Update the documentation for the latest release.

eb37fbcc · Pierre Cazenave · bd1b624c · eb37fbcc · eb37fbcc · eb37fbcc
Commit eb37fbcc authored Jul 29, 2014 by Pierre Cazenave
225 changed files
--- a/doc/fvcom_postproc/README.html
+++ b/doc/fvcom_postproc/README.html
@@ -59,6 +59,6 @@ This function is called by:
 0007 <span class="comment">% Revision history</span>
 0008 <span class="comment">%</span>
 0009 <span class="comment">%==============================================================================</span></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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_postproc/example_surface_plot.html
+++ b/doc/fvcom_postproc/example_surface_plot.html
@@ -184,6 +184,6 @@ This function is called by:
 0120 <span class="comment">% vector plots requires correct lat and lon for u and v positions: FVCOM.xc</span>
 0121 <span class="comment">% and FVCOM.yc. Remember to extract them</span>
 0122 PLotoutV=do_vector_plot(plotOPTS,FVCOM)</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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_postproc/graph.html
+++ b/doc/fvcom_postproc/graph.html
@@ -19,11 +19,11 @@
 <center>
 <img src="graph.png" usemap="#mainmap" alt="Dependency Graph for fvcom_postproc" border="2" style="color:#000;">  
 <map name="mainmap">
-<area shape="poly" id="node1" href="README.html" title="README" alt="" coords="144,31 141,23 131,16 116,10 96,6 75,5 53,6 34,10 18,16 8,23 5,31 8,39 18,46 34,51 53,55 75,56 96,55 116,51 131,46 141,39">
-<area shape="poly" id="node2" href="example_surface_plot.html" title="example_surface_plot" alt="" coords="426,31 420,23 402,16 373,10 337,6 297,5 257,6 221,10 193,16 174,23 168,31 174,39 193,46 221,51 257,55 297,56 337,55 373,51 402,46 420,39">
+<area shape="poly" id="node1" href="README.html" title="README" alt="" coords="133,29,130,22,121,15,107,10,89,7,69,5,50,7,32,10,17,15,8,22,5,29,8,37,17,43,32,49,50,52,69,53,89,52,107,49,121,43,130,37">
+<area shape="poly" id="node2" href="example_surface_plot.html" title="example_surface_plot" alt="" coords="395,29,389,22,372,15,346,10,313,7,276,5,239,7,206,10,180,15,163,22,157,29,163,37,180,43,206,49,239,52,276,53,313,52,346,49,372,43,389,37">
 </map> 
 </center>

-<hr><address>Generated on Tue 04-Jun-2013 12:12:56 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 Tue 29-Jul-2014 15:11:01 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_postproc/graph.map
+++ b/doc/fvcom_postproc/graph.map
-<area shape="poly" id="node1" href="README.html" title="README" alt="" coords="144,31 141,23 131,16 116,10 96,6 75,5 53,6 34,10 18,16 8,23 5,31 8,39 18,46 34,51 53,55 75,56 96,55 116,51 131,46 141,39">
-<area shape="poly" id="node2" href="example_surface_plot.html" title="example_surface_plot" alt="" coords="426,31 420,23 402,16 373,10 337,6 297,5 257,6 221,10 193,16 174,23 168,31 174,39 193,46 221,51 257,55 297,56 337,55 373,51 402,46 420,39">
+<area shape="poly" id="node1" href="README.html" title="README" alt="" coords="133,29,130,22,121,15,107,10,89,7,69,5,50,7,32,10,17,15,8,22,5,29,8,37,17,43,32,49,50,52,69,53,89,52,107,49,121,43,130,37">
+<area shape="poly" id="node2" href="example_surface_plot.html" title="example_surface_plot" alt="" coords="395,29,389,22,372,15,346,10,313,7,276,5,239,7,206,10,180,15,163,22,157,29,163,37,180,43,206,49,239,52,276,53,313,52,346,49,372,43,389,37">
--- a/doc/fvcom_postproc/graph.png
+++ b/doc/fvcom_postproc/graph.png
--- a/doc/fvcom_postproc/index.html
+++ b/doc/fvcom_postproc/index.html
@@ -29,6 +29,6 @@
 <ul style="list-style-image:url(../simulinkicon.gif)">
 <li>View the <a href="graph.html">Graph</a>.</li>
 </ul>
-<hr><address>Generated on Tue 04-Jun-2013 12:12:54 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 Tue 29-Jul-2014 15:10:59 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/README.html
+++ b/doc/fvcom_prepro/README.html
@@ -73,6 +73,6 @@ This function is called by:
 0014 <span class="comment">% Revision history</span>
 0015 <span class="comment">%</span>
 0016 <span class="comment">%==============================================================================</span></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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_coriolis.html
+++ b/doc/fvcom_prepro/add_coriolis.html
@@ -62,7 +62,7 @@ This function calls:
 </ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="example.html" class="code" title="">example</a>	example demonstrating reading in a 2DM file and constructing a model</li></ul>
+<li><a href="example.html" class="code" title="">example</a>	example demonstrating reading in a 2DM file and constructing a model</li><li><a href="read_grid_mesh.html" class="code" title="function [Mobj] = read_grid_mesh(varargin)">read_grid_mesh</a>	Read .grid mesh files into Matlab mesh object</li></ul>
 <!-- crossreference -->


@@ -144,6 +144,6 @@ This function is called by:
 0074 
 0075 
 0076</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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_obc_nodes_graphic.html
+++ b/doc/fvcom_prepro/add_obc_nodes_graphic.html
@@ -160,6 +160,6 @@ This function is called by:
 0088   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0089 <span class="keyword">end</span>;
 0090</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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_obc_nodes_list.html
+++ b/doc/fvcom_prepro/add_obc_nodes_list.html
@@ -51,10 +51,13 @@
 Author(s):  
    Geoff Cowles (University of Massachusetts Dartmouth)
    Pierre Cazenave (Plymouth Marine Laboratory)
-
+    Karen Amoudry (National Oceanography Centre, Liverpool)

 Revision history:
    2012-11-26 Add ability to turn off the figures.
+    2013-01-02 KJA bug fix: amended usage of 'unique' in line 53 to
+    prevent it from sorting the values it returns. Amended by Pierre to
+    support pre-2012 versions of MATLAB whilst giving the same result.
   
 ==========================================================================</pre></div>

@@ -97,69 +100,75 @@ 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>
+0027 <span class="comment">%    Karen Amoudry (National Oceanography Centre, Liverpool)</span>
 0028 <span class="comment">%</span>
 0029 <span class="comment">% Revision history:</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_obc_nodes'</span>;
-0034 <span class="keyword">global</span> ftbverbose
-0035 <span class="keyword">if</span>(ftbverbose)
-0036   fprintf(<span class="string">'\n'</span>)
-0037   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
-0038 <span class="keyword">end</span>
-0039 
-0040 <span class="comment">% Do we want a figure showing how we're getting along?</span>
-0041 <span class="keyword">if</span> nargin == 4
-0042     plotFig = 0;
-0043 <span class="keyword">end</span>
-0044 
-0045 <span class="comment">%--------------------------------------------------------------------------</span>
-0046 <span class="comment">% Get a unique list and make sure they are in the range of node numbers</span>
-0047 <span class="comment">%--------------------------------------------------------------------------</span>
-0048 Nlist = unique(Nlist);
-0049 
-0050 <span class="keyword">if</span>(max(Nlist) &gt; Mobj.nVerts);
-0051   fprintf(<span class="string">'your open boundary node number exceed the total number of nodes in the domain\n'</span>);
-0052   error(<span class="string">'stopping...\n'</span>)
-0053 <span class="keyword">end</span>
-0054 
-0055 <span class="comment">%--------------------------------------------------------------------------</span>
-0056 <span class="comment">% Plot the mesh</span>
-0057 <span class="comment">%--------------------------------------------------------------------------</span>
-0058 <span class="keyword">if</span> plotFig == 1
-0059     <span class="keyword">if</span> strcmpi(Mobj.nativeCoords(1:3), <span class="string">'car'</span>)
-0060         x = Mobj.x;
-0061         y = Mobj.y;
-0062     <span class="keyword">else</span>
-0063         x = Mobj.lon;
-0064         y = Mobj.lat;
-0065     <span class="keyword">end</span>
-0066 
-0067     figure
-0068     patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
-0069             <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>);
-0070     hold on;
-0071     whos Nlist
-0072     plot(x(Nlist),y(Nlist),<span class="string">'ro'</span>);
-0073     axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
-0074     title(<span class="string">'open boundary nodes'</span>);
-0075 <span class="keyword">end</span>
-0076 
-0077 <span class="comment">% add to mesh object</span>
-0078 npts = numel(Nlist);
-0079 Mobj.nObs = Mobj.nObs + 1;
-0080 Mobj.nObcNodes(Mobj.nObs) = npts; 
-0081 Mobj.obc_nodes(Mobj.nObs,1:npts) = Nlist;
-0082 Mobj.obc_name{Mobj.nObs} = ObcName;
-0083 Mobj.obc_type(Mobj.nObs) = ObcType;
-0084 
-0085 
-0086 <span class="keyword">if</span>(ftbverbose)
-0087   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0088 <span class="keyword">end</span>
-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>
+0031 <span class="comment">%    2013-01-02 KJA bug fix: amended usage of 'unique' in line 53 to</span>
+0032 <span class="comment">%    prevent it from sorting the values it returns. Amended by Pierre to</span>
+0033 <span class="comment">%    support pre-2012 versions of MATLAB whilst giving the same result.</span>
+0034 <span class="comment">%</span>
+0035 <span class="comment">%==========================================================================</span>
+0036 subname = <span class="string">'add_obc_nodes'</span>;
+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 == 4
+0045     plotFig = 0;
+0046 <span class="keyword">end</span>
+0047 
+0048 <span class="comment">%--------------------------------------------------------------------------</span>
+0049 <span class="comment">% Get a unique list and make sure they are in the range of node numbers</span>
+0050 <span class="comment">%--------------------------------------------------------------------------</span>
+0051 <span class="comment">% Make this works in versions of MATLAB older than 2012a (newer versions</span>
+0052 <span class="comment">% can just use unique(A, 'stable'), but checking versions is a pain).</span>
+0053 [~, Nidx] = unique(Nlist);
+0054 Nlist = Nlist(sort(Nidx));
+0055 
+0056 <span class="keyword">if</span> max(Nlist) &gt; Mobj.nVerts
+0057   fprintf(<span class="string">'your open boundary node number exceed the total number of nodes in the domain\n'</span>);
+0058   error(<span class="string">'stopping...'</span>)
+0059 <span class="keyword">end</span>
+0060 
+0061 <span class="comment">%--------------------------------------------------------------------------</span>
+0062 <span class="comment">% Plot the mesh</span>
+0063 <span class="comment">%--------------------------------------------------------------------------</span>
+0064 <span class="keyword">if</span> plotFig == 1
+0065     <span class="keyword">if</span> strcmpi(Mobj.nativeCoords(1:3), <span class="string">'car'</span>)
+0066         x = Mobj.x;
+0067         y = Mobj.y;
+0068     <span class="keyword">else</span>
+0069         x = Mobj.lon;
+0070         y = Mobj.lat;
+0071     <span class="keyword">end</span>
+0072 
+0073     figure
+0074     patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
+0075             <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>);
+0076     hold on;
+0077     whos Nlist
+0078     plot(x(Nlist),y(Nlist),<span class="string">'ro'</span>);
+0079     axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
+0080     title(<span class="string">'open boundary nodes'</span>);
+0081 <span class="keyword">end</span>
+0082 
+0083 <span class="comment">% add to mesh object</span>
+0084 npts = numel(Nlist);
+0085 Mobj.nObs = Mobj.nObs + 1;
+0086 Mobj.nObcNodes(Mobj.nObs) = npts; 
+0087 Mobj.obc_nodes(Mobj.nObs,1:npts) = Nlist;
+0088 Mobj.obc_name{Mobj.nObs} = ObcName;
+0089 Mobj.obc_type(Mobj.nObs) = ObcType;
+0090 
+0091 
+0092 <span class="keyword">if</span>(ftbverbose)
+0093   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0094 <span class="keyword">end</span>
+0095</pre></div>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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_river_nodes_graphic.html
+++ b/doc/fvcom_prepro/add_river_nodes_graphic.html
@@ -46,12 +46,14 @@

 Author(s):  
    Geoff Cowles (University of Massachusetts Dartmouth)
+    Pierre Cazenave (Plymouth Marine Laboratory)

 Note:
    Uses ginput2 which allows zooming before selecting points and displays
    clicked points realtime

 Revision history
+    2014-05-20 Set boolean flag to true to indicate rivers.
   
 ==============================================================================</pre></div>

@@ -89,78 +91,81 @@ This function is called by:
 0019 <span class="comment">%</span>
 0020 <span class="comment">% Author(s):</span>
 0021 <span class="comment">%    Geoff Cowles (University of Massachusetts Dartmouth)</span>
-0022 <span class="comment">%</span>
-0023 <span class="comment">% Note:</span>
-0024 <span class="comment">%    Uses ginput2 which allows zooming before selecting points and displays</span>
-0025 <span class="comment">%    clicked points realtime</span>
-0026 <span class="comment">%</span>
-0027 <span class="comment">% Revision history</span>
-0028 <span class="comment">%</span>
-0029 <span class="comment">%==============================================================================</span>
-0030 subname = <span class="string">'add_river_nodes'</span>;
-0031 <span class="keyword">global</span> ftbverbose
-0032 <span class="keyword">if</span>(ftbverbose)
-0033   fprintf(<span class="string">'\n'</span>)
-0034   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
-0035 <span class="keyword">end</span>;
-0036 
-0037 
-0038 <span class="comment">%------------------------------------------------------------------------------</span>
-0039 <span class="comment">% Plot the mesh</span>
+0022 <span class="comment">%    Pierre Cazenave (Plymouth Marine Laboratory)</span>
+0023 <span class="comment">%</span>
+0024 <span class="comment">% Note:</span>
+0025 <span class="comment">%    Uses ginput2 which allows zooming before selecting points and displays</span>
+0026 <span class="comment">%    clicked points realtime</span>
+0027 <span class="comment">%</span>
+0028 <span class="comment">% Revision history</span>
+0029 <span class="comment">%    2014-05-20 Set boolean flag to true to indicate rivers.</span>
+0030 <span class="comment">%</span>
+0031 <span class="comment">%==============================================================================</span>
+0032 subname = <span class="string">'add_river_nodes'</span>;
+0033 <span class="keyword">global</span> ftbverbose
+0034 <span class="keyword">if</span>(ftbverbose)
+0035   fprintf(<span class="string">'\n'</span>)
+0036   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0037 <span class="keyword">end</span>;
+0038 
+0039 
 0040 <span class="comment">%------------------------------------------------------------------------------</span>
-0041 
-0042 <span class="keyword">if</span>(lower(Mobj.nativeCoords(1:3)) == <span class="string">'car'</span>)
-0043     x = Mobj.x;
-0044     y = Mobj.y;
-0045 <span class="keyword">else</span>
-0046     x = Mobj.lon;
-0047     y = Mobj.lat;
-0048 <span class="keyword">end</span>;
-0049 
-0050 figure
-0051 patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
-0052         <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>);
-0053 hold on;
-0054 
-0055 <span class="comment">% use ginput2 (which allows zooming and plots points as they are clicked) to let</span>
-0056 <span class="comment">% user select the boundary points</span>
-0057 fprintf(<span class="string">'click the river nodes in the model\n'</span>)
-0058 fprintf(<span class="string">'left click:  zoom\n'</span>);
-0059 fprintf(<span class="string">'delete:  delete last point\n'</span>);
-0060 fprintf(<span class="string">'drag mouse: pan\n'</span>);
-0061 fprintf(<span class="string">'right click: select point\n'</span>);
-0062 fprintf(<span class="string">'enter (return): finished selecting points\n'</span>);
-0063 [xselect] = ginput2(true,<span class="string">'r+'</span>);
-0064 
-0065 
-0066 [npts,jnk] = size(xselect);
+0041 <span class="comment">% Plot the mesh</span>
+0042 <span class="comment">%------------------------------------------------------------------------------</span>
+0043 
+0044 <span class="keyword">if</span>(lower(Mobj.nativeCoords(1:3)) == <span class="string">'car'</span>)
+0045     x = Mobj.x;
+0046     y = Mobj.y;
+0047 <span class="keyword">else</span>
+0048     x = Mobj.lon;
+0049     y = Mobj.lat;
+0050 <span class="keyword">end</span>;
+0051 
+0052 figure
+0053 patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
+0054         <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>);
+0055 hold on;
+0056 
+0057 <span class="comment">% use ginput2 (which allows zooming and plots points as they are clicked) to let</span>
+0058 <span class="comment">% user select the boundary points</span>
+0059 fprintf(<span class="string">'click the river nodes in the model\n'</span>)
+0060 fprintf(<span class="string">'left click:  zoom\n'</span>);
+0061 fprintf(<span class="string">'delete:  delete last point\n'</span>);
+0062 fprintf(<span class="string">'drag mouse: pan\n'</span>);
+0063 fprintf(<span class="string">'right click: select point\n'</span>);
+0064 fprintf(<span class="string">'enter (return): finished selecting points\n'</span>);
+0065 [xselect] = ginput2(true,<span class="string">'r+'</span>);
+0066 
 0067 
-0068 <span class="keyword">if</span>(npts == 0)
-0069     fprintf(<span class="string">'you didn''t select any points'</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 fprintf(<span class="string">'you selected %d points\n'</span>,npts)
-0074 
-0075 <span class="comment">% snap to the closest vertices</span>
-0076 <span class="keyword">for</span> i=1:npts
-0077     [ipt(i),dist] = <a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>(xselect(i,1),xselect(i,2),Mobj);
-0078 <span class="keyword">end</span>;
-0079 
-0080 <span class="comment">% replot domain with snapped vertices</span>
-0081 plot(x(ipt),y(ipt),<span class="string">'ro'</span>);
-0082 
-0083 <span class="comment">% add to mesh object</span>
-0084 Mobj.nRivers = Mobj.nRivers + 1;
-0085 Mobj.nRivNodes(Mobj.nRivers) = npts;
-0086 Mobj.riv_nodes(Mobj.nRivers,1:npts) = ipt;
-0087 Mobj.riv_name{Mobj.nRivers} = RiverName;
-0088 
-0089 
-0090 <span class="keyword">if</span>(ftbverbose)
-0091   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0092 <span class="keyword">end</span>;
-0093</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>
+0068 [npts,jnk] = size(xselect);
+0069 
+0070 <span class="keyword">if</span>(npts == 0)
+0071     fprintf(<span class="string">'you didn''t select any points'</span>)
+0072     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0073     <span class="keyword">return</span>
+0074 <span class="keyword">end</span>;
+0075 fprintf(<span class="string">'you selected %d points\n'</span>,npts)
+0076 
+0077 <span class="comment">% snap to the closest vertices</span>
+0078 <span class="keyword">for</span> i=1:npts
+0079     [ipt(i),dist] = <a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>(xselect(i,1),xselect(i,2),Mobj);
+0080 <span class="keyword">end</span>;
+0081 
+0082 <span class="comment">% replot domain with snapped vertices</span>
+0083 plot(x(ipt),y(ipt),<span class="string">'ro'</span>);
+0084 
+0085 <span class="comment">% add to mesh object</span>
+0086 Mobj.nRivers = Mobj.nRivers + 1;
+0087 Mobj.nRivNodes(Mobj.nRivers) = npts;
+0088 Mobj.riv_nodes(Mobj.nRivers,1:npts) = ipt;
+0089 Mobj.riv_name{Mobj.nRivers} = RiverName;
+0090 
+0091 Mobj.have_rivers = true;
+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 Tue 29-Jul-2014 15:11:16 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_river_nodes_list.html
+++ b/doc/fvcom_prepro/add_river_nodes_list.html
--- a/doc/fvcom_prepro/add_sigma_forDT.html
+++ b/doc/fvcom_prepro/add_sigma_forDT.html
@@ -91,6 +91,6 @@ This function is called by:
 0045 nc = close(nc);
 0046 
 0047</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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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.html
+++ b/doc/fvcom_prepro/add_sponge_nodes.html
@@ -157,6 +157,6 @@ This function is called by:
 0085 
 0086 fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0087</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>
+<hr><address>Generated on Tue 29-Jul-2014 15:11:16 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
@@ -169,6 +169,6 @@ This function is called by:
 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 Tue 04-Jun-2013 12:12:57 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 Tue 29-Jul-2014 15:11:16 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_stations_list.html
+++ b/doc/fvcom_prepro/add_stations_list.html
@@ -177,6 +177,6 @@ This function is called by:
 0098         fprintf(<span class="string">'No stations found within the model domain.\n'</span>)
 0099     <span class="keyword">end</span>
 0100 <span class="keyword">end</span></pre></div>
-<hr><address>Generated on Tue 04-Jun-2013 12:12:57 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 Tue 29-Jul-2014 15:11:16 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_var_FVCOM_river.html
+++ b/doc/fvcom_prepro/add_var_FVCOM_river.html
@@ -172,6 +172,6 @@ This function is called by:
 0098   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0099 <span class="keyword">end</span>;
 0100</pre></div>
-<hr><address>Generated on Tue 04-Jun-2013 12:12:57 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 Tue 29-Jul-2014 15:11:16 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
@@ -49,7 +49,15 @@
    spongeRadius = calc_sponge_radius(Mobj,Nlist)

 Author(s)
-    Karen Thurston (National Oceanography Centre, Liverpool)
+    Karen Amoudry (National Oceanography Centre, Liverpool)
+    Pierre Cazenave (Plymouth Marine Laboratory)
+
+ Revision history:
+    2013-01-02 KJA bug fix: amended usage of 'unique' to prevent it from
+    sorting the values it returns. Amended by Pierre to support pre-2012
+    versions of MATLAB whilst giving the same result.
+    2013-07-16 KJA: adapted function to remove dependency on the Matlab
+    Mapping Toolbox.

 ==========================================================================</pre></div>

@@ -90,51 +98,78 @@ This function is called by:
 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>
+0025 <span class="comment">%    Karen Amoudry (National Oceanography Centre, Liverpool)</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">%    2013-01-02 KJA bug fix: amended usage of 'unique' to prevent it from</span>
+0030 <span class="comment">%    sorting the values it returns. Amended by Pierre to support pre-2012</span>
+0031 <span class="comment">%    versions of MATLAB whilst giving the same result.</span>
+0032 <span class="comment">%    2013-07-16 KJA: adapted function to remove dependency on the Matlab</span>
+0033 <span class="comment">%    Mapping Toolbox.</span>
+0034 <span class="comment">%</span>
+0035 <span class="comment">%==========================================================================</span>
+0036 subname = <span class="string">'calc_sponge_radius'</span>;
+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">%--------------------------------------------------------------------------</span>
+0044 <span class="comment">% Get a unique list and make sure they are in the range of node numbers</span>
+0045 <span class="comment">%--------------------------------------------------------------------------</span>
+0046 <span class="comment">% Make this work in versions of MATLAB older than 2012a (newer versions</span>
+0047 <span class="comment">% can just use unique(A, 'stable'), but checking versions is a pain).</span>
+0048 [~, Nidx] = unique(Nlist);
+0049 Nlist = Nlist(sort(Nidx));
+0050 
+0051 spongeRadius = 100000+zeros(size(Nlist));
+0052 
+0053 <span class="comment">% For each node on the open boundary</span>
+0054 <span class="keyword">for</span> i =1:length(Nlist)
+0055     <span class="comment">% Find the neighbouring nodes</span>
+0056     [r,c]=find(Mobj.tri==Nlist(i));
+0057     neighbours = Mobj.tri(r,:);
+0058     [~,neighidx] = unique(Mobj.tri(r,:));
+0059     neighbours = neighbours(sort(neighidx));
+0060     
+0061     <span class="comment">% Remove the node of interest from the neighbours list</span>