Add updated documentation for the newly added and amended function

40602d75 · Pierre Cazenave · 75844713 · 40602d75 · 40602d75 · 40602d75
Commit 40602d75 authored Feb 04, 2013 by Pierre Cazenave
--- a/doc/fvcom_postproc/index.html
+++ b/doc/fvcom_postproc/index.html
@@ -24,8 +24,8 @@

 <h2>Subsequent directories:</h2>
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li>mat</li><li>plots</li><li>surface_plots</li><li>timeseries</li><li>transect_plots</li></ul>
+<li>plots</li><li>surface_plots</li><li>transect_plots</li></ul>

-<hr><address>Generated on Tue 18-Dec-2012 12:37:29 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Mon 04-Feb-2013 14:22:26 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file
--- a/doc/fvcom_prepro/add_sponge_nodes_list.html
+++ b/doc/fvcom_prepro/add_sponge_nodes_list.html
@@ -51,10 +51,12 @@
 Author(s):  
    Geoff Cowles (University of Massachusetts Dartmouth)
    Pierre Cazenave (Plymouth Marine Laboratory)
+    Karen Thurston (National Oceanography Centre, Liverpool)

 Revision history
    Modifed from add_sponge_nodes to read in nodes from a supplied list.
    2012-11-26 Add ability to turn off the figures.
+    2013-01-18 Added support for variable sponge radius
   
 ==============================================================================</pre></div>

@@ -97,69 +99,76 @@ This function is called by:
 0024 <span class="comment">% Author(s):</span>
 0025 <span class="comment">%    Geoff Cowles (University of Massachusetts Dartmouth)</span>
 0026 <span class="comment">%    Pierre Cazenave (Plymouth Marine Laboratory)</span>
-0027 <span class="comment">%</span>
-0028 <span class="comment">% Revision history</span>
-0029 <span class="comment">%    Modifed from add_sponge_nodes to read in nodes from a supplied list.</span>
-0030 <span class="comment">%    2012-11-26 Add ability to turn off the figures.</span>
-0031 <span class="comment">%</span>
-0032 <span class="comment">%==============================================================================</span>
-0033 subname = <span class="string">'add_sponge_nodes'</span>;
-0034 
-0035 <span class="keyword">global</span> ftbverbose
-0036 <span class="keyword">if</span>(ftbverbose)
-0037   fprintf(<span class="string">'\n'</span>)
-0038   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
-0039 <span class="keyword">end</span>
-0040 
-0041 <span class="comment">% Do we want a figure showing how we're getting along?</span>
-0042 <span class="keyword">if</span> nargin == 5
-0043     plotFig = 0;
-0044 <span class="keyword">end</span>
-0045 
-0046 <span class="comment">%------------------------------------------------------------------------------</span>
-0047 <span class="comment">% Plot the mesh</span>
+0027 <span class="comment">%    Karen Thurston (National Oceanography Centre, Liverpool)</span>
+0028 <span class="comment">%</span>
+0029 <span class="comment">% Revision history</span>
+0030 <span class="comment">%    Modifed from add_sponge_nodes to read in nodes from a supplied list.</span>
+0031 <span class="comment">%    2012-11-26 Add ability to turn off the figures.</span>
+0032 <span class="comment">%    2013-01-18 Added support for variable sponge radius</span>
+0033 <span class="comment">%</span>
+0034 <span class="comment">%==============================================================================</span>
+0035 subname = <span class="string">'add_sponge_nodes'</span>;
+0036 
+0037 <span class="keyword">global</span> ftbverbose
+0038 <span class="keyword">if</span>(ftbverbose)
+0039     fprintf(<span class="string">'\n'</span>)
+0040     fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0041 <span class="keyword">end</span>
+0042 
+0043 <span class="comment">% Do we want a figure showing how we're getting along?</span>
+0044 <span class="keyword">if</span> nargin == 5
+0045     plotFig = 0;
+0046 <span class="keyword">end</span>
+0047 
 0048 <span class="comment">%------------------------------------------------------------------------------</span>
-0049 <span class="keyword">if</span> plotFig == 1
-0050     <span class="keyword">if</span>(lower(Mobj.nativeCoords(1:3)) == <span class="string">'car'</span>)
-0051         x = Mobj.x;
-0052         y = Mobj.y;
-0053     <span class="keyword">else</span>
-0054         x = Mobj.lon;
-0055         y = Mobj.lat;
-0056     <span class="keyword">end</span>
-0057 
-0058     figure
-0059     patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
-0060             <span class="string">'Cdata'</span>,Mobj.h,<span class="string">'edgecolor'</span>,<span class="string">'k'</span>,<span class="string">'facecolor'</span>,<span class="string">'interp'</span>);
-0061     hold on;
-0062     plot(x(SpongeList),y(SpongeList),<span class="string">'wx'</span>)
-0063     axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
-0064 <span class="keyword">end</span>
-0065 
-0066 npts = size(SpongeList,2);
-0067 
-0068 <span class="keyword">if</span>(npts == 0)
-0069     fprintf(<span class="string">'No points in given list'</span>)
-0070     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0071     <span class="keyword">return</span>
-0072 <span class="keyword">end</span>
-0073 <span class="keyword">if</span>(ftbverbose)
-0074     fprintf(<span class="string">'%d points provided\n'</span>,npts)
+0049 <span class="comment">% Plot the mesh</span>
+0050 <span class="comment">%------------------------------------------------------------------------------</span>
+0051 
+0052 <span class="keyword">if</span> plotFig == 1
+0053     <span class="keyword">if</span>(lower(Mobj.nativeCoords(1:3)) == <span class="string">'car'</span>)
+0054         x = Mobj.x;
+0055         y = Mobj.y;
+0056     <span class="keyword">else</span>
+0057         x = Mobj.lon;
+0058         y = Mobj.lat;
+0059     <span class="keyword">end</span>
+0060 
+0061     figure
+0062     patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
+0063             <span class="string">'Cdata'</span>,Mobj.h,<span class="string">'edgecolor'</span>,<span class="string">'k'</span>,<span class="string">'facecolor'</span>,<span class="string">'interp'</span>);
+0064     hold on;
+0065     plot(x(SpongeList),y(SpongeList),<span class="string">'wx'</span>)
+0066     axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
+0067 <span class="keyword">end</span>
+0068 
+0069 npts = length(SpongeList);
+0070 
+0071 <span class="keyword">if</span>(npts == 0)
+0072     fprintf(<span class="string">'No points in given list'</span>)
+0073     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0074     <span class="keyword">return</span>
 0075 <span class="keyword">end</span>
-0076 
-0077 <span class="comment">% add to mesh object</span>
-0078 Mobj.nSponge = Mobj.nSponge + 1;
-0079 Mobj.nSpongeNodes(Mobj.nSponge) = npts;
-0080 Mobj.sponge_nodes(Mobj.nSponge,1:npts) = SpongeList;
-0081 Mobj.sponge_name{Mobj.nSponge} = SpongeName;
-0082 Mobj.sponge_rad(Mobj.nSponge) = SpongeRadius;
-0083 Mobj.sponge_fac(Mobj.nSponge) = SpongeCoeff;
-0084 
-0085 <span class="keyword">if</span>(ftbverbose)
-0086   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0087 <span class="keyword">end</span>
-0088 
-0089</pre></div>
-<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+0076 <span class="keyword">if</span>(ftbverbose)
+0077     fprintf(<span class="string">'%d points provided\n'</span>,npts)
+0078 <span class="keyword">end</span>
+0079 
+0080 <span class="comment">% add to mesh object</span>
+0081 Mobj.nSponge = Mobj.nSponge + 1;
+0082 Mobj.nSpongeNodes(Mobj.nSponge) = npts;
+0083 Mobj.sponge_nodes(Mobj.nSponge,1:npts) = SpongeList;
+0084 Mobj.sponge_name{Mobj.nSponge} = SpongeName;
+0085 Mobj.sponge_fac(Mobj.nSponge) = SpongeCoeff;
+0086 
+0087 <span class="keyword">if</span> max(size(SpongeRadius))==1   <span class="comment">% if you have a constant sponge radius</span>
+0088     Mobj.sponge_rad(Mobj.nSponge) = SpongeRadius;
+0089 <span class="keyword">else</span>    <span class="comment">% if you have a variable sponge radius</span>
+0090     Mobj.sponge_rad(Mobj.nSponge,1:npts) = SpongeRadius;
+0091 <span class="keyword">end</span>
+0092 
+0093 <span class="keyword">if</span>(ftbverbose)
+0094     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0095 <span class="keyword">end</span>
+0096</pre></div>
+<hr><address>Generated on Mon 04-Feb-2013 14:22:28 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file
--- a/doc/fvcom_prepro/calc_sponge_radius.html
+++ b/doc/fvcom_prepro/calc_sponge_radius.html
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+                "http://www.w3.org/TR/REC-html40/loose.dtd">
+<html>
+<head>
+  <title>Description of calc_sponge_radius</title>
+  <meta name="keywords" content="calc_sponge_radius">
+  <meta name="description" content="Calculate a variable sponge radius based on distance to the boundary">
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+  <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
+  <meta name="robots" content="index, follow">
+  <link type="text/css" rel="stylesheet" href="../m2html.css">
+</head>
+<body>
+<a name="_top"></a>
+<div><a href="../index.html">Home</a> &gt;  <a href="index.html">fvcom_prepro</a> &gt; calc_sponge_radius.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
+<td align="right"><a href="index.html">Index for fvcom_prepro&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>-->
+
+<h1>calc_sponge_radius
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>Calculate a variable sponge radius based on distance to the boundary</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>function [spongeRadius] = calc_sponge_radius(Mobj,Nlist) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> Calculate a variable sponge radius based on distance to the boundary
+ node's furthest neighbour.
+ (Adapted from Phil Hall's 'produce_netcdf_input_data.py')
+
+ spongeRadius = calc_sponge_radius(Mobj,Nlist) 
+
+ DESCRIPTION
+    Calculates the sponge radius for each node on the open boundary, based
+    on the minimum of either the distance to the node's furthest
+    neighbour, or 100 km.
+
+ INPUT
+    Mobj = Matlab mesh object
+    Nlist = List of nodes
+
+ OUTPUT
+    spongeRadius = List of variable sponge radii
+
+ EXAMPLE USAGE
+    spongeRadius = calc_sponge_radius(Mobj,Nlist)
+
+ Author(s)
+    Karen Thurston (National Oceanography Centre, Liverpool)
+
+==========================================================================</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+This function is called by:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [spongeRadius] = calc_sponge_radius(Mobj,Nlist) </a>
+0002 
+0003 <span class="comment">% Calculate a variable sponge radius based on distance to the boundary</span>
+0004 <span class="comment">% node's furthest neighbour.</span>
+0005 <span class="comment">% (Adapted from Phil Hall's 'produce_netcdf_input_data.py')</span>
+0006 <span class="comment">%</span>
+0007 <span class="comment">% spongeRadius = calc_sponge_radius(Mobj,Nlist)</span>
+0008 <span class="comment">%</span>
+0009 <span class="comment">% DESCRIPTION</span>
+0010 <span class="comment">%    Calculates the sponge radius for each node on the open boundary, based</span>
+0011 <span class="comment">%    on the minimum of either the distance to the node's furthest</span>
+0012 <span class="comment">%    neighbour, or 100 km.</span>
+0013 <span class="comment">%</span>
+0014 <span class="comment">% INPUT</span>
+0015 <span class="comment">%    Mobj = Matlab mesh object</span>
+0016 <span class="comment">%    Nlist = List of nodes</span>
+0017 <span class="comment">%</span>
+0018 <span class="comment">% OUTPUT</span>
+0019 <span class="comment">%    spongeRadius = List of variable sponge radii</span>
+0020 <span class="comment">%</span>
+0021 <span class="comment">% EXAMPLE USAGE</span>
+0022 <span class="comment">%    spongeRadius = calc_sponge_radius(Mobj,Nlist)</span>
+0023 <span class="comment">%</span>
+0024 <span class="comment">% Author(s)</span>
+0025 <span class="comment">%    Karen Thurston (National Oceanography Centre, Liverpool)</span>
+0026 <span class="comment">%</span>
+0027 <span class="comment">%==========================================================================</span>
+0028 subname = <span class="string">'calc_sponge_radius'</span>;
+0029 <span class="keyword">global</span> ftbverbose
+0030 <span class="keyword">if</span>(ftbverbose)
+0031   fprintf(<span class="string">'\n'</span>)
+0032   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0033 <span class="keyword">end</span>
+0034 
+0035 <span class="comment">%--------------------------------------------------------------------------</span>
+0036 <span class="comment">% Get a unique list and make sure they are in the range of node numbers</span>
+0037 <span class="comment">%--------------------------------------------------------------------------</span>
+0038 Nlist = unique(Nlist);
+0039 
+0040 spongeRadius = 100000+zeros(size(Nlist));
+0041 
+0042 <span class="comment">% For each node on the open boundary</span>
+0043 <span class="keyword">for</span> i =1:length(Nlist)
+0044     <span class="comment">% Find the neighbouring nodes</span>
+0045     [r,c]=find(Mobj.tri==Nlist(i));
+0046     neighbours = unique(Mobj.tri(r,:));
+0047     
+0048     <span class="comment">% Remove the node of interest from the neighbours list</span>
+0049     n = find(neighbours~=Nlist(i));
+0050     neighbours = neighbours(n);
+0051     
+0052     <span class="comment">% Calculate the arc length (in degrees) between the node and its</span>
+0053     <span class="comment">% neighbours</span>
+0054     arclen = distance(Mobj.lat(Nlist(i)),Mobj.lon(Nlist(i)),<span class="keyword">...</span>
+0055         Mobj.lat(neighbours),Mobj.lon(neighbours));
+0056     
+0057     <span class="comment">% Convert from degrees to whole metres</span>
+0058     arclen = ceil(1000*deg2km(arclen));
+0059     
+0060     <span class="comment">% If the smallest distance is less than 100km, keep it</span>
+0061     <span class="keyword">if</span> min(arclen)&lt;spongeRadius(i)
+0062         spongeRadius(i)=min(arclen);
+0063     <span class="keyword">end</span>
+0064 <span class="keyword">end</span>
+0065 
+0066 <span class="keyword">if</span>(ftbverbose)
+0067   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0068 <span class="keyword">end</span>
+0069</pre></div>
+<hr><address>Generated on Mon 04-Feb-2013 14:22:28 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+</body>
+</html>
\ No newline at end of file
--- a/doc/fvcom_prepro/get_AMM.html
+++ b/doc/fvcom_prepro/get_AMM.html
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+                "http://www.w3.org/TR/REC-html40/loose.dtd">
+<html>
+<head>
+  <title>Description of get_AMM</title>
+  <meta name="keywords" content="get_AMM">
+  <meta name="description" content="Extract boundary forcing information from NOC Operational Tide Surge">
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+  <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
+  <meta name="robots" content="index, follow">
+  <link type="text/css" rel="stylesheet" href="../m2html.css">
+</head>
+<body>
+<a name="_top"></a>
+<div><a href="../index.html">Home</a> &gt;  <a href="index.html">fvcom_prepro</a> &gt; get_AMM.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
+<td align="right"><a href="index.html">Index for fvcom_prepro&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>-->
+
+<h1>get_AMM
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>Extract boundary forcing information from NOC Operational Tide Surge</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>function [Mobj] = get_AMM(Mobj,StartDate,EndDate,ModelFolder) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> Extract boundary forcing information from NOC Operational Tide Surge
+ Model output output  
+
+ function get_AMM(Mobj,StartDate,EndDate,ModelFolder)
+
+ DESCRIPTION:
+    Extract boundary forcing information from NOC Operational Tide Surge
+    Model output and interpolate to FVCOM open boundary nodes.
+
+ INPUT
+    Mobj          = Matlab mesh object
+    StartDate     = Start date and time for FVCOM run
+    EndDate       = End date and time for FVCOM run
+    ModelFolder   = Location of AMM/S12 hourly outputs
+ 
+ OUTPUT:
+    Mobj.surfaceElevation = Addition to Matlab mesh object
+
+ EXAMPLE USAGE
+    function get_AMM(Mobj,StartDate,EndDate,ModelFolder)
+
+ Author(s):  
+    Karen Thurston (National Oceanography Centre Liverpool)
+
+ Revision history
+    2012-12-04 First version.
+   
+==============================================================================</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+This function is called by:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [Mobj] = get_AMM(Mobj,StartDate,EndDate,ModelFolder)</a>
+0002 
+0003 <span class="comment">% Extract boundary forcing information from NOC Operational Tide Surge</span>
+0004 <span class="comment">% Model output output</span>
+0005 <span class="comment">%</span>
+0006 <span class="comment">% function get_AMM(Mobj,StartDate,EndDate,ModelFolder)</span>
+0007 <span class="comment">%</span>
+0008 <span class="comment">% DESCRIPTION:</span>
+0009 <span class="comment">%    Extract boundary forcing information from NOC Operational Tide Surge</span>
+0010 <span class="comment">%    Model output and interpolate to FVCOM open boundary nodes.</span>
+0011 <span class="comment">%</span>
+0012 <span class="comment">% INPUT</span>
+0013 <span class="comment">%    Mobj          = Matlab mesh object</span>
+0014 <span class="comment">%    StartDate     = Start date and time for FVCOM run</span>
+0015 <span class="comment">%    EndDate       = End date and time for FVCOM run</span>
+0016 <span class="comment">%    ModelFolder   = Location of AMM/S12 hourly outputs</span>
+0017 <span class="comment">%</span>
+0018 <span class="comment">% OUTPUT:</span>
+0019 <span class="comment">%    Mobj.surfaceElevation = Addition to Matlab mesh object</span>
+0020 <span class="comment">%</span>
+0021 <span class="comment">% EXAMPLE USAGE</span>
+0022 <span class="comment">%    function get_AMM(Mobj,StartDate,EndDate,ModelFolder)</span>
+0023 <span class="comment">%</span>
+0024 <span class="comment">% Author(s):</span>
+0025 <span class="comment">%    Karen Thurston (National Oceanography Centre Liverpool)</span>
+0026 <span class="comment">%</span>
+0027 <span class="comment">% Revision history</span>
+0028 <span class="comment">%    2012-12-04 First version.</span>
+0029 <span class="comment">%</span>
+0030 <span class="comment">%==============================================================================</span>
+0031 subname = <span class="string">'get_AMM'</span>;
+0032 <span class="keyword">global</span> ftbverbose;
+0033 <span class="keyword">if</span>(ftbverbose);
+0034   fprintf(<span class="string">'\n'</span>)
+0035   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0036 <span class="keyword">end</span>;
+0037 
+0038 <span class="comment">%% Put the open boundary nodes into a single array for convenience</span>
+0039 count = 0;
+0040 ObcNodes = nan(1,sum(Mobj.nObcNodes));
+0041 <span class="keyword">for</span> ob=1:Mobj.nObs
+0042     nObcs = Mobj.nObcNodes(ob);
+0043     <span class="keyword">for</span> j=1:nObcs
+0044         count = count + 1;
+0045         ObcNodes(count) = Mobj.obc_nodes(ob,j);  <span class="comment">% set the open boundary nodes</span>
+0046     <span class="keyword">end</span>
+0047 <span class="keyword">end</span>
+0048 
+0049 <span class="comment">% Create an array of hourly timesteps</span>
+0050 timesteps = datevec(datenum(StartDate):1/24:datenum(EndDate));
+0051 
+0052 <span class="comment">% Initialise an array for the sea surface elevation</span>
+0053 SurfaceElevation = nan(count,size(timesteps,1));
+0054 
+0055 <span class="comment">% For each timestep, find the appropriate AMM/S12 file and extract the</span>
+0056 <span class="comment">% surface elevation</span>
+0057 <span class="keyword">for</span> i=1:size(timesteps,1)
+0058     <span class="comment">% Create AMM/S12 output filename from date</span>
+0059     <span class="comment">% First, accommodate Operational Model idiosyncracy about output times</span>
+0060     <span class="keyword">if</span> timesteps(i,3)==1 &amp;&amp; sum(timesteps(i,4:6)) == 0
+0061         tempdate = datevec(addtodate(datenum(timesteps(i,:)),-1,<span class="string">'month'</span>));
+0062         AMMfile=[ModelFolder,num2str(tempdate(1)),<span class="string">'-'</span>,num2str(tempdate(2),<span class="string">'%02i'</span>),<span class="string">'.nc'</span>];
+0063     <span class="keyword">else</span>
+0064         AMMfile=[ModelFolder,num2str(timesteps(i,1)),<span class="string">'-'</span>,num2str(timesteps(i,2),<span class="string">'%02i'</span>),<span class="string">'.nc'</span>];
+0065     <span class="keyword">end</span>
+0066     
+0067     <span class="comment">% Convert FVCOM timestep into AMM/S12 output (seconds since</span>
+0068     <span class="comment">% 20071101:000000)</span>
+0069     AMM_time = etime(timesteps(i,:),[2007,11,01,0,0,0]);
+0070     
+0071     <span class="comment">% Load the timeseries from the AMM/S12 output file</span>
+0072     AMM_timeseries = ncread(AMMfile,<span class="string">'time'</span>);
+0073     
+0074     <span class="comment">% Locate the appropriate timestep number</span>
+0075     AMM_timestep = find(AMM_timeseries==AMM_time);
+0076 
+0077     <span class="comment">% Load the sea surface elevation ouptut, lat and lon</span>
+0078     AMM_elev = ncread(AMMfile,<span class="string">'zet'</span>,[1 1 AMM_timestep],[Inf Inf 1])';
+0079     AMM_lat = ncread(AMMfile,<span class="string">'lat'</span>);
+0080     AMM_lon = ncread(AMMfile,<span class="string">'lon'</span>);
+0081     
+0082     <span class="comment">% Interpolate the sea surface elevation output to the open boundary</span>
+0083     <span class="comment">% nodes</span>
+0084     [X,Y]=meshgrid(AMM_lon,AMM_lat);
+0085     SurfaceElevation(:,i) = interp2(X,Y,AMM_elev,Mobj.lon(ObcNodes),<span class="keyword">...</span>
+0086         Mobj.lat(ObcNodes));    
+0087 <span class="keyword">end</span>
+0088 
+0089 Mobj.surfaceElevation = SurfaceElevation;
+0090 
+0091 <span class="keyword">if</span>(ftbverbose);
+0092     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>]);
+0093 <span class="keyword">end</span></pre></div>
+<hr><address>Generated on Mon 04-Feb-2013 14:22:28 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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+  <title>Description of get_HYCOM_forcing</title>
+  <meta name="keywords" content="get_HYCOM_forcing">
+  <meta name="description" content="Get mean flow, temperature and salinity data from HYCOM model outputs">
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+<div><a href="../index.html">Home</a> &gt;  <a href="index.html">fvcom_prepro</a> &gt; get_HYCOM_forcing.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
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+
+<h1>get_HYCOM_forcing
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>Get mean flow, temperature and salinity data from HYCOM model outputs</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>function data = get_HYCOM_forcing(Mobj, modelTime) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> Get mean flow, temperature and salinity data from HYCOM model outputs
+ through their OPeNDAP server. 
+ 
+ data = get_HYCOM_forcing(Mobj, modelTime)
+ 
+ DESCRIPTION:
+   Using OPeNDAP, extract the necessary parameters to create an FVCOM
+   forcing file. Requires the OPeNDAP toolbox (see below for where to get
+   it).
+ 
+ INPUT: 
+   Mobj - MATLAB mesh object
+   modelTime - Modified Julian Date start and end times
+ 
+ OUTPUT:
+   data - struct of the data necessary to force FVCOM. These can be
+   interpolated onto an unstructured grid in Mobj using
+   grid2fvcom.m.
+ 
+ The parameters which are obtained from the HYCOM data are:
+     - temperature
+     - salinity
+     - u flow component
+     - v flow component
+     - sea surface height (ssh)
+ 
+ REQUIRES:
+   The OPeNDAP toolbox:
+       http://www.opendap.org/pub/contributed/source/ml-toolbox/
+ 
+ Author(s)
+   Pierre Cazenave (Plymouth Marine Laboratory)
+ 
+ Revision history:
+   2013-01-31 First version.
+ 
+==========================================================================</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+This function is called by:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function data = get_HYCOM_forcing(Mobj, modelTime)</a>
+0002 <span class="comment">% Get mean flow, temperature and salinity data from HYCOM model outputs</span>
+0003 <span class="comment">% through their OPeNDAP server.</span>
+0004 <span class="comment">%</span>
+0005 <span class="comment">% data = get_HYCOM_forcing(Mobj, modelTime)</span>
+0006 <span class="comment">%</span>
+0007 <span class="comment">% DESCRIPTION:</span>
+0008 <span class="comment">%   Using OPeNDAP, extract the necessary parameters to create an FVCOM</span>
+0009 <span class="comment">%   forcing file. Requires the OPeNDAP toolbox (see below for where to get</span>
+0010 <span class="comment">%   it).</span>
+0011 <span class="comment">%</span>
+0012 <span class="comment">% INPUT:</span>
+0013 <span class="comment">%   Mobj - MATLAB mesh object</span>
+0014 <span class="comment">%   modelTime - Modified Julian Date start and end times</span>
+0015 <span class="comment">%</span>
+0016 <span class="comment">% OUTPUT:</span>
+0017 <span class="comment">%   data - struct of the data necessary to force FVCOM. These can be</span>
+0018 <span class="comment">%   interpolated onto an unstructured grid in Mobj using</span>
+0019 <span class="comment">%   grid2fvcom.m.</span>
+0020 <span class="comment">%</span>
+0021 <span class="comment">% The parameters which are obtained from the HYCOM data are:</span>
+0022 <span class="comment">%     - temperature</span>
+0023 <span class="comment">%     - salinity</span>
+0024 <span class="comment">%     - u flow component</span>
+0025 <span class="comment">%     - v flow component</span>
+0026 <span class="comment">%     - sea surface height (ssh)</span>
+0027 <span class="comment">%</span>
+0028 <span class="comment">% REQUIRES:</span>
+0029 <span class="comment">%   The OPeNDAP toolbox:</span>
+0030 <span class="comment">%       http://www.opendap.org/pub/contributed/source/ml-toolbox/</span>
+0031 <span class="comment">%</span>
+0032 <span class="comment">% Author(s)</span>
+0033 <span class="comment">%   Pierre Cazenave (Plymouth Marine Laboratory)</span>
+00