8.3.3. PTRACERS Package¶
8.3.3.1. 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 gchem Package.
Can use up tp 3843 tracers. But can not use the diagnostics package with more than about 90 tracers. Use utils/matlab/ioLb2num.m and 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).
8.3.3.2. Equations¶
8.3.3.3. Key subroutines and parameters¶
The only code you should have to modify is: PTRACERS_SIZE.h where you need to set in the number of tracers to be used in the experiment: PTRACERS_num.
Run time parameters set in data.ptracers:
PTRACERS_Iter0 which is the integer timestep when the tracer experiment is initialized. If
nIter0=PTRACERS_Iter0then the tracers are initialized to zero or from initial files. IfnIter0\(>\)PTRACERS_Iter0then tracers (and previous timestep tendency terms) are read in from a the ptracers pickup file. Note that tracers of zeros will be carried around ifnIter0\(<\)PTRACERS_Iter0.PTRACERS_numInUse: number of tracers to be used in the run (needs to be \(<=\)
PTRACERS_numset in PTRACERS_SIZE.h)PTRACERS_dumpFreq: defaults to dumpFreq (set in data)
PTRACERS_taveFreq: defaults to taveFreq (set in data)
PTRACERS_monitorFreq: defaults to monitorFreq (set in data)
PTRACERS_timeave_mnc: needs useMNC, timeave_mnc, default to false
PTRACERS_snapshot_mnc: needs useMNC , snapshot_mnc, default to false
PTRACERS_monitor_mnc: needs useMNC, monitor_mnc, default to false
PTRACERS_pickup_write_mnc: needs useMNC, pickup_write_mnc, default to false
PTRACERS_pickup_read_mnc: needs useMNC, pickup_read_mnc, default to false
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):
PTRACERS_advScheme (iTrc) will default to saltAdvScheme (set in data). For other options see Table MITgcm Advection Schemes.
PTRACERS_ImplVertAdv (iTrc): implicit vertical advection flag, defaults to false.
PTRACERS_diffKh (iTrc): horizontal Laplacian Diffusivity, defaults to diffKhS (set in data).
PTRACERS_diffK4 (iTrc): Biharmonic Diffusivity, defaults to diffK4S (set in data).
PTRACERS_diffKr (iTrc): vertical diffusion, defaults to un-set.
PTRACERS_diffKrNr (k,iTrc): level specific vertical diffusion, defaults to diffKrNrS. Will be set to PTRACERS_diffKr if this is set.
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 PTRACERS_EvPrRn (iTrc) is set and convertFW2Salt (set in data) is set to something other than -1 (note default is convertFW2Salt = 35).
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.
PTRACERS_useGMRedi (iTrc): apply GM or not. Defaults to useGMREdi.
PTRACERS_useKPP (iTrc): apply KPP or not. Defaults to useKPP.
PTRACERS_initialFile (iTrc): file with initial tracer concentration. Will be used if
PTRACERS_Iter0\(=\)nIter0. Default is no name, in which case tracer is initialised as zero. IfPTRACERS_Iter0\(<\)nIter0, then tracer concentration will come frompickup_ptracer.PTRACERS_names (iTrc): tracer name. Needed for netcdf. Defaults to nothing.
PTRACERS_long_names (iTrc): optional name in long form of tracer.
PTRACERS_units (iTrc): optional units of tracer.
8.3.3.4. 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.
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<-Name->|<- code ->|<-- Units -->|<- Tile (max=80c)
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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)