\hypertarget{namespacecoord__sigma}{}\section{coord\+\_\+sigma Module Reference} \label{namespacecoord__sigma}\index{coord\+\_\+sigma@{coord\+\_\+sigma}} \subsection{Detailed Description} Regrid columns for the sigma coordinate. \subsection*{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} \subsection*{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} \subsection{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}} \subsubsection{\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{\tt in} & {\em cs} & Coordinate control structure\\ \hline \mbox{\tt in} & {\em depth} & Depth of ocean bottom (positive \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]})\\ \hline \mbox{\tt in} & {\em totalthickness} & Column thickness (positive \mbox{[}H $\sim$$>$ m or kg m-\/2\mbox{]})\\ \hline \mbox{\tt 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} 64 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{intent(in)} :: CS\textcolor{comment}{ !< Coordinate control structure} 65 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{intent(in)} :: depth\textcolor{comment}{ !< Depth of ocean bottom (positive [H ~> m or kg m-2])} 66 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{intent(in)} :: totalThickness\textcolor{comment}{ !< Column thickness (positive [H ~> m or kg m-2])} 67 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(CS%nk+1)}, \textcolor{keywordtype}{intent(inout)} :: zInterface\textcolor{comment}{ !< Absolute positions of interfaces [H ~> m or kg m-2]} 68 69 \textcolor{comment}{! Local variables} 70 \textcolor{keywordtype}{integer} :: k 71 72 zinterface(cs%nk+1) = -depth 73 \textcolor{keywordflow}{do} k = cs%nk,1,-1 74 zinterface(k) = zinterface(k+1) + (totalthickness * cs%coordinateResolution(k)) 75 \textcolor{comment}{! Adjust interface position to accommodate inflating layers} 76 \textcolor{comment}{! without disturbing the interface above} 77 \textcolor{keywordflow}{if} (zinterface(k) < (zinterface(k+1) + cs%min\_thickness)) \textcolor{keywordflow}{then} 78 zinterface(k) = zinterface(k+1) + cs%min\_thickness 79 \textcolor{keywordflow}{ endif} 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}} \subsubsection{\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} 43 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Coordinate control structure} 44 45 \textcolor{comment}{! nothing to do} 46 \textcolor{keywordflow}{if} (.not. \textcolor{keyword}{associated}(cs)) \textcolor{keywordflow}{return} 47 \textcolor{keyword}{deallocate}(cs%coordinateResolution) 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}} \subsubsection{\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{\tt in} & {\em nk} & Number of layers in the grid\\ \hline \mbox{\tt in} & {\em coordinateresolution} & Nominal coordinate resolution \mbox{[}nondim\mbox{]} \\ \hline \end{DoxyParams} Definition at line 29 of file coord\+\_\+sigma.\+F90. \begin{DoxyCode} 29 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Unassociated pointer to hold the control structure} 30 \textcolor{keywordtype}{integer}, \textcolor{keywordtype}{intent(in)} :: nk\textcolor{comment}{ !< Number of layers in the grid} 31 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{dimension(:)}, \textcolor{keywordtype}{intent(in)} :: coordinateResolution\textcolor{comment}{ !< Nominal coordinate resolution [nondim]} 32 33 \textcolor{keywordflow}{if} (\textcolor{keyword}{associated}(cs)) \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"init\_coord\_sigma: CS already associated!"}) 34 \textcolor{keyword}{allocate}(cs) 35 \textcolor{keyword}{allocate}(cs%coordinateResolution(nk)) 36 37 cs%nk = nk 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}} \subsubsection{\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{\tt 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} 53 \textcolor{keywordtype}{type}(sigma\_CS), \textcolor{keywordtype}{pointer} :: CS\textcolor{comment}{ !< Coordinate control structure} 54 \textcolor{keywordtype}{real}, \textcolor{keywordtype}{optional}, \textcolor{keywordtype}{intent(in)} :: min\_thickness\textcolor{comment}{ !< Minimum allowed thickness [H ~> m or kg m-2]} 55 56 \textcolor{keywordflow}{if} (.not. \textcolor{keyword}{associated}(cs)) \textcolor{keyword}{call }mom\_error(fatal, \textcolor{stringliteral}{"set\_sigma\_params: CS not associated"}) 57 58 \textcolor{keywordflow}{if} (\textcolor{keyword}{present}(min\_thickness)) cs%min\_thickness = min\_thickness \end{DoxyCode}