)
a435e833b1 Mart*10510 * enable at compile-time via
3ed7687b4d Patr*10511 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
10512 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1014465bd0 Patr*10513 * Absolute scale somewhat unclear so far
10514 * no area weighting was included since no other cost term does so far
0330ceca59 Jean*10515
0e6056cd20 Jean*10516 checkpoint57y_post (2005/12/08)
3488aaba5f Patr*10517 First step for a NLFS adjoint
10518 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
10519 o new init. routines for calc_r_star, calc_surf_dr
10520 o still need to deal with ini_masks_etc
10521 o testreport seemed happy
0e6056cd20 Jean*10522 checkpoint57y_pre (2005/12/08)
7df36fd6a0 Patr*10523
94e76af995 Jean*10524 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1023fa2ba2 Step*10525 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
81b06b0cda Step*10526 o add new offset feature to offline pkg (plus minor cleanup)
10527 o cfc fixes for final year of integration
10528 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
10529 be in GCHEM_OPTIONS).
10530
0e6056cd20 Jean*10531 checkpoint57x_post (2005/12/04)
7392df2720 Jean*10532 o fix testreport Pb in multiple test experiment.
4212cfbd21 Ed H*10533 o cleanup our namelist syntax in verification:
10534 - make it more F95 standards compliant (some work still needed)
10535 - allows the vast majority of our tests to work with gfortran
f3a828f7e4 Jean*10536 o Non-Hydrostatic:
10537 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
10538 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
f56826ff51 Jean*10539 o Allow to apply AB on T,S rather than on AB(gT,gS):
10540 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
10541 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
10542 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
10543 - need a "clever" read_pickup to restart from the other AB formulation
a435e833b1 Mart*10544 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
31a33cd878 Jean*10545 o remove some unused variables (reduces number of compiler warnings)
812e613baf Patr*10546 o adjoint
10547 * Disable useVariableViscosity for adjoint for time being
10548 (there are a number of extensive recomputations)
10549 * Initialize certain variables needed for adjoint
31a33cd878 Jean*10550
0e6056cd20 Jean*10551 checkpoint57w_post (2005/11/03)
b0d5c3a79b Jean*10552 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
10553 fix the singleCpuIO RS version of MDSWRITEFIELD
10554 and add a WARNING if using globalFiles=T with multi-processors.
1b9b94d610 Jean*10555 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
10556 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
b0d5c3a79b Jean*10557 o tracer advection scheme:
a435e833b1 Mart*10558 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
10559 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
dcc36c3b47 Jean*10560 was not very convenient).
a435e833b1 Mart*10561 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
dcc36c3b47 Jean*10562 (further tests needed for the implicit DST & Flux-Limiter schemes).
1ccb4070a2 Mart*10563 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
10564 and sRef for convenience, handy, when you want to initialize
10565 ptracers in a large domain with a constant non-zero value. Also,
10566 untangle ptracers_init.F a little.
10567
0e6056cd20 Jean*10568 checkpoint57v_post (2005/10/13)
5e507d5445 Jean*10569 o change dome exp. to use variable viscosity in side-drag terms.
2f98dc7b12 Ed H*10570 o remove all the files from the cfc_offline test since they are now
10571 incorporated into tutorial_cfc_offline which has been producing
10572 identical results for a few days of testing
7053a0bdbe Jean*10573 o add new parameter: sideDragFactor to enable half-slip-side BC
10574 and change side-drag S/R to use viscosity from mom_calc_visc
a435e833b1 Mart*10575 (can switch back by setting sideDragFactor=0.); affects results at
10576 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
7053a0bdbe Jean*10577 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
a435e833b1 Mart*10578 o vorticity & strain are now computed without masking, to account for
cc95ee1c31 Jean*10579 no-slip-side BC in variable viscosity calculation ; mask is applied
10580 anyway later on, before computing advection/coriolis terms.
1ccb4070a2 Mart*10581 o modify exp4 to test new obcs support for reading from external files
58bf89d65c Mart*10582 and for passive tracers
a435e833b1 Mart*10583 o fix behavior of ptracers_monitor when monitor output is written to a
c760cf3af0 Mart*10584 netcdf-file; still not independent of monitor.F (writes in the same
10585 file).
a435e833b1 Mart*10586 o change default value of tRef (put a uniform, meaningful value for ocean
9807caa0b1 Jean*10587 & atmos) and initialize sRef (was missing, as Martin mentioned).
a435e833b1 Mart*10588 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
e2b2bf4d90 Bayl*10589 to be proportional to enstrophy dissipation length. Thus,
10590 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
10591 This is now consistent with Smagorinsky and with the manual.
10592
ca1cda04e8 Mart*10593 checkpoint57u_post
ae51cb4320 Mart*10594 o OBCS and PTRACERS: add open boundary support for passive tracers
a435e833b1 Mart*10595 - either use homogenous (pseudo) v.Neumann conditions or prescribe
ae51cb4320 Mart*10596 OB-values from file; this is not different from the way theta and salinity
10597 are treated
10598 - however, Orlanski-radiation conditions are not supported, and the model
a435e833b1 Mart*10599 will stop if you use pTracers and Orlanski at the same time.
ae51cb4320 Mart*10600 - beefed up the rountine obcs_external_fields_load: now only those open
a435e833b1 Mart*10601 boundary values are overwritten with values from files for which there
ae51cb4320 Mart*10602 are really files, otherwise the OB-fields remain untouched. This makes
a435e833b1 Mart*10603 it possible to use different OBs at different ends of the domain (as
ae51cb4320 Mart*10604 with EXF)
a435e833b1 Mart*10605 o reduce number of exch calls in shap_filt (s2).
10606 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
20e058fdde Jean*10607 truncation level) 4/5 MLAdjust test results (11&12 digits match).
10608
0e6056cd20 Jean*10609 checkpoint57t_post (2005/10/03)
c126063c4a Jean*10610 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
10611 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
10612 same truncation, independent of the face number: affects affects several
10613 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
02b02f5c36 Jean*10614 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
c126063c4a Jean*10615 note that biharmonic viscosity + no-slip was not tested in any experiment.
76b60848db Jean*10616 o fix bug in non-linear free-surf side-drag ; generate new output for
10617 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
b22b541fe9 Ed H*10618 o make mnc honor the writeBinaryPrec flag for most kinds of output
8b81bca38d Ed H*10619 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
f28ad821d5 Jean*10620 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
10621 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
b39b0f289d Jean*10622 o add brackets in multi-terms sum to get same truncation, independent of
10623 the face number (manage to get exactly same value of gU,gV at the cs-edge)
10624 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1e9e8678dd Bayl*10625 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
10626 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
10627 a maximum grid-scale Reynolds number. Also, changes all length calculations
10628 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
a435e833b1 Mart*10629 Suggested values of viscosity parameters found in mom_calc_visc.
1e9e8678dd Bayl*10630 Many new viscosity diagnostics available.
96c813b2a5 Jean*10631
0e6056cd20 Jean*10632 checkpoint57s_post (2005/09/20)
a435e833b1 Mart*10633 o Add clearing-house for viscosity calculations, mom_calc_visc and
10634 correct numerous bugs in LeithD and Smagorinsky discretizations.
10635 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
10636 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
188fd32c24 Bayl*10637 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
a435e833b1 Mart*10638 and with Strain-Tension viscous term calculation (mom_hdissip.F).
188fd32c24 Bayl*10639 The Strain-Tension form is now called with useStrainTensonVisc=.true.
10640 ViscAhStrain and viscAhTension are now retired.
96c813b2a5 Jean*10641 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
f7f6e70984 Ed H*10642 o In response to JMC's bug report, genmake2 now ignores any soft-links
10643 that it finds in the *current* directory when searching for files.
10644 Soft-links found in any other source directories will still work as
10645 they did before.
a435e833b1 Mart*10646 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
df91541502 Ed H*10647 a C routine to unlimit the stack size
157ea9ae8e Ed H*10648 o mnc-ify pkg/aim snapshot vars
cf701ea57b Ed H*10649 o mnc-ify pkg/land as requested by Daniel
5bc9611487 Ed H*10650 o various changes to mnc including:
10651 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
a435e833b1 Mart*10652 - output can now be grouped so that all files within a group
5bc9611487 Ed H*10653 change the ITER portion of their names in lock-step together
10654 - can now read ("global") PER-FACE (in addition to PER-TILE) files
10655 and works with both EXCH1 and EXCH2 (but needs more testing)
10656 - writing works for all verification test cases w/ g77 on Linux
10657
0e6056cd20 Jean*10658 checkpoint57r_post (2005/09/07)
88d5fee2bf Ed H*10659 o make MNC variable initialization happen earlier
84386989cd Jean*10660 o add diagnostics for (almost) each term of the momentum Eq.
66f83c2ede Jean*10661 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2be058fac5 Jean*10662 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
a435e833b1 Mart*10663 o remove MINIMAL_TAVE_OUTPUT option ;
2be058fac5 Jean*10664 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
69a417565e Jean*10665 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
10666 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5d1838d198 Patr*10667 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
10668 o add time-dependent SST, SSS control
7e2510a0ae Patr*10669 o cost terms in ecco/ modularized (new cost_generic.F)
10670 o cost_averages routines are modularized (new cost_averagesgeneric.F)
10671 o new infrastructure for seaice model vs. obs misfits in seaice/
10672 * driver from the_main_loop.F is seaice_cost_driver.F
10673 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
10674 * gradient check in Exp. 6a of natl_box_adjoint/
10675 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
10676 (see README file)
69a417565e Jean*10677
0e6056cd20 Jean*10678 checkpoint57q_post (2005/08/19)
fa355923ad Jean*10679 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1660a6b12d Ed H*10680 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
10681 - bug was reported by Jean-Michel and Ian Fenty
e8d8f0b10f Jean*10682 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
a435e833b1 Mart*10683 update exp. cpl_aim+ocn output.
9caa94febf Patr*10684 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
a435e833b1 Mart*10685 Needed for high-res. runs with large global files
9caa94febf Patr*10686 to be able to limit tapelev size
10687 o Changed some tests for adjoint:
10688 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
10689 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
10690 * global_ocean.90x40x15/ back to default 3-level checkpointing
9094bd878c Patr*10691 o Modifications to enable scripted COMMON to MODULE conversion
10692 * verification/OpenAD/code/ has necessary scripts and description;
10693 * converts, compiles and runs successfully;
9caa94febf Patr*10694
0e6056cd20 Jean*10695 checkpoint57p_post (2005/08/01)
62807350a8 Jean*10696 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
10697 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
10698 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
10699 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
f39b9d8a97 Jean*10700 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
10701 (was already the case for dissipation with mom_vecinv,
10702 and also the case for grad.PhiHyd when staggered-timeStep)
10703 This will allow to put dissipation out-off the AB time-stepping.
10704 Unfortunately, affects truncation error. Update output of exp. that "fails"
10705 (cg2d matching number) and leave the others for later: front_relax(10),
10706 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
10707 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
10708
0e6056cd20 Jean*10709 checkpoint57o_post (2005/07/30)
a435e833b1 Mart*10710 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
50653b81f1 Ed H*10711 (2) its ready to be documented during the 20050801 DocFest
a435e833b1 Mart*10712 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
e2d47178e0 Ed H*10713 for ideal_2D_oce and lab_sea on linux_ia32_g77
f48a8b1137 Patr*10714 o set to #undef CTRL_SET_OLD_MAXCVARS_30
10715 in global1x1_tot/code_seaice_adj to access indices 32, 33
10716 (worth another tag)
e2d47178e0 Ed H*10717
0e6056cd20 Jean*10718 checkpoint57n_post (2005/07/29)
fbb2516727 Patr*10719 o adding precip control xx_precip 32
10720 o adding swflux control xx_swflux 33
53a1c5d19a Patr*10721 o Replacing 10 forcing penalty cost routines by 1 generic.
10722 o Implementing partitioning in time-mean and variable adjustment
10723 for atmos. state.
10724 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
08f22f958d Patr*10725 o in natl_box_adjoint:
a435e833b1 Mart*10726 * updated exp 1 to 10
53a1c5d19a Patr*10727 (but does not have time-mean vs. variable split results yet)
455751fbdb Patr*10728 o updated global1x1/*_seaice_adj/
10729 to incorporate latest changes
df05ad6e2a Patr*10730 o enable useSingleCpuIO for mdsio vector routines
10731 (applies in particular to tapelev I/O)
10732 o removed inefficient K-loop in all active_file*control*.F
3d0327d769 Patr*10733
0e6056cd20 Jean*10734 checkpoint57m_post (2005/07/28)
c0c2091c08 Jean*10735 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
10736 and advect_cs (use EXCH-2 and standard cs-32 grid files).
a435e833b1 Mart*10737 o pkg/exch2: filling of face-corner halo regions is optional
d6f0fdc2ab Jean*10738 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
10739
0e6056cd20 Jean*10740 checkpoint57l_post (2005/07/14)
a435e833b1 Mart*10741 tag before updating tutorials (pre-release-2)
9ce7209758 Jean*10742 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
10743 for output and interpolation of input fields onto model grid)
10744 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
10745 Affects results of exp. rotating_tank ; update output.txt.
27356e724c Jean*10746 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
6e29458d64 Jean*10747 and taking the square quantity and/or using a fraction-weight field.
27356e724c Jean*10748 o fix aim_diagnostics_init.F mate numbers.
10749 o add mnc output capability to diagnostics/diagstat and update
106a65ba8a Ed H*10750 our cvsignore files for the ACSII output generated
10751
0e6056cd20 Jean*10752 checkpoint57k_post (2005/07/02)
508b8225ad Patr*10753 o lab_sea now uses diagnostics package and provides a suite of
10754 new EXF diagnostics output.
10755
0e6056cd20 Jean*10756 checkpoint57j_post (2005/06/30)
61b6aef6a7 Patr*10757 o exf
10758 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
10759 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
10760 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
10761 * extended diagnostics output
10762 - now includes all EXF variables
10763 - hs, hl moved to common block
10764 - separate S/R for diagnostics, called after ctrl vector is added
10765 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
10766 - EXFqnet contains true Qnet (i.e. includes qsw)
10767 * updated verif. lab_sea, global_with_exf
10768 * Rearranging hflux (exf_mapfields -> exf_getforcing)
10769 to ensure that diagnostics sees a true EXFqnet
f529aaf45d Jean*10770 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
f4f7b96c0e Jean*10771 o diagnostics pkg: change pointers so that 1 diagnostic can be used
10772 several times with different frequencies.
df4e8f7bcf Ed H*10773 o mnc-ify the thsice package as requested by Daniel Enderton
10774 - the monitor--MNC output needs work
10775 - many attributes need to be added (most are currently blank)
10776 o mnc-ify theaim_v23 package as requested by Daniel Enderton
10777 - many attributes need to be added (most are currently blank)
24babd248d Jean*10778 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
cafbc21546 Jean*10779 o add Sadourny like discretization to the 4th.O vorticity advection scheme
a435e833b1 Mart*10780 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
a3075797a1 Jean*10781 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
10782 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
85f899f51b Jean*10783 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
10784 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
10785
0e6056cd20 Jean*10786 checkpoint57i_post (2005/06/19)
d1a9b8a2b9 Andr*10787 o Diagnostics package was changed: diagnostic allocation is now deactivated
10788 by setting an empty file name in the namelist (used to be by setting 0 frequency)
78a781bbae Jean*10789 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
10790 add 1rst Order upwind vertical Shear.
eb47174845 Ed H*10791 o add a quick fix for A/B checkpointing in OFFLINE mode
4b08b6ee66 Ed H*10792 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
10793 end-run around the C/Fortran linking horror in eesup/src/timers.F
2e9be4c81e Alis*10794 o added pkg/runclock: allows user to terminate run based on wall clock
10795 o added non-hydrostatic scaling parameter: nh_am2
8fef4b1a57 Mart*10796 o pkg/my82: futile attempt to make results compiler-independent by adding
10797 some "_d 0", etc. no effect.
a435e833b1 Mart*10798 o for mnc output, fill the 'T' coordinate var with myTime and create a
987ff12cb6 Ed H*10799 separate 'iter' variable for iteration count
a435e833b1 Mart*10800 o pkg/diagnostics:
37224b77cb Jean*10801 add new capability: output of Global/Regional & per-level statistics ;
10802 tested against monitor output (including land & thSIce) on various exp.
10803 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
b9d81c4350 Jean*10804
0e6056cd20 Jean*10805 checkpoint57h_done (2005/05/19)
a435e833b1 Mart*10806 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
74630d4888 Jean*10807 data.diagnostics, data.gchem, data.ptracers) is done.
10808
a435e833b1 Mart*10809 o pkg/diagnostics: prepare for Global/Regional statistics.
10810 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
83f253cab3 Jean*10811 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
10812 and rename it: DIFFERENT_MULTIPLE
10813
0e6056cd20 Jean*10814 checkpoint57h_post (2005/05/14)
8e5ee067a3 Jean*10815 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
0da48370b7 Jean*10816 o pkg/diagnostics: change output frequency, now in seconds (instead
10817 of Nb of iterations). This requires to change data.diagnostics.
0e6056cd20 Jean*10818 checkpoint57h_pre (2005/05/12)
51dd5bf40e Jean*10819
41ce3f2380 Ed H*10820 o in mnc, let the user create the output dir if both mnc_outdir_date
10821 and mnc_outdir_num are false
06fffa8fd5 Ed H*10822 o add fflags() to pkg/diagnostics which allows one to specify, on a
10823 per-file basis, the file precision [default behavior is unchanged]
7e819019d5 Dimi*10824 o added diagnostics to pkg/kpp, including computation of mixed layer
10825 depth based on a temperature/density criterion
10826 o updated verification/natl_box to test the new pkg/kpp diagnostics
7bc0d239f7 Jean*10827 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
300c0d54fc Jean*10828 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
9a87ea5e43 Ed H*10829 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
10830 not mnc -- this mistake was found by JMC and is now corrected
10831
0e6056cd20 Jean*10832 checkpoint57g_post (2005/04/15)
79e87d2e6d Jean*10833 o add Adams-Bashforth 3rd Order time stepping:
10834 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
10835 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
0e6056cd20 Jean*10836 checkpoint57g_pre (2005/04/15)
af908d3f0e Jean*10837
5ab5d7f263 Patr*10838 o make lambda[Theta,Salt]ClimRelax spatially varying
10839 (default remains spatially uniform constant based on tau)
ce442b4534 Patr*10840 o added new control variables
10841 * init. uVel, vVel, etanN
10842 * lambda[Theta,Salt]ClimRelax
10843 o separate masks used for ctrl_pack/unpack 'from write_grid' output
10844 (suggested by G. Forget)
5ab5d7f263 Patr*10845
0e6056cd20 Jean*10846 checkpoint57f_post (2005/04/06)
a80a5e8cfd Jean*10847 o add parameter "baseTime" = model base time = time at iteration zero
a435e833b1 Mart*10848 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
a80a5e8cfd Jean*10849 account for baseTime shift
10850 o move Coriolis arrays from PARAMS.h to GRID.h
0e6056cd20 Jean*10851 checkpoint57f_pre (2005/04/06)
ee61c20a30 Jean*10852
de859229b1 Ed H*10853 o mnc-ifying the seaice package
de01be390b Alis*10854 o introduced an alternative length scale calculation for use in the limiting
10855 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2d80ef5b25 Patr*10856 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
a435e833b1 Mart*10857 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
b4b9669a6b Bayl*10858 as well as grad(vort3). Made it compatible with both approximate form
10859 for the cubed sphere and full form of these gradients. Added flag
a435e833b1 Mart*10860 useFullLeith to select between approximate and full form.
02718ea810 Jean*10861 o add "d0" in getcon.F to reduce differences between compilers/platforms
10862 update output.txt of exp. fizhi-gridalt-hs
5103c42ce9 Jean*10863 o change port_rand funtion to allow to set the seed.
409155d7b6 Ed H*10864 o fix obscure MNC bug involving conversion between reals and integers
a435e833b1 Mart*10865 - it caused no problems with certain (eg. gcc, ifc) compilers but the
409155d7b6 Ed H*10866 new version is now more standards-compliant
4645654aba Patr*10867 o adjoint-related modifications
10868 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
10869 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
10870 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
409155d7b6 Ed H*10871
0e6056cd20 Jean*10872 checkpoint57e_post (2005/02/28)
a4f6b487ba Patr*10873 o Adding eddy stress controls a la Ferreira et al.
5245708a89 Jean*10874 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
f30908c65d Patr*10875
eee5dc53df Jean*10876 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
10877 update output.txt of exp. fizhi-gridalt-hs
2cc3b69a26 Ed H*10878 o add more "Z" dimensions and associated coordinate vars to MNC
c098ac3e0d Dimi*10879 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
fc64655a31 Dimi*10880 o parameter calendarDumps: when set, approximate months (30-31 days) and years
10881 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
10882 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
10883 months and years. Requires pkg/cal.
ee2e7fad64 Ed H*10884 o diagnostics: add pickup functionality
10885 - off by default for backwards compatibility
10886 - current version only uses MDSIO -- MNC will be added
9723cb5244 Jean*10887 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
26c7db4c78 Jean*10888 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
10889
0e6056cd20 Jean*10890 checkpoint57d_post (2005/02/11)
06d5464476 Jean*10891 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
a435e833b1 Mart*10892 o modify verification/ideal_2D_oce so that it tests the creation of mnc
91cf1175df Ed H*10893 output from the diagnostics package
24ef99fe7f Jean*10894 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
6554790d1c Ed H*10895 o make genmake2 more portable by using ".$FS" instead of ".f" for more
10896 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
e8743b4419 Ed H*10897 o add coordinate variables to the MNC output from the diagnostics package
a629410b0b Jean*10898 o change MNC-flags default value: true when useMNC=TRUE
e808c5b132 Ed H*10899 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
a435e833b1 Mart*10900 the ability (off by default) to read the grid information using MNC
7a3f7c0b47 Jean*10901 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
0557aa5c83 Jean*10902 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
a435e833b1 Mart*10903 o do snap-shot diagnostics at the middle of the time-interval (instead of
fde699a81e Jean*10904 at the end).
40893cb58a Jean*10905 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
10906 new test for AIM with thSIce + slab-ocean
dd3fb239f5 Jean*10907 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
440b7157f3 Jean*10908 o move state variable diagnostics to the beginning of the time step ;
10909 (note: still needs some work specially for snap-shot diagnostics)
10910 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
10911
0e6056cd20 Jean*10912 checkpoint57c_post (2005/01/27)
c130fcff71 Jean*10913 o Change testing option (-ieee) to get closer agreement between g77 & ifort
10914 o generate new output.txt files on faulks with g77 & the new -ieee option
0e6056cd20 Jean*10915 checkpoint57c_pre (2005/01/27)
7ba28f2af1 Jean*10916
10917 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5a35007c50 Jean*10918 update output.txt of exp. global_ocean.90x40x15
a435e833b1 Mart*10919 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
6643de8305 Jean*10920 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5f46ec9135 Jean*10921 o add saltFlux(+File) forcing capability with periodicExternalForcing
97038d3c07 Jean*10922 o allow to use pkg diagnostics for GM-Redi & ThSIce output
10923 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
35ef3a0982 Ed H*10924 o improvements for the MNC output from DIAGNOSTICS:
10925 - correct handling of the unlimitied dimension
10926 - all dims now have associated coordinate variables
10927 - variables located at U, V, and Corner ("Z") points are now written
a435e833b1 Mart*10928 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
35ef3a0982 Ed H*10929 *all* data points are output
8d9f2d1888 Dimi*10930 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
e1a538cff8 Dimi*10931 o added pkg/seaice/seaice_monitor.F
fcf5946e08 Dimi*10932 o mdsio_readfield.F can now read files visible only to master MPI process.
714116e714 Dimi*10933 o pkg/seaice: some test code for ice-modified ocean stress
4aa81846e7 Dimi*10934 o exf_getffields interpolation defaults to bilinear for all scalar forcing
10935 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
10936 spurious negative numbers for precipitation and humidity. Will cause
10937 some small numerical differences for integrations using pkg/exf/exf_interp.F.
a3296ad516 Patr*10938 o pkg/ctrl/
10939 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
10940 May be enabled via doPackDiag
a435e833b1 Mart*10941 * introduce z-scaling of
10942 + gradient (doZscalePack) and
a3296ad516 Patr*10943 + control (doZscaleUnpack)
10944 o pkg/mdsio/
10945 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
10946 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4aa81846e7 Dimi*10947
0e6056cd20 Jean*10948 checkpoint57b_post (2004/12/20)
0cf6e0ada1 Jean*10949 o simplify options in diagnostics_fill arguments (remove weird combinations)
2f38f768b3 Ed H*10950 o fix MNC coordinate variables so that they now contain per-face index
a435e833b1 Mart*10951 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2f38f768b3 Ed H*10952 general, EXCH2 grids are only aligned to a "local" coordinate system
34bd0f9de0 Jean*10953 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
10954 o Implement instantaneous output within pkg diagnostics:
10955 setting a negative frequency in data.diagnostics produces
10956 "snap-shot" output (as opposed to time-average if freq > 0)
ed27c6ee8e Jean*10957 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
a435e833b1 Mart*10958 NOTE: change ptracer diagnostics name: use 2 characters to work with
ed27c6ee8e Jean*10959 more than 9 tracers. Add also diagnostics of advect & diffus flux.
a435e833b1 Mart*10960 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
18eb3f79fd Ed H*10961 becomes the coordinate variable for the 'T' dimension
d77e828db7 Ed H*10962 o add CF-style coordinate variables to MNC
a435e833b1 Mart*10963 - just a first cut: numbers are meaningless on the cubesphere and
d77e828db7 Ed H*10964 missing along the T axis but otherwise it works!
e07cbe4110 Dimi*10965 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
047c5644f3 Jean*10966 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
9a922069e0 Jean*10967 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
10968 this is based directly on what the model compute, so that the content of
10969 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
10970 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
a435e833b1 Mart*10971 o clean up build options files for SunOS, in particular
e8f00bfc75 Mart*10972 - remove -traditional from xmakedepend
10973 - change -xarch=v9 to -xarch=native for f77
10974 - restore use of make (not gmake)
10975 - add CC=gcc if using g77
7af35f0733 Ed H*10976 o changes per discussion of AM, JMC, & EH3 today:
a435e833b1 Mart*10977 - move redundant "grid" variables out of "state" -- in preparation of
10978 creating proper CF-style coordinate variables and in recognition
10979 that any/all grid variables can be easily copied (eg. w/NCO) from
7af35f0733 Ed H*10980 the grid files into any of the other NetCDF files
a435e833b1 Mart*10981 - *always* output grid variables with MDSIO (this will eventually be
7af35f0733 Ed H*10982 changed)
10983 - output MNC grid file if useMNC is true
a435e833b1 Mart*10984 o every instance of _END_MASTER() has been found and replaced with
10985 _END_MASTER( myThid ) in order to satisfy certain picky Sun
ea6e02f692 Ed H*10986 preprocessors
ee5c9de779 Jean*10987 o re-arrange diagnostics pkg initialisation:
10988 - allow each package to extend the available diagnostics list
10989 - add some checking and fix small problems (multi-threaded, ...)
10990 - new S/R diagnostics_fill (replace fill_diagnostics):
10991 look through the short list of active diag. (instead of the long list)
10992 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
617e9c07f6 Ed H*10993
0e6056cd20 Jean*10994 checkpoint57a_post (2004/12/10)
6ff6896d7d Patr*10995 o this set of changes restores TAMC compatibility
10996 tested for global_ocean.90x40x15 adjoint on trough
10997 (what a pain)
10998
0e6056cd20 Jean*10999 checkpoint57a_pre (2004/12/10)
4161b94ac5 Patr*11000 o some modifs in tools/build_options for sunos
11001 o call ctrl_pack for ctrl at end for optimcycle=0
11002
0e6056cd20 Jean*11003 checkpoint57 (2004/12/09)
7bcb6cc723 Mart*11004 o add horizontal bi-harmonic viscosity for vertical velocity
11005 - new parameter viscA4W (defaults to viscA4)
11006 - affects only non-hydrostatic code
11007 - to be done: no-slip lateral boundary conditions
af994d39e8 Dimi*11008 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
f9712caa2c Jean*11009 o implement Implicit Vertical advection for pTracers
2c4cea51ae Jean*11010 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
e97e7f4284 Jean*11011 (implemented also for implicit vertical diffusion & advection)
5428496056 Mart*11012 o OBCS: extend application of tracer open boundary conditions
11013 to a strip beyond the boundary of width Olx/Oly
14137e831b Patr*11014 o add call monitor to TAF set of required calls (flow directives)
11015 and include in natl_box_adjoint
11016 o untangle a few ifdefs related to cost, ctrl, autodiff
11017 untangel a few ALLOW_ECCO_OPTIMIZATION
e5d44c8b0d Patr*11018 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
11019 (theta2, salt2 in ecco_cost_weights)
5428496056 Mart*11020
0e6056cd20 Jean*11021 checkpoint56c_post (2004/12/03)
93ea71777b Mart*11022 o OBCS as control variables
11023 - update ctrl_ad_diff.list, obcs_ad_diff.list
11024 - remove balance of obcs controls from default
11025 - fix index bug nobcs in ctrl_init
11026 - fix dummy fields filen in ctrl_pack
11027 - add dummy weights for obcs
11028 o lsopt: comment out fort.94 output
a435e833b1 Mart*11029 o optim:
93ea71777b Mart*11030 - remove unnecessary header files
11031 - adjusted namelists
11032 - add xerbla.F to Makefile
a435e833b1 Mart*11033 o exf:
93ea71777b Mart*11034 - multiple modifications of exf_check_range
11035 - unit change in exf_init_runoff from [m/year] to [m/s]
11036 o mdsio:
11037 - i/o-vector change debugLevel from debLevA to debLevB
11038
0e6056cd20 Jean*11039 checkpoint56b_post (2004/12/01)
8a588e179e Mart*11040 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
11041 is called from DO_THE_MODEL_IO
11042 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
11043 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
11044 - clean up PTRACERS_WRITE_TIMEAVE a little
233b414ed8 Mart*11045 o add another verification experiment that tests both the cfc-pkg and
a435e833b1 Mart*11046 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
233b414ed8 Mart*11047 reactive tendencies treated inline with regular timestepping
d8c583b49a Mart*11048 o testreport previously did a lousy job of comparing small numbers, so
11049 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
11050 implemented in the little c-progam tmp_cmpnum.c which is embedded in
a435e833b1 Mart*11051 testreport.
d8c583b49a Mart*11052 o ptracers_monitor: bug fix for MPI
11053
0e6056cd20 Jean*11054 checkpoint56a_post (2004/11/28)
bdb2728325 Mart*11055 o GCHEM: finish reorganizating the package
a435e833b1 Mart*11056 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
bdb2728325 Mart*11057 (introduces another 3D-array for each passive tracer, but only if
11058 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
11059 gchemTendency is not needed because the timestep is done separately)
11060 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
11061 - GCHEM is now---more or less cleanly---separate from PTRACERS
11062 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
11063 so clear to me how that should be done in a general way.
11064 o CFC: improve formatting of output in CFC_ATMOS
11065 o PTRACERS:
11066 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
11067 that ALL experiments with ptracers enable can be checked. This makes
11068 GCHEM_MONITOR obsolete.
11069 - include a runtime parameter PTRACERS_monitorFreq that defaults to
11070 monitorFreq
a435e833b1 Mart*11071 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
68c34fd102 Ed H*11072 o add PTRACERS (PTR0[1-5]) to testreport output
b3bbb0d458 Patr*11073 o exf_check_range:
11074 * default changed to .TRUE.
11075 * will check values for niter0 if debLevA, every timestep if debLevB
11076 * STOP in exf_check_range if 'out of range'
11077 * range chosen generous to allow for potential extema
11078 TBD: a version with stricter range
11079 permitted range would be runtime parameters
5f42c34bbe Jean*11080 o GMredi:
11081 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
11082 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
11083 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
a435e833b1 Mart*11084 o GCHEM:
31940778af Mart*11085 - move call to GCHEM_FORCING_SEP, so that it is now called before
11086 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
a435e833b1 Mart*11087 - introduced a useGCHEM runtime flag and applied it everywhere.
26bcdcd4f0 Mart*11088 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
11089 this flag is now only visible within GCHEM-pkg routines.
11090 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
a435e833b1 Mart*11091 be replaced by a 3D array that is computed before thermodynamics; for
26bcdcd4f0 Mart*11092 this, the tracer ID iTracer had to be included into the parameter list
11093 of ptracers_forcing
a435e833b1 Mart*11094 - set up forward_step to call gchem_forcing, that will replace
26bcdcd4f0 Mart*11095 gchem_forcing_int in ptracers_forcing
11096 - cleaning up
3e021cd85f Jean*11097 o small cleaning of exch2: remove files that are also in eesupp/src
30a55c64a0 Mart*11098
0e6056cd20 Jean*11099 checkpoint56 (2004/11/17)
0608749963 Jean*11100 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2f14a1f812 Ed H*11101 o mnc: cleanup "full" files--fixes out-of-memory problem
c715d0b027 Patr*11102 o ECCO-GODAE
11103 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
11104 * fully merged and updated from SIO code
11105 windstress sign change affects
11106 - exf_inscal_[u/v]stress
11107 - sign of xx_tau[u/v] adjustments
11108 - signs in cost_scat
11109 * ctrl_get_gen: avoid update of tau[u/v] for first few days
11110 * natl_box_adjoint updated and compressed
11111 * 2-level checkpoint switch added
11112 (tested in EXP. 1 of natl_box_adjoint)
11113 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
11114 o SVD
11115 * first complete, non-hacked version for SVD calculations
11116 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
11117 performed via direct access files admtlm_vector.it????
11118 (via ctrl_[un]pack)
11119 * optimcycle is used for ARPACK iteration counter
11120 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
11121 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
a435e833b1 Mart*11122 and add linear transforms where necessary
c715d0b027 Patr*11123 * controls are initial/final SST, SSS (can be extended; need to check
11124 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
11125 o mdsio: filename info to both stderr, stdout
11126 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
a435e833b1 Mart*11127 from sign change
2f14a1f812 Ed H*11128
0e6056cd20 Jean*11129 checkpoint55j_post (2004/11/10)
4c23dd3d61 Jean*11130 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
11131 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
617e9c07f6 Ed H*11132 o add consistent build directories and .cvsignore files to verification
070e727a0d Dimi*11133 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
a435e833b1 Mart*11134 o make all subroutines 30 or less characters in length for certain older
11135 compilers to work (a thorough search only turns up two routines in
064f472621 Ed H*11136 pkg/ptracers)
a435e833b1 Mart*11137 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
7066de6cf6 Jean*11138 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
11139
0e6056cd20 Jean*11140 checkpoint55i_post (2004/10/28)
92cbe40bc9 Jean*11141 o change arrays for total vertical diffusivity (2.D if explicit,
11142 3.D if implicit) ; each ptracer uses its own background value.
73983c4f5f Ed H*11143 o added mnc/NetCDF output capability to ocn_compon_interf
a435e833b1 Mart*11144 - added bits to verification/cpl_aim+ocn so that it can run on
73983c4f5f Ed H*11145 ITRDA and other clusters without the mpirun "-wd" option
0de9c264f0 Andr*11146 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
a435e833b1 Mart*11147 configuration
11148 o give MNC the ability to create additional files rather than
11149 exceeding a specified file size limit "MNC_MAX_FILESIZE"
11150 - the default is just less than 2GB which is a practical limit
ab11ba1276 Ed H*11151 on many systems
a435e833b1 Mart*11152 o Compute the non-local term using either KPP vertical diffusivity (=default)
60fa91c126 Jean*11153 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
9f675e95f9 Jean*11154
0e6056cd20 Jean*11155 checkpoint55h_post (2004/10/20)
19afae78f4 Jean*11156 o add verification test "vermix"
ff63a227b0 Ed H*11157 o remove all the *_ioinc flags and replace with the single global
11158 outputTypesInclusive flag
69377f8682 Jean*11159 o allow to set a vertical profile of vertical diffusivity for T & S
19afae78f4 Jean*11160 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
11161 o useMNC moved from data.mnc to data.pkg
69377f8682 Jean*11162
0e6056cd20 Jean*11163 checkpoint55g_post (2004/10/14)
6b1c25ae7b Patr*11164 o Renaming carbon AD experiments to comply with testreport conventions
11165 o Updating adjoint of Held-Suarez hs94.1x64x5
11166 o Fixing directives for non-ECCO forward_step, after ECCO directives
11167 have been fixed to avoid recomp. of do_oceanic_phys
11168 Works well for global_ocean.90x40x15,
11169 but recomp. issue remains for carbon
a435e833b1 Mart*11170 o Updating adjoint output for natl_box_adjoint after
6b1c25ae7b Patr*11171 pkg/ecco has been modified (see taga c55d_post)
11172
0e6056cd20 Jean*11173 checkpoint55f_post (2004/10/13)
8a3e9d877a Ed H*11174 o rename to timeave_init_fixed
11175
0e6056cd20 Jean*11176 checkpoint55e_post (2004/10/13)
d6be6cad8f Patr*11177 o some delicate re-shuffle of store directives to avoid one
11178 extra call of do_oceanic_physics
11179 affects ecco_the_main_loop.F, do_oceanic_physics.F
11180 checkpoint_lev1_directives.h
11181 o NB: this may break global_ocean adjoint temporarily,
11182 but it is clear how to fix it. Will do later, need this now.
11183
0e6056cd20 Jean*11184 checkpoint55d_post (2004/10/11)
75d667876f Patr*11185 o ECCO specific cost function terms (up-to-date with 1x1 runs)
11186 o ecco_cost_weights is modified to 1x1 runs
11187 o modifs to allow observations to be read in as
11188 single file or yearly files
11189 o enable to read exf forcing fields as either
11190 single file or yearly files (flag useExfYearlyFields)
0e6056cd20 Jean*11191 checkpoint55d_pre (2004/10/08)
75d667876f Patr*11192
11193 o switch between 2-level and 3-level checkpointing
a435e833b1 Mart*11194 o add ability of MNC to write local and "partial" (eg. 2D slices where
cb356b4c5f Ed H*11195 the full 3D field is never actually stored) arrays to NetCDF files
a435e833b1 Mart*11196 with the correct (that is, the complete multi-dimensional) set of
cb356b4c5f Ed H*11197 array indicies
11198 - used in mom_vecinv() to write the diagFreq output
11199 - tested (demonstrated) in verification/aim.5l_cs
c9c3d7103f Ed H*11200 o further mnc-ification
11201 - add verification/lab_sea to the list with mnc setups
11202 - fix undefined mnc v-names in cd_code
11203 - add kpp to mnc output (both snapshot and timeave)
6deb815953 Mart*11204 o non-hydrostatic code
11205 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
11206 in calc_gw.F
11207 - defaults to viscAh
11208 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
a435e833b1 Mart*11209 friction or Leith) in non-hydrostatic mode, as long as there is
6deb815953 Mart*11210 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
449f3c105b Patr*11211 o pkg/cost
11212 extend simple cost functions to treat time mean quantities
11213 (T,U,V) via cost_accumulate_state from cost_tile
4ddf54cc90 Jean*11214 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
11215 be 2 times larger than the minimum size the advection scheme requires.
11216 now get a perfect conservation of salt in advect_cs test-exp (updated)
76f580e1f0 Mart*11217 o GGL90 (Gaspar's TKE mixed layer)
a435e833b1 Mart*11218 - add horizontal diffusion of TKE, requires exchanges in
11219 do_fields_blocking_exchanges, horizontal diffusivity is zero by
11220 default. In OPA there is no horizontal diffusion of TKE but the
76f580e1f0 Mart*11221 mixing coefficients are computed from a horizontal average of TKE of
11222 6 points or so. I think that diffusion has a little more physical
11223 justification.
a435e833b1 Mart*11224 - clean up ggl90_calc in the hope of reducing memory usage (this hope
76f580e1f0 Mart*11225 was in vain)
11226 - mask tke-variable in ggl90_init
3c38934f04 Jean*11227 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
11228 o fix biharmonic diffusion on CS-grid.
78800a222d Mart*11229 o more obcs stuff
11230 - added obcs_external_fields_load as an alternative to the EXF-pkg option
a435e833b1 Mart*11231 for reading boundary values. This routine is called from
78800a222d Mart*11232 obcs_prescribe_read
11233 - updated obcs_check
965df15d92 Mart*11234 - changed sponge layer relaxation parameter units for days to seconds
11235 - turned off sponge layer by default
5720994acc Patr*11236 - changed argument list of OBCS_CALC to myTime+deltaTclock
b67ae883c8 Mart*11237 - fixed about 35 bugs in obcs_external_fields_load
78800a222d Mart*11238
0e6056cd20 Jean*11239 checkpoint55c_post (2004/09/23)
38224ac59a Patr*11240 o obcs stuff
11241 - new runtime flags useOBCSprescribe, useOBCSbalance
11242 - re-arranged obcs_calc
11243 - moved exf_getobcs to obcs_prescibe_read
11244 obcs_prescibe_read is called after ORLANSKI stuff
11245 and independent of it (executable can contain all).
11246 - updated obcs_check
64e4c8fd27 Patr*11247 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
11248 These may be necessary only if tangential velocities are
11249 prescribed at OB, not sure, needs testing.
2509c39694 Ed H*11250 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
11251 which simplifies the calls and passes the ifc check-bounds test
11252
0e6056cd20 Jean*11253 checkpoint55b_post (2004/09/22)
6fdcc18f80 Jean*11254 o add a 2D scalar, Z location, exchange_2 routine.
9f675e95f9 Jean*11255 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
11256 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
11257 affects advect_cs results (for the wrong reason): update output.txt
a435e833b1 Mart*11258 o use a more standard discretization for biharmonic viscosity ;
df39a169f0 Jean*11259 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
a435e833b1 Mart*11260 affects results of dome set-up: update output.txt
df39a169f0 Jean*11261 o fix gad_advection.F (CubedSphere part), back to version 1.23
11262 o fix bug in mom_vi_del2uv.F (CubedSphere part).
58031354dd Mart*11263
0e6056cd20 Jean*11264 checkpoint55a_post (2004/09/20)
a435e833b1 Mart*11265 o merged code to
96bbd4e2a5 Patr*11266 * prescribe/read time-dependent open boundaries
11267 (works in conjunction with exf, cal)
11268 * sponge layer code for open boundaries
11269 * each boundary N/S/E/W now has its own CPP option
11270 (healthy for the adjoint)
11271
0e6056cd20 Jean*11272 checkpoint55 (2004/09/17)
334b55a5b0 Patr*11273 o up-to-date adjoint of previous breaks
11274 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
11275 - global_ocean_ebm: adjoint still needs fix (TLM ok)
11276 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
11277 - carbon: * remove tr1-related adjoint verification
11278 * add ptracer as control variable
11279 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
11280 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
11281
0e6056cd20 Jean*11282 checkpoint54f_post (2004/09/16)
d3c81fef04 Patr*11283 o in verification/carbin/ remove experiment related to
11284 ALLOW_PASSIVE_TRACER (array tr1 etc)
11285 code_ad/ input_ad/ results_ad
11286
b8e554ea44 Mart*11287 o add two new packages
11288 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
11289 + subject to optimization (memory)
11290 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
11291 + subject to reordering (many GOTOs in the original code)
11292 + so far opps is called for every (i,j) point, and then operates in
11293 the vertical; one may want to reorder the scheme in order operate in
a435e833b1 Mart*11294 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
b8e554ea44 Mart*11295 fields)
e05d966902 Ed H*11296 o overhaul of IO so that we now have flags for MDSIO and/or MNC
11297 - all verification tests compile and run with linux_ia32_g77
a435e833b1 Mart*11298 - defaults are compatible with current input files--nothing
e05d966902 Ed H*11299 should change if you were not previously using MNC
11300 - MNC output has been added in numerous places (eg. timeave)
11301 but there are still a few writes not yet do-able with MNC
11302 (this is in progress)
a435e833b1 Mart*11303 - flags now allow for either/or/both use of MDSIO and MNC and
e05d966902 Ed H*11304 documentation will soon follow
11305 - numerous small formatting cleanups for ProTeX
1f6288729b Ed H*11306 o add version info (via BUILD_INFO.h) to MNC and stdout
11307
0e6056cd20 Jean*11308 checkpoint54e_post (2004/09/02)
58031354dd Mart*11309 o add two new packages
a435e833b1 Mart*11310 - pp81 (Packanowski and Philander, 1981), Richardson number and
58031354dd Mart*11311 stratification dependent mixing
11312 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
a435e833b1 Mart*11313 - these scheme operate in a similar manner as KPP (without ghat, of
58031354dd Mart*11314 course), however there is only one diffusivity that is used for both
58378fc26e Mart*11315 temperature and salinity (and passive tracers)
ff0dde6fdb Step*11316 o add offline package
c7bf664228 Ed H*11317 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
11318 provided by Stephanie Dutkiewicz
e8a04cb645 Ed H*11319 o genmake2: add ability to search for C compilers and cleanup test output
11320 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
11321
0e6056cd20 Jean*11322 checkpoint54d_post (2004/07/27)
999e18a3ba Alis*11323 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
a435e833b1 Mart*11324 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
1c7ec5d18e Jean*11325 leading to additional shift by 5 days each year of integration
11326 (i.e. leading to considerable offset over the years)
3eb6e74bad Jean*11327 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
11328 o start with no AB and no initial filtering (staggerTimeStep):
11329 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
11330 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
11331 (external loading & cpl import/export stay in forward_step.F)
11332 o update coupling interface to work with new staggerTimeStep
11333 o change MDSIO ptracers_pickup.
f8f693c946 Jean*11334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
353dc202ae Ed H*11335 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
f8f693c946 Jean*11336 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
353dc202ae Ed H*11337
0e6056cd20 Jean*11338 checkpoint54c_post (2004/07/18)
1a73c8a0cc Jean*11339 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
11340 this affects (truncation error) output.txt of test-exp:
11341 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
11342 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
b59159bd17 Jean*11343 o change Qnet to always be the net heat flux, (+upward).
11344 affects (truncation error) output of natl_box exp.: updated
43f9f92e51 Jean*11345 o define the max number of passive tracers in PTRACERS_SIZE.h
11346 o start to test mnc routinely in exp0
11347 o add sea-ice loading (sIceLoad) as a new forcing field.
11348
0e6056cd20 Jean*11349 checkpoint54b_post (2004/07/08)
a435e833b1 Mart*11350 o add testreport "-j JOBS" option for parallel builds (tested and pretty
8c9e835c69 Ed H*11351 impressive on Altix and Opteron systems)
bc1bd3388a Ed H*11352 o diagnostics can now write NetCDF files through the mnc package
b71b8cc969 Jean*11353 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
a435e833b1 Mart*11354 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
f04695194c Jean*11355 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
11356 affects (truncation error) output of lab_sea & natl_box exp.: updated
11357 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
11358
0e6056cd20 Jean*11359 checkpoint54a_post (2004/07/06)
89aa0d86bf Jean*11360 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
11361 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
11362 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
11363 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
11364 + internal_wave (shift in writing cg2d_ini_res)
0e6056cd20 Jean*11365 checkpoint54a_pre (2004/07/05)
33e1cd7241 Jean*11366
0f1d4cfc8d Dimi*11367 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
11368 - modified verification/lab_sea and natl_box_adjoint accordingly
11369
0e6056cd20 Jean*11370 checkpoint54 (2004/07/02)
11371 checkpoint53g_post (2004/07/02)
e5b80f023f Jean*11372 o prepare splitting of thermodynamics: store convect.counter in common block
8ac0de89ba Jean*11373 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
11374 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
e73e2206ff Dimi*11375 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
1cf497b67b Jean*11376 o new parameter "nShapS": allow to treat differently S from T (nShapT)
11377 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
9e38639d14 Patr*11378 o restore adjointability
1cf497b67b Jean*11379
0e6056cd20 Jean*11380 checkpoint53f_post (2004/06/25)
f4437bef13 Jean*11381 o modifications that affect AIM experiment results (update output.txt):
a435e833b1 Mart*11382 - no advection of S at top interface Nr (pkg/generic_advdiff)
f4437bef13 Jean*11383 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
71989a1d2f Jean*11384 o AIM pkg:
11385 - include stability function into surf.Flux derivative relative to Tsurf
11386 - calculate clear-sky radiation & surface temp. change (for diagnostics)
a435e833b1 Mart*11387
9583d821f1 Andr*11388 checkpoint53e_post
11389 o merged cylindrical coord configuration
11390 o added rotating_tank experiment
db2e27b728 Andr*11391 checkpoint53e_pre
11392
0e6056cd20 Jean*11393 checkpoint53d_post (2004/06/14)
27134ca433 Jean*11394 o faulks upgraded: re-generate output.txt that have changed:
11395 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
19ec94aecc Alis*11396 o Added Bryan and Lewis, 1979, vertical diffusivity profile
a435e833b1 Mart*11397 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5d5fff3a81 Alis*11398 o added Sadourny discretization of Coriolis
11399 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
11400 - re-enabled use of omega3 (useAbsVorticity)
e46ec53fc5 Alis*11401 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
52f1ebc9d7 Jean*11402 vector-invariant equations
e46ec53fc5 Alis*11403 - note: does *NOT* yet use same variable visc. for no-slip BC's.
8a9329e700 Mart*11404 o recoded the lateral boundary conditions for non-hydrostatic w, this time
11405 hopefully without new bugs
11406 - still to do: biharmonic friction for non-hydrostatic w
4855f667f0 Alis*11407 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
11408 o regenerated output for global_ocean_ebm (using -ieee)
647a06f20c Alis*11409 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
11410 of mom_common/
11411 - simple re-arrangement of instructions within computing loop
0e6056cd20 Jean*11412 checkpoint53d_pre (2004/05/21)
647a06f20c Alis*11413
0e6056cd20 Jean*11414 checkpoint53c_post (2004/05/21)
1ad8306ce0 Jean*11415 o new version of coupler for AIM+thSIce and Ocean models
11416 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
11417 - land: change Evaporation of snow
11418 - aim with thSIce: fix bug in snow-precip.
fbdf55c31a Mart*11419 o changes to calc_gw.F
11420 - bug fix for w^2 term near the bottom boundary
11421 - (hopefully) improve the lateral slip boundary condtions for use with
11422 partial/looped cells
11423 - because the bug fix changes two verification experiments anyway (exp5
11424 and plume on slope), change the lateral boundary condition from half slip
11425 to the value of no_slip_sides
4e8c9bded2 Patr*11426 o ebm package wasnt quite up to the parallel task. Fixed that.
8c7ad6d151 Patr*11427 o Adjoint of EBM package + verification
11428 * TLM OK
11429 * ADM not sufficient accuracy yet (needs further testing)
fbdf55c31a Mart*11430
0e6056cd20 Jean*11431 checkpoint53b_post (2004/05/14)
f86a3c0e0c Patr*11432 o Commiting new energy balance model to repository
11433 * package is pkg/ebm
11434 * verif. is verification/global_ocean_ebm
11435 * references are in ebm_driver.F
11436 C * X. Wang, P. Stone and J. Marotzke, 1999:
11437 C Global thermohaline circulation. Part I:
11438 C Sensitivity to atmospheric moisture transport.
11439 C J. Climate 12(1), 71-82
11440 C * X. Wang, P. Stone and J. Marotzke, 1999:
11441 C Global thermohaline circulation. Part II:
11442 C Sensitivity with interactive transport.
11443 C J. Climate 12(1), 83-91
11444 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
11445 C Destabilization of the thermohaline circulation
11446 C by atmospheric eddy transports.
11447 C J. Climate 7(12), 1870-1882
11448 o Will need long integration testing.
0e6056cd20 Jean*11449 checkpoint53b_pre (2004/05/14)
89dadec0f0 Patr*11450
9c05b3873e Alis*11451 o created pkg/mom_common in preparation for variable viscosity code
11452 o renamed and split ini_mnc_io
f4a07a4bc7 Jean*11453 o pkg/land: only liquid water can diffuse or run-off
11454 o AIM using land: soil wetness availability account for snow
53c7d996f6 Dimi*11455 o added printMapIncludesZeros to EEPARMS namelist
11456
0e6056cd20 Jean*11457 checkpoint53a_post (2004/05/11)
e7f1536c88 Patr*11458 o restore TAMC compatiility for exf_constants.h
11459 (no usage of _d in .h)
11460 o Additional storing in KPP in an attempt to fix
11461 TAMC problem with adjoint of KPP code.
11462 (no success...)
11463 Identical code works fine with TAF.
0b07ed3507 Dimi*11464 o Fixed verification/natl_box_adjoint experiments.
11465 Initial conditions for Experiments 4 and 5 are now
11466 set to "SEAICE_initialHEFF=0", which is more reasonable,
11467 and hence gives results closer to that of Experiment 2.
11468 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
e7f1536c88 Patr*11469
0e6056cd20 Jean*11470 checkpoint53 (2004/05/06)
8522e3c798 Chri*11471 o stable checkpoint with up to date adjoint
11472 TLM tests only run for 1st grdchk at the moment. Its unclear if
11473 this is a code problem or a problem with resetting code for g_
11474 variables that is being autogenerated wrong.
11475 Otherwise:
a435e833b1 Mart*11476 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
11477 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
8522e3c798 Chri*11478 are both still in chaos following their security messes.
11479
0e6056cd20 Jean*11480 checkpoint52n_post (2004/05/06)
f989ca6313 Ed H*11481 o various build (mostly genmake2) changes including:
11482 - ability to build/run more easily within Cygwin and MacOS X
11483 - more complicated Makefiles with a stronger dependence on Gnu Make
4634ed4578 Dimi*11484 o pkg/seaice modifications
f4fcd985ee Dimi*11485 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
11486 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
11487 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
a435e833b1 Mart*11488 - changed proxy for geostrophic velocity and updated
28d826540b Dimi*11489 verification/lab_sea/results/* accordingly
4634ed4578 Dimi*11490 - removed ADI dynamic solver from pkg/seaice
11491 - replaced all occurrences of 1/CSTICE or 1/CSUICE
11492 they caused a segmentation fault under certain circumstances
9976df0ac5 Mart*11493 - removed unused field WATR
b055761890 Mart*11494 o bug fix in exf-package:
11495 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
11496 now reflect that.
386eadb044 Mart*11497 o small fixes in the cal-package:
11498 - set reference date to first of January for the 'model'-calendar
11499 - failing of cal_CheckDate in cal_FullDate now actually results in a
11500 warning
df66ce88b0 Mart*11501 o small modifications in exf-package to increase flexibility:
11502 - change climtempfreeze from a constant to a runtime parameter that
11503 is specified in data.exf_clim (default = -1.9)
11504 - introduce runtime parameter windstressmax (default = 2.0) that is
11505 specified in data.exf
351ee82bec Jean*11506 o fix in pkg/thsice:
11507 - update Evap (Tsf changes) to be consistent with Latent heat flux
11508 - maintain snow precipitation unchanged (even if Tsf >=0).
11509 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
11510
0e6056cd20 Jean*11511 checkpoint52m_post (2004/04/18)
329dcc48c4 Mart*11512 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
11513 this does not change any of the results, because myIter=0 in swfrac always
11514 lead to jwtype=2 (the default anyway), but the call makes little sense
11515 as a default
222786db83 Jean*11516 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
1395c36e8a Jean*11517 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
11518 atmospheric model (AIM) to use it ; add a "slab ocean" component.
11519 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
11520 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
7b6ef96a80 Dimi*11521 o extending useSingleCpuIO option to work with new exch2 I/O format
11522 - old-style, missing-tile I/O is still accessible by defining CPP
11523 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
7e019df062 Ed H*11524 o monitor package can write to NetCDF files and/or STDOUT
11525 o fix re-definition bug in MNC_GRID_INIT_ALL()
8a37d3da43 Ed H*11526 o doc/api_reference added
11527 - a framework for building an API Reference Manual using all
11528 the "protex" comments embedded in the code
11529 - see pkg/generic_advdiff, pkg/mnc for examples
b297381f9a Ed H*11530 o MNC:
11531 - make myThid the last argument for all subroutines
11532 - new default for the grid files: NO halos
cba009f524 Ed H*11533 - add useMNC and other run-time flags
11534 - separate per-file-group handling of the unlimited dimension
a435e833b1 Mart*11535 - early initialization of MNC w/ flags read at the eeboot stage
cba009f524 Ed H*11536 and lookup tables set in initialize_fixed
11537 - write all MNC output to a freshly-created directory
47e4defd15 Jean*11538 o thermodynamics sea-ice (thsice) is now tested with testreport.
11539 o test exp. advect_cs: use the standard cs32 grid ; update output.
cd56948b28 Patr*11540 o Added functionality to grdchk:
11541 pick global i,j,k position (or nearest wet) where to perform check.
9fa8dff5bb Jean*11542
0e6056cd20 Jean*11543 checkpoint52l_post (2004/03/11)
63585e25d4 Jean*11544 o new land formulation:
11545 a) use ground enthalpy as prognostic variable to ensure exact
11546 energy conservation.
11547 b) account for water temperature and for latent heat of freezing
11548 in all processes (rain, run-off, ground storage)
11549 c) compute surface and ground temperature implicitly.
11550 o aim_v23 modification for new land model:
11551 a) Treat separately land / ocean / sea-ice surface fluxes
11552 to allow implicit computation of land & sea-ice surface temp.
11553 b) add snow precipitation.
0e6056cd20 Jean*11554 checkpoint52l_pre (2004/03/11)
9fa8dff5bb Jean*11555
af5663a801 Jean*11556 o fix problem (when 1 tile is empty) in min/max monitor.
a435e833b1 Mart*11557 o fix bug in timeAve (u,vZetatave in common block)
76a3a9dce3 Dimi*11558 o no restoring terms under ice for pkg/seaice
36f6faaf99 Dimi*11559 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
11560 o bug fix for pkg/seaice pickups
070ec0f1ad Ed H*11561 o change MNC call locations and add coordinate attributes
3777bd4e33 Jean*11562 o mask vorticity at the corner ; affects global_ocean.cs output
11563 o fix ini_curvilinear_grid ; test CS experiments with mpi
831771ecb4 Jean*11564 o aim.5l_cs: modify sea-ice fraction input file ; update output
73ca73937b Patr*11565 o exf: Adding simple range check routine for exf fields after read
e06eab71ce Jean*11566
0e6056cd20 Jean*11567 checkpoint52k_post (2004/02/23)
c99437d93a Alis*11568 o removed top-level directory "diags"
11569 - we migrated these functions to pkg/timeave a long time ago
11570 o fixed bug introduced in pkg/monitor
171b0dbf72 Patr*11571 o accuracy ctrlprec = 32 insuffient for gradient checks using
11572 averaged fields (I/O via cost_averages)
11573 -> use ctrl.h in active_file*.F to control I/O precision.
11574 o paramter list of CALL ADTHE_MAIN_LOOP
11575 o added initial do_the_model_io to ecco
11576 o set all ...Freq to zero after cost_final
11577 taveFreq, dumpFreq, pChkptFreq
4f02768964 Patr*11578 o MAIN and ECCO differentiability restored
c99437d93a Alis*11579
0e6056cd20 Jean*11580 checkpoint52j_post (2004/02/18)
37b568618c Patr*11581 o fix nchklev in tamc.h for global_ocean...
11582 o Bringing flow and store directives up-to-date
11583 o Really weird thing!
11584 call do_the_model_io from the_main_loop with parameters
a435e833b1 Mart*11585 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
37b568618c Patr*11586 TAF places a faulty re-call of initialise_varia
11587 after cost_final call which should not be there!
0e6056cd20 Jean*11588 checkpoint52j_pre (2004/02/03)
37b568618c Patr*11589
63ae023a6f Andr*11590 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
11591 error messages
e06eab71ce Jean*11592 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
7ecbd3c2aa Andr*11593 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
11594 debug output
bd481ce0ad Andr*11595 o modfied mdsio_writefield.F to handle non-global files under exch2
65c905ad22 Jean*11596 o update AIM Cubed-Sphere exp (aim.5l_cs):
11597 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
11598 o update AIM Equatorial Channel exp:
11599 use standard aim_v23 pkg and change the SST fields to be more realistic.
6b7f81d27b Andr*11600 o globalFile now works with exch2
a435e833b1 Mart*11601 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
e06eab71ce Jean*11602 mon_vort3.F to make exch2 friendly with >1 tile per cube face
e7f0a9dbe1 Dimi*11603 o limit timeave output for hi-res integrations
404487e0d3 Andr*11604
0e6056cd20 Jean*11605 checkpoint52i_post (2004/01/21)
6989afdf96 Alis*11606 o removed CPP_EEOPTIONS.h from verification/*/code
11607 o updated the tiling for global_ocean_pressure
0e6056cd20 Jean*11608 checkpoint52i_pre (2004/01/20)
6989afdf96 Alis*11609
a435e833b1 Mart*11610 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
1e2193d0c9 Jean*11611 the old pkg/aim).
11612
0e6056cd20 Jean*11613 checkpoint52h_pre (2004/01/20)
27e400a76e Andr*11614 o shortened offending lines in exch2_send_rx?.template
8c93ce9839 Andr*11615 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
65592d1bf7 Ed H*11616 o genmake2: add build & execute test for NetCDF code
52d06eb5f9 Andr*11617 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
11618 old grid files, moved CPP_EEMACROS.h to pkg/exch2
f02794c1c2 Dimi*11619 o added useSingleCPUIO flag to monitor.F and mon_out.F
d3ec31b5f6 Dimi*11620 o added temporary hack for sea-ice dynamics on the cube:
11621 metric terms are ignored and it is assumed that
11622 there is no sea-ice on cube faces 1, 2, 4, and 5.
f02794c1c2 Dimi*11623
0e6056cd20 Jean*11624 checkpoint52f_post (2004/01/09)
046fd16d1c Andr*11625 o added exch2 cube routines to pkg/exch2
11626 o modified hs94.cs-32x32x5 to use it
11627 o added new grid files to hs94.cs-32x32x5
0e6056cd20 Jean*11628 checkpoint52f_pre (2004/01/07)
046fd16d1c Andr*11629
0e6056cd20 Jean*11630 checkpoint52e_post (2004/01/07)
67b14118a3 Jean*11631 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
11632 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
1cead955c0 Jean*11633 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
11634 to work with implicit vertical advection and AB ;
11635 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
11636 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
11637 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
0e6056cd20 Jean*11638 checkpoint52e_pre (2004/01/02)
caad9f4c67 Jean*11639
11640 o fix bug in impldiff when Nr=1 or Nr=2.
7d401e1f11 Jean*11641 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
11642 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
157d0c5b42 Jean*11643 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
11644 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
7e230c5c02 Dimi*11645 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
7fd609fd20 Dimi*11646 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
11647 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
7e230c5c02 Dimi*11648
0e6056cd20 Jean*11649 checkpoint52d_post (2003/12/16)
8b7b5f4e88 Alis*11650 o re-tiled many expts to allow comparison in multi-processor mode
11651 - updated output accordingly
11652 - changed hs94.128x64x5 to use intial T from file rather than use the
11653 random number generator
bcea5a4765 Andr*11654 o add infrastructure in model routines for fizhi and gridalt packages
6b0a2bb136 Jean*11655 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
8ac0e9b3ce Dimi*11656 o changes to permit hi-res, cubed-sphere, configuration
11657 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
11658 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
11659 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
11660 of surface winds for the cube
11661 (A verification experiment, based on global_ocean.cs32x15, but with
11662 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
11663 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
11664 complete with example surface forcing files and matlab scripts to look
11665 at the output and compare it with that of global_ocean.cs32x15.)
4b82b202ac Jean*11666 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
11667 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
11668 to conform to the common rule.
a435e833b1 Mart*11669 o check-in the first version of the coupler + interfaces for multi-components
bf18de4739 Jean*11670 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
11671 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
a435e833b1 Mart*11672 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
bf18de4739 Jean*11673 - ocean and atmos. share the same horizontal grid (no interpolation).
11674 - exchanges between component and coupler is done in forward_step
a435e833b1 Mart*11675 o new verification experiment, cpl_aim+ocn:
11676 coupled ocean - AIM atmosphere on cs32 grid.
6b0a2bb136 Jean*11677
0e6056cd20 Jean*11678 checkpoint52d_pre (2003/12/06)
a435e833b1 Mart*11679 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
803573887e Jean*11680 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
269d31530a Jean*11681
0e6056cd20 Jean*11682 checkpoint52c_post (2003/11/25)
7c799abcad Patr*11683 o Fixing OPTIONS files for use of exf:
11684 - ALLOW_ECCO not needed
11685 - ECCO_CPPOPTIONS.h should not be included from
11686 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
11687 as has been the case in the past
11688 - All cal/exf related options are currently set in
11689 single header file. Should remain so until we
11690 agree on a consistent new policy.
2a563ee529 Patr*11691 o Removed all CPP options for cal package.
11692 cal has no more CPP options.
9682a51356 Patr*11693 o modified STOREs in GAD_ADVECTION
11694 o corrected key comp. for passkey
7c799abcad Patr*11695
0e6056cd20 Jean*11696 checkpoint52b_post (2003/11/23)
dfac86e1ec Jean*11697 o new version: "thsice" of thermodynamic sea-ice pkg:
a435e833b1 Mart*11698 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
dfac86e1ec Jean*11699 - modify fluxes but do not change theta directly;
11700 - light cleaning of bulk_force pkg (still needed with thsice).
a435e833b1 Mart*11701 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
dfac86e1ec Jean*11702 + output_thsice.txt to test thsice & bulk_force pkgs.
11703 o put back grid & coriolis monitor output.
0e6056cd20 Jean*11704 checkpoint52b_pre (2003/11/23)
7966caf364 Jean*11705
a435e833b1 Mart*11706 o call "do_the_model_io" at the beginning (=> dump initial state)
7966caf364 Jean*11707 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6dbdc867be Patr*11708 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
11709 (need info on NUMBER_OF_PTRACERS)
11710 o missing PTRACERS headers in some routines
11711 o default tamc.h in pkg/autodiff supposed to crash
11712 to ensure proper customization
11713
0e6056cd20 Jean*11714 checkpoint52a_post (2003/11/17)
fa690556aa Jean*11715 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
9d36aec500 Dimi*11716 - moved surfaceTendencyTice from pkg/seaice to main code
fa690556aa Jean*11717 - subroutine FREEZE_SURFACE now limits only surface temperature
11718 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
11719 => new output.txt for global_ocean.cs32x15 & global_with_exf
11720 - keep the old version of FREEZE for backward compatibility;
11721 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
915eb1cffa Patr*11722 - corresponding modifs for TAF directives
9d36aec500 Dimi*11723 o added surface flux output variables to TIMEAVE_STATVARS
11724 o time-averaged output for pkg/ptracers
915eb1cffa Patr*11725 o fix problem with ECCO-related divided adjoint
11726 snapshot file was missing some ad-variables,
11727 but no warning issued by TAF
fa1dae9534 Dimi*11728
0e6056cd20 Jean*11729 checkpoint52a_pre (2003/11/12)
fa1dae9534 Dimi*11730 o some bug fixes for #undef REAL4_IS_SLOW
11731
aca4df70a2 Patr*11732 checkpoint52 = ecco_c52_e35
11733 o after testing adjoints of checkpoint51u_post
11734
0e6056cd20 Jean*11735 checkpoint51u_post (2003/11/06)
909a9f878d Patr*11736 o this is the post-merge tag of the ecco-branch
11737 (needs another clean checkout and re-testing)
11738 o various natl_box_adjoint configs and results
11739 but no input fields
11740 o obcs adjoint not yet merged!
11741 o adding ECCO global 1x1 and 2x2 degree configs
11742 o updated/extended some store directives for seaice
11743 o pkg/ecco now containes ecco-specific part of cost function
11744 o top level routines the_main_loop, forward_step
11745 supersede those in model/src/
11746 previous input data.cost now in data.ecco
11747 (new namelist ecco_cost_nml)
11748 o in ctrl/ cleaned some cross-dependencies and updated CPP options
11749
0e6056cd20 Jean*11750 checkpoint51t_post (2003/11/04)
909a9f878d Patr*11751 o this is the pre-merge tag of the ecco-branch
11752
0e6056cd20 Jean*11753 checkpoint51s_post (2003/11/04)
ef651d0d5f Ed H*11754 o cleanup: removed various obsolete #define-s
909a9f878d Patr*11755 o pkg/grdchk
11756 - renamed 'ph-grd 3' to 'grad-res'
a435e833b1 Mart*11757 - merged from ecco-branch
909a9f878d Patr*11758 (remaining bug fixes for obcs gradient checks)
11759 - additional high-precision output for testreport
11760 (grep for 'precision_grdchk_result')
ef651d0d5f Ed H*11761
0e6056cd20 Jean*11762 checkpoint51r_post (2003/11/03)
16add2227d Ed H*11763 o cleaned up or removed CPP_OPTIONS.h files
11764 o updated results for some of the tests to reflect the new
11765 optfiles (-ieee: -O0 instead of -O3)
11766
0e6056cd20 Jean*11767 checkpoint51q_post (2003/10/30)
cb574bfa04 Patr*11768 o cd_code:
11769 - moved cd_scheme.F -> cd_code_scheme.F
11770 - separate read_checkpoint from cd_code_ini_vars.F
11771 - separated cd_code part from write_checkpoint
11772 - updated AD_SOURCE, generated .flow
11773 - added CD_CODE_VARS.h to the_main_loop
11774 - Moving cd_code specific store dir.s to pkg/cd_code
11775 o ctrl package totally restructured
11776 - pack/unpack now optional and decoupled from
11777 xx_/adxx_ I/O
11778 - ctrl_pack/unpack cleaned
11779 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
11780 - confined inclusion of AD_CONFIG.h to where necessary.
11781 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
11782
0e6056cd20 Jean*11783 checkpoint51p_post (2003/10/30)
138482fdf6 Ed H*11784 o create initial cd_code package
a5bd9cbb61 Ed H*11785 - WARNING: the initialization of fields within packages
11786 is broken because INI_FIELDS (where READ_CHECKPOINT is
11787 called) is called *before* PACKAGES_INIT_VARIABLES.
11788 This seems to be backwards since
a435e833b1 Mart*11789 1) its important to initially zero the entire field including
a5bd9cbb61 Ed H*11790 the "halo" region
11791 2) zeroing needs to be done *before* reading pickup info
a435e833b1 Mart*11792 and the pickup call might or might not happen in any
a5bd9cbb61 Ed H*11793 particular run
11794 - this needs an overhaul for R2
138482fdf6 Ed H*11795 o cleanup verification/*/code/GMREDI_OPTIONS.h
11796 o cleanup testreport
11797
0e6056cd20 Jean*11798 checkpoint51o_post (2003/10/27)
8a8c81fb3e Patr*11799 o bringing AD-related verif's up to date with genmake2
11800 - carbon/
11801 - global_ocean.90x40x15/
11802 - hs.94.1x64x5/
11803 - (front_relax/ )
11804 o (more) consistent directory structure for AD-related verif.'s
11805 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
11806 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
11807 o bug fix in find_alpha.F for MDJWF:
11808 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
11809 change rho -> rho-rhoConst
11810 - replace call find_rho to find_rhonum
11811 o initialisation of rFlx extended to full array (required by TAF)
11812 and shifted to thermodynamics
11813 o removed PTRACERS.h in ptracers routine
11814 o added surfacetendencyPtr to S/R parameter list pracers_forcing
11815 o Correcting initialisations for fVerU, fVerV.
11816 o helping TAF to recognize dependency on kUp for
11817 fVerU, fVerV
11818 o Replacing delZ by delR in pkg/ctrl/
0e6056cd20 Jean*11819 checkpoint51o_pre (2003/10/24)
8a8c81fb3e Patr*11820
51701379d8 Ed H*11821 o undid all of cp51 pending some cleanups and discussion
a435e833b1 Mart*11822 o added the [#include "AD_CONFIG.h"] statement to all files that need
406902c2ea Patr*11823 it for adjoint/tl #defines
11824 o re-worked the build logic in genmake2 to support AD_CONFIG.h
11825 o removed tools/genmake since it no longer works
c9cb668a47 Dimi*11826
0e6056cd20 Jean*11827 checkpoint51n_post (2003/10/23)
c9cb668a47 Dimi*11828 o modifications to make FREEZE flux visible to pkg/kpp
11829 - moved surfaceTendencyTice from pkg/seaice to main code
11830 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
11831 - subroutine FREEZE now limits only surface temperature
11832 (this means new output.txt for global_ocean.90x40x15,
11833 global_ocean.cs32x15, and global_with_exf)
11834 o added surface flux output variables to TIMEAVE_STATVARS
11835
0e6056cd20 Jean*11836 checkpoint51n_pre (2003/10/23)
d7f6e03355 Dimi*11837 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4a967b9107 Ed H*11838 o added [#include "AD_CONFIG.h"] to all files that use the following
11839 defines:
11840 - ALLOW_ADJOINT_RUN
11841 - ALLOW_TANGENTLINEAR_RUN
11842 - ALLOW_ECCO_OPTIMIZATION
d7f6e03355 Dimi*11843
0e6056cd20 Jean*11844 checkpoint51m_post (2003/10/21)
668b211e58 Ed H*11845 o incorporating changes to get TAMC/TAF working in genmake2
11846 - added new TAMC/TAF targets to the Makefile
11847 - various cleanups related to package handling
fea3c3e36d Ed H*11848 - these changes should have no impact on the forward model
668b211e58 Ed H*11849
0e6056cd20 Jean*11850 checkpoint51l_post (2003/10/20)
c84f6b7c89 Dimi*11851 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
11852 - faster algorithm for cal_addtime.F
11853 - higher precision arithmetic, where needed
11854 - pkg/exf *startdate variables changed from calendar date to
11855 model integration time
11856
0e6056cd20 Jean*11857 checkpoint51l_pre (2003/10/17)
d33aea2a79 Jean*11858 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
11859 o enable to apply restoring on S & T only in a latitude band.
11860 o update output (external_forcing_surf modif. change truncation errors)
11861 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
06c869d156 Patr*11862
0e6056cd20 Jean*11863 checkpoint51k_post (2003/10/16)
f9e188eb72 Jean*11864 o change default to: useNHMTerms=.FALSE.
11865 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
11866 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
11867 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
11868 exp1, ideal_2D_oce
11869 - change data file of oceanic exp (leave the results unchanged for now)
11870 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
11871 o set gravitySign automatically according to the vertical coordinate used
11872 (and change sign: back to "logical" value: +1 when R increases downward)
a435e833b1 Mart*11873 o added an include barrier to the default CPP_OPTIONS.h and
9eb494b0cb Ed H*11874 removed the #include "PACKAGES_CONFIG.h" from it
f9e188eb72 Jean*11875 o fix a bug in mom_fluxform (from chk51j_post)
9eb494b0cb Ed H*11876
0e6056cd20 Jean*11877 checkpoint51j_post (2003/10/10)
0b85d93038 Patr*11878 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
11879 o adjusted some flow directives (dynamics, thermodynamics)
11880 o added cubed-sphere case to test cost function
11881 o heckpoint_lev?_directives.h now include
11882 pkg-specific directives, whenever those are enabled.
11883 o Moving pkg-specific flow directives to corresponding pkg
11884 Moving pkg-specific differentiation list to corresponding pkg
11885 Moving pkg-specific checkpoint-lev storing to corresponding pkg
11886 ---> conventions are
11887 - pkg_ad.flow
11888 - pkg_ad_diff.list
11889 - pkg_ad_check_lev?_dir.h
11890
0e6056cd20 Jean*11891 checkpoint51i_post (2003/10/09)
6d54cf9ca1 Ed H*11892 o merge of the branch-genmake2
11893 - knowingly breaks the older genmake
11894 - automatic generation of all ALLOW_${PKG_NAME} defines
11895 - new testreport supersedes older testscript
11896 o large number of package inclusion and header cleanups
0e6056cd20 Jean*11897 checkpoint51i_pre (2003/10/08)
6d54cf9ca1 Ed H*11898
b95c3843ab Ed H*11899 o new output for adjoin of global ocean vector invariant
11900 o fix for checkpoint of thermodynamic seaice and bulk_force
11901 o Steph gchem various cleanups
11902
46a4243beb Step*11903 checkpoint 51h_pre
b95c3843ab Ed H*11904 o fixed some single quotes
46a4243beb Step*11905 o modify gchem pkg to be more versatile
11906 o modifications to clean up dic pkg
11907 o add pkg/cfc
11908
0e6056cd20 Jean*11909 checkpoint51g_post (2003/10/02)
8c13754326 Patr*11910 o provide links for ARPACK and ADM*TLM
11911 o start removing verification/vero/
11912 o update AD-related stuff
11913 (in particular some IF-statements in model/src/ routines)
11914 o adding to verification/global_ocean.90x40x15/ adjoint of
11915 vector invariant setup
11916
0e6056cd20 Jean*11917 checkpoint51f_post (2003/10/02)
57c1eda489 Jean*11918 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6eb9516f3f Dimi*11919 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
34fdea0d95 Dimi*11920 of tracer Green's fucntions for ocean inversion project.
11921
0e6056cd20 Jean*11922 checkpoint51f_pre (2003/08/07)
981f32514d Dimi*11923 o Added on-the-fly spatial interpolation capability
11924 "USE_EXF_INTERPOLATION" to pkg/exf.
bda7c25f4a Dimi*11925 - This is a temporary Cartesian-grid hack until
981f32514d Dimi*11926 the super-duper ESMF coupler becomes available.
bda7c25f4a Dimi*11927 - See verification/global_with_exf/README for usage example.
11928 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
11929 flags and modified pkg/seaice accordingly.
981f32514d Dimi*11930 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
11931 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
11932 non-local transport term.
11933
0e6056cd20 Jean*11934 checkpoint51e_post (2003/08/03)
a435e833b1 Mart*11935 o pkg/mom_vecinv:
542c6d36a4 Jean*11936 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
11937 - add time-ave diagnostic of vorticity advection.
11938 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
a435e833b1 Mart*11939 o atmospheric geopotential: - include water vapor effect;
542c6d36a4 Jean*11940 - use p^kappa in p* scaling.
c886fcc85e Jean*11941 o land pkg: read initial state from files.
11942 o AIM : add stratospheric drag in the upper level
11943
0e6056cd20 Jean*11944 checkpoint51d_post (2003/07/18)
c886fcc85e Jean*11945 o change function ILNBLNK (=> last non-blank char.) to return zero
11946 (instead of the string length) when the string. char is empty
8cd26a84aa Jean*11947 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
06c869d156 Patr*11948 o modif's to restore TAMC compatibility
11949 - avoid "_d" constructs in PARAMETER declarations
11950 - avoid interrupting lines by comment lines
11951 o Use cluster local disks for purely local I/O
11952 vs. globally visible disks needed for ctrl stuff
11953 (merged from ecco-branch)
11954 - new active_file_loc... and mdsio_..._loc routines
11955 - affected packages: autodiff, ctrl, grdchk, mdsio
f171be8f2a Alis*11956
0e6056cd20 Jean*11957 checkpoint51c_post (2003/07/08)
494ad43bae Patr*11958 o introducing integer flag debugLevel
11959 - debLevZero: suppress all output
11960 - debLevA: standard
11961 - debLevB: equivalent to current debugMode=.TRUE.
11962 o introducing pathname variable mdsioLocalDir for mdsio
11963 that can be specified at runtime
11964 (relevant for cluster I/O to local disk)
11965 `
f35a23c575 Patr*11966 >>>checkpoint51b_post
11967 adjoint of ptracers
11968 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
11969 o extended state in checkpoint_lev?, etc.
11970 o alternative ctrl/cost with tr1 or ptracer
11971 o new comlev1_bibj_ptracers
11972 o new ptracers.flow
11973 o made ptracers_forcing same as external_forcing_s
11974 o added verification for adjoint with ptracers
11975 - adm. grdchk fail so far
11976 - tlm. grdchk OK
11977 - checked tapelev/comlev recomputations: OK
11978 <<<checkpoint51b_pre
11979
0e6056cd20 Jean*11980 checkpoint51a_post (2003/06/25)
f04468175c Step*11981 o added code for biogeochemistry package
11982 - new pkgs: dic, gchem
11983 - new subroutine in ptracers
11984 o modify code for biogeo packages
11985 - in model/src and pkg/ptracers
11986
0e6056cd20 Jean*11987 checkpoint51 (2003/06/24)
5949b565e2 Patr*11988 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
11989 - autodiff, ctrl, exf, grdchk, seaice
11990 kept separate packages
11991 - cost, ecco, obcs
f535eb56d5 Patr*11992 o updating verification/internal_wave, verification/lab_sea
11993 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5949b565e2 Patr*11994
0e6056cd20 Jean*11995 checkpoint50i_post (2003/06/23)
3cd89c6ea4 Patr*11996 o Preparing next differentiable checkpoint and sync
11997 of MAIN vs. ecco-branch
11998 - 1st step: this one is differentiable
a435e833b1 Mart*11999 - 2nd step: next(! not this) checkpoint will have updated packages
3cd89c6ea4 Patr*12000 from ecco-branch)
12001
0e6056cd20 Jean*12002 checkpoint50h_post (2003/06/20)
8f5c8e08bc Jean*12003 o new package "land": provide surface BC for AIM.
12004 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
a435e833b1 Mart*12005 o AIM: use true log-P extrapolation for near surface temp (= as in
568bb87ebb Jean*12006 F.Molteni paper) ; update aim.5l_cs output.
8aafdaabe9 Alis*12007 o New variable in PARM03 for more flexible pickups
61893791a0 Patr*12008 o somewhat cleaned package initialisation sequence for
12009 ctrl/ cost/ ecco/ in packages_... routines
568bb87ebb Jean*12010
0e6056cd20 Jean*12011 checkpoint50g_post (2003/05/23)
09510da3bb Dimi*12012 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
12013 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
12014 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
12015 made the default because of faster convergence than ADI
12016
0e6056cd20 Jean*12017 checkpoint50f_post (2003/05/23)
5192502418 Patr*12018 o exf totally restructured
12019 - replaced all exf_set_ routines by one generic exf_set_gen.F
12020 and made sure it's still differentiable
12021 - split exf_getffields.F into new exf_bulkformulae.F
12022 - exf_inscal_/exf_outscal_ suffixes consistent with field names
12023 - updated adjoint/makefile and relevant verif. accordingly
12024
0e6056cd20 Jean*12025 checkpoint50f_pre (2003/05/23)
b8d7339ac7 Jean*12026 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
12027 + change Evap over land. (update aim.5l_cs output)
f171be8f2a Alis*12028 o added missing .cvsignores and made uniform across expts
12029 o changed configuration of tidal_basin_2d expt
12030 o added pkg/debug functions for tracing code in fatal crashes
12031 o tidied pkg/monitor to use MONITOR_OPTIONS.h
12032 o new fn in pkg/monitor to stop model if solution grows too big
12033 o removed lots of single quotes from comments
12034
0e6056cd20 Jean*12035 checkpoint50e_post (2003/05/14)
1a1e1d268a Mart*12036 o make KPP work with PTRACERS
12037 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
12038 nearly a copy of kpp_transport_s
a435e833b1 Mart*12039 - there is no analogue to SurfaceTendencyS, so I have to use
1a1e1d268a Mart*12040 gPtr(of the surface layer) instead
12041 o add a new platform SunFire+mpi (SunFire 15000) to genmake
0e6056cd20 Jean*12042 checkpoint50e_pre (2003/05/13)
1a1e1d268a Mart*12043
0e6056cd20 Jean*12044 checkpoint50d_post (2003/05/13)
a435e833b1 Mart*12045 o change kpp output from multiple-record state files to single-record state
3ff61f337e Mart*12046 files analogous to write_state.F
a435e833b1 Mart*12047 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
12048 analogous to the cg2d-related output.
12049 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
1a1e1d268a Mart*12050 so that writing to internal file fn (with length 512) fails.
0e6056cd20 Jean*12051 checkpoint50d_pre (2003/05/12)
dd4e4e2846 Patr*12052
0e6056cd20 Jean*12053 checkpoint50c_post (2003/05/12)
36b01f3eb4 Jean*12054 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
a07df11acd Jean*12055 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
956742bd08 Jean*12056 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
12057 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
12058 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
12059
0e6056cd20 Jean*12060 checkpoint50c_pre (2003/04/30)
460cb5f999 Dimi*12061 Merging from release1_p13:
12062 o bug fix for pkg/seaice dynamic solver
12063 o Added SEAICE_initialHEFF to pkg/seaice
12064
0e6056cd20 Jean*12065 checkpoint50b_post (2003/04/17)
b95ba5a50f Jean*12066 o store u*,v* in gU,V instead of in guNm1,gvNm1
12067 o in order to put the momForcing out of the Adams-Bashforth:
12068 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
12069 to timestep.F
12070 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
12071 o re-generate output for highly sensitive test-exp:
12072 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
12073
0e6056cd20 Jean*12074 checkpoint50b_pre (2003/04/17)
3228e22c96 Jean*12075 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
a435e833b1 Mart*12076 o corrected CPP option mismatch in exf_Bulk... functions for case
5ef1561d49 Patr*12077 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
12078
0e6056cd20 Jean*12079 checkpoint50a_post (2003/03/21)
011884106d Patr*12080 o Bug fix for merging between c50 and KPP.
12081 ikey was passed from thermodynamics to kpp_calc via
12082 common block rather than being recomputed in kpp_calc,
12083 in contradiction with new key itdkey.
12084 New key ikppkey created, and tamc.h headers updated.
12085
0e6056cd20 Jean*12086 checkpoint50 (2003/03/08)
19c7b39f75 Patr*12087 - 2nd step of merge with ecco-branch:
12088 merge changes in ecco-branch back into main trunk
12089 - bug fix in find_alpha
12090 - more storing in gmredi_calc_tensor.F, kpp_routines.F
12091 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
12092 - merged some sliced AD support routines
12093
0e6056cd20 Jean*12094 checkpoint49 (2003/03/06)
a2ac993b88 Patr*12095 merged from ecco-branch:
12096 o exf:
a435e833b1 Mart*12097 - Enable initialisation of forcing fields to constant
a2ac993b88 Patr*12098 (runtime) values.
12099 - in exf_getffields.F
12100 Reduce i-/j-loop to interior domain, discarding overlaps.
12101 That also fixes wrong TAF-key computations for key_1, key_2
12102 with bulf formulae.
12103 - exf_init.F modify #ifdef for exf_init_evap
12104 - exf_getffieldrec.F, ctrl_getrec.F
12105 The following INT-usages are not safe:
12106 fldsecs = int(fldsecs/fldperiod)*fldperiod
12107 fldcount = int(fldsecs/fldperiod) + 1
12108 and were modified.
12109 o autodiff: checkpoint_lev...
12110 - updated storing for bulk formulae (some arrays were missing)
12111 - added state for seaice package
12112 - synchronized with main branch
12113 o DIVA:
12114 Modif.s in
19c7b39f75 Patr*12115 - the_main_loop.F
12116 - the_model_main.F
a2ac993b88 Patr*12117 and added cost_final_restore.F cost_final_store.F
12118 o With these changes, it is possible to fully separate
12119 the first forward run to compute the cost function (mdthe_main_loop)
12120 and adjoint runs over individual DIVA intervals (adthe_main_loop)
12121 into separate model executions.
12122 This enables better tuning of DIVA to given queue sizes.
12123 o Loss of cost function value in consecutive DIVA runs is
12124 fixed by storing to 'costfinal' file.
a435e833b1 Mart*12125 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
a2ac993b88 Patr*12126 beginning/end of adjoint integration is accounted for.
12127 The current changes apply to TAF-1.4.26.
12128 TAF has one remaining bug, requiring one manual change
12129 (see MITgcm manual).
12130 o cal: synchronized between MAIN and ecco-branch
12131
0e6056cd20 Jean*12132 checkpoint48i_post (2003/03/05)
eae13cfd04 Patr*12133 o Changes to restore differentiability of code w.r.t. previous tag
12134 (mostly adding new routines to make list and replacing
12135 pressure by totPhiHyd).
12136 o Updated and merged grdchk package
12137 - has both ADM and TLM checks
12138 - works for single- and multi-proc.
12139 - output cleaned
12140 - worked successfully for parallel DIVA
12141 o genmake:
12142 - Adding -platform=SP4
12143 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
12144 o Modif. for DIVA:
12145 ctrl_unpack should not be called in intermediate DIVA interval.
12146 (similar thing would apply for active files such as
12147 tbar, sbar, psbar, which should not be reinitialised;
12148 only relevant for ecco-branch)
12149
0e6056cd20 Jean*12150 checkpoint48h_post (2003/02/28)
c05a259eac Jean*12151 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
190e1777cb Dimi*12152 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
12153 o Added SEAICE_initialHEFF to pkg/seaice
d0702b49e9 Dimi*12154 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
190e1777cb Dimi*12155
0e6056cd20 Jean*12156 checkpoint48g_post (2003/02/18)
2959c7b521 Jean*12157 --- EOS:
12158 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
12159 store total Potential in totPhyHyd for diagnostics & EOS.
12160 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
12161 --- Pressure/geopotential gradient:
12162 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
12163 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
12164 ( changes results of global_ocean_pressure )
12165 o NLFS + z-coord.: add eta*Rho' contribution.
12166 o accurate phiHyd when using interface-W at the middle between 2 centers
12167 ( changes results of ideal_2D_oce )
12168 o includes r* 2nd term in potential gradient.
12169
0e6056cd20 Jean*12170 checkpoint48f_post (2003/02/18)
6060ec2938 Dimi*12171 Merging from release1_p12:
12172 o Modifications for using pkg/exf with pkg/seaice
12173 - improved description of the various forcing configurations
12174 - added basic radiation bulk formulae to pkg/exf
12175 - units/sign fix for evap computation in exf_getffields.F
12176 - updated verification/global_with_exf/results/output.txt
12177 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
12178 (SBO) core products, including oceanic mass, center-of-mass,
12179 angular, and bottom pressure (see pkg/sbo/README.sbo).
12180 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
12181 to avoid negative values in shallow regions.
12182 - updated verification/natl_box/results/output.txt
12183 - updated verification/lab_sea/results/output.txt
12184 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
12185 o Added useSingleCpuIO option (see PARAMS.h).
12186 o Updated useSingleCpuIO option in mdsio_writefield.F to
12187 work with multi-field files, e.g., for single-file pickup.
12188 o pkg/seaice:
12189 - bug fix in growth.F: QNET for no shortwave case
12190 - added HeffFile for specifying initial sea-ice thickness
12191 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
12192 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
12193 kpp_transport_t.F, forward_step.F, and the_main_loop.F
12194 o pkg/seaice:
12195 - adjoint-friendly modifications
12196 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
12197
0e6056cd20 Jean*12198 checkpoint48e_post (2003/02/12)
6f90d97ce9 Jean*12199 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5f7a0a65d1 Jean*12200 o dynamics: change definition of computational domain & adapt mom_fluxform
a435e833b1 Mart*12201 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5f7a0a65d1 Jean*12202 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
12203 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
bc5ef4cea8 Jean*12204 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
a435e833b1 Mart*12205 global_ocean.90x40x15 global_with_exf global_ocean_pressure
5f7a0a65d1 Jean*12206 inverted_barometer solid-body.cs-32x32x1
12207 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6f90d97ce9 Jean*12208
0e6056cd20 Jean*12209 checkpoint48d_post (2003/02/09)
fa86c7bd0e Jean*12210 o in preparation for r*:
12211 a) use pre-computed gradient of hydrostatic potential:
12212 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
12213 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
a435e833b1 Mart*12214 => affects results of glob_oce_pressure (different truncation error)
fa86c7bd0e Jean*12215 update output.txt of ideal_2D_oce & global_ocean_pressure
12216
0e6056cd20 Jean*12217 checkpoint48d_pre (2003/02/08)
395300a99d Jean*12218 o in preparation for r*:
12219 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
12220 pass the 2 comp. of the grad. as arguments to momentum S/R.
a435e833b1 Mart*12221 but for the moment, only used if it does not change the results.
395300a99d Jean*12222 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
12223
0e6056cd20 Jean*12224 checkpoint48c_post (2003/02/06)
da25c1b1f0 Patr*12225 Modifications in treatment of initial flux forcing controls
12226 to avoid extra storing of flux fields.
12227
0e6056cd20 Jean*12228 checkpoint48c_pre (2003/01/21)
6201ebed0f Alis*12229 o Added tidal_basin_2d experiment (currently 1D!)
a435e833b1 Mart*12230 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
ed1ae133b9 Jean*12231
0e6056cd20 Jean*12232 checkpoint48b_post (2003/01/27)
1bf124dbfd Jean*12233 o r* coordinate added in #ifdef NONLIN_FRSURF block.
12234 (modification to pressure gradient not yet implemented)
12235 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
12236 (for U & V) that are used for vertical advection of momentum.
12237
0e6056cd20 Jean*12238 checkpoint48a_post (2003/01/24)
5c72e2cee7 Jean*12239 o In preparation for r*, use temp. array to compute vertical transport
a435e833b1 Mart*12240 in flux-form momentum pkg. => change results of few test-exp.
12241 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5c72e2cee7 Jean*12242 lab_sea, natl_box & plume_on_slope
12243
0e6056cd20 Jean*12244 checkpoint48 (2003/01/23)
3fa5200144 Jean*12245 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
12246
0e6056cd20 Jean*12247 checkpoint47j_post (2003/01/21)
d15fa5f8eb Jean*12248 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
dd4e4e2846 Patr*12249 o moved adexch from forward_step to addummy_in_stepping
12250 o added exch in ctrl_map_...
12251 o aveFreq.=0. at end of cost_final to avoid overwrite in
12252 reverse checkpointing loop
12253 o Yet more changes in gmredi:
12254 * adgmredi_calc_tensor
12255 avoiding all recomputation of gmredi_slope_limit
12256 * adgmredi_x/y/rtransport
12257 added flag for excessive storing to avoid recomp. of
12258 u/v/rtans, dTdx/y/z
12259 -> this is not really necessary and very memory-consuming
12260 * adgmredi_slope_psi:
12261 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
12262 * gmredi_slope_limit
12263 re-activated full calculation of taperfct for case 'ac02'
12264 o updating verification/ adjoints of carbon, global_ocean.90x40x15
d537a7f0b2 Patr*12265
0e6056cd20 Jean*12266 checkpoint47i_post (2003/01/13)
a934d97f06 Jean*12267 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
12268 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
12269 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
a435e833b1 Mart*12270 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
a934d97f06 Jean*12271 o gmredi: fix few bugs.
12272
ba5e34915b Alis*12273 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
d537a7f0b2 Patr*12274 This will be a good checkpoint to plug into the ecco-branch.
12275 o few modif.'s to get latest version adjointed
12276 (mainly kick out code in ini_linear_phisurf)
12277 o modif's to run adjoint with exactConserv
12278 o case GM_BOLUS_ADVEC should be cleaned
12279 S/R gmredi_slope_psi should be cleaned
12280 o verification/carbon now has exactConserv=.TRUE.
0501ef9fb3 Patr*12281
0e6056cd20 Jean*12282 checkpoint47g_post (2003/01/10)
6d8d3f40dd Jean*12283 o time-average AIM output: becomes independent from statvars time-average
12284 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
88844f54ad Patr*12285 o After TAF bug fix:
12286 Tested adjoint of gmredi package.
12287 Tests were done with checkpoint47 rather than with latest
12288 checkpoint47f_post since the latter is broken for the adjoint
12289 verification/carbon/ contains both ADM and TLM gradient checks.
12290 Here they are, before they get changed/lost/stolen.
12291 Mostly modif.'s to fix numerical sensitivities.
12292 Gradient checks OK for
12293 - GM_taper_scheme:
12294 * clipping
12295 * ac02
12296 * linear
12297 * glw91
12298 * dm95
12299 * ldd97
12300 - GMREDI_OPTIONS:
12301 * GM_VISBECK_VARIABLE_K
12302 * GM_NON_UNITY_DIAGONAL
12303 * GM_EXTRA_DIAGONAL
12304 * GM_BOLUS_ADVEC
12305 in conjunction with data.gmredi parameters to be checked in
12306 in a few minutes under verification/carbon/code/
6d8d3f40dd Jean*12307
0e6056cd20 Jean*12308 checkpoint47f_post (2002/12/28)
cee16b76ae Dimi*12309 Merging from release1_p10:
12310 o modifications for using pkg/exf with pkg/seaice
12311 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
12312 and SEAICE_EXTERNAL_FLUXES
12313 - pkg/exf CPP options EXF_READ_EVAP and
12314 EXF_NO_BULK_COMPUTATIONS
12315 - usage examples are Experiments 8 and 9 in
12316 verification/lab_sea/README
12317 - verification/lab_sea default experiment now uses
12318 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
12319
0e6056cd20 Jean*12320 checkpoint47e_post (2002/12/27)
2d0f62a494 Curt*12321 o created a tag prior to creating a branch
12322
0e6056cd20 Jean*12323 checkpoint47d_post (2002/12/16)
a435e833b1 Mart*12324 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
2672305b1d Mart*12325 at the bottom boundary had an erroneous half slip boundary condition
a435e833b1 Mart*12326 o added bottom drag and no slip boundary condition capabilities to
2672305b1d Mart*12327 oceanic pressure coordinates code
12328 o added new verification experiment global_ocean_pressure, this experiment is
12329 also described in the tutorial section of the manual
0e6056cd20 Jean*12330 checkpoint47d_pre (2002/12/16)
2672305b1d Mart*12331
0e6056cd20 Jean*12332 checkpoint47c_post (2002/12/16)
03456d021e Curt*12333 o Added a verification experiment for a global cubed-sphere ocean run
12334 - verification/global_ocean.cubed32x32x30
12335 - uses pkg/therm_seaice and pkg/bulk_forcing
12336
4195ef17c2 Jean*12337 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
12338 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
12339 when using P-coordinate; only implemented for atmospheric config.
12340 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
12341 NOTES: requires option NONLIN_FRSURF to be "#define".
12342 o update advect_xz/results/output.txt (left from checkpoint44g_post)
12343
0e6056cd20 Jean*12344 checkpoint47b_post (2002/12/05)
baa476eeba Dimi*12345 Merging from release1_p9:
12346 o pkg/seaice
12347 - removed GOTO's and added taf directives
12348 - double precision constants to reduce the g77 (Linux)
12349 to F77 (SGI) differences reported in release1_p8
12350 o tools/genmake
12351 - added SGI options
12352 o verification/testscript
12353 - updated to that of checkpoint47a_post
12354 o verification/global_ocean.90x40x15/input/eedata
12355 - modified for SGI f77 compatibility
12356 o verification/lab_sea
12357 - added description of sea-ice model
12358 - added missing matlab routines
12359 - added test of thermodynamics parallelization
12360
0e6056cd20 Jean*12361 checkpoint47a_post (2002/11/23)
a435e833b1 Mart*12362 o new pkg: aim_v23
12363 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
9a923a4cdc Jean*12364 for now, keep the same surface forcing as before.
12365 - Part-Cell implemented into AIM; check that Heat & Water are conserved
12366 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
12367 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
12368 o add diagnostic of surface correction term in monitor output
12369
a435e833b1 Mart*12370 o bulk_force and therm_seaice
c9bad82272 Curt*12371 - Two packages: bulk_force (Bulk forcing)
12372 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
12373 - Earlier integration from Stephaine Dutkiewicz
12374 and Patrick Heimbach.
12375 - Two ifdef statements for compile time,
12376 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
0ae80337bd Jean*12377
0e6056cd20 Jean*12378 checkpoint47 (2002/11/15)
d66d6a3f19 Patr*12379 differentiable version of checkpoint46n_post
12380 o bug fix in quasihydrostaticterms
12381 o * "clean" adjoint code (in terms of extensive recomputations)
a435e833b1 Mart*12382 can now be obtained for all GMREDI options (i.e. for
d66d6a3f19 Patr*12383 - GM_VISBECK_VARIABLE_K
12384 - GM_NON_UNITY_DIAGONAL
12385 - GM_EXTRA_DIAGONAL
12386 - GM_BOLUS_ADVEC )
12387 * However, wrong gradient check problem remains unsolved.
12388 * New CPP options have been introduced for different
12389 tapering schemes
12390 o external_fields_load now part of differentiation list
12391 o pressure needs multiple storing;
12392 would be nice to have store_pressure at beginning or
12393 end of forward_step, e.g. by having phiHyd global (5-dim.)
12394 (NB: pressure is needed for certain cases in find_rho,
12395 which is also invoked through convective_adjustment).
a435e833b1 Mart*12396 o recomputations in find_rho for cases
d66d6a3f19 Patr*12397 'JMD95'/'UNESCO' or 'MDJWF' are OK.
12398 o #define ATMOSPHERIC_LOADING should be differentiable
12399 o ini_forcing shifted to begining of initialise_varia
12400 o Incorporating QNVS line search routines into MITgcm
12401 (this is separate code, and therefore not under pkg)
12402 lsopt/, optim/
12403 o Updated verification/carbon/
12404 - #define GM_VISBECK_VARIABLE_K
a435e833b1 Mart*12405 - GM_taper_scheme = 'ldd97'
d66d6a3f19 Patr*12406
0e6056cd20 Jean*12407 checkpoint46n_post (2002/11/12)
5553098c72 Patr*12408 Merging from release1_p8:
12409 o verification/natl_box:
12410 updating new external_fields_load routine
12411 o New package: pkg/seaice
12412 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
12413 The sea-ice code is based on Hibler (1979-1980).
12414 Two sea-ice dynamic solvers, ADI and LSR, are included.
a435e833b1 Mart*12415 In addition to computing prognostic sea-ice variables and diagnosing
12416 the forcing/external data fields that drive the ocean model,
5553098c72 Patr*12417 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
a435e833b1 Mart*12418 The implied surface heat flux is then stored in variable
12419 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
12420 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
12421 non-local transport term. Because this call precedes model
12422 thermodynamics, temperature under sea-ice may not be "exactly" at
5553098c72 Patr*12423 the freezing point by the time theta is dumped or time-averaged.
12424 N.B.: fairly large differences in accuracy occur across
12425 different platforms/compilers; comparison between
a435e833b1 Mart*12426 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5553098c72 Patr*12427 generated output gives:
12428 T S U V
12429 C D M c m s m s m s m s
12430 n p a R g m m e . m m e . m m e . m m e .
12431 f n k u 2 i a a d i a a d i a a d i a a d
12432 g d e n d n x n . n x n . n x n . n x n .
12433
12434 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*12435 o GAD:
5553098c72 Patr*12436 - generated new common blocks to account for call of
12437 same gad routines with differing traceridentities
12438 (needed to modify tracerIdentity indices in GAD.h)
12439 - generated separate common blocks for case useCubedSphereExchange
12440 (Department of Futurology)
12441 - parameter lists to gmredi_?transport: added tracerIdentity
12442 - added new key indices to tamc.h
12443 o external_fields_load:
12444 - added this routine to TAF list
12445 - needed to make some common blocks global and additional storing
12446 along the same lines as exf package (checkpoint_lev?_directives.h)
12447 o exf:
12448 updated external forcing package
12449 - bug fixes carried over from ecco-branch
12450 (missing OBCS_OPTIONS.h in two routines)
12451 - enable easy to use "no forcing".
12452 - added exf I/O for atmospheric loading
12453 - added exf I/O for runoff data
12454 - transfered scaling between exf <-> MITgcm to exf namelist
12455 o Adding new verification experiment global_with_exf.
12456 This verification experiment is almost identical to the
12457 global_ocean.90x40x15 experiment, except that it uses
12458 the exf (and cal) package instead of the
12459 external_fields_load routine (cf README file).
12460
0e6056cd20 Jean*12461 checkpoint46m_post (2002/11/07)
a435e833b1 Mart*12462 o modified testscript to return -- when there are no lines of "%MON" output
775ad00e06 Alis*12463 o added new flag "quasiHydrostatic" for QH mode
12464 and new routine quasihydrostaticterms()
c5990018f4 Alis*12465 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
12466 New routine: mom_u_coriolis_nh()
8d87f02f4b Alis*12467 o fixed sign of non-hydrostatic metric terms in u and v equations.
12468 Depend on correct sign of gravitySign.
574be91465 Alis*12469 o added work.pc* to .cvsignore in aim directories using ifc
faaa70ed68 Alis*12470 o introduced flag for controllin non-hydrostatic metric terms
a22df31c5b Alis*12471 o removed gravitySign from PARM04
4cc3ac93d0 Alis*12472 o switched to g77/ifc from pgf77 in aim experiments
12473
0e6056cd20 Jean*12474 checkpoint46l_post (2002/11/01)
59e59b79d8 Mart*12475 o made convective adjustment work with pressure coordinates:
12476 - changed the direction of k-loop in convective_adjustment.F for the
12477 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
12478 - adjusted the reference pressure k-index in convective_adjustment.F
12479 - adjusted the convection condition in convect.F (in analogy to
12480 calc_ivdc.F)
12481 - convective_adjustment no longer computes anything on the halos
12482 - removed the warnings about negative salinity from find_rho.F and
12483 find_alpha.F; instead the new routine look_for_neg_salinity, called
a435e833b1 Mart*12484 at the beginning of find_rho, find_alpha, and find_beta, does a
12485 check of the entire slice, if CPP-option
59e59b79d8 Mart*12486 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
0e6056cd20 Jean*12487 checkpoint46l_pre (2002/10/23)
59e59b79d8 Mart*12488
0e6056cd20 Jean*12489 checkpoint46k_post (2002/10/23)
19ec7ca2f5 Mart*12490 o fixed the verification/global_ocean.90x40x15 experiment:
12491 - new bathymetry (the world according to A., JMC, and M.)
12492 - new initial fields and forcing fields (*.bin files)
12493 - new POLY3.COEFFS (for the next release one should switch to a full
12494 equation of state: JMD95P or MDJWF)
12495 - fixed several errors and redundancies in the data file
12496 - experiment uses looped cells
12497 - added matlab directory with diagnostic scripts for plotting of output
12498
1b947e4f16 Jean*12499 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
12500 - read AIM physics parameters from a file (data.aimphys)
12501 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
12502
0e6056cd20 Jean*12503 checkpoint46j_post (2002/10/07)
3d1716969e Jean*12504 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
12505 o move wVel computation at the end of the time step, in S/R integr_continuity
12506 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
12507 o update timeave pkg for wVel diagnostic.
0e6056cd20 Jean*12508 checkpoint46j_pre (2002/09/27)
3d1716969e Jean*12509
0e6056cd20 Jean*12510 checkpoint46i_post (2002/09/25)
e16ef9be6a Jean*12511 o Clean up AIM package (and keep the results unchanged):
a435e833b1 Mart*12512 include CPP_OPTION and use IMPLICT NONE in all routines ;
e16ef9be6a Jean*12513 declare all the variables _RL ; use _d 0 for all numerical constants.
12514 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
e305438401 Mart*12515
0e6056cd20 Jean*12516 checkpoint46h_post (2002/09/25)
a435e833b1 Mart*12517 o cleaned up the use of rhoNil and rhoConst.
12518 - rhoNil should only appear in the LINEAR equation of state, everywhere
e305438401 Mart*12519 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
12520 and the dynamical equations are all divided by rhoConst
a435e833b1 Mart*12521 o introduced new parameter rhoConstFresh, a reference density of fresh
e305438401 Mart*12522 water, to remove the fresh water flux's dependence on rhoNil. The default
12523 value is 999.8 kg/m^3
12524 o cleanup up external_forcing.F and external_forcing_surf.F
12525 - can now be used by both OCEANIC and OCEANICP
0e6056cd20 Jean*12526 checkpoint46h_pre (2002/09/18)
e305438401 Mart*12527
12528 Added code to convert surface volume flux (fresh water) into
12529 a mass flux when using P coordinates in the ocean (OCEANICP).
12530 Note: It assumes you have set rho0=rhoConst=density of fresh water.
12531
0e6056cd20 Jean*12532 checkpoint46g_post (2002/09/18)
60c223928f Mart*12533 o Include a new diagnostic variable phiHydLow for the ocean model
12534 - in z-coordinates, it is the bottom pressure anomaly
12535 - in p-coordinates, it is the sea surface elevation
12536 - in both cases, these variable have global drift, reflecting the mass
12537 drift in z-coordinates and the volume drift in p-coordinates
12538 - included time averaging for phiHydLow, be aware of the drift!
a435e833b1 Mart*12539 o depth-dependent computation of Bo_surf for pressure coordinates
60c223928f Mart*12540 in the ocean (buoyancyRelation='OCEANICP')
a435e833b1 Mart*12541 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
12542 Theta, Salinity, and Pressure in the parameter list. This routine is
60c223928f Mart*12543 presently contained in find_rho.F. This routine does not give the
12544 correct density for 'POLY3', which would be a z-dependent reference
12545 density.
12546 o cleaned up find_rho
12547 - removed obsolete 'eqn' from the parameter list.
12548 o added two new verification experiments: gop and goz
12549 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
0e6056cd20 Jean*12550 checkpoint46g_pre (2002/09/16)
60c223928f Mart*12551
0e6056cd20 Jean*12552 checkpoint46f_post (2002/09/16)
77d659325b Patr*12553 o Enable tangent linear (forward mode) gradient checks:
12554 - extended active file handling to g_... files
12555 - added TANGENT_SIMULATION to theSimulationMode
12556 - extended grdchk package accordingly
12557 o added tangent linear setup in verification/carbon/code_ftl
12558 o added adjoint setup in verification/front_relax/code_ad
12559
0e6056cd20 Jean*12560 checkpoint46e_post (2002/09/05)
31a5949e20 Mart*12561 o Added new equation of state -> MDJWF
12562 - EOS of McDougall et al., 2002, JAOT, submitted
12563 - caveat: the equation of state is only valid for a smaller (more
12564 realistic?) range of values than JMD95P/Z and UNESCO
12565 - added masks to the calculation of pressure in store_pressure
a435e833b1 Mart*12566 - added more check values for density in check_eos (ini_eos.F), some of
31a5949e20 Mart*12567 the old check values are out of the range of the MDJWF-eos, so don't
a435e833b1 Mart*12568 expect perfect matches for those
0e6056cd20 Jean*12569 checkpoint46e_pre (2002/08/19)
31a5949e20 Mart*12570
0e6056cd20 Jean*12571 checkpoint46d_post (2002/08/19)
9b1fb10894 Mart*12572 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
a435e833b1 Mart*12573 'OCEANICP', also initialised field pressure correctly in ini_eos in the
12574 case of pressure coordinates. eosType='JMD95Z' in
9b1fb10894 Mart*12575 combination with buoyancyRelation='OCEANICP' now causes an error.
12576 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
12577 in find_alpha/beta.
0e6056cd20 Jean*12578 checkpoint46d_pre (2002/08/15)
9b1fb10894 Mart*12579
12580 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
a435e833b1 Mart*12581 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
9b1fb10894 Mart*12582
0e6056cd20 Jean*12583 checkpoint46c_post (2002/08/15)
9e5f2093d3 Alis*12584 o Changes necessary for ocean in p-coordinates
12585 - Added new buoyancy relation = 'OCEANICP'
12586 - Added new parameters = gravitySign (this used to be contained inside
12587 the factor dRdZ which I added when we first switched to R coordinates).
12588 X GM/Redi is not compatible (yet)
12589 X bottom drag and no-slip need to be debugged.
0e6056cd20 Jean*12590 checkpoint46c_pre (2002/08/07)
9e5f2093d3 Alis*12591
0e6056cd20 Jean*12592 checkpoint46b_post (2002/08/07)
a37a13034c Mart*12593 o Added new equation of state -> JMD95Z and JMD95P
31a5949e20 Mart*12594 - EOS of Jackett and McDougall, 1995, JAOT
a37a13034c Mart*12595 - moved all EOS parameters into EOS.h
12596 - new routines ini_eos.F, store_pressure.F
a435e833b1 Mart*12597 o Added UNESCO EOS, but not recommended because it requires
a37a13034c Mart*12598 in-situ temperature (see JMD95)
12599 o Modified formatting for knudsen2.f in utils/knudsen2 and added
12600 unesco.f to be used with POLY3
0e6056cd20 Jean*12601 checkpoint46b_pre (2002/07/31)
a37a13034c Mart*12602
0e6056cd20 Jean*12603 checkpoint46a_post (2002/07/31)
395b093796 Mart*12604 o Added (atmospheric) pressure loading
12605 - new field in FFIELDS.h, etc...
12606 - new cpp flag ATMOSPHERIC_LOADING
12607 o Changed hFacC to _hFacC in calc_phi_hyd.F
12608 o Added SHORTWAVE_HEATING to some files for consistency
0e6056cd20 Jean*12609 checkpoint46a_pre (2002/07/13)
395b093796 Mart*12610
0e6056cd20 Jean*12611 checkpoint46 (2002/07/13)
0501ef9fb3 Patr*12612 further merges from release1_p5
12613 o new ctrl package
12614 - adopted from ECCO environment to enable optimization
12615 - added Eliassen Palm fluxes to controls
12616 o added Eliassen Palm flux controls to gradient check package
12617 o cost package
12618 - Compatible with new ctrl package
12619 - added Eliassen Palm cost hooks
12620 - modif's of existing cost functions
12621 o Adjoint-related bug fixes in kpp:
12622 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
12623 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
12624 o autodiff package
12625 - flow directives:
12626 + new for S/R do_the_model_io
12627 + enhanced for S/R checkpoint
12628 + new gmredi.flow
12629 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
12630 disable adcommon.h/g_common.h by default.
12631 - fixed problem for adjoint of global_max
12632 o modified verification/carbon/
12633 o New setup for adjoint of global_ocean
12634 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
12635 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
12636 o incorporated hooks for sponge layer code (external_forcing.F)
12637
0e6056cd20 Jean*12638 checkpoint45d_post (2002/07/12)
9d1e859170 Jean*12639 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
fe84d1c123 Jean*12640 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
12641 (affects plume_on_slope "cg2d" output)
9d1e859170 Jean*12642 o add new parameter deltaTfreesurf for free-surface time stepping
a435e833b1 Mart*12643 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
40a013c787 Jean*12644 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
5a6e38b5cb Jean*12645 o change phiMin in exp1 (to agree with documentation)
a435e833b1 Mart*12646 o add new flags:
5a6e38b5cb Jean*12647 - T,S forcing inside/outside Adams-Bashforth
12648 - turn off temp,salt advection and/or forcing
12649 - for each tracer, define internal flag for multiDimAdvection & A-B
12650 o monitor: change definition of KE to check conservation of Energy
fda4da40f3 Jean*12651
0e6056cd20 Jean*12652 checkpoint45c_post (2002/05/30)
cda7963c0f Patr*12653 o Removed f90 comments ("!")
12654 o Modified initialisations to enable exf package for MITgcm
12655 (without invoking ECCO_PACKAGE).
12656 o modifications to gradient check package (Martin Losch)
12657 - enable centered differences
12658 - modified format of standard output
12659
0e6056cd20 Jean*12660 checkpoint45b_post (2002/05/30)
778263fdd2 Patr*12661 o cleaned exchange calls in cg2d
12662 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
12663 o included CPP option SINGLE_LAYER_MODE in thermodynamics
12664 to configure barotropic setup (Martin Losch)
12665 o moved some initialisations within bi,bj loop in dynamics
12666 (TAF flow dependency)
12667 o in initialise_varia, moved call packages_init_variables
12668 before convective_adjustment_init
12669 (corresponding adjustment of TAF tape initialisation).
12670 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
12671
0e6056cd20 Jean*12672 checkpoint45a_post (2002/05/01)
23b8953dcb Jean*12673 o compute Rho over the whole domain (extend iMin,jMin indices)
12674 o specific exchange for X-slice domain (case Ny=1)
58071f7ded Jean*12675 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
12676 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
12677
f2f05cab96 Patr*12678 checkpoint44h_post = checkpoint45
12679 o Fix to restore differentiability:
12680 place at which packages_init_variables is called in
12681 initialise_varia is crucial for reverse control flow.
12682 o modifications in GMRedi to enable stable adjoint
12683 (corresponding modif's in thermodynamics, dynamics)
12684 o added missing hook for sponge layer code in external_forcing
12685 o modified test cost functions
12686 o storing in gad_advection (plus removal of write(0,*)!
12687 o missing headers TR1.h added in convective_adjustment routines
12688 o errorMessageUnit set non-equal zero in eeboot
12689 (conflict on some platforms, e.g. IBM SP3)
12690 o modified carbon verif.
12691
0e6056cd20 Jean*12692 checkpoint44h_pre (2002/03/14)
e5968d5db8 Jean*12693 o vertical grid option: allow to put the Interface at the middle between
12694 2 cell-centers ; replace delZ in pkg/kpp by drF.
3f61bba06d Jean*12695 o GM Advective form: Tracers are advected using the residual transport (=
12696 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
12697
0e6056cd20 Jean*12698 checkpoint44g_post (2002/03/05)
a435e833b1 Mart*12699 o fix surface correction term in multiDimAdvection (affects plume_on_slope
d459353a4c Jean*12700 results) ; ifdef missing in thermodynamics.F
12701
5c43c390b6 Alis*12702 checkpoint44f_pre,checkpoint44f_post
12703 o added PTRACERS package
12704 This allows an arbitrary number of passive tracers to be integrated
12705 forward simultaneously with the dynamicaly model.
12706 + Implemented so far:
12707 - basic forward algorithm (time-stepping, advection, diffusion, convection)
12708 - I/O and checkpointing
12709 - GM/Redi *but* using the GM/Redi coefficient of Salt
12710 + Not implemented so far:
12711 - KPP
12712 - OBCS
12713 + No specific example supplied (yet) but global_ocean.90x40x15 has the
12714 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
12715 line in data.pkg.
12716 + This package is disabled by default since it increases storage.
12717
12718
658a1753bb Alis*12719 o testscript: added -cleanup option
f4ba6d3695 Jean*12720 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
12721 b) enable to filter 2D fields.
d427b861ca Jean*12722
3e6bf4af46 Alis*12723 checkpoint44e_pre,post
12724 o re-wrote convective adjustment to use pre-calculated weights
12725 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
12726 Adds: model/src/convective_weights.F, convectively_mixtracer.F
12727 Original calls to convect() still in place.
12728
2014c6d62b Patr*12729 chkpt44d_pre,post
12730 o added missing EXCLUDE_MONITOR flags
12731 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
12732 (incompatible typ in MIN/MAX expressions caused problems
12733 on IBM SP3)
12734 o in genmake added variable MAKEDEPEND
12735 plus resetting for case SunOS
12736 o added timer_stats.c routine for IBM SP3
12737 o removed variables in dynamics
12738 !!! I forgot to create tag chkpt44d_pre !!!
12739 !!! But chkpt44d_pre = chkpt44c_post !!!
12740
f4ba6d3695 Jean*12741 o real fresh water flux implemented with non-linear free-surface.
12742
d645283517 Jean*12743 chkpt44c_pre,post
a435e833b1 Mart*12744 o few fix (mask in shap_s2, EmPmR in external_field_load,
12745 USE_NATURAL_BCS in solve_for_P);
d645283517 Jean*12746 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
12747
de416ebcde Patr*12748 checkpoint44b_pre/_post
12749 o merge of relevant stuff from the ecco-branch:
12750 - genmake: removed $S64 overwrite for case SunOS
12751 - pkg/exf: update and corrections for field swapping and obcs
12752 - pkg/ecco: parameter lists for the_model_main, the_main_loop
12753 harmonized between ECCO and MITgcm
12754 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
12755 updated checkpointing_lev... lists for obcs
12756 - model/src: minor changes in forward_step, plot_field
12757 added directive for divided adjoint in the_main_loop
12758 - pkg/mdsio: added mdsio_gl_slice
12759
fda4da40f3 Jean*12760 o check parameters & config (chkpt44a_pre,post)
5fc9e00fa1 Jean*12761 o OBC and NonLin_FrSurf.
12762
0e6056cd20 Jean*12763 checkpoint44 (2002/01/18)
beeff87535 Jean*12764 o fix bug in mom_vi_del2uv
5fc9e00fa1 Jean*12765 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
12766 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
12767 o update AIM experiments (NCEP input files)
12768 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
b07345cdda Patr*12769 o added some stuff for AD
84a1eca0f1 Patr*12770
0e6056cd20 Jean*12771 checkpoint43 (2001/09/28)
7205c731d1 Alis*12772 o added two new advection tests
12773 o added global 4x4 degree ocean test
12774 o added test of H&S94 with free surface on cube
12775 o some final mods for gradient check, adjoint,...
12776
0e6056cd20 Jean*12777 checkpoint42 (2001/09/27)
9620337c26 Patr*12778 Fixed AD-related problems:
12779 o Store directives up-to-date with re-arranged Adams-Bashforth
12780 (mainly thermodynamics.F)
12781 o New store directives for multi-dim. advection schemes
12782 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
12783 * new common block and key passkey
12784 (mainly gad_advection.F)
12785 o Modified store directives for split of dynamics/thermodynamics
12786 for the case ALLOW_KPP
12787 o Cleaned argument list for timestep_tracer.F
12788
0e6056cd20 Jean*12789 checkpoint41 (2001/09/27)
aafb52f44c Alis*12790 o re-formatted/added comments in prologues of key subroutines
12791 to work with protex
12792
0e6056cd20 Jean*12793 checkpoint40 (2001/09/27)
07eb89f7e7 Alis*12794 o moved calc_gs, calc_gt and calc_tr1 back to model/src
12795 o added FLT (floats) package from Arne along with demo. experiment
12796 o re-arranged Adams-Bashforth scheme for tracers to allow easier
12797 implementation of forward-in-time forcing terms
12798 o more mods for non-linear free-surface including new variable
12799 o modified multi-dim method to work on cube
12800 o bug fix in KPP (from DM)
12801
0e6056cd20 Jean*12802 checkpoint40pre9 (2001/09/27)
76bfa80e3f Alis*12803 o added DST advection schemes
12804 o fix MPI bug on SGI's
12805 o modifications for non-linear free-surface
12806 o fixed conditionals for fixed flow/passive tracer only mode
12807 o added tension/strain form of stress tensor
12808 o changes to commenting of arguments for TAF/TAMC
12809 o added/updated many matlab scripts
07eb89f7e7 Alis*12810 o added multi-dimensional advection method for tracers
a435e833b1 Mart*12811
0e6056cd20 Jean*12812 checkpoint40pre8 (2001/09/05)
c710cbecfb Patr*12813 o new package rw/
12814 Added method for dumping intermediate local arrays:
12815 mdsio_writetile - same as mdsio_writefield except works from inside
12816 bi,bj loop
12817 mdsio_writelocal - same as mdsio_writetile except works for local
12818 arrays
12819 write_local_r? - higher-level wrapper for mdsio_writelocal
12820 Controlled by diagFreq. Defaults to zero (ie. no dumps)
12821 Example given at end of mom_vecinv.F that dumps some local arrays.
12822 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
12823 control flux-form versus vector invariant code.
12824 Switch is runtime flag vectorInvariantMomentum (defaults to false)
12825 or genmake -DISABLE ...
12826 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
12827 (additional storing is now needed for case vecinv;
12828 currently nothing implemented to switch this storing off
12829 in case fluxform is used since no CPP flag available).
12830
0e6056cd20 Jean*12831 checkpoint40pre7 (2001/08/14)
11252a3870 Patr*12832 o bug fix in dynamics.F
12833 calc_viscosity called before k=1,Nr loop.
12834 o added some #ifdef's ALLOW_PASSIVE_TRACER
12835 o cleaned initialisations in ctrl_map_ini
12836 related to TAF
12837
0e6056cd20 Jean*12838 checkpoint40pre6 (2001/08/13)
b2d3fccd49 Patr*12839 o split dynamics into thermodynamics & dynamics
12840 o corresponding split of calc_diffusivity into
12841 calc_diffusivity, calc_viscosity
12842 (kpp_calc_diff, kpp_calc_visc).
12843 o Added diffkr, kapgm to control variables
12844 o bug fix in gmredi_slope_limit for ldd97
12845
0e6056cd20 Jean*12846 checkpoint40pre5 (2001/07/31)
2277c012d1 Alis*12847 o proper initialization of Adams-Bashforth time stepping
12848 + uses forward step for very first step of model (iter=0)
12849 o re-generated *all* output since almost all output is modified by this
12850 change (sorry but we've been putting this one off for about 2 years)
12851 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
12852 *not* regenerated since they are already out of date and I don't
12853 want to create the impression that they are suddenly working.
12854 o removed KAP stuff for DEC's
12855 o modified/added many .cvsignore files in */code and */input
12856 o added new expt "solid-body.cs-32x32x1"
12857 + this uses an alternative form of ini_curvilinear_grid.F which
12858 is not necessarily any better than the current one...
12859
0e6056cd20 Jean*12860 checkpoint40pre4 (2001/07/30)
84a1eca0f1 Patr*12861 o added re-initialisations of utrans,vtrans,rtrans in
12862 calc_common_factors which are crucial for TAF.
12863 o extended iMin,jMin range for calc_common_factors,
12864 calc_diffusivity
12865 o added option ALLOW_PASSIVE_TRACER
12866 o a few minor updates and fixes
12867
0e6056cd20 Jean*12868 checkpoint40pre3 (2001/07/13)
8970237877 Patr*12869 o created calc_gtr1.F for gad package
12870 o split the_main_loop and re-introduced forward_step
12871 o some recomputations of nIter0 for TAMC
12872
0e6056cd20 Jean*12873 checkpoint40pre2 (2001/07/13)
12b269a63b Patr*12874 o Updated to latest branch of AJA, JMC
12875 o Added gradient check package
12876 o Added routines for passive tracer handling
12877 o Added carbon sequestration sensitivity experiment
12878
0e6056cd20 Jean*12879 checkpoint39 (2001/05/14)
0a8108926c Patr*12880 o Modifications and fixes to support TAMC
12881 (mainly missing or wrong directives)
12882 o Corrected common blocks when fooling TAMC to produce adjoint I/O
12883 in addummy_in_stepping
12884 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
12885 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
12886 o Included following packages:
12887 cal: calendar
12888 exf: external forcing
12889 ecco: essential routines to control use of cal, exf
12890 (NB: this is not the full ECCO environment)
160e0619c9 Patr*12891 o disabled some packages by default in genmake
0a8108926c Patr*12892
0e6056cd20 Jean*12893 checkpoint38 (2001/04/10)
2cfc9d59a2 Patr*12894 o see notes_c37_adj.txt
12895 o corrected wrong layer index in external_forcing_t
12896 o replaced the_main_loop/forward_step by the_main_loop
12897 o removed forceoutput from write_state
12898 (replaced criteria for initial/final state)
12899 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
b7a12fbe29 Chri*12900
0e6056cd20 Jean*12901 checkpoint37 (2001/03/13)
2a60a6d948 Jean*12902 o mdsio.F routine split and packaged in pkg/mdsio
12903 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
12904 used unless genmake -disable=mdsio)
12905 o allow a more precise surface-geopotential gradient for the atmosphere
12906 taking into account the change in space of Alpha (=1/rho) at the surface.
12907 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
12908 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
12909 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
12910 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
12911 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
12912 o Time-Average diagnostics defined as a pseudo package "timeave".
12913 o pickup files : old pickup (before c35) did not work with new code (c35
12914 and after) unless activating 2 commented lines in initialise-varia.
12915 o Non-Hydrostatic pickup file Pb fixed.
a435e833b1 Mart*12916 o bug with Rigid-lid version (since c35) fixed.
2a60a6d948 Jean*12917
0e6056cd20 Jean*12918 checkpoint36 (2001/02/20)
2a60a6d948 Jean*12919 o implement Crank-Nickelson barotropic time-stepping
3d3ffaaedb Jean*12920 o recover Time-Average diagnostics
a435e833b1 Mart*12921 o fix Pb in checkpoint (PR#19)
3d3ffaaedb Jean*12922 o AIM become a standard package ; clean unused CPP_kees
12923
0e6056cd20 Jean*12924 checkpoint35 (2001/02/08)
47b446e27e Jean*12925 o subtantial rewrite of dynamics.f
12926 o allows staggered time-stepping
12927 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
12928 o added bottom drag (linear + quadratic)
12929
0e6056cd20 Jean*12930 checkpoint34 (2001/01/30)
ea8b6560ce Patr*12931 o Modified exchange routines for correct reverse simulation.
12932 o Added verification output to comply with bug fix in impldiff.F
12933 as of c33 (exp2, natl_box).
12934 o Corrected store directives in dynamics.F
12935 o Corrected array boundaries in impldiff.F
12936 o Corrected array dimensions in gmredi.
12937 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
c3ddfd9c4c Patr*12938 o Added routine GLOBAL_SUM_INT to global_sum.F
ea8b6560ce Patr*12939 o Added mdsio_gl.F for ECCO purposes.
12940
0e6056cd20 Jean*12941 checkpoint33 (2000/11/30)
7a9ddade78 Alis*12942 o Fixed bug in lower BC in impldiff.F
12943 o Fixed confusion about units of forcing arrays in FFIELDS.h
12944 namely Fu,Fv,Qnet,Qsw,EmPmR:
12945 - Removed verification/natl_box/code/external_fields_scale.F
12946 (did not differ from that in model/src)
12947 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
12948 (see FFIELDS.h for description)
12949 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
12950 kpp_calc.F and kpp_transport_t.F
12951 - Removed model/src/external_fields_scale.F and calls to it
12952 - verification/natl_box uses flux data with "atmospheric" sign so
12953 a special version of external_fields_load.F is used to
12954 change the data as it's read in. This way, the arrays
12955 have the right units and signs at all times tha a user could
12956 possibly use them.
12957 o Corrected genmake to delete a temporary file during configuration
12958
0e6056cd20 Jean*12959 checkpoint32 (2000/11/13)
cfb3cd1ea2 Patr*12960 o Scaling of forcing fields moved from external_forcing.F to
12961 external_fields_scale.F, called directly after loading fields.
12962 o Surface relaxation terms added to surface tendency fields in
12963 extra subroutine.
12964 o impldiff.F changed to avoid storing by TAMC of huge intermediate
12965 fields.
12966 o Changes in GMRedi to comply with packaging structure.
12967 o Modifications and bug fixes in KPP package.
12968 o Verification experiment for KPP added (verification/nat_box/)
12969
0e6056cd20 Jean*12970 checkpoint31 (2000/09/11)
dde6192d54 Patr*12971 o Packages interface brought in line with defined standard
12972 -> new routines packages_...F
12973 -> changes in initialise_fixed.F, initialise_varia.F
12974 -> enables initialisation interface for ECCO package
12975 o Rescaling of external forcing fields immediately after read
a435e833b1 Mart*12976 (removed from external_forcing.F)
dde6192d54 Patr*12977 -> new: surface_fields_scale.F
12978 -> affects ini_foorcing.F, external_fields_load.F
12979 o Computation of surface tendencies before tendency updates.
12980 -> new: external_forcing_surf.F
12981 o Change of variable names useGMRedi, useKPP, useECCO
12982 o Further changes in dynamics.F, impldiff.F for TAMC
12983 o Tested for experiments 0, 2, 4.
12984 - not yet tested for GMRedi.
12985 - not yet tested for KPP.
12986
0e6056cd20 Jean*12987 checkpoint30 (2000/07/13)
7eedb26c3d Alis*12988 o Updates for OBCs
12989 o New experiment for test OBCs (internal_wave)
12990 o New output.txt in verification/exp4/results/
12991 o Updates for KPP: calculation of viscosity corrected, new variables
12992 kpp_dumpFreq and kpp_taveFreq
12993 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
12994 and entry for T90 in genmake
12995
0e6056cd20 Jean*12996 checkpoint29 (2000/06/21)
c53ad8dc62 Alis*12997 o packaged KPP and GM/Redi
12998
0e6056cd20 Jean*12999 checkpoint28 (2000/06/09)
56096ca40a Patr*13000 o Corrected initialization of hFacMin for difference vertical coordinates
13001 o Modified calculation of partial cell thickness to more robust algorithm
13002 o config_summary.F: replaced write_1D_... by write_0D_...
13003 read_write.F: added subroutines write_0D_...
13004 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
13005 included some initialisations required for TAMC.
a435e833b1 Mart*13006 o routine calc_isoslopes: modified sqrt computation to make it
56096ca40a Patr*13007 differentiable for zero argument.
13008 o routines dynamics, impldiff:
13009 included store directives and tape key computations required for TAMC.
13010 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
13011
0e6056cd20 Jean*13012 checkpoint27 (2000/04/10)
5b679adde0 Alis*13013 o fixed calc_isoslopes() to so that cancellation of terms in tensor
13014 formulation works properly with variable resolution.
13015 o restructured the calling tree between the_model_main() and dynamics()
13016 o split initialise() into initialise_fixed() and initialise_varia()
13017 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
13018 in new routine ini_psurf()
13019
0e6056cd20 Jean*13020 checkpoint26 (2000/04/05)
ab1673a65c Alis*13021 o moved some #ifdef in optional routines to encompass everything
13022 except the argument declarations. This was using up some memory.
13023 o fixed macros like _ADT to work with both versions of Linux cpp
13024 o cleaned up some unused and uninitialized variables
13025 (helps when debugging with strict compile options)
13026 o split up CPP_EEOPTIONS.h into options and macros
13027 (macros are now in eesupp/inc/CPP_EEMACROS.h)
13028 o patch for 2 processor JAM mode
13029
0e6056cd20 Jean*13030 checkpoint25 (2000/03/15)
c19cdd9408 Alis*13031 o updates for OBCs and NH
13032 o dramatically reduced memory usage
13033 o added "JAM" routines for use on Artic network
13034 o parameterization of convection by implicit vertical diffusion
13035 o added a diagnostic of convective index
13036 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
13037 (this is was partly for OBCs and NH but also in anticipation of
13038 an explicit free-surface option)
13039 o initial state input files for U and V
13040
0e6056cd20 Jean*13041 checkpoint24 (1999/08/02)
090b7007c7 Alis*13042 o Removed some spurious "REAL"s
13043 o Updated KPP to latest version from JPL
13044 o Added a COS(latitude) in horizontal viscosity
13045
0e6056cd20 Jean*13046 checkpoint23 (1999/05/26)
8f6e5ef29b Alis*13047 o Added del^4 diffusion for salt and temperature
13048 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
13049
0e6056cd20 Jean*13050 checkpoint22 (1999/05/18)
b3d4b567f6 Alis*13051 o Made many small changes: implicit none, format(i5), etc...
13052 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
13053
0e6056cd20 Jean*13054 checkpoint21 (1999/05/18)
dccdad8bbd Alis*13055 o Introduced new I/O package that supports direct-access records (mdsio.F)
13056 o Split-up mid-level I/O routines
13057 o Updated input data for experiments 0,1,2,4 and 5
13058 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
13059
0e6056cd20 Jean*13060 checkpoint20 (1999/03/22)
e92aabed24 Alis*13061 o Tidied up open-boundaries some more
13062 o Added non-hydrostatic code
13063 o Fixed some input data
13064 o Modified MPI start-up to work in "coupled" context.
13065
0e6056cd20 Jean*13066 checkpoint19 (1998/12/15)
337ad8328b Alis*13067 o Tidied up directory structure for verification experiments.
13068 o Added new code for open boundaries.
13069 o Corrected advective terms near boundaries.
13070 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
13071 o Implemented free-slip/no-slip BCs and del^4 dissipation.
e92aabed24 Alis*13072 o Split default parameters out of ini_parms.F into set_defaults.F.
337ad8328b Alis*13073
0e6056cd20 Jean*13074 checkpoint18 (1998/11/30)
a435e833b1 Mart*13075 o Further changes for optional code generation with
632baf6c85 Chri*13076 CPP - ugh!
13077
0e6056cd20 Jean*13078 checkpoint17 (1998/11/03)
6d71ac9cce Chri*13079 o Beginning to incorporating modularity
13080 for supporting atmos. and ocean configs.
13081 o Small changes for TAMC complinace
13082 o New ultra simple test case. Barotropic box
13083 configuration "exp0".
13084
0e6056cd20 Jean*13085 checkpoint16 (1998/10/28)
a435e833b1 Mart*13086 o Minor changes to exchange routines to support
8c88443df3 Chri*13087 accumulation in reverse mode. Adjoint of an
13088 assignment is an addition.
a435e833b1 Mart*13089 o Changes to support compilation by TAMC (LR(1)
8c88443df3 Chri*13090 syntax) and by g77 under Linux ( 72 character
13091 limit ).
13092
0e6056cd20 Jean*13093 checkpoint15 (1998/09/29)
048ce7bdb7 Chri*13094 Rewrote exchange routines to allow
13095 o General tile <-> tile connectivity.
13096 o TAMC reverse mode flag ( is this really needed? )
13097 o Variable width overlap and exchange region widths.
a435e833b1 Mart*13098 o Hooks for sharing data via DMA, Arctic, Memory Channel,
13099 shmput/shmget, VIA, SYSV shmem and every other cool
048ce7bdb7 Chri*13100 communication method.
13101
0e6056cd20 Jean*13102 checkpoint14 (1998/09/09)
e83f632bdc Chri*13103 Consistent isomorphism chages made. These allow dynamical core
13104 to support both pressure and meters as a vertical coordinate.
13105
0e6056cd20 Jean*13106 checkpoint13 (1998/07/17)
b472be50f6 Chri*13107 Release which corrects global_max problem and a couple
13108 of KGM time-averaging diagnostic errors. Also contains
13109 a double-gyre experiment setup as well as the baseline
13110 4 degree global template. The double gyre template is
13111 organised to allow it to be applied automatically to
13112 the baseline configuration.
13113
6b85e5319c Alis*13114 branch-point-rdot
13115 A few tidy-ups have been made bt the real point of this
13116 check-point (excuse the pun) is to allow a branch to be
13117 made for the purposes of adding the rDot alterations.
13118 I don't want to commit the rDot to the main-trunk until
13119 we've actually tested it...
13120
0e6056cd20 Jean*13121 checkpoint12 (1998/07/08)
713eeb0b71 Chri*13122 Tidy up and added generic genmake script (formerly
a435e833b1 Mart*13123 configure script).
713eeb0b71 Chri*13124 Released to testers.
13125
0e6056cd20 Jean*13126 checkpoint11 (1998/07/02)
8e14856263 Alis*13127 Re-arranged initialise() and introduced ini_vertical_grid()
13128 and ini_masks_etc().
13129
0e6056cd20 Jean*13130 checkpoint10 (1998/07/01)
bef276faee Alis*13131 Introduced the configure script.
13132 Separated out the diags package.
13133 Added template for writing time-averages of tile/intermediate quantities.
13134 Updated SIZE.h in exp2 and made the data big-endian.
13135
0e6056cd20 Jean*13136 checkpoint9 (1998/06/22)
455e14887b Alis*13137 MPI fix. Filename changes (meta/data). salbin*y stuff.
13138 General tidy-up.
13139 SST.bin SSS.bin added to verification/exp2
13140
0e6056cd20 Jean*13141 checkpoint8 (1998/06/22)
81be42c716 Alis*13142 Inludes time-dependant forcing and time-averaging.
13143 Works at 4x4 and 2.8125x2.8125 global
13144
13145 checkpoint7-4degree-ref
13146 Branch from checkpoint7. Released for application to
13147 global modeling and general modeling - process studies, regional
a435e833b1 Mart*13148 model etc..
81be42c716 Alis*13149 Configured for verification/exp2 - 4 degree global, two process.
13150
0e6056cd20 Jean*13151 checkpoint7 (1998/06/15)
42bd47f06f Chri*13152 Created by cnh
a435e833b1 Mart*13153 Simple 4 degree global simulation
42bd47f06f Chri*13154 configuration.
a435e833b1 Mart*13155 Includes climatological wind,
42bd47f06f Chri*13156 hydrography, bathymetry etc
13157 Does not include Heat Flux and E-P
13158
0e6056cd20 Jean*13159 checkpoint6 (1998/06/08)
a82990e8c1 Chri*13160 Created by cnh
a435e833b1 Mart*13161 merged checkpoint5 with CD and
13162 spherical polar code.
a82990e8c1 Chri*13163 Still some problems with GM Redi
13164 abd full topography.
13165
0e6056cd20 Jean*13166 checkpoint5 (1998/06/08)
41a4b13446 Chri*13167 Created by AJA
13168 contains updates to GM Redi
13169 and reordered timestepping loop
13170 for Implicit Diffusion.
13171
0e6056cd20 Jean*13172 checkpoint4 (1998/05/30)
b7a12fbe29 Chri*13173 Created by cnh
13174 Contains memory saving macros ( _rdxc etc..) for when
13175 grid variations are limited.
13176 Contains polynomial coeffs for EOS and knudsen program
13177 for generation.
13178
0e6056cd20 Jean*13179 checkpoint3 (1998/05/26)
addde852ed Chri*13180 Created by cnh
13181 Added extra flags for runtime options
13182 Added this file
13183 Added implicit free-surface
13184 Added pre-conditioner
13185 Put compare01 into repository ( compare01/... )
13186 Put data and eedata into repository ( verification/exp1 )
13187
13188 checkpoint2
13189 Created by AJA
13190 Added GM/Redi
13191
13192 checkpoint1
13193 Created by AJA
13194 Restructured kloop in dynamics.F
13195 Added non-linear EOS
13196
b7a12fbe29 Chri*13197 baseline
13198 Original checked in code
