.. _sub_phys_pkg_ptracers: PTRACERS Package ---------------- Introduction ++++++++++++ This is a ''passive'' tracer package. Passive here means that the tracers don’t affect the density of the water (as opposed to temperature and salinity) so no not actively affect the physics of the ocean. Tracers are initialized, advected, diffused and various outputs are taken care of in this package. For methods to add additional sources and sinks of tracers use the :ref:`gchem Package `. Can use up tp 3843 tracers. But can not use the :ref:`diagnostics package ` with more than about 90 tracers. Use :filelink:`utils/matlab/ioLb2num.m` and :filelink:`num2ioLb.m ` to find correspondence between tracer number and tracer designation in the code for more than 99 tracers (since tracers only have two digit designations). Equations +++++++++ Key subroutines and parameters ++++++++++++++++++++++++++++++ The only code you should have to modify is: :filelink:`PTRACERS_SIZE.h ` where you need to set in the number of tracers to be used in the experiment: :varlink:`PTRACERS_num`. Run time parameters set in :code:`data.ptracers`: - :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``. - :varlink:`PTRACERS_numInUse`: number of tracers to be used in the run (needs to be :math:`<=` ``PTRACERS_num`` set in :filelink:`PTRACERS_SIZE.h `) - :varlink:`PTRACERS_dumpFreq`: defaults to :varlink:`dumpFreq` (set in data) - :varlink:`PTRACERS_taveFreq`: defaults to :varlink:`taveFreq` (set in data) - :varlink:`PTRACERS_monitorFreq`: defaults to :varlink:`monitorFreq` (set in data) - :varlink:`PTRACERS_timeave_mnc`: needs :varlink:`useMNC`, :varlink:`timeave_mnc`, default to false - :varlink:`PTRACERS_snapshot_mnc`: needs :varlink:`useMNC` , :varlink:`snapshot_mnc`, default to false - :varlink:`PTRACERS_monitor_mnc`: needs :varlink:`useMNC`, :varlink:`monitor_mnc`, default to false - :varlink:`PTRACERS_pickup_write_mnc`: needs :varlink:`useMNC`, :varlink:`pickup_write_mnc`, default to false - :varlink:`PTRACERS_pickup_read_mnc`: needs :varlink:`useMNC`, :varlink:`pickup_read_mnc`, default to false - :varlink:`PTRACERS_useRecords`: defaults to false. If true, will write all tracers in a single file, otherwise each tracer in a seperate file. The following can be set for each tracer (tracer number iTrc): - :varlink:`PTRACERS_advScheme` (iTrc) will default to :varlink:`saltAdvScheme` (set in data). For other options see Table :ref:`adv_scheme_summary`. - :varlink:`PTRACERS_ImplVertAdv` (iTrc): implicit vertical advection flag, defaults to false. - :varlink:`PTRACERS_diffKh` (iTrc): horizontal Laplacian Diffusivity, defaults to :varlink:`diffKhS` (set in data). - :varlink:`PTRACERS_diffK4` (iTrc): Biharmonic Diffusivity, defaults to :varlink:`diffK4S` (set in data). - :varlink:`PTRACERS_diffKr` (iTrc): vertical diffusion, defaults to un-set. - :varlink:`PTRACERS_diffKrNr` (k,iTrc): level specific vertical diffusion, defaults to :varlink:`diffKrNrS`. Will be set to :varlink:`PTRACERS_diffKr` if this is set. - :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). - :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. - :varlink:`PTRACERS_useGMRedi` (iTrc): apply GM or not. Defaults to :varlink:`useGMREdi`. - :varlink:`PTRACERS_useKPP` (iTrc): apply KPP or not. Defaults to :varlink:`useKPP`. - :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``. - :varlink:`PTRACERS_names` (iTrc): tracer name. Needed for netcdf. Defaults to nothing. - :varlink:`PTRACERS_long_names` (iTrc): optional name in long form of tracer. - :varlink:`PTRACERS_units` (iTrc): optional units of tracer. .. _ptracers_diagnostics: PTRACERS Diagnostics ++++++++++++++++++++ Note that beyond 99 ptracers, diagnostics will be labeled with letters in addition to numbers, e.g., the diagnostic for the 100th ptracer is TRAC0a, etc. :: --------------------------------------------------------------- <-Name->|<- code ->|<-- Units -->|<- Tile (max=80c) --------------------------------------------------------------- TRAC01 |SMR MR|mol/m^3 |Dissolved Inorganic Carbon (DIC) [mol C/m^3] concentration UTRAC01 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of DIC VTRAC01 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of DIC WTRAC01 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of DIC ForcTr01|SMR MR|mol/m^3/s |DIC forcing tendency AB_gTr01|SMR MR|mol/m^3/s |DIC tendency from Adams-Bashforth Tp_gTr01|SMR MR|mol/m^3/s |DIC total transport tendency (before gchem_forcing_sep) ADVrTr01|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DIC ADVxTr01|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DIC ADVyTr01|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DIC DFrETr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Explicit part) DFxETr01|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DIC DFyETr01|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DIC DFrITr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Implicit part) TRAC02 |SMR MR|mol/m^3 |Alkalinity (Alk) [mol eq/m^3] concentration UTRAC02 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of Alk VTRAC02 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of Alk WTRAC02 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of Alk ForcTr02|SMR MR|mol/m^3/s |Alk forcing tendency AB_gTr02|SMR MR|mol/m^3/s |Alk tendency from Adams-Bashforth Tp_gTr02|SMR MR|mol/m^3/s |Alk total transport tendency (before gchem_forcing_sep) ADVrTr02|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of Alk ADVxTr02|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of Alk ADVyTr02|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of Alk DFrETr02|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of Alk (Explicit part) DFxETr02|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of Alk DFyETr02|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of Alk DFrITr02|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of Alk (Implicit part) TRAC03 |SMR MR|mol/m^3 |Phosphate (PO4) [mol P/m^3] concentration UTRAC03 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of PO4 VTRAC03 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of PO4 WTRAC03 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of PO4 ForcTr03|SMR MR|mol/m^3/s |PO4 forcing tendency AB_gTr03|SMR MR|mol/m^3/s |PO4 tendency from Adams-Bashforth Tp_gTr03|SMR MR|mol/m^3/s |PO4 total transport tendency (before gchem_forcing_sep) ADVrTr03|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of PO4 ADVxTr03|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of PO4 ADVyTr03|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of PO4 DFrETr03|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of PO4 (Explicit part) DFxETr03|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of PO4 DFyETr03|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of PO4 DFrITr03|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of PO4 (Implicit part) TRAC04 |SMR MR|mol/m^3 |Dissolved Organic Phosphorus (DOP) [mol P/m^3] concentration UTRAC04 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of DOP VTRAC04 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of DOP WTRAC04 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of DOP ForcTr04|SMR MR|mol/m^3/s |DOP forcing tendency AB_gTr04|SMR MR|mol/m^3/s |DOP tendency from Adams-Bashforth Tp_gTr04|SMR MR|mol/m^3/s |DOP total transport tendency (before gchem_forcing_sep) ADVrTr04|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DOP ADVxTr04|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DOP ADVyTr04|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DOP DFrETr04|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DOP (Explicit part) DFxETr04|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DOP DFyETr04|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DOP DFrITr04|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DOP (Implicit part) TRAC05 |SMR MR|mol/m^3 |Dissolved Oxygen (O2) [mol O/m^3] concentration UTRAC05 |UUr MR|mol/m^3.m/s |Zonal Mass-Weighted Transp of O2 VTRAC05 |VVr MR|mol/m^3.m/s |Merid Mass-Weighted Transp of O2 WTRAC05 |WM MR|mol/m^3.m/s |Vert Mass-Weighted Transp of O2 ForcTr05|SMR MR|mol/m^3/s |O2 forcing tendency AB_gTr05|SMR MR|mol/m^3/s |O2 tendency from Adams-Bashforth Tp_gTr05|SMR MR|mol/m^3/s |O2 total transport tendency (before gchem_forcing_sep) ADVrTr05|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of O2 ADVxTr05|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of O2 ADVyTr05|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of O2 DFrETr05|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of O2 (Explicit part) DFxETr05|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of O2 DFyETr05|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of O2 DFrITr05|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of O2 (Implicit part) Do’s and Don’ts +++++++++++++++ Reference Material ++++++++++++++++++