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molod |
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\subsection {PTRACERS Package} |
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\label{sec:pkg:ptracers} |
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\begin{rawhtml} |
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<!-- CMIREDIR:package_ptracers: --> |
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\end{rawhtml} |
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\subsubsection {Introduction} |
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stephd |
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This is a "passive" tracer package. Passive here means that the |
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tracers don't affect the density of the water (as opposed to |
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temperature and salinity) so no not actively affect the |
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physics of the ocean. Tracers are initialized, advected, diffused |
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and various outputs are taken care of in this package. |
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For methods to add additional sources and sinks of tracers use the pkg/gchem |
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(section \ref{sec:pkg:gchem}). |
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Can use up tp 3843 tracers. But can not use pkg/diagnostics with more |
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than about 90 tracers. |
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Use utils/matlab/ioLb2num.m and num2ioLb.m to find correspondence |
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between tracer number and tracer designation in the code for more |
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than 99 tracers (since |
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tracers only have two digit designations). |
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molod |
1.1 |
\subsubsection {Equations} |
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\subsubsection {Key subroutines and parameters} |
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stephd |
1.3 |
The only code you shoul dhave to modify is: |
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{\bf PTRACERS\_SIZE.h} where you need to set in the number of tracers to |
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be used in the experiment: PTRACERS\_num. |
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\vspace{.5cm} |
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\noindent |
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{bf RUN TIME PARAMETERS SET IN {\bf data.ptracers}}: \\ |
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$\bullet$ {\bf PTRACERS\_Iter0} |
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which is the integer timestep when the tracer experiment |
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is initialized. If nIter0 $=$ PTRACERS\_Iter0 then the tracers |
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are initialized to zero or from initial files. If nIter0 $>$ |
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PTRACERS\_Iter0 then tracers (and previous timestep tendency terms) |
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stephd |
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are read in from a the ptracers pickup file. Note that tracers |
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stephd |
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of zeros will be carried around if nIter0 $<$ PTRACERS\_Iter0.\\ |
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$\bullet$ {\bf PTRACERS\_numInUse}: number of tracers to be used in the |
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run (needs to be $<=$ PTRACERS\_num set in PTRACERS\_SIZE.h)\\ |
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$\bullet$ {\bf PTRACERS\_dumpFreq}: defaults to dumpFreq (set in data)\\ |
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$\bullet$ {\bf PTRACERS\_taveFreq}: defaults to taveFreq (set in data)\\ |
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$\bullet$ {\bf PTRACERS\_monitorFreq}: defaults to monitorFreq (set in data)\\ |
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$\bullet$ {\bf PTRACERS\_timeave\_mnc}: needs useMNC, timeave\_mnc, default to false\\ |
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$\bullet$ {\bf PTRACERS\_snapshot\_mnc}: needs useMNC, snapshot\_mnc, default to false \\ |
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$\bullet$ {\bf PTRACERS\_monitor\_mnc}: needs useMNC, monitor\_mnc, default to false\\ |
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$\bullet$ {\bf PTRACERS\_pickup\_write\_mnc}: needs useMNC, pickup\_write\_mnc, default to false\\ |
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$\bullet$ {\bf PTRACERS\_pickup\_read\_mnc}: needs useMNC, pickup\_read\_mnc, default to false\\ |
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$\bullet$ {\bf PTRACERS\_useRecords}: defaults to false. If true, will write |
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all tracers in a single file, otherwise each tracer in a seperate file.\\ |
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\vspace{.5cm} |
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The following can be set for each tracer (tracer number iTrc):\\ |
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$\bullet$ {\bf PTRACERS\_advScheme(iTrc)} will default to saltAdvScheme (set in data). For other options see Table \ref {tab:advectionShemes_summary}.\\ |
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$\bullet$ {\bf PTRACERS\_ImplVertAdv(iTrc)}: implicit vertical advection flag, |
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default to .FALSE.\\ |
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$\bullet$ {\bf PTRACERS\_diffKh(iTrc)}: horizontal Laplacian Diffusivity, |
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dafaults to diffKhS (set in data).\\ |
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$\bullet$ {\bf PTRACERS\_diffK4(iTrc)}: Biharmonic Diffusivity, defaults to |
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diffK4S (set in data).\\ |
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$\bullet$ {\bf PTRACERS\_diffKr(iTrc)}: vertical diffusion, defaults to un-set.\\ |
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$\bullet$ {\bf PTRACERS\_diffKrNr(k,iTrc)}: level specific vertical diffusion, |
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defaults to diffKrNrS. Will be set to PTRACERS\_diffKr if this is set.\\ |
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$\bullet$ {\bf PTRACERS\_ref(k,iTrc)}: reference tracer value for each level k, |
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defaults to 0. Currently only used for |
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dilution/concentration of tracers at surface if PTRACERS\_EvPrRn(iTrc) is |
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set and convertFW2Salt (set in data) is set to something other than -1 |
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(note default is convertFW2Salt=35).\\ |
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$\bullet$ {\bf PTRACERS\_EvPrRn(iTrc)}: tracer concentration in freshwater. |
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Needed for calculation of dilution/concentration in surface layer due to |
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freshwater addition/evaporation. Defaults to un-set in which case no |
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dilution/concentration occurs.\\ |
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$\bullet$ {\bf PTRACERS\_useGMRedi(iTrc)}: apply GM or not. Defaults to |
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useGMREdi.\\ |
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$\bullet$ {\bf PTRACERS\_useKPP(iTrc)}: apply KPP or not. Defaults to |
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useKPP.\\ |
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$\bullet$ {\bf PTRACERS\_initialFile(iTrc)}: file with initial tracer |
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concentration. Will be used if PTRACERS\_Iter0 $=$ nIter0. Default |
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is no name, in which case tracer is initialised as zero. If |
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PTRACERS\_Iter0 $<$ nIter0, then tracer concentration will come |
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from pickup\_ptracer.\\ |
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$\bullet$ {\bf PTRACERS\_names(iTrc)}: tracer name. Needed for netcdf. |
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Defaults to nothing.\\ |
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$\bullet$ {\bf PTRACERS\_long\_names(iTrc)}: optional name in long form |
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of tracer.\\ |
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$\bullet$ {\bf PTRACERS\_units(iTrc)}: optional units of tracer. |
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stephd |
1.2 |
\\ |
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molod |
1.1 |
\subsubsection{PTRACERS Diagnostics} |
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\label{sec:pkg:ptracers:diagnostics} |
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stephd |
1.3 |
Note that these will only work for 90 or less tracers (some |
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problems with the numbering/designation over this number) |
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molod |
1.1 |
{\footnotesize |
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\begin{verbatim} |
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------------------------------------------------------------------------ |
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<-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) |
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------------------------------------------------------------------------ |
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TRAC01 | 15 |SM P MR |mol C/m |Mass-Weighted Dissolved Inorganic Carbon |
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UTRAC01 | 15 |UU 171MR |mol C/m.m/s |Zonal Mass-Weighted Transp of Dissolved Inorganic Carbon |
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VTRAC01 | 15 |VV 170MR |mol C/m.m/s |Merid Mass-Weighted Transp of Dissolved Inorganic Carbon |
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WTRAC01 | 15 |WM MR |mol C/m.m/s |Vert Mass-Weighted Transp of Dissolved Inorganic Carbon |
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ADVrTr01| 15 |WM LR |mol C/m.m^3/s |Vertical Advective Flux of Dissolved Inorganic Carbon |
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ADVxTr01| 15 |UU 175MR |mol C/m.m^3/s |Zonal Advective Flux of Dissolved Inorganic Carbon |
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ADVyTr01| 15 |VV 174MR |mol C/m.m^3/s |Meridional Advective Flux of Dissolved Inorganic Carbon |
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DFrETr01| 15 |WM LR |mol C/m.m^3/s |Vertical Diffusive Flux of Dissolved Inorganic Carbon (Explicit part) |
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DIFxTr01| 15 |UU 178MR |mol C/m.m^3/s |Zonal Diffusive Flux of Dissolved Inorganic Carbon |
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DIFyTr01| 15 |VV 177MR |mol C/m.m^3/s |Meridional Diffusive Flux of Dissolved Inorganic Carbon |
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DFrITr01| 15 |WM LR |mol C/m.m^3/s |Vertical Diffusive Flux of Dissolved Inorganic Carbon (Implicit part) |
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TRAC02 | 15 |SM P MR |mol eq/ |Mass-Weighted Alkalinity |
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UTRAC02 | 15 |UU 182MR |mol eq/.m/s |Zonal Mass-Weighted Transp of Alkalinity |
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VTRAC02 | 15 |VV 181MR |mol eq/.m/s |Merid Mass-Weighted Transp of Alkalinity |
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WTRAC02 | 15 |WM MR |mol eq/.m/s |Vert Mass-Weighted Transp of Alkalinity |
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ADVrTr02| 15 |WM LR |mol eq/.m^3/s |Vertical Advective Flux of Alkalinity |
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ADVxTr02| 15 |UU 186MR |mol eq/.m^3/s |Zonal Advective Flux of Alkalinity |
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ADVyTr02| 15 |VV 185MR |mol eq/.m^3/s |Meridional Advective Flux of Alkalinity |
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DFrETr02| 15 |WM LR |mol eq/.m^3/s |Vertical Diffusive Flux of Alkalinity (Explicit part) |
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DIFxTr02| 15 |UU 189MR |mol eq/.m^3/s |Zonal Diffusive Flux of Alkalinity |
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DIFyTr02| 15 |VV 188MR |mol eq/.m^3/s |Meridional Diffusive Flux of Alkalinity |
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DFrITr02| 15 |WM LR |mol eq/.m^3/s |Vertical Diffusive Flux of Alkalinity (Implicit part) |
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TRAC03 | 15 |SM P MR |mol P/m |Mass-Weighted Phosphate |
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UTRAC03 | 15 |UU 193MR |mol P/m.m/s |Zonal Mass-Weighted Transp of Phosphate |
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VTRAC03 | 15 |VV 192MR |mol P/m.m/s |Merid Mass-Weighted Transp of Phosphate |
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WTRAC03 | 15 |WM MR |mol P/m.m/s |Vert Mass-Weighted Transp of Phosphate |
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ADVrTr03| 15 |WM LR |mol P/m.m^3/s |Vertical Advective Flux of Phosphate |
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ADVxTr03| 15 |UU 197MR |mol P/m.m^3/s |Zonal Advective Flux of Phosphate |
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ADVyTr03| 15 |VV 196MR |mol P/m.m^3/s |Meridional Advective Flux of Phosphate |
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DFrETr03| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Phosphate (Explicit part) |
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DIFxTr03| 15 |UU 200MR |mol P/m.m^3/s |Zonal Diffusive Flux of Phosphate |
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------------------------------------------------------------------------ |
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<-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) |
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------------------------------------------------------------------------ |
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DIFyTr03| 15 |VV 199MR |mol P/m.m^3/s |Meridional Diffusive Flux of Phosphate |
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DFrITr03| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Phosphate (Implicit part) |
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TRAC04 | 15 |SM P MR |mol P/m |Mass-Weighted Dissolved Organic Phosphorus |
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UTRAC04 | 15 |UU 204MR |mol P/m.m/s |Zonal Mass-Weighted Transp of Dissolved Organic Phosphorus |
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VTRAC04 | 15 |VV 203MR |mol P/m.m/s |Merid Mass-Weighted Transp of Dissolved Organic Phosphorus |
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WTRAC04 | 15 |WM MR |mol P/m.m/s |Vert Mass-Weighted Transp of Dissolved Organic Phosphorus |
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ADVrTr04| 15 |WM LR |mol P/m.m^3/s |Vertical Advective Flux of Dissolved Organic Phosphorus |
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ADVxTr04| 15 |UU 208MR |mol P/m.m^3/s |Zonal Advective Flux of Dissolved Organic Phosphorus |
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ADVyTr04| 15 |VV 207MR |mol P/m.m^3/s |Meridional Advective Flux of Dissolved Organic Phosphorus |
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DFrETr04| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Dissolved Organic Phosphorus (Explicit part) |
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DIFxTr04| 15 |UU 211MR |mol P/m.m^3/s |Zonal Diffusive Flux of Dissolved Organic Phosphorus |
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DIFyTr04| 15 |VV 210MR |mol P/m.m^3/s |Meridional Diffusive Flux of Dissolved Organic Phosphorus |
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DFrITr04| 15 |WM LR |mol P/m.m^3/s |Vertical Diffusive Flux of Dissolved Organic Phosphorus (Implicit part) |
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TRAC05 | 15 |SM P MR |mol O/m |Mass-Weighted Dissolved Oxygen |
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UTRAC05 | 15 |UU 215MR |mol O/m.m/s |Zonal Mass-Weighted Transp of Dissolved Oxygen |
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VTRAC05 | 15 |VV 214MR |mol O/m.m/s |Merid Mass-Weighted Transp of Dissolved Oxygen |
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WTRAC05 | 15 |WM MR |mol O/m.m/s |Vert Mass-Weighted Transp of Dissolved Oxygen |
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ADVrTr05| 15 |WM LR |mol O/m.m^3/s |Vertical Advective Flux of Dissolved Oxygen |
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ADVxTr05| 15 |UU 219MR |mol O/m.m^3/s |Zonal Advective Flux of Dissolved Oxygen |
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ADVyTr05| 15 |VV 218MR |mol O/m.m^3/s |Meridional Advective Flux of Dissolved Oxygen |
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DFrETr05| 15 |WM LR |mol O/m.m^3/s |Vertical Diffusive Flux of Dissolved Oxygen (Explicit part) |
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DIFxTr05| 15 |UU 222MR |mol O/m.m^3/s |Zonal Diffusive Flux of Dissolved Oxygen |
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DIFyTr05| 15 |VV 221MR |mol O/m.m^3/s |Meridional Diffusive Flux of Dissolved Oxygen |
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DFrITr05| 15 |WM LR |mol O/m.m^3/s |Vertical Diffusive Flux of Dissolved Oxygen (Implicit part) |
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\end{verbatim} |
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} |
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\subsubsection{Do's and Don'ts} |
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\subsubsection{Reference Material} |
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