\hypertarget{namespacecoord__sigma}{}\doxysection{coord\+\_\+sigma Module Reference} \label{namespacecoord__sigma}\index{coord\_sigma@{coord\_sigma}} \doxysubsection{Detailed Description} Regrid columns for the sigma coordinate. \doxysubsection*{Data Types} \begin{DoxyCompactItemize} \item type \mbox{\hyperlink{structcoord__sigma_1_1sigma__cs}{sigma\+\_\+cs}} \begin{DoxyCompactList}\small\item\em Control structure containing required parameters for the sigma coordinate. \end{DoxyCompactList}\end{DoxyCompactItemize} \doxysubsection*{Functions/\+Subroutines} \begin{DoxyCompactItemize} \item subroutine, public \mbox{\hyperlink{namespacecoord__sigma_adce9c462a3b61ba3791035534e1d8b2a}{init\+\_\+coord\+\_\+sigma}} (CS, nk, coordinate\+Resolution) \begin{DoxyCompactList}\small\item\em Initialise a sigma\+\_\+\+CS with pointers to parameters. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacecoord__sigma_ac2489166e8a1e3e891b2e05df3b8d422}{end\+\_\+coord\+\_\+sigma}} (CS) \begin{DoxyCompactList}\small\item\em This subroutine deallocates memory in the control structure for the \mbox{\hyperlink{namespacecoord__sigma}{coord\+\_\+sigma}} module. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacecoord__sigma_aceccbaf232379cea8182c04130c03f5a}{set\+\_\+sigma\+\_\+params}} (CS, min\+\_\+thickness) \begin{DoxyCompactList}\small\item\em This subroutine can be used to set the parameters for the \mbox{\hyperlink{namespacecoord__sigma}{coord\+\_\+sigma}} module. \end{DoxyCompactList}\item subroutine, public \mbox{\hyperlink{namespacecoord__sigma_af3954fd955a967aa2ff11c2fc115dc19}{build\+\_\+sigma\+\_\+column}} (CS, depth, total\+Thickness, z\+Interface) \begin{DoxyCompactList}\small\item\em Build a sigma coordinate column. \end{DoxyCompactList}\end{DoxyCompactItemize} \doxysubsection{Function/\+Subroutine Documentation} \mbox{\Hypertarget{namespacecoord__sigma_af3954fd955a967aa2ff11c2fc115dc19}\label{namespacecoord__sigma_af3954fd955a967aa2ff11c2fc115dc19}} \index{coord\_sigma@{coord\_sigma}!build\_sigma\_column@{build\_sigma\_column}} \index{build\_sigma\_column@{build\_sigma\_column}!coord\_sigma@{coord\_sigma}} \doxysubsubsection{\texorpdfstring{build\_sigma\_column()}{build\_sigma\_column()}} {\footnotesize\ttfamily subroutine, public coord\+\_\+sigma\+::build\+\_\+sigma\+\_\+column (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structcoord__sigma_1_1sigma__cs}{sigma\+\_\+cs}}), intent(in)}]{CS, }\item[{real, intent(in)}]{depth, }\item[{real, intent(in)}]{total\+Thickness, }\item[{real, dimension(cs\%nk+1), intent(inout)}]{z\+Interface }\end{DoxyParamCaption})} Build a sigma coordinate column. \begin{DoxyParams}[1]{Parameters} \mbox{\texttt{ in}} & {\em cs} & Coordinate control structure \\ \hline \mbox{\texttt{ in}} & {\em depth} & Depth of ocean bottom (positive \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}) \\ \hline \mbox{\texttt{ in}} & {\em totalthickness} & Column thickness (positive \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]}) \\ \hline \mbox{\texttt{ in,out}} & {\em zinterface} & Absolute positions of interfaces \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]} \\ \hline \end{DoxyParams} Definition at line 64 of file coord\+\_\+sigma.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{64 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{intent(in)} :: CS\textcolor{comment}{ !< Coordinate control structure}} \DoxyCodeLine{65 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{intent(in)} :: depth\textcolor{comment}{ !< Depth of ocean bottom (positive [H \string~> m or kg m-\/2])}} \DoxyCodeLine{66 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{intent(in)} :: totalThickness\textcolor{comment}{ !< Column thickness (positive [H \string~> m or kg m-\/2])}} \DoxyCodeLine{67 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(CS\%nk+1)}, \textcolor{keywordtype}{intent(inout)} :: zInterface\textcolor{comment}{ !< Absolute positions of interfaces [H \string~> m or kg m-\/2]}} \DoxyCodeLine{68 } \DoxyCodeLine{69 \textcolor{comment}{! Local variables}} \DoxyCodeLine{70 \textcolor{keywordtype}{integer} :: k} \DoxyCodeLine{71 } \DoxyCodeLine{72 zinterface(cs\%nk+1) = -\/depth} \DoxyCodeLine{73 \textcolor{keywordflow}{do} k = cs\%nk,1,-\/1} \DoxyCodeLine{74 zinterface(k) = zinterface(k+1) + (totalthickness * cs\%coordinateResolution(k))} \DoxyCodeLine{75 \textcolor{comment}{! Adjust interface position to accommodate inflating layers}} \DoxyCodeLine{76 \textcolor{comment}{! without disturbing the interface above}} \DoxyCodeLine{77 \textcolor{keywordflow}{if} (zinterface(k) < (zinterface(k+1) + cs\%min\_thickness)) \textcolor{keywordflow}{then}} \DoxyCodeLine{78 zinterface(k) = zinterface(k+1) + cs\%min\_thickness} \DoxyCodeLine{79 \textcolor{keywordflow}{ endif}} \DoxyCodeLine{80 \textcolor{keywordflow}{ enddo}} \end{DoxyCode} \mbox{\Hypertarget{namespacecoord__sigma_ac2489166e8a1e3e891b2e05df3b8d422}\label{namespacecoord__sigma_ac2489166e8a1e3e891b2e05df3b8d422}} \index{coord\_sigma@{coord\_sigma}!end\_coord\_sigma@{end\_coord\_sigma}} \index{end\_coord\_sigma@{end\_coord\_sigma}!coord\_sigma@{coord\_sigma}} \doxysubsubsection{\texorpdfstring{end\_coord\_sigma()}{end\_coord\_sigma()}} {\footnotesize\ttfamily subroutine, public coord\+\_\+sigma\+::end\+\_\+coord\+\_\+sigma (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structcoord__sigma_1_1sigma__cs}{sigma\+\_\+cs}}), pointer}]{CS }\end{DoxyParamCaption})} This subroutine deallocates memory in the control structure for the \mbox{\hyperlink{namespacecoord__sigma}{coord\+\_\+sigma}} module. \begin{DoxyParams}{Parameters} {\em cs} & Coordinate control structure \\ \hline \end{DoxyParams} Definition at line 43 of file coord\+\_\+sigma.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{43 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Coordinate control structure}} \DoxyCodeLine{44 } \DoxyCodeLine{45 \textcolor{comment}{! nothing to do}} \DoxyCodeLine{46 \textcolor{keywordflow}{if} (.not. \textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return}} \DoxyCodeLine{47 \textcolor{keyword}{deallocate}(cs\%coordinateResolution)} \DoxyCodeLine{48 \textcolor{keyword}{deallocate}(cs)} \end{DoxyCode} \mbox{\Hypertarget{namespacecoord__sigma_adce9c462a3b61ba3791035534e1d8b2a}\label{namespacecoord__sigma_adce9c462a3b61ba3791035534e1d8b2a}} \index{coord\_sigma@{coord\_sigma}!init\_coord\_sigma@{init\_coord\_sigma}} \index{init\_coord\_sigma@{init\_coord\_sigma}!coord\_sigma@{coord\_sigma}} \doxysubsubsection{\texorpdfstring{init\_coord\_sigma()}{init\_coord\_sigma()}} {\footnotesize\ttfamily subroutine, public coord\+\_\+sigma\+::init\+\_\+coord\+\_\+sigma (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structcoord__sigma_1_1sigma__cs}{sigma\+\_\+cs}}), pointer}]{CS, }\item[{integer, intent(in)}]{nk, }\item[{real, dimension(\+:), intent(in)}]{coordinate\+Resolution }\end{DoxyParamCaption})} Initialise a sigma\+\_\+\+CS with pointers to parameters. \begin{DoxyParams}[1]{Parameters} & {\em cs} & Unassociated pointer to hold the control structure \\ \hline \mbox{\texttt{ in}} & {\em nk} & Number of layers in the grid \\ \hline \mbox{\texttt{ in}} & {\em coordinateresolution} & Nominal coordinate resolution \mbox{[}nondim\mbox{]} \\ \hline \end{DoxyParams} Definition at line 29 of file coord\+\_\+sigma.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{29 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Unassociated pointer to hold the control structure}} \DoxyCodeLine{30 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{intent(in)} :: nk\textcolor{comment}{ !< Number of layers in the grid}} \DoxyCodeLine{31 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(in)} :: coordinateResolution\textcolor{comment}{ !< Nominal coordinate resolution [nondim]}} \DoxyCodeLine{32 } \DoxyCodeLine{33 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"init\_coord\_sigma: CS already associated!"})} \DoxyCodeLine{34 \textcolor{keyword}{allocate}(cs)} \DoxyCodeLine{35 \textcolor{keyword}{allocate}(cs\%coordinateResolution(nk))} \DoxyCodeLine{36 } \DoxyCodeLine{37 cs\%nk = nk} \DoxyCodeLine{38 cs\%coordinateResolution = coordinateresolution} \end{DoxyCode} \mbox{\Hypertarget{namespacecoord__sigma_aceccbaf232379cea8182c04130c03f5a}\label{namespacecoord__sigma_aceccbaf232379cea8182c04130c03f5a}} \index{coord\_sigma@{coord\_sigma}!set\_sigma\_params@{set\_sigma\_params}} \index{set\_sigma\_params@{set\_sigma\_params}!coord\_sigma@{coord\_sigma}} \doxysubsubsection{\texorpdfstring{set\_sigma\_params()}{set\_sigma\_params()}} {\footnotesize\ttfamily subroutine, public coord\+\_\+sigma\+::set\+\_\+sigma\+\_\+params (\begin{DoxyParamCaption}\item[{type(\mbox{\hyperlink{structcoord__sigma_1_1sigma__cs}{sigma\+\_\+cs}}), pointer}]{CS, }\item[{real, intent(in), optional}]{min\+\_\+thickness }\end{DoxyParamCaption})} This subroutine can be used to set the parameters for the \mbox{\hyperlink{namespacecoord__sigma}{coord\+\_\+sigma}} module. \begin{DoxyParams}[1]{Parameters} & {\em cs} & Coordinate control structure \\ \hline \mbox{\texttt{ in}} & {\em min\+\_\+thickness} & Minimum allowed thickness \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]} \\ \hline \end{DoxyParams} Definition at line 53 of file coord\+\_\+sigma.\+F90. \begin{DoxyCode}{0} \DoxyCodeLine{53 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Coordinate control structure}} \DoxyCodeLine{54 \textcolor{keywordtype}{ real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: min\_thickness\textcolor{comment}{ !< Minimum allowed thickness [H \string~> m or kg m-\/2]}} \DoxyCodeLine{55 } \DoxyCodeLine{56 \textcolor{keywordflow}{if} (.not. \textcolor{keyword}{associated}(cs)) \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"set\_sigma\_params: CS not associated"})} \DoxyCodeLine{57 } \DoxyCodeLine{58 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(min\_thickness)) cs\%min\_thickness = min\_thickness} \end{DoxyCode}