\hypertarget{namespacemom__generic__tracer}{}\section{mom\+\_\+generic\+\_\+tracer Module Reference} \label{namespacemom__generic__tracer}\index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsection{Detailed Description} Drives the generic version of tracers T\+O\+P\+AZ and C\+FC and other G\+F\+DL B\+GC components. \subsection*{Data Types} \begin{DoxyCompactItemize} \item type \mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}} \begin{DoxyCompactList}\small\item\em Control structure for generic tracers. \end{DoxyCompactList}\end{DoxyCompactItemize} \subsection*{Functions/\+Subroutines} \begin{DoxyCompactItemize} \item logical function, public \mbox{\hyperlink{namespacemom__generic__tracer_a5714b64160c8c96b30f1b641de5ff764}{register\+\_\+mom\+\_\+generic\+\_\+tracer}} (HI, GV, param\+\_\+file, CS, tr\+\_\+\+Reg, restart\+\_\+\+CS) \begin{DoxyCompactList}\small\item\em Initializes the generic tracer packages and adds their tracers to the list Adds the tracers in the list of generic tracers to the set of M\+OM tracers (i.\+e., M\+O\+M-\/register them) Register these tracers for restart. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_a5a103d836debaf2815b39a3ccb8ae850}{initialize\+\_\+mom\+\_\+generic\+\_\+tracer}} (restart, day, G, GV, US, h, param\+\_\+file, diag, O\+BC, CS, sponge\+\_\+\+C\+Sp, A\+L\+E\+\_\+sponge\+\_\+\+C\+Sp) \begin{DoxyCompactList}\small\item\em Initialize phase II\+: Initialize required variables for generic tracers There are some steps of initialization that cannot be done in register\+\_\+\+M\+O\+M\+\_\+generic\+\_\+tracer This is the place and time to do them\+: Set the grid mask and initial time for all generic tracers. Diag\+\_\+register them. Z\+\_\+diag\+\_\+register them. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_aa0ea1e7080c580a5598b5bede9ebd017}{mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics}} (h\+\_\+old, h\+\_\+new, ea, eb, fluxes, Hml, dt, G, GV, CS, tv, optics, evap\+\_\+\+C\+F\+L\+\_\+limit, minimum\+\_\+forcing\+\_\+depth) \begin{DoxyCompactList}\small\item\em Column physics for generic tracers. Get the coupler values for generic tracers that exchange with atmosphere Update generic tracer concentration fields from sources and sinks. Vertically diffuse generic tracer concentration fields. Update generic tracers from bottom and their bottom reservoir. \end{DoxyCompactList}\item integer function, public \mbox{\hyperlink{namespacemom__generic__tracer_a873bcaf0549f1840a111f031e549c5cd}{mom\+\_\+generic\+\_\+tracer\+\_\+stock}} (h, stocks, G, GV, CS, names, units, stock\+\_\+index) \begin{DoxyCompactList}\small\item\em This subroutine calculates mass-\/weighted integral on the PE either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of stocks it has calculated. If the stock\+\_\+index is present, only the stock corresponding to that coded index is returned. \end{DoxyCompactList}\item integer function, public \mbox{\hyperlink{namespacemom__generic__tracer_af5c635964fd7dfa7aea41fd17b3b3824}{mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max}} (ind\+\_\+start, got\+\_\+minmax, gmin, gmax, xgmin, ygmin, zgmin, xgmax, ygmax, zgmax, G, CS, names, units) \begin{DoxyCompactList}\small\item\em This subroutine find the global min and max of either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of tracers it has gone through. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_a4ba8950c78d0aef988f00cbf74a691d5}{mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state}} (sfc\+\_\+state, h, G, CS) \begin{DoxyCompactList}\small\item\em This subroutine calculates the surface state and sets coupler values for those generic tracers that have flux exchange with atmosphere. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_ac7ac1e5cc988131c4bcb1ea11e901a29}{mom\+\_\+generic\+\_\+flux\+\_\+init}} (verbosity) \item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_ac7e6d764d4df3376baeaf5ae4db7ba90}{mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate}} (flux\+\_\+tmp, weight) \item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_a3890163ae69f4c113abd4523c20510e4}{mom\+\_\+generic\+\_\+tracer\+\_\+get}} (name, member, array, CS) \begin{DoxyCompactList}\small\item\em Copy the requested tracer into an array. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacemom__generic__tracer_ada9424751eae6d320b5de26faa03a923}{end\+\_\+mom\+\_\+generic\+\_\+tracer}} (CS) \begin{DoxyCompactList}\small\item\em This subroutine deallocates the memory owned by this module. \end{DoxyCompactList}\end{DoxyCompactItemize} \subsection*{Variables} \begin{DoxyCompactItemize} \item \mbox{\Hypertarget{namespacemom__generic__tracer_adc781c54c3513e29b19d79bd8ef4cba4}\label{namespacemom__generic__tracer_adc781c54c3513e29b19d79bd8ef4cba4}} logical \mbox{\hyperlink{namespacemom__generic__tracer_adc781c54c3513e29b19d79bd8ef4cba4}{g\+\_\+registered}} = .false. \begin{DoxyCompactList}\small\item\em An state hidden in module data that is very much not allowed in M\+O\+M6. \end{DoxyCompactList}\end{DoxyCompactItemize} \subsection{Function/\+Subroutine Documentation} \mbox{\Hypertarget{namespacemom__generic__tracer_ada9424751eae6d320b5de26faa03a923}\label{namespacemom__generic__tracer_ada9424751eae6d320b5de26faa03a923}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!end\+\_\+mom\+\_\+generic\+\_\+tracer@{end\+\_\+mom\+\_\+generic\+\_\+tracer}} \index{end\+\_\+mom\+\_\+generic\+\_\+tracer@{end\+\_\+mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{end\+\_\+mom\+\_\+generic\+\_\+tracer()}{end\_mom\_generic\_tracer()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::end\+\_\+mom\+\_\+generic\+\_\+tracer (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS }\end{DoxyParamCaption})} This subroutine deallocates the memory owned by this module. \begin{DoxyParams}{Parameters} {\em cs} & Pointer to the control structure for this module. \\ \hline \end{DoxyParams} Definition at line 822 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 822 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 823 824 \textcolor{keyword}{call }generic\_tracer\_end() 825 826 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{then} 827 \textcolor{keyword}{deallocate}(cs) 828 \textcolor{keywordflow}{ endif} \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_a5a103d836debaf2815b39a3ccb8ae850}\label{namespacemom__generic__tracer_a5a103d836debaf2815b39a3ccb8ae850}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!initialize\+\_\+mom\+\_\+generic\+\_\+tracer@{initialize\+\_\+mom\+\_\+generic\+\_\+tracer}} \index{initialize\+\_\+mom\+\_\+generic\+\_\+tracer@{initialize\+\_\+mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{initialize\+\_\+mom\+\_\+generic\+\_\+tracer()}{initialize\_mom\_generic\_tracer()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::initialize\+\_\+mom\+\_\+generic\+\_\+tracer (\begin{DoxyParamCaption}\item[{logical, intent(in)}]{restart, }\item[{type(time\+\_\+type), intent(in), target}]{day, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(inout)}]{G, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{type(unit\+\_\+scale\+\_\+type), intent(in)}]{US, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h, }\item[{type(param\+\_\+file\+\_\+type), intent(in)}]{param\+\_\+file, }\item[{type(diag\+\_\+ctrl), intent(in), target}]{diag, }\item[{type(ocean\+\_\+obc\+\_\+type), pointer}]{O\+BC, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{type(sponge\+\_\+cs), pointer}]{sponge\+\_\+\+C\+Sp, }\item[{type(ale\+\_\+sponge\+\_\+cs), pointer}]{A\+L\+E\+\_\+sponge\+\_\+\+C\+Sp }\end{DoxyParamCaption})} Initialize phase II\+: Initialize required variables for generic tracers There are some steps of initialization that cannot be done in register\+\_\+\+M\+O\+M\+\_\+generic\+\_\+tracer This is the place and time to do them\+: Set the grid mask and initial time for all generic tracers. Diag\+\_\+register them. Z\+\_\+diag\+\_\+register them. This subroutine initializes the N\+TR tracer fields in tr(\+:,\+:,\+:,\+:) and it sets up the tracer output. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em restart} & .true. if the fields have already been read from a restart file.\\ \hline \mbox{\tt in} & {\em day} & Time of the start of the run.\\ \hline \mbox{\tt in,out} & {\em g} & The ocean\textquotesingle{}s grid structure\\ \hline \mbox{\tt in} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure\\ \hline \mbox{\tt in} & {\em us} & A dimensional unit scaling type\\ \hline \mbox{\tt in} & {\em h} & Layer thicknesses \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}\\ \hline \mbox{\tt in} & {\em param\+\_\+file} & A structure to parse for run-\/time parameters\\ \hline \mbox{\tt in} & {\em diag} & Regulates diagnostic output.\\ \hline & {\em obc} & This open boundary condition type specifies whether, where, and what open boundary conditions are used.\\ \hline & {\em cs} & Pointer to the control structure for this module.\\ \hline & {\em sponge\+\_\+csp} & Pointer to the control structure for the sponges.\\ \hline & {\em ale\+\_\+sponge\+\_\+csp} & Pointer to the control structure for the A\+LE sponges. \\ \hline \end{DoxyParams} Definition at line 232 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 232 \textcolor{keywordtype}{logical}, \textcolor{keywordtype}{intent(in)} :: restart\textcolor{comment}{ !< .true. if the fields have already been} 233 \textcolor{comment}{ !! read from a restart file.} 234 \textcolor{keywordtype}{type}(time\_type), \textcolor{keywordtype}{target}, \textcolor{keywordtype}{intent(in)} :: day\textcolor{comment}{ !< Time of the start of the run.} 235 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(inout)} :: G\textcolor{comment}{ !< The ocean's grid structure} 236 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure} 237 \textcolor{keywordtype}{type}(unit\_scale\_type), \textcolor{keywordtype}{intent(in)} :: US\textcolor{comment}{ !< A dimensional unit scaling type} 238 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \textcolor{keywordtype}{intent(in)} :: h\textcolor{comment}{ !< Layer thicknesses [H ~> m or kg m-2]} 239 \textcolor{keywordtype}{type}(param\_file\_type), \textcolor{keywordtype}{intent(in)} :: param\_file\textcolor{comment}{ !< A structure to parse for run-time parameters} 240 \textcolor{keywordtype}{type}(diag\_ctrl), \textcolor{keywordtype}{target}, \textcolor{keywordtype}{intent(in)} :: diag\textcolor{comment}{ !< Regulates diagnostic output.} 241 \textcolor{keywordtype}{type}(ocean\_OBC\_type), \textcolor{keywordtype}{pointer} :: OBC\textcolor{comment}{ !< This open boundary condition type specifies whether,} 242 \textcolor{comment}{ !! where, and what open boundary conditions are used.} 243 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 244 \textcolor{keywordtype}{type}(sponge\_CS), \textcolor{keywordtype}{pointer} :: sponge\_CSp\textcolor{comment}{ !< Pointer to the control structure for the sponges.} 245 \textcolor{keywordtype}{type}(ALE\_sponge\_CS), \textcolor{keywordtype}{pointer} :: ALE\_sponge\_CSp\textcolor{comment}{ !< Pointer to the control structure for the} 246 \textcolor{comment}{ !! ALE sponges.} 247 248 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'initialize\_MOM\_generic\_tracer'} 249 \textcolor{keywordtype}{logical} :: OK 250 \textcolor{keywordtype}{integer} :: i, j, k, isc, iec, jsc, jec, nk 251 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer,g\_tracer\_next 252 \textcolor{keywordtype}{character(len=fm\_string\_len)} :: g\_tracer\_name 253 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_field 254 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_ptr 255 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(G%isd:G%ied, G%jsd:G%jed,1:G%ke)} :: grid\_tmask 256 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{dimension(G%isd:G%ied, G%jsd:G%jed)} :: grid\_kmt 257 258 \textcolor{comment}{!! 2010/02/04 Add code to re-initialize Generic Tracers if needed during a model simulation} 259 \textcolor{comment}{!! By default, restart cpio should not contain a Generic Tracer IC file and step below will be skipped.} 260 \textcolor{comment}{!! Ideally, the generic tracer IC file should have the tracers on Z levels.} 261 262 isc = g%isc ; iec = g%iec ; jsc = g%jsc ; jec = g%jec ; nk = g%ke 263 264 cs%diag=>diag 265 \textcolor{comment}{!Get the tracer list} 266 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(cs%g\_tracer\_list)) \textcolor{keyword}{call }mom\_error(fatal, trim(sub\_name)//& 267 \textcolor{stringliteral}{": No tracer in the list."}) 268 \textcolor{comment}{!For each tracer name get its fields} 269 g\_tracer=>cs%g\_tracer\_list 270 271 \textcolor{keywordflow}{do} 272 \textcolor{keywordflow}{if} (index(cs%IC\_file, \textcolor{stringliteral}{'\_NULL\_'}) /= 0) \textcolor{keywordflow}{then} 273 \textcolor{keyword}{call }mom\_error(warning, \textcolor{stringliteral}{"The name of the IC\_file "}//trim(cs%IC\_file)//& 274 \textcolor{stringliteral}{" indicates no MOM initialization was asked for the generic tracers."}//& 275 \textcolor{stringliteral}{"Bypassing the MOM initialization of ALL generic tracers!"}) 276 \textcolor{keywordflow}{exit} 277 \textcolor{keywordflow}{ endif} 278 \textcolor{keyword}{call }g\_tracer\_get\_alias(g\_tracer,g\_tracer\_name) 279 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'field'},tr\_field) 280 tr\_ptr => tr\_field(:,:,:,1) 281 282 \textcolor{keywordflow}{if} (.not.restart .or. (cs%tracers\_may\_reinit .and. & 283 .not.query\_initialized(tr\_ptr, g\_tracer\_name, cs%restart\_CSp))) \textcolor{keywordflow}{then} 284 285 \textcolor{keywordflow}{if} (g\_tracer%requires\_src\_info ) \textcolor{keywordflow}{then} 286 \textcolor{keyword}{call }mom\_error(note,\textcolor{stringliteral}{"initialize\_MOM\_generic\_tracer: "}//& 287 \textcolor{stringliteral}{"initializing generic tracer "}//trim(g\_tracer\_name)//& 288 \textcolor{stringliteral}{" using MOM\_initialize\_tracer\_from\_Z "}) 289 290 \textcolor{keyword}{call }mom\_initialize\_tracer\_from\_z(h, tr\_ptr, g, gv, us, param\_file, & 291 src\_file = g\_tracer%src\_file, & 292 src\_var\_nam = g\_tracer%src\_var\_name, & 293 src\_var\_unit\_conversion = g\_tracer%src\_var\_unit\_conversion,& 294 src\_var\_record = g\_tracer%src\_var\_record, & 295 src\_var\_gridspec = g\_tracer%src\_var\_gridspec ) 296 297 \textcolor{comment}{!Check/apply the bounds for each g\_tracer} 298 \textcolor{keywordflow}{do} k=1,nk ; \textcolor{keywordflow}{do} j=jsc,jec ; \textcolor{keywordflow}{do} i=isc,iec 299 \textcolor{keywordflow}{if} (tr\_ptr(i,j,k) /= cs%tracer\_land\_val) \textcolor{keywordflow}{then} 300 \textcolor{keywordflow}{if} (tr\_ptr(i,j,k) < g\_tracer%src\_var\_valid\_min) tr\_ptr(i,j,k) = g\_tracer%src\_var\_valid\_min 301 \textcolor{comment}{!Jasmin does not want to apply the maximum for now} 302 \textcolor{comment}{!if (tr\_ptr(i,j,k) > g\_tracer%src\_var\_valid\_max) tr\_ptr(i,j,k) = g\_tracer%src\_var\_valid\_max} 303 \textcolor{keywordflow}{ endif} 304 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 305 306 \textcolor{comment}{!jgj: Reset CASED to 0 below K=1} 307 \textcolor{keywordflow}{if} ( (trim(g\_tracer\_name) == \textcolor{stringliteral}{'cased'}) .or. (trim(g\_tracer\_name) == \textcolor{stringliteral}{'ca13csed'}) ) \textcolor{keywordflow}{then} 308 \textcolor{keywordflow}{do} k=2,nk ; \textcolor{keywordflow}{do} j=jsc,jec ; \textcolor{keywordflow}{do} i=isc,iec 309 \textcolor{keywordflow}{if} (tr\_ptr(i,j,k) /= cs%tracer\_land\_val) \textcolor{keywordflow}{then} 310 tr\_ptr(i,j,k) = 0.0 311 \textcolor{keywordflow}{ endif} 312 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 313 \textcolor{keywordflow}{ endif} 314 \textcolor{keywordflow}{elseif}(.not. g\_tracer%requires\_restart) \textcolor{keywordflow}{then} 315 \textcolor{comment}{!Do nothing for this tracer, it is initialized by the tracer package} 316 \textcolor{keyword}{call }mom\_error(note,\textcolor{stringliteral}{"initialize\_MOM\_generic\_tracer: "}//& 317 \textcolor{stringliteral}{"skip initialization of generic tracer "}//trim(g\_tracer\_name)) 318 \textcolor{keywordflow}{else} \textcolor{comment}{!Do it old way if the tracer is not registered to start from a specific source file.} 319 \textcolor{comment}{!This path should be deprecated if all generic tracers are required to start from specified sources.} 320 \textcolor{keywordflow}{if} (len\_trim(cs%IC\_file) > 0) \textcolor{keywordflow}{then} 321 \textcolor{comment}{! Read the tracer concentrations from a netcdf file.} 322 \textcolor{keywordflow}{if} (.not.file\_exists(cs%IC\_file)) \textcolor{keyword}{call }mom\_error(fatal, & 323 \textcolor{stringliteral}{"initialize\_MOM\_Generic\_tracer: Unable to open "}//cs%IC\_file) 324 \textcolor{keywordflow}{if} (cs%Z\_IC\_file) \textcolor{keywordflow}{then} 325 ok = tracer\_z\_init(tr\_ptr, h, cs%IC\_file, g\_tracer\_name, g, us) 326 \textcolor{keywordflow}{if} (.not.ok) \textcolor{keywordflow}{then} 327 ok = tracer\_z\_init(tr\_ptr, h, cs%IC\_file, trim(g\_tracer\_name), g, us) 328 \textcolor{keywordflow}{if} (.not.ok) \textcolor{keyword}{call }mom\_error(fatal,\textcolor{stringliteral}{"initialize\_MOM\_Generic\_tracer: "}//& 329 \textcolor{stringliteral}{"Unable to read "}//trim(g\_tracer\_name)//\textcolor{stringliteral}{" from "}//& 330 trim(cs%IC\_file)//\textcolor{stringliteral}{"."}) 331 \textcolor{keywordflow}{ endif} 332 \textcolor{keyword}{call }mom\_error(note,\textcolor{stringliteral}{"initialize\_MOM\_generic\_tracer: "}//& 333 \textcolor{stringliteral}{"initialized generic tracer "}//trim(g\_tracer\_name)//& 334 \textcolor{stringliteral}{" using Generic Tracer File on Z: "}//cs%IC\_file) 335 \textcolor{keywordflow}{else} 336 \textcolor{comment}{! native grid} 337 \textcolor{keyword}{call }mom\_error(note,\textcolor{stringliteral}{"initialize\_MOM\_generic\_tracer: "}//& 338 \textcolor{stringliteral}{"Using Generic Tracer IC file on native grid "}//trim(cs%IC\_file)//& 339 \textcolor{stringliteral}{" for tracer "}//trim(g\_tracer\_name)) 340 \textcolor{keyword}{call }mom\_read\_data(cs%IC\_file, trim(g\_tracer\_name), tr\_ptr, g%Domain) 341 \textcolor{keywordflow}{ endif} 342 \textcolor{keywordflow}{else} 343 \textcolor{keyword}{call }mom\_error(fatal,\textcolor{stringliteral}{"initialize\_MOM\_generic\_tracer: "}//& 344 \textcolor{stringliteral}{"check Generic Tracer IC filename "}//trim(cs%IC\_file)//& 345 \textcolor{stringliteral}{" for tracer "}//trim(g\_tracer\_name)) 346 \textcolor{keywordflow}{ endif} 347 348 \textcolor{keywordflow}{ endif} 349 \textcolor{keywordflow}{ endif} 350 351 \textcolor{comment}{!traverse the linked list till hit NULL} 352 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 353 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 354 g\_tracer=>g\_tracer\_next 355 \textcolor{keywordflow}{ enddo} 356 \textcolor{comment}{!! end section to re-initialize generic tracers} 357 358 359 \textcolor{comment}{!Now we can reset the grid mask, axes and time to their true values} 360 \textcolor{comment}{!Note that grid\_tmask must be set correctly on the data domain boundary} 361 \textcolor{comment}{!so that coast mask can be deduced from it.} 362 grid\_tmask(:,:,:) = 0.0 363 grid\_kmt(:,:) = 0 364 \textcolor{keywordflow}{do} j = g%jsd, g%jed ; \textcolor{keywordflow}{do} i = g%isd, g%ied 365 \textcolor{keywordflow}{if} (g%mask2dT(i,j) > 0) \textcolor{keywordflow}{then} 366 grid\_tmask(i,j,:) = 1.0 367 grid\_kmt(i,j) = g%ke \textcolor{comment}{! Tell the code that a layer thicker than 1m is the bottom layer.} 368 \textcolor{keywordflow}{ endif} 369 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 370 \textcolor{keyword}{call }g\_tracer\_set\_common(g%isc,g%iec,g%jsc,g%jec,g%isd,g%ied,g%jsd,g%jed,& 371 gv%ke,1,cs%diag%axesTL%handles,grid\_tmask,grid\_kmt,day) 372 373 \textcolor{comment}{! Register generic tracer modules diagnostics} 374 375 \textcolor{preprocessor}{#ifdef \_USE\_MOM6\_DIAG} 376 \textcolor{preprocessor}{} \textcolor{keyword}{call }g\_tracer\_set\_csdiag(cs%diag) 377 \textcolor{preprocessor}{#endif} 378 \textcolor{preprocessor}{} \textcolor{keyword}{call }generic\_tracer\_register\_diag() 379 \textcolor{preprocessor}{#ifdef \_USE\_MOM6\_DIAG} 380 \textcolor{preprocessor}{} \textcolor{keyword}{call }g\_tracer\_set\_csdiag(cs%diag) 381 \textcolor{preprocessor}{#endif} 382 \textcolor{preprocessor}{} 383 cs%H\_to\_m = gv%H\_to\_m 384 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_ac7ac1e5cc988131c4bcb1ea11e901a29}\label{namespacemom__generic__tracer_ac7ac1e5cc988131c4bcb1ea11e901a29}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+flux\+\_\+init@{mom\+\_\+generic\+\_\+flux\+\_\+init}} \index{mom\+\_\+generic\+\_\+flux\+\_\+init@{mom\+\_\+generic\+\_\+flux\+\_\+init}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+flux\+\_\+init()}{mom\_generic\_flux\_init()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+flux\+\_\+init (\begin{DoxyParamCaption}\item[{integer, intent(in), optional}]{verbosity }\end{DoxyParamCaption})} \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em verbosity} & A 0-\/9 integer indicating a level of verbosity. \\ \hline \end{DoxyParams} Definition at line 763 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 763 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: verbosity\textcolor{comment}{ !< A 0-9 integer indicating a level of verbosity.} 764 765 \textcolor{keywordtype}{integer} :: ind 766 \textcolor{keywordtype}{character(len=fm\_string\_len)} :: g\_tracer\_name,longname, package,units,old\_package,file\_in,file\_out 767 \textcolor{keywordtype}{real} :: const\_init\_value 768 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_flux\_init'} 769 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer\_list,g\_tracer,g\_tracer\_next 770 771 \textcolor{keywordflow}{if} (.not. g\_registered) \textcolor{keywordflow}{then} 772 \textcolor{keyword}{call }generic\_tracer\_register() 773 g\_registered = .true. 774 \textcolor{keywordflow}{ endif} 775 776 \textcolor{keyword}{call }generic\_tracer\_get\_list(g\_tracer\_list) 777 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_list)) \textcolor{keywordflow}{then} 778 \textcolor{keyword}{call }mom\_error(warning, trim(sub\_name)// \textcolor{stringliteral}{": No generic tracer in the list."}) 779 \textcolor{keywordflow}{return} 780 \textcolor{keywordflow}{ endif} 781 782 g\_tracer=>g\_tracer\_list 783 \textcolor{keywordflow}{do} 784 785 \textcolor{keyword}{call }g\_tracer\_flux\_init(g\_tracer) \textcolor{comment}{!, verbosity=verbosity) !### Add this after ocean shared is updated.} 786 787 \textcolor{comment}{! traverse the linked list till hit NULL} 788 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 789 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 790 g\_tracer=>g\_tracer\_next 791 792 \textcolor{keywordflow}{ enddo} 793 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_aa0ea1e7080c580a5598b5bede9ebd017}\label{namespacemom__generic__tracer_aa0ea1e7080c580a5598b5bede9ebd017}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics@{mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics@{mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics()}{mom\_generic\_tracer\_column\_physics()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+column\+\_\+physics (\begin{DoxyParamCaption}\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h\+\_\+old, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h\+\_\+new, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{ea, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{eb, }\item[{type(forcing), intent(in)}]{fluxes, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed), intent(in)}]{Hml, }\item[{real, intent(in)}]{dt, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{type(thermo\+\_\+var\+\_\+ptrs), intent(in)}]{tv, }\item[{type(optics\+\_\+type), intent(in)}]{optics, }\item[{real, intent(in), optional}]{evap\+\_\+\+C\+F\+L\+\_\+limit, }\item[{real, intent(in), optional}]{minimum\+\_\+forcing\+\_\+depth }\end{DoxyParamCaption})} Column physics for generic tracers. Get the coupler values for generic tracers that exchange with atmosphere Update generic tracer concentration fields from sources and sinks. Vertically diffuse generic tracer concentration fields. Update generic tracers from bottom and their bottom reservoir. This subroutine applies diapycnal diffusion and any other column tracer physics or chemistry to the tracers from this file. C\+F\+Cs are relatively simple, as they are passive tracers. with only a surface flux as a source. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em g} & The ocean\textquotesingle{}s grid structure\\ \hline \mbox{\tt in} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure\\ \hline \mbox{\tt in} & {\em h\+\_\+old} & Layer thickness before entrainment \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}.\\ \hline \mbox{\tt in} & {\em h\+\_\+new} & Layer thickness after entrainment \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}.\\ \hline \mbox{\tt in} & {\em ea} & The amount of fluid entrained from the layer\\ \hline \mbox{\tt in} & {\em eb} & The amount of fluid entrained from the layer\\ \hline \mbox{\tt in} & {\em fluxes} & A structure containing pointers to thermodynamic and tracer forcing fields.\\ \hline \mbox{\tt in} & {\em hml} & Mixed layer depth \mbox{[}Z $\sim$$>$ m\mbox{]}\\ \hline \mbox{\tt in} & {\em dt} & The amount of time covered by this call \mbox{[}s\mbox{]}\\ \hline & {\em cs} & Pointer to the control structure for this module.\\ \hline \mbox{\tt in} & {\em tv} & A structure pointing to various thermodynamic variables\\ \hline \mbox{\tt in} & {\em optics} & The structure containing optical properties.\\ \hline \mbox{\tt in} & {\em evap\+\_\+cfl\+\_\+limit} & Limits how much water can be fluxed out of the top layer Stored previously in diabatic CS.\\ \hline \mbox{\tt in} & {\em minimum\+\_\+forcing\+\_\+depth} & The smallest depth over which fluxes can be applied \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]} \\ \hline \end{DoxyParams} Definition at line 399 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 399 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< The ocean's grid structure} 400 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure} 401 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, & 402 \textcolor{keywordtype}{intent(in)} :: h\_old\textcolor{comment}{ !< Layer thickness before entrainment [H ~> m or kg m-2].} 403 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, & 404 \textcolor{keywordtype}{intent(in)} :: h\_new\textcolor{comment}{ !< Layer thickness after entrainment [H ~> m or kg m-2].} 405 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, & 406 \textcolor{keywordtype}{intent(in)} :: ea\textcolor{comment}{ !< The amount of fluid entrained from the layer} 407 \textcolor{comment}{ !! above during this call [H ~> m or kg m-2].} 408 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, & 409 \textcolor{keywordtype}{intent(in)} :: eb\textcolor{comment}{ !< The amount of fluid entrained from the layer} 410 \textcolor{comment}{ !! below during this call [H ~> m or kg m-2].} 411 \textcolor{keywordtype}{type}(forcing), \textcolor{keywordtype}{intent(in)} :: fluxes\textcolor{comment}{ !< A structure containing pointers to thermodynamic} 412 \textcolor{comment}{ !! and tracer forcing fields.} 413 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G))}, \textcolor{keywordtype}{intent(in)} :: Hml\textcolor{comment}{ !< Mixed layer depth [Z ~> m]} 414 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{intent(in)} :: dt\textcolor{comment}{ !< The amount of time covered by this call [s]} 415 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 416 \textcolor{keywordtype}{type}(thermo\_var\_ptrs), \textcolor{keywordtype}{intent(in)} :: tv\textcolor{comment}{ !< A structure pointing to various thermodynamic variables} 417 \textcolor{keywordtype}{type}(optics\_type), \textcolor{keywordtype}{intent(in)} :: optics\textcolor{comment}{ !< The structure containing optical properties.} 418 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: evap\_CFL\_limit\textcolor{comment}{ !< Limits how much water can be fluxed out of} 419 \textcolor{comment}{ !! the top layer Stored previously in diabatic CS.} 420 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: minimum\_forcing\_depth\textcolor{comment}{ !< The smallest depth over which fluxes} 421 \textcolor{comment}{ !! can be applied [H ~> m or kg m-2]} 422 \textcolor{comment}{! Stored previously in diabatic CS.} 423 \textcolor{comment}{! The arguments to this subroutine are redundant in that} 424 \textcolor{comment}{! h\_new(k) = h\_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)} 425 426 \textcolor{comment}{! Local variables} 427 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_tracer\_column\_physics'} 428 429 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer, g\_tracer\_next 430 \textcolor{keywordtype}{character(len=fm\_string\_len)} :: g\_tracer\_name 431 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:)}, \textcolor{keywordtype}{pointer} :: stf\_array,trunoff\_array,runoff\_tracer\_flux\_array 432 433 \textcolor{keywordtype}{real} :: surface\_field(SZI\_(G),SZJ\_(G)) 434 \textcolor{keywordtype}{real} :: dz\_ml(SZI\_(G),SZJ\_(G)) \textcolor{comment}{! The mixed layer depth in the MKS units used for generic tracers [m]} 435 \textcolor{keywordtype}{real} :: sosga 436 437 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(G%isd:G%ied,G%jsd:G%jed,G%ke)} :: rho\_dzt, dzt 438 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))} :: h\_work 439 \textcolor{keywordtype}{integer} :: i, j, k, isc, iec, jsc, jec, nk 440 441 isc = g%isc ; iec = g%iec ; jsc = g%jsc ; jec = g%jec ; nk = g%ke 442 443 \textcolor{comment}{!Get the tracer list} 444 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(cs%g\_tracer\_list)) \textcolor{keyword}{call }mom\_error(fatal,& 445 trim(sub\_name)//\textcolor{stringliteral}{": No tracer in the list."}) 446 447 \textcolor{preprocessor}{#ifdef \_USE\_MOM6\_DIAG} 448 \textcolor{preprocessor}{} \textcolor{keyword}{call }g\_tracer\_set\_csdiag(cs%diag) 449 \textcolor{preprocessor}{#endif} 450 \textcolor{preprocessor}{} 451 \textcolor{comment}{!} 452 \textcolor{comment}{!Extract the tracer surface fields from coupler and update tracer fields from sources} 453 \textcolor{comment}{!} 454 \textcolor{comment}{!call generic\_tracer\_coupler\_get(fluxes%tr\_fluxes)} 455 \textcolor{comment}{!Niki: This is moved out to ocean\_model\_MOM.F90 because if dt\_therm>dt\_cpld we need to average} 456 \textcolor{comment}{! the fluxes without coming into this subroutine.} 457 \textcolor{comment}{! MOM5 has to modified to conform.} 458 459 \textcolor{comment}{!} 460 \textcolor{comment}{!Add contribution of river to surface flux} 461 \textcolor{comment}{!} 462 g\_tracer=>cs%g\_tracer\_list 463 \textcolor{keywordflow}{do} 464 \textcolor{keywordflow}{if} (\_allocated(g\_tracer%trunoff)) \textcolor{keywordflow}{then} 465 \textcolor{keyword}{call }g\_tracer\_get\_alias(g\_tracer,g\_tracer\_name) 466 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'stf'}, stf\_array) 467 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'trunoff'},trunoff\_array) 468 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'runoff\_tracer\_flux'},runoff\_tracer\_flux\_array) 469 \textcolor{comment}{!nnz: Why is fluxes%river = 0?} 470 runoff\_tracer\_flux\_array(:,:) = trunoff\_array(:,:) * & 471 g%US%RZ\_T\_to\_kg\_m2s*fluxes%lrunoff(:,:) 472 stf\_array = stf\_array + runoff\_tracer\_flux\_array 473 \textcolor{keywordflow}{ endif} 474 475 \textcolor{comment}{!traverse the linked list till hit NULL} 476 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 477 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 478 g\_tracer=>g\_tracer\_next 479 480 \textcolor{keywordflow}{ enddo} 481 482 \textcolor{comment}{!} 483 \textcolor{comment}{!Prepare input arrays for source update} 484 \textcolor{comment}{!} 485 486 rho\_dzt(:,:,:) = gv%H\_to\_kg\_m2 * gv%Angstrom\_H 487 \textcolor{keywordflow}{do} k = 1, nk ; \textcolor{keywordflow}{do} j = jsc, jec ; \textcolor{keywordflow}{do} i = isc, iec \textcolor{comment}{!\{} 488 rho\_dzt(i,j,k) = gv%H\_to\_kg\_m2 * h\_old(i,j,k) 489 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} \textcolor{comment}{!\}} 490 491 dzt(:,:,:) = 1.0 492 \textcolor{keywordflow}{do} k = 1, nk ; \textcolor{keywordflow}{do} j = jsc, jec ; \textcolor{keywordflow}{do} i = isc, iec \textcolor{comment}{!\{} 493 dzt(i,j,k) = gv%H\_to\_m * h\_old(i,j,k) 494 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} \textcolor{comment}{!\}} 495 dz\_ml(:,:) = 0.0 496 \textcolor{keywordflow}{do} j=jsc,jec ; \textcolor{keywordflow}{do} i=isc,iec 497 surface\_field(i,j) = tv%S(i,j,1) 498 dz\_ml(i,j) = g%US%Z\_to\_m * hml(i,j) 499 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 500 sosga = global\_area\_mean(surface\_field, g) 501 502 \textcolor{comment}{!} 503 \textcolor{comment}{!Calculate tendencies (i.e., field changes at dt) from the sources / sinks} 504 \textcolor{comment}{!} 505 \textcolor{keywordflow}{if} ((g%US%L\_to\_m == 1.0) .and. (g%US%RZ\_to\_kg\_m2 == 1.0) .and. (g%US%s\_to\_T == 1.0)) \textcolor{keywordflow}{then} 506 \textcolor{comment}{! Avoid unnecessary copies when no unit conversion is needed.} 507 \textcolor{keyword}{call }generic\_tracer\_source(tv%T, tv%S, rho\_dzt, dzt, dz\_ml, g%isd, g%jsd, 1, dt, & 508 g%areaT, get\_diag\_time\_end(cs%diag), & 509 optics%nbands, optics%max\_wavelength\_band, optics%sw\_pen\_band, optics%opacity\_band, & 510 internal\_heat=tv%internal\_heat, frunoff=fluxes%frunoff, sosga=sosga) 511 \textcolor{keywordflow}{else} 512 \textcolor{keyword}{call }generic\_tracer\_source(tv%T, tv%S, rho\_dzt, dzt, dz\_ml, g%isd, g%jsd, 1, dt, & 513 g%US%L\_to\_m**2*g%areaT(:,:), get\_diag\_time\_end(cs%diag), & 514 optics%nbands, optics%max\_wavelength\_band, optics%sw\_pen\_band, optics%opacity\_band, & 515 internal\_heat=g%US%RZ\_to\_kg\_m2*tv%internal\_heat(:,:), & 516 frunoff=g%US%RZ\_T\_to\_kg\_m2s*fluxes%frunoff(:,:), sosga=sosga) 517 \textcolor{keywordflow}{ endif} 518 519 \textcolor{comment}{! This uses applyTracerBoundaryFluxesInOut to handle the change in tracer due to freshwater fluxes} 520 \textcolor{comment}{! usually in ALE mode} 521 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(evap\_cfl\_limit) .and. \textcolor{keyword}{present}(minimum\_forcing\_depth)) \textcolor{keywordflow}{then} 522 g\_tracer=>cs%g\_tracer\_list 523 \textcolor{keywordflow}{do} 524 \textcolor{keywordflow}{if} (g\_tracer\_is\_prog(g\_tracer)) \textcolor{keywordflow}{then} 525 \textcolor{keywordflow}{do} k=1,nk ;\textcolor{keywordflow}{do} j=jsc,jec ; \textcolor{keywordflow}{do} i=isc,iec 526 h\_work(i,j,k) = h\_old(i,j,k) 527 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 528 \textcolor{keyword}{call }applytracerboundaryfluxesinout(g, gv, g\_tracer%field(:,:,:,1), g%US%s\_to\_T*dt, & 529 fluxes, h\_work, evap\_cfl\_limit, minimum\_forcing\_depth) 530 \textcolor{keywordflow}{ endif} 531 532 \textcolor{comment}{!traverse the linked list till hit NULL} 533 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 534 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 535 g\_tracer=>g\_tracer\_next 536 \textcolor{keywordflow}{ enddo} 537 \textcolor{keywordflow}{ endif} 538 539 \textcolor{comment}{!} 540 \textcolor{comment}{!Update Tr(n)%field from explicit vertical diffusion} 541 \textcolor{comment}{!} 542 \textcolor{comment}{! Use a tridiagonal solver to determine the concentrations after the} 543 \textcolor{comment}{! surface source is applied and diapycnal advection and diffusion occurs.} 544 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(evap\_cfl\_limit) .and. \textcolor{keyword}{present}(minimum\_forcing\_depth)) \textcolor{keywordflow}{then} 545 \textcolor{comment}{! Last arg is tau which is always 1 for MOM6} 546 \textcolor{keyword}{call }generic\_tracer\_vertdiff\_g(h\_work, ea, eb, dt, gv%kg\_m2\_to\_H, gv%m\_to\_H, 1) 547 \textcolor{keywordflow}{else} 548 \textcolor{comment}{! Last arg is tau which is always 1 for MOM6} 549 \textcolor{keyword}{call }generic\_tracer\_vertdiff\_g(h\_old, ea, eb, dt, gv%kg\_m2\_to\_H, gv%m\_to\_H, 1) 550 \textcolor{keywordflow}{ endif} 551 552 \textcolor{comment}{! Update bottom fields after vertical processes} 553 554 \textcolor{comment}{! Second arg is tau which is always 1 for MOM6} 555 \textcolor{keyword}{call }generic\_tracer\_update\_from\_bottom(dt, 1, get\_diag\_time\_end(cs%diag)) 556 557 \textcolor{comment}{!Output diagnostics via diag\_manager for all generic tracers and their fluxes} 558 \textcolor{keyword}{call }g\_tracer\_send\_diag(cs%g\_tracer\_list, get\_diag\_time\_end(cs%diag), tau=1) 559 \textcolor{preprocessor}{#ifdef \_USE\_MOM6\_DIAG} 560 \textcolor{preprocessor}{} \textcolor{keyword}{call }g\_tracer\_set\_csdiag(cs%diag) 561 \textcolor{preprocessor}{#endif} 562 \textcolor{preprocessor}{} \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_ac7e6d764d4df3376baeaf5ae4db7ba90}\label{namespacemom__generic__tracer_ac7e6d764d4df3376baeaf5ae4db7ba90}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate@{mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate@{mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate()}{mom\_generic\_tracer\_fluxes\_accumulate()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+fluxes\+\_\+accumulate (\begin{DoxyParamCaption}\item[{type(forcing), intent(in)}]{flux\+\_\+tmp, }\item[{real, intent(in)}]{weight }\end{DoxyParamCaption})} \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em flux\+\_\+tmp} & A structure containing pointers to thermodynamic and tracer forcing fields.\\ \hline \mbox{\tt in} & {\em weight} & A weight for accumulating this flux \\ \hline \end{DoxyParams} Definition at line 797 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 797 \textcolor{keywordtype}{type}(forcing), \textcolor{keywordtype}{intent(in)} :: flux\_tmp\textcolor{comment}{ !< A structure containing pointers to} 798 \textcolor{comment}{ !! thermodynamic and tracer forcing fields.} 799 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{intent(in)} :: weight\textcolor{comment}{ !< A weight for accumulating this flux} 800 801 \textcolor{keyword}{call }generic\_tracer\_coupler\_accumulate(flux\_tmp%tr\_fluxes, weight) 802 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_a3890163ae69f4c113abd4523c20510e4}\label{namespacemom__generic__tracer_a3890163ae69f4c113abd4523c20510e4}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+get@{mom\+\_\+generic\+\_\+tracer\+\_\+get}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+get@{mom\+\_\+generic\+\_\+tracer\+\_\+get}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+get()}{mom\_generic\_tracer\_get()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+get (\begin{DoxyParamCaption}\item[{character(len=$\ast$), intent(in)}]{name, }\item[{character(len=$\ast$), intent(in)}]{member, }\item[{real, dimension(\+:,\+:,\+:), intent(out)}]{array, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS }\end{DoxyParamCaption})} Copy the requested tracer into an array. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em name} & Name of requested tracer.\\ \hline \mbox{\tt in} & {\em member} & The tracer element to return.\\ \hline \mbox{\tt out} & {\em array} & Array filled by this routine.\\ \hline & {\em cs} & Pointer to the control structure for this module. \\ \hline \end{DoxyParams} Definition at line 807 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 807 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{intent(in)} :: name\textcolor{comment}{ !< Name of requested tracer.} 808 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{intent(in)} :: member\textcolor{comment}{ !< The tracer element to return.} 809 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{intent(out)} :: array\textcolor{comment}{ !< Array filled by this routine.} 810 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 811 812 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{pointer} :: array\_ptr 813 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_tracer\_get'} 814 815 \textcolor{keyword}{call }g\_tracer\_get\_pointer(cs%g\_tracer\_list,name,member,array\_ptr) 816 array(:,:,:) = array\_ptr(:,:,:) 817 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_af5c635964fd7dfa7aea41fd17b3b3824}\label{namespacemom__generic__tracer_af5c635964fd7dfa7aea41fd17b3b3824}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max@{mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max@{mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max()}{mom\_generic\_tracer\_min\_max()}} {\footnotesize\ttfamily integer function, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+min\+\_\+max (\begin{DoxyParamCaption}\item[{integer, intent(in)}]{ind\+\_\+start, }\item[{logical, dimension(\+:), intent(out)}]{got\+\_\+minmax, }\item[{real, dimension(\+:), intent(out)}]{gmin, }\item[{real, dimension(\+:), intent(out)}]{gmax, }\item[{real, dimension(\+:), intent(out)}]{xgmin, }\item[{real, dimension(\+:), intent(out)}]{ygmin, }\item[{real, dimension(\+:), intent(out)}]{zgmin, }\item[{real, dimension(\+:), intent(out)}]{xgmax, }\item[{real, dimension(\+:), intent(out)}]{ygmax, }\item[{real, dimension(\+:), intent(out)}]{zgmax, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{character(len=$\ast$), dimension(\+:), intent(out)}]{names, }\item[{character(len=$\ast$), dimension(\+:), intent(out)}]{units }\end{DoxyParamCaption})} This subroutine find the global min and max of either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of tracers it has gone through. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em ind\+\_\+start} & The index of the tracer to start with\\ \hline \mbox{\tt out} & {\em got\+\_\+minmax} & Indicates whether the global min and max are found for each tracer\\ \hline \mbox{\tt out} & {\em gmin} & Global minimum of each tracer, in kg times concentration units.\\ \hline \mbox{\tt out} & {\em gmax} & Global maximum of each tracer, in kg times concentration units.\\ \hline \mbox{\tt out} & {\em xgmin} & The x-\/position of the global minimum\\ \hline \mbox{\tt out} & {\em ygmin} & The y-\/position of the global minimum\\ \hline \mbox{\tt out} & {\em zgmin} & The z-\/position of the global minimum\\ \hline \mbox{\tt out} & {\em xgmax} & The x-\/position of the global maximum\\ \hline \mbox{\tt out} & {\em ygmax} & The y-\/position of the global maximum\\ \hline \mbox{\tt out} & {\em zgmax} & The z-\/position of the global maximum\\ \hline \mbox{\tt in} & {\em g} & The ocean\textquotesingle{}s grid structure\\ \hline & {\em cs} & Pointer to the control structure for this module.\\ \hline \mbox{\tt out} & {\em names} & The names of the stocks calculated.\\ \hline \mbox{\tt out} & {\em units} & The units of the stocks calculated.\\ \hline \end{DoxyParams} \begin{DoxyReturn}{Returns} Return value, the number of tracers done here. \end{DoxyReturn} Definition at line 636 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 636 \textcolor{keywordtype}{use }mpp\_utilities\_mod, \textcolor{keywordtype}{only}: mpp\_array\_global\_min\_max 637 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{intent(in)} :: ind\_start\textcolor{comment}{ !< The index of the tracer to start with} 638 \textcolor{keywordtype}{logical}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: got\_minmax\textcolor{comment}{ !< Indicates whether the global min and} 639 \textcolor{comment}{ !! max are found for each tracer} 640 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: gmin\textcolor{comment}{ !< Global minimum of each tracer, in kg} 641 \textcolor{comment}{ !! times concentration units.} 642 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: gmax\textcolor{comment}{ !< Global maximum of each tracer, in kg} 643 \textcolor{comment}{ !! times concentration units.} 644 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: xgmin\textcolor{comment}{ !< The x-position of the global minimum} 645 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: ygmin\textcolor{comment}{ !< The y-position of the global minimum} 646 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: zgmin\textcolor{comment}{ !< The z-position of the global minimum} 647 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: xgmax\textcolor{comment}{ !< The x-position of the global maximum} 648 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: ygmax\textcolor{comment}{ !< The y-position of the global maximum} 649 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: zgmax\textcolor{comment}{ !< The z-position of the global maximum} 650 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< The ocean's grid structure} 651 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 652 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: names\textcolor{comment}{ !< The names of the stocks calculated.} 653 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: units\textcolor{comment}{ !< The units of the stocks calculated.} 654 \textcolor{keywordtype}{integer} :: MOM\_generic\_tracer\_min\_max\textcolor{comment}{ !< Return value, the} 655 \textcolor{comment}{ !! number of tracers done here.} 656 657 \textcolor{comment}{! Local variables} 658 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer, g\_tracer\_next 659 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_field 660 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_ptr 661 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_tracer\_min\_max'} 662 663 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)},\textcolor{keywordtype}{pointer} :: grid\_tmask 664 \textcolor{keywordtype}{integer} :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau 665 666 \textcolor{keywordtype}{integer} :: i, j, k, is, ie, js, je, nz, m 667 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{allocatable}, \textcolor{keywordtype}{dimension(:)} :: geo\_z 668 669 is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec ; nz = g%ke 670 671 mom\_generic\_tracer\_min\_max = 0 672 \textcolor{keywordflow}{if} (.not.\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return} 673 674 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(cs%g\_tracer\_list)) \textcolor{keywordflow}{return} \textcolor{comment}{! No stocks.} 675 676 677 \textcolor{keyword}{call }g\_tracer\_get\_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,grid\_tmask=grid\_tmask) 678 679 \textcolor{comment}{! Because the use of a simple z-coordinate can not be assumed, simply} 680 \textcolor{comment}{! use the layer index as the vertical label.} 681 \textcolor{keyword}{allocate}(geo\_z(nk)) 682 \textcolor{keywordflow}{do} k=1,nk ; geo\_z(k) = \textcolor{keywordtype}{real(k)} ; enddo 683 684 m=ind\_start ; g\_tracer=>cs%g\_tracer\_list 685 \textcolor{keywordflow}{do} 686 \textcolor{keyword}{call }g\_tracer\_get\_alias(g\_tracer,names(m)) 687 \textcolor{keyword}{call }g\_tracer\_get\_values(g\_tracer,names(m),\textcolor{stringliteral}{'units'},units(m)) 688 units(m) = trim(units(m))//\textcolor{stringliteral}{" kg"} 689 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,names(m),\textcolor{stringliteral}{'field'},tr\_field) 690 691 gmin(m) = -1.0 692 gmax(m) = -1.0 693 694 tr\_ptr => tr\_field(:,:,:,1) 695 696 \textcolor{keyword}{call }mpp\_array\_global\_min\_max(tr\_ptr, grid\_tmask,isd,jsd,isc,iec,jsc,jec,nk , gmin(m), gmax(m), & 697 g%geoLonT,g%geoLatT,geo\_z,xgmin(m), ygmin(m), zgmin(m), & 698 xgmax(m), ygmax(m), zgmax(m)) 699 700 got\_minmax(m) = .true. 701 702 \textcolor{comment}{!traverse the linked list till hit NULL} 703 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 704 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 705 g\_tracer=>g\_tracer\_next 706 m = m+1 707 \textcolor{keywordflow}{ enddo} 708 709 mom\_generic\_tracer\_min\_max = m 710 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_a873bcaf0549f1840a111f031e549c5cd}\label{namespacemom__generic__tracer_a873bcaf0549f1840a111f031e549c5cd}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+stock@{mom\+\_\+generic\+\_\+tracer\+\_\+stock}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+stock@{mom\+\_\+generic\+\_\+tracer\+\_\+stock}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+stock()}{mom\_generic\_tracer\_stock()}} {\footnotesize\ttfamily integer function, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+stock (\begin{DoxyParamCaption}\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h, }\item[{real, dimension(\+:), intent(out)}]{stocks, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{character(len=$\ast$), dimension(\+:), intent(out)}]{names, }\item[{character(len=$\ast$), dimension(\+:), intent(out)}]{units, }\item[{integer, intent(in), optional}]{stock\+\_\+index }\end{DoxyParamCaption})} This subroutine calculates mass-\/weighted integral on the PE either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of stocks it has calculated. If the stock\+\_\+index is present, only the stock corresponding to that coded index is returned. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em g} & The ocean\textquotesingle{}s grid structure\\ \hline \mbox{\tt in} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure\\ \hline \mbox{\tt in} & {\em h} & Layer thicknesses \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}\\ \hline \mbox{\tt out} & {\em stocks} & The mass-\/weighted integrated amount of each tracer, in kg times concentration units \mbox{[}kg conc\mbox{]}.\\ \hline & {\em cs} & Pointer to the control structure for this module.\\ \hline \mbox{\tt out} & {\em names} & The names of the stocks calculated.\\ \hline \mbox{\tt out} & {\em units} & The units of the stocks calculated.\\ \hline \mbox{\tt in} & {\em stock\+\_\+index} & The coded index of a specific stock being sought.\\ \hline \end{DoxyParams} \begin{DoxyReturn}{Returns} Return value, the number of stocks calculated here. \end{DoxyReturn} Definition at line 571 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 571 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< The ocean's grid structure} 572 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure} 573 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \textcolor{keywordtype}{intent(in)} :: h\textcolor{comment}{ !< Layer thicknesses [H ~> m or kg m-2]} 574 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: stocks\textcolor{comment}{ !< The mass-weighted integrated amount of each} 575 \textcolor{comment}{ !! tracer, in kg times concentration units [kg conc].} 576 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 577 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: names\textcolor{comment}{ !< The names of the stocks calculated.} 578 \textcolor{keywordtype}{character(len=*)}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(out)} :: units\textcolor{comment}{ !< The units of the stocks calculated.} 579 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: stock\_index\textcolor{comment}{ !< The coded index of a specific stock} 580 \textcolor{comment}{ !! being sought.} 581 \textcolor{keywordtype}{integer} :: MOM\_generic\_tracer\_stock\textcolor{comment}{ !< Return value, the} 582 \textcolor{comment}{ !! number of stocks calculated here.} 583 584 \textcolor{comment}{! Local variables} 585 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer, g\_tracer\_next 586 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_field 587 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_ptr 588 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_tracer\_stock'} 589 590 \textcolor{keywordtype}{integer} :: i, j, k, is, ie, js, je, nz, m 591 is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec ; nz = g%ke 592 593 mom\_generic\_tracer\_stock = 0 594 \textcolor{keywordflow}{if} (.not.\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return} 595 596 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(stock\_index)) \textcolor{keywordflow}{then} ; \textcolor{keywordflow}{if} (stock\_index > 0) \textcolor{keywordflow}{then} 597 \textcolor{comment}{! Check whether this stock is available from this routine.} 598 599 \textcolor{comment}{! No stocks from this routine are being checked yet. Return 0.} 600 \textcolor{keywordflow}{return} 601 \textcolor{keywordflow}{ endif} ;\textcolor{keywordflow}{ endif} 602 603 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(cs%g\_tracer\_list)) \textcolor{keywordflow}{return} \textcolor{comment}{! No stocks.} 604 605 m=1 ; g\_tracer=>cs%g\_tracer\_list 606 \textcolor{keywordflow}{do} 607 \textcolor{keyword}{call }g\_tracer\_get\_alias(g\_tracer,names(m)) 608 \textcolor{keyword}{call }g\_tracer\_get\_values(g\_tracer,names(m),\textcolor{stringliteral}{'units'},units(m)) 609 units(m) = trim(units(m))//\textcolor{stringliteral}{" kg"} 610 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,names(m),\textcolor{stringliteral}{'field'},tr\_field) 611 612 stocks(m) = 0.0 613 tr\_ptr => tr\_field(:,:,:,1) 614 \textcolor{keywordflow}{do} k=1,nz ; \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie 615 stocks(m) = stocks(m) + tr\_ptr(i,j,k) * & 616 (g%mask2dT(i,j) * g%US%L\_to\_m**2*g%areaT(i,j) * h(i,j,k)) 617 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} 618 stocks(m) = gv%H\_to\_kg\_m2 * stocks(m) 619 620 \textcolor{comment}{!traverse the linked list till hit NULL} 621 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 622 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 623 g\_tracer=>g\_tracer\_next 624 m = m+1 625 \textcolor{keywordflow}{ enddo} 626 627 mom\_generic\_tracer\_stock = m 628 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_a4ba8950c78d0aef988f00cbf74a691d5}\label{namespacemom__generic__tracer_a4ba8950c78d0aef988f00cbf74a691d5}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state@{mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state}} \index{mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state@{mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state()}{mom\_generic\_tracer\_surface\_state()}} {\footnotesize\ttfamily subroutine, public mom\+\_\+generic\+\_\+tracer\+::mom\+\_\+generic\+\_\+tracer\+\_\+surface\+\_\+state (\begin{DoxyParamCaption}\item[{type(surface), intent(inout)}]{sfc\+\_\+state, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS }\end{DoxyParamCaption})} This subroutine calculates the surface state and sets coupler values for those generic tracers that have flux exchange with atmosphere. This subroutine sets up the fields that the coupler needs to calculate the C\+FC fluxes between the ocean and atmosphere. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em g} & The ocean\textquotesingle{}s grid structure\\ \hline \mbox{\tt in,out} & {\em sfc\+\_\+state} & A structure containing fields that describe the surface state of the ocean.\\ \hline \mbox{\tt in} & {\em h} & Layer thicknesses \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}\\ \hline & {\em cs} & Pointer to the control structure for this module. \\ \hline \end{DoxyParams} Definition at line 720 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 720 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< The ocean's grid structure} 721 \textcolor{keywordtype}{type}(surface), \textcolor{keywordtype}{intent(inout)} :: sfc\_state\textcolor{comment}{ !< A structure containing fields that} 722 \textcolor{comment}{ !! describe the surface state of the ocean.} 723 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \textcolor{keywordtype}{intent(in)} :: h\textcolor{comment}{ !< Layer thicknesses [H ~> m or kg m-2]} 724 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module.} 725 726 \textcolor{comment}{! Local variables} 727 \textcolor{keywordtype}{real} :: sosga 728 729 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'MOM\_generic\_tracer\_surface\_state'} 730 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(G%isd:G%ied,G%jsd:G%jed,1:G%ke,1)} :: rho0 731 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(G%isd:G%ied,G%jsd:G%jed,1:G%ke)} :: dzt 732 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer 733 734 \textcolor{comment}{!Set coupler values} 735 \textcolor{comment}{!nnz: fake rho0} 736 rho0=1.0 737 738 dzt(:,:,:) = cs%H\_to\_m * h(:,:,:) 739 740 sosga = global\_area\_mean(sfc\_state%SSS, g) 741 742 \textcolor{keyword}{call }generic\_tracer\_coupler\_set(sfc\_state%tr\_fields,& 743 st=sfc\_state%SST,& 744 ss=sfc\_state%SSS,& 745 rho=rho0,& \textcolor{comment}{!nnz: required for MOM5 and previous versions.} 746 ilb=g%isd, jlb=g%jsd,& 747 dzt=dzt,& \textcolor{comment}{!This is needed for the Mocsy method of carbonate system vars} 748 tau=1,sosga=sosga,model\_time=get\_diag\_time\_end(cs%diag)) 749 750 \textcolor{comment}{!Output diagnostics via diag\_manager for all tracers in this module} 751 \textcolor{comment}{! if (.NOT. associated(CS%g\_tracer\_list)) call MOM\_error(FATAL, trim(sub\_name)//&} 752 \textcolor{comment}{! "No tracer in the list.")} 753 \textcolor{comment}{! call g\_tracer\_send\_diag(CS%g\_tracer\_list, get\_diag\_time\_end(CS%diag), tau=1)} 754 \textcolor{comment}{!Niki: The problem with calling diagnostic outputs here is that this subroutine is called every dt\_cpld} 755 \textcolor{comment}{! hence if dt\_therm > dt\_cpld we get output (and contribution to the mean) at times that tracers} 756 \textcolor{comment}{! had not been updated.} 757 \textcolor{comment}{! Moving this to the end of column physics subrotuine fixes this issue.} 758 \end{DoxyCode} \mbox{\Hypertarget{namespacemom__generic__tracer_a5714b64160c8c96b30f1b641de5ff764}\label{namespacemom__generic__tracer_a5714b64160c8c96b30f1b641de5ff764}} \index{mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}!register\+\_\+mom\+\_\+generic\+\_\+tracer@{register\+\_\+mom\+\_\+generic\+\_\+tracer}} \index{register\+\_\+mom\+\_\+generic\+\_\+tracer@{register\+\_\+mom\+\_\+generic\+\_\+tracer}!mom\+\_\+generic\+\_\+tracer@{mom\+\_\+generic\+\_\+tracer}} \subsubsection{\texorpdfstring{register\+\_\+mom\+\_\+generic\+\_\+tracer()}{register\_mom\_generic\_tracer()}} {\footnotesize\ttfamily logical function, public mom\+\_\+generic\+\_\+tracer\+::register\+\_\+mom\+\_\+generic\+\_\+tracer (\begin{DoxyParamCaption}\item[{type(hor\+\_\+index\+\_\+type), intent(in)}]{HI, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{type(param\+\_\+file\+\_\+type), intent(in)}]{param\+\_\+file, }\item[{type(\mbox{\hyperlink{structmom__generic__tracer_1_1mom__generic__tracer__cs}{mom\+\_\+generic\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{type(tracer\+\_\+registry\+\_\+type), pointer}]{tr\+\_\+\+Reg, }\item[{type(mom\+\_\+restart\+\_\+cs), pointer}]{restart\+\_\+\+CS }\end{DoxyParamCaption})} Initializes the generic tracer packages and adds their tracers to the list Adds the tracers in the list of generic tracers to the set of M\+OM tracers (i.\+e., M\+O\+M-\/register them) Register these tracers for restart. \begin{DoxyParams}[1]{Parameters} \mbox{\tt in} & {\em hi} & Horizontal index ranges\\ \hline \mbox{\tt in} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure\\ \hline \mbox{\tt in} & {\em param\+\_\+file} & A structure to parse for run-\/time parameters\\ \hline & {\em cs} & Pointer to the control structure for this module\\ \hline & {\em tr\+\_\+reg} & Pointer to the control structure for the tracer advection and diffusion module.\\ \hline & {\em restart\+\_\+cs} & Pointer to the restart control structure. \\ \hline \end{DoxyParams} Definition at line 98 of file M\+O\+M\+\_\+generic\+\_\+tracer.\+F90. \begin{DoxyCode} 98 \textcolor{keywordtype}{type}(hor\_index\_type), \textcolor{keywordtype}{intent(in)} :: HI\textcolor{comment}{ !< Horizontal index ranges} 99 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure} 100 \textcolor{keywordtype}{type}(param\_file\_type), \textcolor{keywordtype}{intent(in)} :: param\_file\textcolor{comment}{ !< A structure to parse for run-time parameters} 101 \textcolor{keywordtype}{type}(MOM\_generic\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Pointer to the control structure for this module} 102 \textcolor{keywordtype}{type}(tracer\_registry\_type), \textcolor{keywordtype}{pointer} :: tr\_Reg\textcolor{comment}{ !< Pointer to the control structure for the tracer} 103 \textcolor{comment}{ !! advection and diffusion module.} 104 \textcolor{keywordtype}{type}(MOM\_restart\_CS), \textcolor{keywordtype}{pointer} :: restart\_CS\textcolor{comment}{ !< Pointer to the restart control structure.} 105 106 \textcolor{comment}{! Local variables} 107 \textcolor{keywordtype}{logical} :: register\_MOM\_generic\_tracer 108 109 \textcolor{keywordtype}{character(len=128)}, \textcolor{keywordtype}{parameter} :: sub\_name = \textcolor{stringliteral}{'register\_MOM\_generic\_tracer'} 110 \textcolor{keywordtype}{character(len=200)} :: inputdir \textcolor{comment}{! The directory where NetCDF input files are.} 111 \textcolor{comment}{! These can be overridden later in via the field manager?} 112 113 \textcolor{keywordtype}{integer} :: ntau, k,i,j,axes(3) 114 \textcolor{keywordtype}{type}(g\_tracer\_type), \textcolor{keywordtype}{pointer} :: g\_tracer,g\_tracer\_next 115 \textcolor{keywordtype}{character(len=fm\_string\_len)} :: g\_tracer\_name,longname,units 116 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_field 117 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:,:,:)}, \textcolor{keywordtype}{pointer} :: tr\_ptr 118 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(HI%isd:HI%ied, HI%jsd:HI%jed,GV%ke)} :: grid\_tmask 119 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{dimension(HI%isd:HI%ied, HI%jsd:HI%jed)} :: grid\_kmt 120 121 register\_mom\_generic\_tracer = .false. 122 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{then} 123 \textcolor{keyword}{call }mom\_error(warning, \textcolor{stringliteral}{"register\_MOM\_generic\_tracer called with an "}// & 124 \textcolor{stringliteral}{"associated control structure."}) 125 \textcolor{keywordflow}{return} 126 \textcolor{keywordflow}{ endif} 127 \textcolor{keyword}{allocate}(cs) 128 129 130 \textcolor{comment}{!Register all the generic tracers used and create the list of them.} 131 \textcolor{comment}{!This can be called by ALL PE's. No array fields allocated.} 132 \textcolor{keywordflow}{if} (.not. g\_registered) \textcolor{keywordflow}{then} 133 \textcolor{keyword}{call }generic\_tracer\_register() 134 g\_registered = .true. 135 \textcolor{keywordflow}{ endif} 136 137 138 \textcolor{comment}{! Read all relevant parameters and write them to the model log.} 139 \textcolor{keyword}{call }log\_version(param\_file, sub\_name, version, \textcolor{stringliteral}{""}) 140 \textcolor{keyword}{call }get\_param(param\_file, sub\_name, \textcolor{stringliteral}{"GENERIC\_TRACER\_IC\_FILE"}, cs%IC\_file, & 141 \textcolor{stringliteral}{"The file in which the generic trcer initial values can "}//& 142 \textcolor{stringliteral}{"be found, or an empty string for internal initialization."}, & 143 default=\textcolor{stringliteral}{" "}) 144 \textcolor{keywordflow}{if} ((len\_trim(cs%IC\_file) > 0) .and. (scan(cs%IC\_file,\textcolor{stringliteral}{'/'}) == 0)) \textcolor{keywordflow}{then} 145 \textcolor{comment}{! Add the directory if CS%IC\_file is not already a complete path.} 146 \textcolor{keyword}{call }get\_param(param\_file, sub\_name, \textcolor{stringliteral}{"INPUTDIR"}, inputdir, default=\textcolor{stringliteral}{"."}) 147 cs%IC\_file = trim(slasher(inputdir))//trim(cs%IC\_file) 148 \textcolor{keyword}{call }log\_param(param\_file, sub\_name, \textcolor{stringliteral}{"INPUTDIR/GENERIC\_TRACER\_IC\_FILE"}, cs%IC\_file) 149 \textcolor{keywordflow}{ endif} 150 \textcolor{keyword}{call }get\_param(param\_file, sub\_name, \textcolor{stringliteral}{"GENERIC\_TRACER\_IC\_FILE\_IS\_Z"}, cs%Z\_IC\_file, & 151 \textcolor{stringliteral}{"If true, GENERIC\_TRACER\_IC\_FILE is in depth space, not "}//& 152 \textcolor{stringliteral}{"layer space."},default=.false.) 153 \textcolor{keyword}{call }get\_param(param\_file, sub\_name, \textcolor{stringliteral}{"TRACERS\_MAY\_REINIT"}, cs%tracers\_may\_reinit, & 154 \textcolor{stringliteral}{"If true, tracers may go through the initialization code "}//& 155 \textcolor{stringliteral}{"if they are not found in the restart files. Otherwise "}//& 156 \textcolor{stringliteral}{"it is a fatal error if tracers are not found in the "}//& 157 \textcolor{stringliteral}{"restart files of a restarted run."}, default=.false.) 158 159 cs%restart\_CSp => restart\_cs 160 161 162 ntau=1 \textcolor{comment}{! MOM needs the fields at only one time step} 163 164 165 \textcolor{comment}{! At this point G%mask2dT and CS%diag%axesTL are not allocated.} 166 \textcolor{comment}{! postpone diag\_registeration to initialize\_MOM\_generic\_tracer} 167 168 \textcolor{comment}{!Fields cannot be diag registered as they are allocated and have to registered later.} 169 grid\_tmask(:,:,:) = 0.0 170 grid\_kmt(:,:) = 0.0 171 axes(:) = -1 172 173 \textcolor{comment}{!} 174 \textcolor{comment}{! Initialize all generic tracers} 175 \textcolor{comment}{!} 176 \textcolor{keyword}{call }generic\_tracer\_init(hi%isc,hi%iec,hi%jsc,hi%jec,hi%isd,hi%ied,hi%jsd,hi%jed,& 177 gv%ke,ntau,axes,grid\_tmask,grid\_kmt,set\_time(0,0)) 178 179 180 \textcolor{comment}{!} 181 \textcolor{comment}{! MOM-register the generic tracers} 182 \textcolor{comment}{!} 183 184 \textcolor{comment}{!Get the tracer list} 185 \textcolor{keyword}{call }generic\_tracer\_get\_list(cs%g\_tracer\_list) 186 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(cs%g\_tracer\_list)) \textcolor{keyword}{call }mom\_error(fatal, trim(sub\_name)//& 187 \textcolor{stringliteral}{": No tracer in the list."}) 188 \textcolor{comment}{! For each tracer name get its T\_prog index and get its fields} 189 190 g\_tracer=>cs%g\_tracer\_list 191 \textcolor{keywordflow}{do} 192 \textcolor{keyword}{call }g\_tracer\_get\_alias(g\_tracer,g\_tracer\_name) 193 194 \textcolor{keyword}{call }g\_tracer\_get\_pointer(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'field'},tr\_field) 195 \textcolor{keyword}{call }g\_tracer\_get\_values(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'longname'}, longname) 196 \textcolor{keyword}{call }g\_tracer\_get\_values(g\_tracer,g\_tracer\_name,\textcolor{stringliteral}{'units'},units ) 197 198 \textcolor{comment}{!!nnz: MOM field is 3D. Does this affect performance? Need it be override field?} 199 tr\_ptr => tr\_field(:,:,:,1) 200 \textcolor{comment}{! Register prognastic tracer for horizontal advection, diffusion, and restarts.} 201 \textcolor{keywordflow}{if} (g\_tracer\_is\_prog(g\_tracer)) \textcolor{keywordflow}{then} 202 \textcolor{keyword}{call }register\_tracer(tr\_ptr, tr\_reg, param\_file, hi, gv, & 203 name=g\_tracer\_name, longname=longname, units=units, & 204 registry\_diags=.false., & \textcolor{comment}{!### CHANGE TO TRUE?} 205 restart\_cs=restart\_cs, mandatory=.not.cs%tracers\_may\_reinit) 206 \textcolor{keywordflow}{else} 207 \textcolor{keyword}{call }register\_restart\_field(tr\_ptr, g\_tracer\_name, .not.cs%tracers\_may\_reinit, & 208 restart\_cs, longname=longname, units=units) 209 \textcolor{keywordflow}{ endif} 210 211 \textcolor{comment}{!traverse the linked list till hit NULL} 212 \textcolor{keyword}{call }g\_tracer\_get\_next(g\_tracer, g\_tracer\_next) 213 \textcolor{keywordflow}{if} (.NOT. \textcolor{keyword}{associated}(g\_tracer\_next)) \textcolor{keywordflow}{exit} 214 g\_tracer=>g\_tracer\_next 215 216 \textcolor{keywordflow}{ enddo} 217 218 register\_mom\_generic\_tracer = .true. \end{DoxyCode}