.. _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 these will only work for 90 or less tracers (some problems with the numbering/designation over this number) :: ------------------------------------------------------------------------ <-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) ------------------------------------------------------------------------ TRAC01 | 15 |SM P MR |mol C/m |Mass-Weighted Dissolved Inorganic Carbon UTRAC01 | 15 |UU 171MR |mol C/m.m/s |Zonal Mass-Weighted Transp of Dissolved Inorganic Carbon VTRAC01 | 15 |VV 170MR |mol C/m.m/s |Merid Mass-Weighted Transp of Dissolved Inorganic Carbon WTRAC01 | 15 |WM MR |mol C/m.m/s |Vert Mass-Weighted Transp of Dissolved Inorganic Carbon ADVrTr01| 15 |WM LR |mol C/m.m^3/s |Vertical Advective Flux of Dissolved Inorganic Carbon ADVxTr01| 15 |UU 175MR |mol C/m.m^3/s |Zonal Advective Flux of Dissolved Inorganic Carbon ADVyTr01| 15 |VV 174MR |mol C/m.m^3/s |Meridional Advective Flux of Dissolved Inorganic Carbon DFrETr01| 15 |WM LR |mol C/m.m^3/s |Vertical Diffusive Flux of Dissolved Inorganic Carbon (Explicit part) DIFxTr01| 15 |UU 178MR |mol C/m.m^3/s |Zonal Diffusive Flux of Dissolved Inorganic Carbon DIFyTr01| 15 |VV 177MR |mol C/m.m^3/s |Meridional Diffusive Flux of Dissolved Inorganic Carbon DFrITr01| 15 |WM LR |mol C/m.m^3/s |Vertical Diffusive Flux of Dissolved Inorganic Carbon (Implicit part) TRAC02 | 15 |SM P MR |mol eq/ |Mass-Weighted Alkalinity UTRAC02 | 15 |UU 182MR |mol eq/.m/s |Zonal Mass-Weighted Transp of Alkalinity VTRAC02 | 15 |VV 181MR |mol eq/.m/s |Merid Mass-Weighted Transp of Alkalinity WTRAC02 | 15 |WM MR |mol eq/.m/s |Vert Mass-Weighted Transp of Alkalinity ADVrTr02| 15 |WM LR |mol eq/.m^3/s |Vertical Advective Flux of Alkalinity ADVxTr02| 15 |UU 186MR |mol eq/.m^3/s |Zonal Advective Flux of Alkalinity ADVyTr02| 15 |VV 185MR |mol eq/.m^3/s |Meridional Advective Flux of Alkalinity DFrETr02| 15 |WM LR |mol eq/.m^3/s |Vertical Diffusive Flux of Alkalinity (Explicit part) DIFxTr02| 15 |UU 189MR |mol eq/.m^3/s |Zonal Diffusive Flux of Alkalinity DIFyTr02| 15 |VV 188MR |mol eq/.m^3/s |Meridional Diffusive Flux of Alkalinity DFrITr02| 15 |WM LR |mol eq/.m^3/s |Vertical Diffusive Flux of Alkalinity (Implicit part) TRAC03 | 15 |SM P MR |mol P/m |Mass-Weighted Phosphate UTRAC03 | 15 |UU 193MR |mol P/m.m/s |Zonal Mass-Weighted Transp of Phosphate VTRAC03 | 15 |VV 192MR |mol P/m.m/s |Merid Mass-Weighted Transp of Phosphate WTRAC03 | 15 |WM MR |mol P/m.m/s |Vert Mass-Weighted Transp of Phosphate ADVrTr03| 15 |WM LR |mol P/m.m^3/s |Vertical Advective Flux of Phosphate ADVxTr03| 15 |UU 197MR |mol P/m.m^3/s |Zonal Advective Flux of Phosphate ADVyTr03| 15 |VV 196MR |mol P/m.m^3/s |Meridional Advective Flux of Phosphate DFrETr03| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Phosphate (Explicit part) DIFxTr03| 15 |UU 200MR |mol P/m.m^3/s |Zonal Diffusive Flux of Phosphate ------------------------------------------------------------------------ <-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) ------------------------------------------------------------------------ DIFyTr03| 15 |VV 199MR |mol P/m.m^3/s |Meridional Diffusive Flux of Phosphate DFrITr03| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Phosphate (Implicit part) TRAC04 | 15 |SM P MR |mol P/m |Mass-Weighted Dissolved Organic Phosphorus UTRAC04 | 15 |UU 204MR |mol P/m.m/s |Zonal Mass-Weighted Transp of Dissolved Organic Phosphorus VTRAC04 | 15 |VV 203MR |mol P/m.m/s |Merid Mass-Weighted Transp of Dissolved Organic Phosphorus WTRAC04 | 15 |WM MR |mol P/m.m/s |Vert Mass-Weighted Transp of Dissolved Organic Phosphorus ADVrTr04| 15 |WM LR |mol P/m.m^3/s |Vertical Advective Flux of Dissolved Organic Phosphorus ADVxTr04| 15 |UU 208MR |mol P/m.m^3/s |Zonal Advective Flux of Dissolved Organic Phosphorus ADVyTr04| 15 |VV 207MR |mol P/m.m^3/s |Meridional Advective Flux of Dissolved Organic Phosphorus DFrETr04| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Dissolved Organic Phosphorus (Explicit part) DIFxTr04| 15 |UU 211MR |mol P/m.m^3/s |Zonal Diffusive Flux of Dissolved Organic Phosphorus DIFyTr04| 15 |VV 210MR |mol P/m.m^3/s |Meridional Diffusive Flux of Dissolved Organic Phosphorus DFrITr04| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Dissolved Organic Phosphorus (Implicit part) TRAC05 | 15 |SM P MR |mol O/m |Mass-Weighted Dissolved Oxygen UTRAC05 | 15 |UU 215MR |mol O/m.m/s |Zonal Mass-Weighted Transp of Dissolved Oxygen VTRAC05 | 15 |VV 214MR |mol O/m.m/s |Merid Mass-Weighted Transp of Dissolved Oxygen WTRAC05 | 15 |WM MR |mol O/m.m/s |Vert Mass-Weighted Transp of Dissolved Oxygen ADVrTr05| 15 |WM LR |mol O/m.m^3/s |Vertical Advective Flux of Dissolved Oxygen ADVxTr05| 15 |UU 219MR |mol O/m.m^3/s |Zonal Advective Flux of Dissolved Oxygen ADVyTr05| 15 |VV 218MR |mol O/m.m^3/s |Meridional Advective Flux of Dissolved Oxygen DFrETr05| 15 |WM LR |mol O/m.m^3/s |Vertical Diffusive Flux of Dissolved Oxygen (Explicit part) DIFxTr05| 15 |UU 222MR |mol O/m.m^3/s |Zonal Diffusive Flux of Dissolved Oxygen DIFyTr05| 15 |VV 221MR |mol O/m.m^3/s |Meridional Diffusive Flux of Dissolved Oxygen DFrITr05| 15 |WM LR |mol O/m.m^3/s |Vertical Diffusive Flux of Dissolved Oxygen (Implicit part) Do’s and Don’ts +++++++++++++++ Reference Material ++++++++++++++++++