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8679f9097b Jeff*0001 .. _sub_phys_pkg_ptracers:
0002
0003 PTRACERS Package
0004 ----------------
0005
0006
0007 Introduction
0008 ++++++++++++
0009
0010 This is a ''passive'' tracer package. Passive here means that the tracers
0011 don’t affect the density of the water (as opposed to temperature and
0012 salinity) so no not actively affect the physics of the ocean. Tracers
0013 are initialized, advected, diffused and various outputs are taken care
0014 of in this package. For methods to add additional sources and sinks of
bf89a37abc Phob*0015 tracers use the :ref:`gchem Package <sub_phys_pkg_gchem>`.
8679f9097b Jeff*0016
bf89a37abc Phob*0017 Can use up tp 3843 tracers. But can not use the :ref:`diagnostics package <sub_outp_pkg_diagnostics>` with more
0018 than about 90 tracers. Use :filelink:`utils/matlab/ioLb2num.m` and :filelink:`num2ioLb.m <utils/matlab/num2ioLB.m>` to
8679f9097b Jeff*0019 find correspondence between tracer number and tracer designation in the
0020 code for more than 99 tracers (since tracers only have two digit
0021 designations).
0022
0023 Equations
0024 +++++++++
0025
0026 Key subroutines and parameters
0027 ++++++++++++++++++++++++++++++
0028
bf89a37abc Phob*0029 The only code you should have to modify is: :filelink:`PTRACERS_SIZE.h <pkg/ptracers/PTRACERS_SIZE.h>` where
8679f9097b Jeff*0030 you need to set in the number of tracers to be used in the experiment:
bf89a37abc Phob*0031 :varlink:`PTRACERS_num`.
8679f9097b Jeff*0032
0033 Run time parameters set in :code:`data.ptracers`:
0034
bf89a37abc Phob*0035 - :varlink:`PTRACERS_Iter0` which is the integer timestep when the tracer experiment is initialized. If ``nIter0`` = ``PTRACERS_Iter0`` then the tracers are initialized to zero or from initial files. If ``nIter0`` :math:`>` ``PTRACERS_Iter0`` then tracers (and previous timestep tendency terms) are read in from a the ptracers pickup file. Note that tracers of zeros will be carried around if ``nIter0`` :math:`<` ``PTRACERS_Iter0``.
0036 - :varlink:`PTRACERS_numInUse`: number of tracers to be used in the run (needs to be :math:`<=` ``PTRACERS_num`` set in :filelink:`PTRACERS_SIZE.h <pkg/ptracers/PTRACERS_SIZE.h>`)
0037 - :varlink:`PTRACERS_dumpFreq`: defaults to :varlink:`dumpFreq` (set in data)
0038 - :varlink:`PTRACERS_taveFreq`: defaults to :varlink:`taveFreq` (set in data)
0039 - :varlink:`PTRACERS_monitorFreq`: defaults to :varlink:`monitorFreq` (set in data)
0040 - :varlink:`PTRACERS_timeave_mnc`: needs :varlink:`useMNC`, :varlink:`timeave_mnc`, default to false
0041 - :varlink:`PTRACERS_snapshot_mnc`: needs :varlink:`useMNC` , :varlink:`snapshot_mnc`, default to false
0042 - :varlink:`PTRACERS_monitor_mnc`: needs :varlink:`useMNC`, :varlink:`monitor_mnc`, default to false
0043 - :varlink:`PTRACERS_pickup_write_mnc`: needs :varlink:`useMNC`, :varlink:`pickup_write_mnc`, default to false
0044 - :varlink:`PTRACERS_pickup_read_mnc`: needs :varlink:`useMNC`, :varlink:`pickup_read_mnc`, default to false
0045 - :varlink:`PTRACERS_useRecords`: defaults to false. If true, will write all tracers in a single file, otherwise each tracer in a seperate file.
8679f9097b Jeff*0046
0047 The following can be set for each tracer (tracer number iTrc):
0048
bf89a37abc Phob*0049 - :varlink:`PTRACERS_advScheme` (iTrc) will default to :varlink:`saltAdvScheme` (set in data). For other options see Table :ref:`adv_scheme_summary`.
0050 - :varlink:`PTRACERS_ImplVertAdv` (iTrc): implicit vertical advection flag, defaults to false.
0051 - :varlink:`PTRACERS_diffKh` (iTrc): horizontal Laplacian Diffusivity, defaults to :varlink:`diffKhS` (set in data).
0052 - :varlink:`PTRACERS_diffK4` (iTrc): Biharmonic Diffusivity, defaults to :varlink:`diffK4S` (set in data).
0053 - :varlink:`PTRACERS_diffKr` (iTrc): vertical diffusion, defaults to un-set.
0054 - :varlink:`PTRACERS_diffKrNr` (k,iTrc): level specific vertical diffusion, defaults to :varlink:`diffKrNrS`. Will be set to :varlink:`PTRACERS_diffKr` if this is set.
0055 - :varlink:`PTRACERS_ref` (k,iTrc): reference tracer value for each level k, defaults to 0. Currently only used for dilution/concentration of tracers at surface if :varlink:`PTRACERS_EvPrRn` (iTrc) is set and :varlink:`convertFW2Salt` (set in data) is set to something other than -1 (note default is :varlink:`convertFW2Salt` = 35).
0056 - :varlink:`PTRACERS_EvPrRn` (iTrc): tracer concentration in freshwater. Needed for calculation of dilution/concentration in surface layer due to freshwater addition/evaporation. Defaults to un-set in which case no dilution/concentration occurs.
0057 - :varlink:`PTRACERS_useGMRedi` (iTrc): apply GM or not. Defaults to :varlink:`useGMREdi`.
0058 - :varlink:`PTRACERS_useKPP` (iTrc): apply KPP or not. Defaults to :varlink:`useKPP`.
0059 - :varlink:`PTRACERS_initialFile` (iTrc): file with initial tracer concentration. Will be used if ``PTRACERS_Iter0`` :math:`=` ``nIter0``. Default is no name, in which case tracer is initialised as zero. If ``PTRACERS_Iter0`` :math:`<` ``nIter0``, then tracer concentration will come from ``pickup_ptracer``.
0060 - :varlink:`PTRACERS_names` (iTrc): tracer name. Needed for netcdf. Defaults to nothing.
654ec02869 Phob*0061 - :varlink:`PTRACERS_long_names` (iTrc): optional name in long form of tracer.
bf89a37abc Phob*0062 - :varlink:`PTRACERS_units` (iTrc): optional units of tracer.
8679f9097b Jeff*0063
9ce7d74115 Jeff*0064 .. _ptracers_diagnostics:
0065
8679f9097b Jeff*0066 PTRACERS Diagnostics
0067 ++++++++++++++++++++
0068
de8afdbdd0 Oliv*0069 Note that beyond 99 ptracers, diagnostics will be labeled with letters in
0070 addition to numbers, e.g., the diagnostic for the 100th ptracer is TRAC0a, etc.
8679f9097b Jeff*0071
0072 ::
0073
bee2303e6c Oliv*0074 ---------------------------------------------------------------
0075 <-Name->|<- code ->|<-- Units -->|<- Tile (max=80c)
0076 ---------------------------------------------------------------
0077 TRAC01 |SMR MR|mol/m^3 |Dissolved Inorganic Carbon (DIC) [mol C/m^3] concentration
0078 UTRAC01 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of DIC
0079 VTRAC01 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of DIC
0080 WTRAC01 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of DIC
0081 ForcTr01|SMR MR|mol/m^3/s |DIC forcing tendency
0082 AB_gTr01|SMR MR|mol/m^3/s |DIC tendency from Adams-Bashforth
0083 Tp_gTr01|SMR MR|mol/m^3/s |DIC total transport tendency (before gchem_forcing_sep)
0084 ADVrTr01|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DIC
0085 ADVxTr01|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DIC
0086 ADVyTr01|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DIC
0087 DFrETr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Explicit part)
0088 DFxETr01|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DIC
0089 DFyETr01|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DIC
0090 DFrITr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Implicit part)
0091 TRAC02 |SMR MR|mol/m^3 |Alkalinity (Alk) [mol eq/m^3] concentration
0092 UTRAC02 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of Alk
0093 VTRAC02 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of Alk
0094 WTRAC02 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of Alk
0095 ForcTr02|SMR MR|mol/m^3/s |Alk forcing tendency
0096 AB_gTr02|SMR MR|mol/m^3/s |Alk tendency from Adams-Bashforth
0097 Tp_gTr02|SMR MR|mol/m^3/s |Alk total transport tendency (before gchem_forcing_sep)
0098 ADVrTr02|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of Alk
0099 ADVxTr02|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of Alk
0100 ADVyTr02|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of Alk
0101 DFrETr02|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of Alk (Explicit part)
0102 DFxETr02|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of Alk
0103 DFyETr02|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of Alk
0104 DFrITr02|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of Alk (Implicit part)
0105 TRAC03 |SMR MR|mol/m^3 |Phosphate (PO4) [mol P/m^3] concentration
0106 UTRAC03 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of PO4
0107 VTRAC03 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of PO4
0108 WTRAC03 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of PO4
0109 ForcTr03|SMR MR|mol/m^3/s |PO4 forcing tendency
0110 AB_gTr03|SMR MR|mol/m^3/s |PO4 tendency from Adams-Bashforth
0111 Tp_gTr03|SMR MR|mol/m^3/s |PO4 total transport tendency (before gchem_forcing_sep)
0112 ADVrTr03|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of PO4
0113 ADVxTr03|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of PO4
0114 ADVyTr03|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of PO4
0115 DFrETr03|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of PO4 (Explicit part)
0116 DFxETr03|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of PO4
0117 DFyETr03|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of PO4
0118 DFrITr03|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of PO4 (Implicit part)
0119 TRAC04 |SMR MR|mol/m^3 |Dissolved Organic Phosphorus (DOP) [mol P/m^3] concentration
0120 UTRAC04 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of DOP
0121 VTRAC04 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of DOP
0122 WTRAC04 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of DOP
0123 ForcTr04|SMR MR|mol/m^3/s |DOP forcing tendency
0124 AB_gTr04|SMR MR|mol/m^3/s |DOP tendency from Adams-Bashforth
0125 Tp_gTr04|SMR MR|mol/m^3/s |DOP total transport tendency (before gchem_forcing_sep)
0126 ADVrTr04|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DOP
0127 ADVxTr04|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DOP
0128 ADVyTr04|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DOP
0129 DFrETr04|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DOP (Explicit part)
0130 DFxETr04|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DOP
0131 DFyETr04|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DOP
0132 DFrITr04|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DOP (Implicit part)
0133 TRAC05 |SMR MR|mol/m^3 |Dissolved Oxygen (O2) [mol O/m^3] concentration
0134 UTRAC05 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of O2
0135 VTRAC05 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of O2
0136 WTRAC05 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of O2
0137 ForcTr05|SMR MR|mol/m^3/s |O2 forcing tendency
0138 AB_gTr05|SMR MR|mol/m^3/s |O2 tendency from Adams-Bashforth
0139 Tp_gTr05|SMR MR|mol/m^3/s |O2 total transport tendency (before gchem_forcing_sep)
0140 ADVrTr05|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of O2
0141 ADVxTr05|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of O2
0142 ADVyTr05|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of O2
0143 DFrETr05|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of O2 (Explicit part)
0144 DFxETr05|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of O2
0145 DFyETr05|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of O2
0146 DFrITr05|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of O2 (Implicit part)
8679f9097b Jeff*0147
0148 Do’s and Don’ts
0149 +++++++++++++++
0150
0151 Reference Material
0152 ++++++++++++++++++
0153
