\hypertarget{namespacergc__tracer}{}\doxysection{rgc\+\_\+tracer Module Reference} \label{namespacergc__tracer}\index{rgc\_tracer@{rgc\_tracer}} \doxysubsection{Detailed Description} This module contains the routines used to set up a dynamically passive tracer. Set up and use passive tracers requires the following\+: (1) register\+\_\+\+R\+G\+C\+\_\+tracer (2) apply diffusion, physics/chemistry and advect the tracer. \doxysubsection*{Data Types} \begin{DoxyCompactItemize} \item type \mbox{\hyperlink{structrgc__tracer_1_1rgc__tracer__cs}{rgc\+\_\+tracer\+\_\+cs}} \begin{DoxyCompactList}\small\item\em tracer control structure \end{DoxyCompactList}\end{DoxyCompactItemize} \doxysubsection*{Functions/\+Subroutines} \begin{DoxyCompactItemize} \item logical function, public \mbox{\hyperlink{namespacergc__tracer_a39b5d56f4cb8c161dd9744e0c2b256de}{register\+\_\+rgc\+\_\+tracer}} (HI, GV, param\+\_\+file, CS, tr\+\_\+\+Reg, restart\+\_\+\+CS) \begin{DoxyCompactList}\small\item\em This subroutine is used to register tracer fields. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacergc__tracer_ad2da37dd791644961aab6e66a2452793}{initialize\+\_\+rgc\+\_\+tracer}} (restart, day, G, GV, h, diag, O\+BC, CS, layer\+\_\+\+C\+Sp, sponge\+\_\+\+C\+Sp) \begin{DoxyCompactList}\small\item\em Initializes the N\+TR tracer fields in tr(\+:,\+:,\+:,\+:) and it sets up the tracer output. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacergc__tracer_ad4ef1aeae0c30402bc2e4d0a2ec248c2}{rgc\+\_\+tracer\+\_\+column\+\_\+physics}} (h\+\_\+old, h\+\_\+new, ea, eb, fluxes, dt, G, GV, US, CS, evap\+\_\+\+C\+F\+L\+\_\+limit, minimum\+\_\+forcing\+\_\+depth) \begin{DoxyCompactList}\small\item\em This subroutine applies diapycnal diffusion and any other column tracer physics or chemistry to the tracers from this file. This is a simple example of a set of advected passive tracers. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacergc__tracer_ac32f863f5b15037d5b44b51ed461c2cd}{rgc\+\_\+tracer\+\_\+end}} (CS) \end{DoxyCompactItemize} \doxysubsection*{Variables} \begin{DoxyCompactItemize} \item \mbox{\Hypertarget{namespacergc__tracer_a92ad5e7af13730e9f0717ff898146982}\label{namespacergc__tracer_a92ad5e7af13730e9f0717ff898146982}} integer, parameter \mbox{\hyperlink{namespacergc__tracer_a92ad5e7af13730e9f0717ff898146982}{ntr}} = 1 \begin{DoxyCompactList}\small\item\em The number of tracers in this module. \end{DoxyCompactList}\end{DoxyCompactItemize} \doxysubsection{Function/\+Subroutine Documentation} \mbox{\Hypertarget{namespacergc__tracer_ad2da37dd791644961aab6e66a2452793}\label{namespacergc__tracer_ad2da37dd791644961aab6e66a2452793}} \index{rgc\_tracer@{rgc\_tracer}!initialize\_rgc\_tracer@{initialize\_rgc\_tracer}} \index{initialize\_rgc\_tracer@{initialize\_rgc\_tracer}!rgc\_tracer@{rgc\_tracer}} \doxysubsubsection{\texorpdfstring{initialize\_rgc\_tracer()}{initialize\_rgc\_tracer()}} {\footnotesize\ttfamily subroutine, public rgc\+\_\+tracer\+::initialize\+\_\+rgc\+\_\+tracer (\begin{DoxyParamCaption}\item[{logical, intent(in)}]{restart, }\item[{type(time\+\_\+type), intent(in), target}]{day, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{real, dimension( g \%isd\+: g \%ied, g \%jsd\+: g \%jed, g \%ke), intent(in)}]{h, }\item[{type(diag\+\_\+ctrl), intent(in), target}]{diag, }\item[{type(ocean\+\_\+obc\+\_\+type), pointer}]{O\+BC, }\item[{type(\mbox{\hyperlink{structrgc__tracer_1_1rgc__tracer__cs}{rgc\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{type(sponge\+\_\+cs), pointer}]{layer\+\_\+\+C\+Sp, }\item[{type(ale\+\_\+sponge\+\_\+cs), pointer}]{sponge\+\_\+\+C\+Sp }\end{DoxyParamCaption})} Initializes the N\+TR tracer fields in tr(\+:,\+:,\+:,\+:) and it sets up the tracer output. \begin{DoxyParams}[1]{Parameters} \mbox{\texttt{ in}} & {\em g} & Grid structure. \\ \hline \mbox{\texttt{ in}} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure. \\ \hline \mbox{\texttt{ in}} & {\em restart} & .true. if the fields have already been read from a restart file. \\ \hline \mbox{\texttt{ in}} & {\em day} & Time of the start of the run. \\ \hline \mbox{\texttt{ in}} & {\em h} & Layer thickness, in m or kg m-\/2. \\ \hline \mbox{\texttt{ in}} & {\em diag} & Structure used to regulate diagnostic output. \\ \hline & {\em obc} & This open boundary condition type specifies whether, where, and what open boundary conditions are used. This is not being used for now. \\ \hline & {\em cs} & The control structure returned by a previous call to R\+G\+C\+\_\+register\+\_\+tracer. \\ \hline & {\em layer\+\_\+csp} & A pointer to the control structure \\ \hline & {\em sponge\+\_\+csp} & A pointer to the control structure for the sponges, if they are in use. Otherwise this may be unassociated. \\ \hline \end{DoxyParams} Definition at line 156 of file R\+G\+C\+\_\+tracer.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{156 } \DoxyCodeLine{157 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< Grid structure.}} \DoxyCodeLine{158 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure.}} \DoxyCodeLine{159 \textcolor{keywordtype}{logical}, \textcolor{keywordtype}{intent(in)} :: restart\textcolor{comment}{ !< .true. if the fields have already}} \DoxyCodeLine{160 \textcolor{comment}{ !! been read from a restart file.}} \DoxyCodeLine{161 \textcolor{keywordtype}{type}(time\_type), \textcolor{keywordtype}{target}, \textcolor{keywordtype}{intent(in)} :: day\textcolor{comment}{ !< Time of the start of the run.}} \DoxyCodeLine{162 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \&} \DoxyCodeLine{163 \textcolor{keywordtype}{intent(in)} :: h\textcolor{comment}{ !< Layer thickness, in m or kg m-\/2.}} \DoxyCodeLine{164 \textcolor{keywordtype}{type}(diag\_ctrl), \textcolor{keywordtype}{target}, \textcolor{keywordtype}{intent(in)} :: diag\textcolor{comment}{ !< Structure used to regulate diagnostic output.}} \DoxyCodeLine{165 \textcolor{keywordtype}{type}(ocean\_OBC\_type), \textcolor{keywordtype}{pointer} :: OBC\textcolor{comment}{ !< This open boundary condition type specifies}} \DoxyCodeLine{166 \textcolor{comment}{ !! whether, where, and what open boundary}} \DoxyCodeLine{167 \textcolor{comment}{ !! conditions are used. This is not being used for now.}} \DoxyCodeLine{168 \textcolor{keywordtype}{type}(RGC\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< The control structure returned by a previous}} \DoxyCodeLine{169 \textcolor{comment}{ !! call to RGC\_register\_tracer.}} \DoxyCodeLine{170 \textcolor{keywordtype}{type}(sponge\_CS), \textcolor{keywordtype}{pointer} :: layer\_CSp\textcolor{comment}{ !< A pointer to the control structure}} \DoxyCodeLine{171 \textcolor{keywordtype}{type}(ALE\_sponge\_CS), \textcolor{keywordtype}{pointer} :: sponge\_CSp\textcolor{comment}{ !< A pointer to the control structure for the}} \DoxyCodeLine{172 \textcolor{comment}{ !! sponges, if they are in use. Otherwise this may be unassociated.}} \DoxyCodeLine{173 } \DoxyCodeLine{174 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{allocatable} :: temp(:,:,:)} \DoxyCodeLine{175 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{pointer}, \textcolor{keywordtype}{dimension(:,:,:)} :: \&} \DoxyCodeLine{176 OBC\_tr1\_u => null(), \& \textcolor{comment}{! These arrays should be allocated and set to}} \DoxyCodeLine{177 obc\_tr1\_v => null() \textcolor{comment}{! specify the values of tracer 1 that should come}} \DoxyCodeLine{178 \textcolor{comment}{! in through u-\/ and v-\/ points through the open}} \DoxyCodeLine{179 \textcolor{comment}{! boundary conditions, in the same units as tr.}} \DoxyCodeLine{180 \textcolor{keywordtype}{character(len=16)} :: name \textcolor{comment}{! A variable's name in a NetCDF file.}} \DoxyCodeLine{181 \textcolor{keywordtype}{character(len=72)} :: longname \textcolor{comment}{! The long name of that variable.}} \DoxyCodeLine{182 \textcolor{keywordtype}{character(len=48)} :: units \textcolor{comment}{! The dimensions of the variable.}} \DoxyCodeLine{183 \textcolor{keywordtype}{character(len=48)} :: flux\_units \textcolor{comment}{! The units for tracer fluxes, usually}} \DoxyCodeLine{184 \textcolor{comment}{! kg(tracer) kg(water)-\/1 m3 s-\/1 or kg(tracer) s-\/1.}} \DoxyCodeLine{185 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{pointer} :: tr\_ptr(:,:,:) => null()} \DoxyCodeLine{186 \textcolor{keywordtype}{ real} :: h\_neglect \textcolor{comment}{! A thickness that is so small it is usually lost}} \DoxyCodeLine{187 \textcolor{comment}{! in roundoff and can be neglected [H ~> m or kg-\/2].}} \DoxyCodeLine{188 \textcolor{keywordtype}{ real} :: e(SZK\_(G)+1), e\_top, e\_bot, d\_tr \textcolor{comment}{! Heights [Z ~> m].}} \DoxyCodeLine{189 \textcolor{keywordtype}{integer} :: i, j, k, is, ie, js, je, isd, ied, jsd, jed, nz, m} \DoxyCodeLine{190 \textcolor{keywordtype}{integer} :: IsdB, IedB, JsdB, JedB} \DoxyCodeLine{191 \textcolor{keywordtype}{integer} :: nzdata} \DoxyCodeLine{192 } \DoxyCodeLine{193 \textcolor{keywordflow}{if} (.not.\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return}} \DoxyCodeLine{194 is = g\%isc ; ie = g\%iec ; js = g\%jsc ; je = g\%jec ; nz = g\%ke} \DoxyCodeLine{195 isd = g\%isd ; ied = g\%ied ; jsd = g\%jsd ; jed = g\%jed} \DoxyCodeLine{196 isdb = g\%IsdB ; iedb = g\%IedB ; jsdb = g\%JsdB ; jedb = g\%JedB} \DoxyCodeLine{197 h\_neglect = gv\%H\_subroundoff} \DoxyCodeLine{198 } \DoxyCodeLine{199 cs\%Time => day} \DoxyCodeLine{200 cs\%diag => diag} \DoxyCodeLine{201 } \DoxyCodeLine{202 \textcolor{keywordflow}{if} (.not.restart) \textcolor{keywordflow}{then}} \DoxyCodeLine{203 \textcolor{keywordflow}{if} (len\_trim(cs\%tracer\_IC\_file) >= 1) \textcolor{keywordflow}{then}} \DoxyCodeLine{204 \textcolor{comment}{! Read the tracer concentrations from a netcdf file.}} \DoxyCodeLine{205 \textcolor{keywordflow}{if} (.not.file\_exists(cs\%tracer\_IC\_file, g\%Domain)) \&} \DoxyCodeLine{206 \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"RGC\_initialize\_tracer: Unable to open "}// \&} \DoxyCodeLine{207 cs\%tracer\_IC\_file)} \DoxyCodeLine{208 \textcolor{keywordflow}{do} m=1,ntr} \DoxyCodeLine{209 \textcolor{keyword}{call }query\_vardesc(cs\%tr\_desc(m), name, caller=\textcolor{stringliteral}{"initialize\_RGC\_tracer"})} \DoxyCodeLine{210 \textcolor{keyword}{call }mom\_read\_data(cs\%tracer\_IC\_file, trim(name), cs\%tr(:,:,:,m), g\%Domain)} \DoxyCodeLine{211 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{212 \textcolor{keywordflow}{else}} \DoxyCodeLine{213 \textcolor{keywordflow}{do} m=1,ntr} \DoxyCodeLine{214 \textcolor{keywordflow}{do} k=1,nz ; \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{215 cs\%tr(i,j,k,m) = 0.0} \DoxyCodeLine{216 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo}} \DoxyCodeLine{217 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{218 m=1} \DoxyCodeLine{219 \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{220 \textcolor{comment}{!set tracer to 1.0 in the surface of the continental shelf}} \DoxyCodeLine{221 \textcolor{keywordflow}{if} (g\%geoLonT(i,j) <= (cs\%CSL)) \textcolor{keywordflow}{then}} \DoxyCodeLine{222 cs\%tr(i,j,1,m) = 1.0 \textcolor{comment}{!first layer}} \DoxyCodeLine{223 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{224 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo}} \DoxyCodeLine{225 } \DoxyCodeLine{226 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{227 \textcolor{keywordflow}{ endif} \textcolor{comment}{! restart}} \DoxyCodeLine{228 } \DoxyCodeLine{229 \textcolor{keywordflow}{if} ( cs\%use\_sponge ) \textcolor{keywordflow}{then}} \DoxyCodeLine{230 \textcolor{comment}{! If sponges are used, this damps values to zero in the offshore boundary.}} \DoxyCodeLine{231 \textcolor{comment}{! For any tracers that are not damped in the sponge, the call}} \DoxyCodeLine{232 \textcolor{comment}{! to set\_up\_sponge\_field can simply be omitted.}} \DoxyCodeLine{233 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(sponge\_csp)) \textcolor{keywordflow}{then} \textcolor{comment}{!ALE mode}} \DoxyCodeLine{234 nzdata = get\_ale\_sponge\_nz\_data(sponge\_csp)} \DoxyCodeLine{235 \textcolor{keywordflow}{if} (nzdata>0) \textcolor{keywordflow}{then}} \DoxyCodeLine{236 \textcolor{keyword}{allocate}(temp(g\%isd:g\%ied,g\%jsd:g\%jed,nzdata))} \DoxyCodeLine{237 \textcolor{keywordflow}{do} k=1,nzdata ; \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{238 \textcolor{keywordflow}{if} (g\%geoLonT(i,j) >= (cs\%lenlon -\/ cs\%lensponge) .AND. g\%geoLonT(i,j) <= cs\%lenlon) \textcolor{keywordflow}{then}} \DoxyCodeLine{239 temp(i,j,k) = 0.0} \DoxyCodeLine{240 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{241 \textcolor{keywordflow}{ enddo} ; enddo;\textcolor{keywordflow}{ enddo}} \DoxyCodeLine{242 \textcolor{keywordflow}{do} m=1,1} \DoxyCodeLine{243 \textcolor{comment}{! This is needed to force the compiler not to do a copy in the sponge calls.}} \DoxyCodeLine{244 tr\_ptr => cs\%tr(:,:,:,m)} \DoxyCodeLine{245 \textcolor{keyword}{call }set\_up\_ale\_sponge\_field(temp, g, tr\_ptr, sponge\_csp)} \DoxyCodeLine{246 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{247 \textcolor{keyword}{deallocate}(temp)} \DoxyCodeLine{248 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{249 } \DoxyCodeLine{250 \textcolor{keywordflow}{elseif} (\textcolor{keyword}{associated}(layer\_csp)) \textcolor{keywordflow}{then} \textcolor{comment}{!layer mode}} \DoxyCodeLine{251 \textcolor{keywordflow}{if} (nz>0) \textcolor{keywordflow}{then}} \DoxyCodeLine{252 \textcolor{keyword}{allocate}(temp(g\%isd:g\%ied,g\%jsd:g\%jed,nz))} \DoxyCodeLine{253 \textcolor{keywordflow}{do} k=1,nz ; \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{254 \textcolor{keywordflow}{if} (g\%geoLonT(i,j) >= (cs\%lenlon -\/ cs\%lensponge) .AND. g\%geoLonT(i,j) <= cs\%lenlon) \textcolor{keywordflow}{then}} \DoxyCodeLine{255 temp(i,j,k) = 0.0} \DoxyCodeLine{256 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{257 \textcolor{keywordflow}{ enddo} ; enddo;\textcolor{keywordflow}{ enddo}} \DoxyCodeLine{258 \textcolor{keywordflow}{do} m=1,1} \DoxyCodeLine{259 tr\_ptr => cs\%tr(:,:,:,m)} \DoxyCodeLine{260 \textcolor{keyword}{call }set\_up\_sponge\_field(temp, tr\_ptr, g, nz, layer\_csp)} \DoxyCodeLine{261 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{262 \textcolor{keyword}{deallocate}(temp)} \DoxyCodeLine{263 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{264 \textcolor{keywordflow}{else}} \DoxyCodeLine{265 \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"RGC\_initialize\_tracer: "}// \&} \DoxyCodeLine{266 \textcolor{stringliteral}{"The pointer to sponge\_CSp must be associated if SPONGE is defined."})} \DoxyCodeLine{267 \textcolor{keywordflow}{ endif} \textcolor{comment}{!selecting mode/calling error if no pointer}} \DoxyCodeLine{268 \textcolor{keywordflow}{ endif} \textcolor{comment}{!using sponge}} \DoxyCodeLine{269 } \end{DoxyCode} \mbox{\Hypertarget{namespacergc__tracer_a39b5d56f4cb8c161dd9744e0c2b256de}\label{namespacergc__tracer_a39b5d56f4cb8c161dd9744e0c2b256de}} \index{rgc\_tracer@{rgc\_tracer}!register\_rgc\_tracer@{register\_rgc\_tracer}} \index{register\_rgc\_tracer@{register\_rgc\_tracer}!rgc\_tracer@{rgc\_tracer}} \doxysubsubsection{\texorpdfstring{register\_rgc\_tracer()}{register\_rgc\_tracer()}} {\footnotesize\ttfamily logical function, public rgc\+\_\+tracer\+::register\+\_\+rgc\+\_\+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{structrgc__tracer_1_1rgc__tracer__cs}{rgc\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{type(tracer\+\_\+registry\+\_\+type), pointer}]{tr\+\_\+\+Reg, }\item[{type(mom\+\_\+restart\+\_\+cs), pointer}]{restart\+\_\+\+CS }\end{DoxyParamCaption})} This subroutine is used to register tracer fields. \begin{DoxyParams}[1]{Parameters} \mbox{\texttt{ in}} & {\em hi} & A horizontal index type structure. \\ \hline \mbox{\texttt{ in}} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure. \\ \hline \mbox{\texttt{ in}} & {\em param\+\_\+file} & A structure indicating the open file to parse for model parameter values. \\ \hline & {\em cs} & A pointer that is set to point to the control structure for this module (in/out). \\ \hline & {\em tr\+\_\+reg} & A pointer to the tracer registry. \\ \hline & {\em restart\+\_\+cs} & A pointer to the restart control structure. \\ \hline \end{DoxyParams} Definition at line 68 of file R\+G\+C\+\_\+tracer.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{68 \textcolor{keywordtype}{type}(hor\_index\_type), \textcolor{keywordtype}{intent(in)} :: HI\textcolor{comment}{ !< A horizontal index type structure.}} \DoxyCodeLine{69 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure.}} \DoxyCodeLine{70 \textcolor{keywordtype}{type}(param\_file\_type), \textcolor{keywordtype}{intent(in)} :: param\_file\textcolor{comment}{ ! null()} \DoxyCodeLine{83 \textcolor{keywordtype}{logical} :: register\_RGC\_tracer} \DoxyCodeLine{84 \textcolor{keywordtype}{integer} :: isd, ied, jsd, jed, nz, m} \DoxyCodeLine{85 isd = hi\%isd ; ied = hi\%ied ; jsd = hi\%jsd ; jed = hi\%jed ; nz = gv\%ke} \DoxyCodeLine{86 } \DoxyCodeLine{87 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{then}} \DoxyCodeLine{88 \textcolor{keyword}{call }mom\_error(warning, \textcolor{stringliteral}{"RGC\_register\_tracer called with an "}// \&} \DoxyCodeLine{89 \textcolor{stringliteral}{"associated control structure."})} \DoxyCodeLine{90 \textcolor{keywordflow}{return}} \DoxyCodeLine{91 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{92 \textcolor{keyword}{allocate}(cs)} \DoxyCodeLine{93 } \DoxyCodeLine{94 \textcolor{comment}{! Read all relevant parameters and write them to the model log.}} \DoxyCodeLine{95 \textcolor{keyword}{call }log\_version(param\_file, mdl, version, \textcolor{stringliteral}{""})} \DoxyCodeLine{96 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"RGC\_TRACER\_IC\_FILE"}, cs\%tracer\_IC\_file, \&} \DoxyCodeLine{97 \textcolor{stringliteral}{"The name of a file from which to read the initial \(\backslash\)n"}//\&} \DoxyCodeLine{98 \textcolor{stringliteral}{"conditions for the RGC tracers, or blank to initialize \(\backslash\)n"}//\&} \DoxyCodeLine{99 \textcolor{stringliteral}{"them internally."}, default=\textcolor{stringliteral}{" "})} \DoxyCodeLine{100 \textcolor{keywordflow}{if} (len\_trim(cs\%tracer\_IC\_file) >= 1) \textcolor{keywordflow}{then}} \DoxyCodeLine{101 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"INPUTDIR"}, inputdir, default=\textcolor{stringliteral}{"."})} \DoxyCodeLine{102 inputdir = slasher(inputdir)} \DoxyCodeLine{103 cs\%tracer\_IC\_file = trim(inputdir)//trim(cs\%tracer\_IC\_file)} \DoxyCodeLine{104 \textcolor{keyword}{call }log\_param(param\_file, mdl, \textcolor{stringliteral}{"INPUTDIR/RGC\_TRACER\_IC\_FILE"}, \&} \DoxyCodeLine{105 cs\%tracer\_IC\_file)} \DoxyCodeLine{106 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{107 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"SPONGE"}, cs\%use\_sponge, \&} \DoxyCodeLine{108 \textcolor{stringliteral}{"If true, sponges may be applied anywhere in the domain. \(\backslash\)n"}//\&} \DoxyCodeLine{109 \textcolor{stringliteral}{"The exact location and properties of those sponges are \(\backslash\)n"}//\&} \DoxyCodeLine{110 \textcolor{stringliteral}{"specified from MOM\_initialization.F90."}, default=.false.)} \DoxyCodeLine{111 } \DoxyCodeLine{112 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"LENLAT"}, cs\%lenlat, \&} \DoxyCodeLine{113 \textcolor{stringliteral}{"The latitudinal or y-\/direction length of the domain"}, \&} \DoxyCodeLine{114 fail\_if\_missing=.true., do\_not\_log=.true.)} \DoxyCodeLine{115 } \DoxyCodeLine{116 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"LENLON"}, cs\%lenlon, \&} \DoxyCodeLine{117 \textcolor{stringliteral}{"The longitudinal or x-\/direction length of the domain"}, \&} \DoxyCodeLine{118 fail\_if\_missing=.true., do\_not\_log=.true.)} \DoxyCodeLine{119 } \DoxyCodeLine{120 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"CONT\_SHELF\_LENGTH"}, cs\%CSL, \&} \DoxyCodeLine{121 \textcolor{stringliteral}{"The length of the continental shelf (x dir, km)."}, \&} \DoxyCodeLine{122 default=15.0)} \DoxyCodeLine{123 } \DoxyCodeLine{124 \textcolor{keyword}{call }get\_param(param\_file, mdl, \textcolor{stringliteral}{"LENSPONGE"}, cs\%lensponge, \&} \DoxyCodeLine{125 \textcolor{stringliteral}{"The length of the sponge layer (km)."}, \&} \DoxyCodeLine{126 default=10.0)} \DoxyCodeLine{127 } \DoxyCodeLine{128 \textcolor{keyword}{allocate}(cs\%tr(isd:ied,jsd:jed,nz,ntr)) ; cs\%tr(:,:,:,:) = 0.0} \DoxyCodeLine{129 \textcolor{keywordflow}{if} (cs\%mask\_tracers) \textcolor{keywordflow}{then}} \DoxyCodeLine{130 \textcolor{keyword}{allocate}(cs\%tr\_aux(isd:ied,jsd:jed,nz,ntr)) ; cs\%tr\_aux(:,:,:,:) = 0.0} \DoxyCodeLine{131 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{132 } \DoxyCodeLine{133 \textcolor{keywordflow}{do} m=1,ntr} \DoxyCodeLine{134 \textcolor{keywordflow}{if} (m < 10) \textcolor{keywordflow}{then} ; \textcolor{keyword}{write}(name,\textcolor{stringliteral}{'("tr\_RGC",I1.1)'}) m} \DoxyCodeLine{135 \textcolor{keywordflow}{else} ; \textcolor{keyword}{write}(name,\textcolor{stringliteral}{'("tr\_RGC",I2.2)'}) m ;\textcolor{keywordflow}{ endif}} \DoxyCodeLine{136 \textcolor{keyword}{write}(longname,\textcolor{stringliteral}{'("Concentration of RGC Tracer ",I2.2)'}) m} \DoxyCodeLine{137 cs\%tr\_desc(m) = var\_desc(name, units=\textcolor{stringliteral}{"kg kg-\/1"}, longname=longname, caller=mdl)} \DoxyCodeLine{138 } \DoxyCodeLine{139 \textcolor{comment}{! This is needed to force the compiler not to do a copy in the registration calls.}} \DoxyCodeLine{140 tr\_ptr => cs\%tr(:,:,:,m)} \DoxyCodeLine{141 \textcolor{comment}{! Register the tracer for horizontal advection \& diffusion.}} \DoxyCodeLine{142 \textcolor{keyword}{call }register\_tracer(tr\_ptr, tr\_reg, param\_file, hi, gv, \&} \DoxyCodeLine{143 name=name, longname=longname, units=\textcolor{stringliteral}{"kg kg-\/1"}, \&} \DoxyCodeLine{144 registry\_diags=.true., flux\_units=\textcolor{stringliteral}{"kg/s"}, \&} \DoxyCodeLine{145 restart\_cs=restart\_cs)} \DoxyCodeLine{146 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{147 } \DoxyCodeLine{148 cs\%tr\_Reg => tr\_reg} \DoxyCodeLine{149 register\_rgc\_tracer = .true.} \end{DoxyCode} \mbox{\Hypertarget{namespacergc__tracer_ad4ef1aeae0c30402bc2e4d0a2ec248c2}\label{namespacergc__tracer_ad4ef1aeae0c30402bc2e4d0a2ec248c2}} \index{rgc\_tracer@{rgc\_tracer}!rgc\_tracer\_column\_physics@{rgc\_tracer\_column\_physics}} \index{rgc\_tracer\_column\_physics@{rgc\_tracer\_column\_physics}!rgc\_tracer@{rgc\_tracer}} \doxysubsubsection{\texorpdfstring{rgc\_tracer\_column\_physics()}{rgc\_tracer\_column\_physics()}} {\footnotesize\ttfamily subroutine, public rgc\+\_\+tracer\+::rgc\+\_\+tracer\+\_\+column\+\_\+physics (\begin{DoxyParamCaption}\item[{real, dimension(szi\+\_\+(g),szj\+\_\+(g),szk\+\_\+(g)), intent(in)}]{h\+\_\+old, }\item[{real, dimension(szi\+\_\+(g),szj\+\_\+(g),szk\+\_\+(g)), intent(in)}]{h\+\_\+new, }\item[{real, dimension(szi\+\_\+(g),szj\+\_\+(g),szk\+\_\+(g)), intent(in)}]{ea, }\item[{real, dimension(szi\+\_\+(g),szj\+\_\+(g),szk\+\_\+(g)), intent(in)}]{eb, }\item[{type(forcing), intent(in)}]{fluxes, }\item[{real, intent(in)}]{dt, }\item[{type(ocean\+\_\+grid\+\_\+type), intent(in)}]{G, }\item[{type(verticalgrid\+\_\+type), intent(in)}]{GV, }\item[{type(unit\+\_\+scale\+\_\+type), intent(in)}]{US, }\item[{type(\mbox{\hyperlink{structrgc__tracer_1_1rgc__tracer__cs}{rgc\+\_\+tracer\+\_\+cs}}), pointer}]{CS, }\item[{real, intent(in), optional}]{evap\+\_\+\+C\+F\+L\+\_\+limit, }\item[{real, intent(in), optional}]{minimum\+\_\+forcing\+\_\+depth }\end{DoxyParamCaption})} This subroutine applies diapycnal diffusion and any other column tracer physics or chemistry to the tracers from this file. This is a simple example of a set of advected passive tracers. \begin{DoxyParams}[1]{Parameters} \mbox{\texttt{ in}} & {\em g} & The ocean\textquotesingle{}s grid structure. \\ \hline \mbox{\texttt{ in}} & {\em gv} & The ocean\textquotesingle{}s vertical grid structure. \\ \hline \mbox{\texttt{ in}} & {\em h\+\_\+old} & Layer thickness before entrainment \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}. \\ \hline \mbox{\texttt{ in}} & {\em h\+\_\+new} & Layer thickness after entrainment \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}. \\ \hline \mbox{\texttt{ in}} & {\em ea} & an array to which the amount of fluid entrained \\ \hline \mbox{\texttt{ in}} & {\em eb} & an array to which the amount of fluid entrained \\ \hline \mbox{\texttt{ in}} & {\em fluxes} & A structure containing pointers to any possible forcing fields. Unused fields have N\+U\+LL ptrs. \\ \hline \mbox{\texttt{ in}} & {\em dt} & The amount of time covered by this call \mbox{[}T $\sim$$>$ s\mbox{]}. \\ \hline \mbox{\texttt{ in}} & {\em us} & A dimensional unit scaling type \\ \hline & {\em cs} & The control structure returned by a previous call. \\ \hline \mbox{\texttt{ in}} & {\em evap\+\_\+cfl\+\_\+limit} & Limit on the fraction of the water that can be fluxed out of the top layer in a timestep \mbox{[}nondim\mbox{]}. \\ \hline \mbox{\texttt{ in}} & {\em minimum\+\_\+forcing\+\_\+depth} & The smallest depth over which fluxes can be applied \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}. \\ \hline \end{DoxyParams} Definition at line 277 of file R\+G\+C\+\_\+tracer.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{277 \textcolor{keywordtype}{type}(ocean\_grid\_type), \textcolor{keywordtype}{intent(in)} :: G\textcolor{comment}{ !< The ocean's grid structure.}} \DoxyCodeLine{278 \textcolor{keywordtype}{type}(verticalGrid\_type), \textcolor{keywordtype}{intent(in)} :: GV\textcolor{comment}{ !< The ocean's vertical grid structure.}} \DoxyCodeLine{279 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \&} \DoxyCodeLine{280 \textcolor{keywordtype}{intent(in)} :: h\_old\textcolor{comment}{ !< Layer thickness before entrainment [H ~> m or kg m-\/2].}} \DoxyCodeLine{281 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \&} \DoxyCodeLine{282 \textcolor{keywordtype}{intent(in)} :: h\_new\textcolor{comment}{ !< Layer thickness after entrainment [H ~> m or kg m-\/2].}} \DoxyCodeLine{283 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \&} \DoxyCodeLine{284 \textcolor{keywordtype}{intent(in)} :: ea\textcolor{comment}{ !< an array to which the amount of fluid entrained}} \DoxyCodeLine{285 \textcolor{comment}{ !! from the layer above during this call will be}} \DoxyCodeLine{286 \textcolor{comment}{ !! added [H ~> m or kg m-\/2].}} \DoxyCodeLine{287 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))}, \&} \DoxyCodeLine{288 \textcolor{keywordtype}{intent(in)} :: eb\textcolor{comment}{ !< an array to which the amount of fluid entrained}} \DoxyCodeLine{289 \textcolor{comment}{ !! from the layer below during this call will be}} \DoxyCodeLine{290 \textcolor{comment}{ !! added [H ~> m or kg m-\/2].}} \DoxyCodeLine{291 \textcolor{keywordtype}{type}(forcing), \textcolor{keywordtype}{intent(in)} :: fluxes\textcolor{comment}{ !< A structure containing pointers to any possible}} \DoxyCodeLine{292 \textcolor{comment}{ !! forcing fields. Unused fields have NULL ptrs.}} \DoxyCodeLine{293 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{intent(in)} :: dt\textcolor{comment}{ !< The amount of time covered by this call [T ~> s].}} \DoxyCodeLine{294 \textcolor{keywordtype}{type}(unit\_scale\_type), \textcolor{keywordtype}{intent(in)} :: US\textcolor{comment}{ !< A dimensional unit scaling type}} \DoxyCodeLine{295 \textcolor{keywordtype}{type}(RGC\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< The control structure returned by a previous call.}} \DoxyCodeLine{296 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: evap\_CFL\_limit\textcolor{comment}{ !< Limit on the fraction of the water that can be}} \DoxyCodeLine{297 \textcolor{comment}{ !! fluxed out of the top layer in a timestep [nondim].}} \DoxyCodeLine{298 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: minimum\_forcing\_depth\textcolor{comment}{ !< The smallest depth over which fluxes}} \DoxyCodeLine{299 \textcolor{comment}{ !! can be applied [H ~> m or kg m-\/2].}} \DoxyCodeLine{300 } \DoxyCodeLine{301 \textcolor{comment}{! The arguments to this subroutine are redundant in that}} \DoxyCodeLine{302 \textcolor{comment}{! h\_new[k] = h\_old[k] + ea[k] -\/ eb[k-\/1] + eb[k] -\/ ea[k+1]}} \DoxyCodeLine{303 } \DoxyCodeLine{304 \textcolor{keywordtype}{ real} :: b1(SZI\_(G)) \textcolor{comment}{! b1 and c1 are variables used by the}} \DoxyCodeLine{305 \textcolor{keywordtype}{ real} :: c1(SZI\_(G),SZK\_(G)) \textcolor{comment}{! tridiagonal solver.}} \DoxyCodeLine{306 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(SZI\_(G),SZJ\_(G),SZK\_(G))} :: h\_work \textcolor{comment}{! Used so that h can be modified}} \DoxyCodeLine{307 \textcolor{keywordtype}{ real} :: in\_flux(SZI\_(G),SZJ\_(G),2) \textcolor{comment}{! total amount of tracer to be injected}} \DoxyCodeLine{308 } \DoxyCodeLine{309 \textcolor{keywordtype}{integer} :: i, j, k, is, ie, js, je, nz, m} \DoxyCodeLine{310 is = g\%isc ; ie = g\%iec ; js = g\%jsc ; je = g\%jec ; nz = g\%ke} \DoxyCodeLine{311 } \DoxyCodeLine{312 \textcolor{keywordflow}{if} (.not.\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return}} \DoxyCodeLine{313 } \DoxyCodeLine{314 in\_flux(:,:,:) = 0.0} \DoxyCodeLine{315 m=1} \DoxyCodeLine{316 \textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{317 \textcolor{comment}{!set tracer to 1.0 in the surface of the continental shelf}} \DoxyCodeLine{318 \textcolor{keywordflow}{if} (g\%geoLonT(i,j) <= (cs\%CSL)) \textcolor{keywordflow}{then}} \DoxyCodeLine{319 cs\%tr(i,j,1,m) = 1.0 \textcolor{comment}{!first layer}} \DoxyCodeLine{320 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{321 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo}} \DoxyCodeLine{322 } \DoxyCodeLine{323 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(evap\_cfl\_limit) .and. \textcolor{keyword}{present}(minimum\_forcing\_depth)) \textcolor{keywordflow}{then}} \DoxyCodeLine{324 \textcolor{keywordflow}{do} m=1,ntr} \DoxyCodeLine{325 \textcolor{keywordflow}{do} k=1,nz ;\textcolor{keywordflow}{do} j=js,je ; \textcolor{keywordflow}{do} i=is,ie} \DoxyCodeLine{326 h\_work(i,j,k) = h\_old(i,j,k)} \DoxyCodeLine{327 \textcolor{keywordflow}{ enddo} ;\textcolor{keywordflow}{ enddo} ; enddo;} \DoxyCodeLine{328 \textcolor{keyword}{call }applytracerboundaryfluxesinout(g, gv, cs\%tr(:,:,:,m) , dt, fluxes, h\_work, \&} \DoxyCodeLine{329 evap\_cfl\_limit, minimum\_forcing\_depth, in\_flux(:,:,m))} \DoxyCodeLine{330 } \DoxyCodeLine{331 \textcolor{keyword}{call }tracer\_vertdiff(h\_work, ea, eb, dt, cs\%tr(:,:,:,m), g, gv)} \DoxyCodeLine{332 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{333 \textcolor{keywordflow}{else}} \DoxyCodeLine{334 \textcolor{keywordflow}{do} m=1,ntr} \DoxyCodeLine{335 \textcolor{keyword}{call }tracer\_vertdiff(h\_old, ea, eb, dt, cs\%tr(:,:,:,m), g, gv)} \DoxyCodeLine{336 \textcolor{keywordflow}{ enddo}} \DoxyCodeLine{337 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{338 } \end{DoxyCode} \mbox{\Hypertarget{namespacergc__tracer_ac32f863f5b15037d5b44b51ed461c2cd}\label{namespacergc__tracer_ac32f863f5b15037d5b44b51ed461c2cd}} \index{rgc\_tracer@{rgc\_tracer}!rgc\_tracer\_end@{rgc\_tracer\_end}} \index{rgc\_tracer\_end@{rgc\_tracer\_end}!rgc\_tracer@{rgc\_tracer}} \doxysubsubsection{\texorpdfstring{rgc\_tracer\_end()}{rgc\_tracer\_end()}} {\footnotesize\ttfamily subroutine, public rgc\+\_\+tracer\+::rgc\+\_\+tracer\+\_\+end (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structrgc__tracer_1_1rgc__tracer__cs}{rgc\+\_\+tracer\+\_\+cs}}), pointer}]{CS }\end{DoxyParamCaption})} \begin{DoxyParams}{Parameters} {\em cs} & The control structure returned by a previous call to R\+G\+C\+\_\+register\+\_\+tracer. \\ \hline \end{DoxyParams} Definition at line 342 of file R\+G\+C\+\_\+tracer.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{342 \textcolor{keywordtype}{type}(RGC\_tracer\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< The control structure returned by a previous call to RGC\_register\_tracer.}} \DoxyCodeLine{343 \textcolor{keywordtype}{integer} :: m} \DoxyCodeLine{344 } \DoxyCodeLine{345 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{then}} \DoxyCodeLine{346 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs\%tr)) \textcolor{keyword}{deallocate}(cs\%tr)} \DoxyCodeLine{347 \textcolor{keyword}{deallocate}(cs)} \DoxyCodeLine{348 \textcolor{keywordflow}{ endif}} \end{DoxyCode}