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fvcom-toolbox
fvcom-toolbox
Commit 3ac27449 authored by Pierre Cazenave's avatar Pierre Cazenave
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Prepare for a new release.

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PML_ChangeLog.txt
View file @ 3ac27449
Pierre Cazenave <pica@pml.ac.uk> fvcom-toolbox ChangeLog
20190220
--------
Minor update.
Thanks to Ricardo Torres and Simon Waldman for their contributions.
README.md
Updated with the current release details.
doc:
Updated for the latest release.
fvcom_postproc:
do_surface_plotMatlabMap
* Cosmetic changes to the plot.
show_max_CFL
* New function to compute the CFL number for a given grid.
fvcom_prepro:
add_obc_node_list
* Fix checks for invalid open boundaries.
add_sponge_nodes_list
* Code cleanup.
add_weights_FVCOM_nested_forcing
* Fix shape of the weights for the nodes.
change_shallow_bathy
* New function to adjust bathymetry in the grid.
find_nesting_region
* Code cleanup.
hybrid_coordinate
* Fix output format for the sigma file.
interp_POLCOMS2FVCOM
* Merge the v1 version of this and remove the duplicate.
make_default_nml
* Tweak the default number format for bed roughness.
read_fabm_variables
* Code cleanup.
read_sigma
* Add complete support for generalised and hyperbolic tangent sigma distributions.
read_sms_mesh
* Allow a given depth file to override values in the .2dm.
set_elevtide_tmd
* Add argument for the location of the TMD data.
write_FVCOM_river_nml
* Add argument to supply a vertical distribution as fractional depths (0-1).
write_FVCOM_tsobcERSEM
* Code cleanup.
utilities:
ComputeMatricRx1_nodes
* New function to calculate the hydrostatic consistency condition.
Times2Datetime
* New function to convert FVCOM 'Times' to MATLAB datetime objects.
concat_by_struct
* New function to concatenate data contained within a structure.
mjul2str
* Make the input always be a double.
plot_fvcom_field
* Add quiver plotting option.
read_FVCOM_river_file
* New function to read in FVCOM river files.
read_netCDF_FVCOM
* Fix loading data with only a single time stamp.
restrict_spatial_indices
* New function to eliminate nodes and elements for some given mask.
sigma_gen
* Add comment about potential bug (not yet fully investigated).
sigma_tanh
* Add option to return the sigma data into the supplied mesh object.
tubine_area_sigma
* Add option to plot into subplots.
20180201
--------
......
README.md
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......@@ -22,6 +22,7 @@ Notes:
The PML version of the toolbox includes tagged releases, which can be downloaded as standalone (and thus relatively stable) versions. See the PML_ChangeLog.txt for details. Links to the direct downloads are:
- v20190220: https://github.com/pwcazenave/fvcom-toolbox/releases/tag/20190120
- v20180201: https://github.com/pwcazenave/fvcom-toolbox/releases/tag/20180201
- v20160811: https://github.com/pwcazenave/fvcom-toolbox/releases/tag/20160811
- v20160218: https://github.com/pwcazenave/fvcom-toolbox/releases/tag/20160218
......
doc/fvcom_postproc/README.html
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......@@ -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 Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
</body>
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doc/fvcom_postproc/do_residual.html
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......@@ -114,6 +114,6 @@ This function is called by:
0061 <span class="comment">% Calculate direction and magnitude.</span>
0062 rDir=atan2(uDiff,vDiff)*(180/pi); <span class="comment">% in degrees.</span>
0063 rMag=sqrt(uDiff.^2+vDiff.^2)/tideDuration; <span class="comment">% in units/s.</span></pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_residual_plot.html
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......@@ -121,6 +121,6 @@ This function is called by:
0076 <span class="keyword">end</span>
0077 <span class="keyword">end</span>
0078</pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_surface_plot.html
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......@@ -168,6 +168,6 @@ This function is called by:
0094
0095 <span class="keyword">return</span>
0096</pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_surface_plotVel.html
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0066
0067 <span class="keyword">return</span>
0068</pre></div>
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<hr><address>Generated on Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_surface_plotVelMatlabMap.html
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......@@ -118,6 +118,6 @@ This function is called by:
0074
0075 <span class="keyword">return</span>
0076</pre></div>
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<hr><address>Generated on Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_transect_plot.html
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......@@ -186,6 +186,6 @@ This function is called by:
0111 plot(X,Y,<span class="string">'r'</span>,<span class="string">'LineWidth'</span>,2.5)
0112 <span class="keyword">end</span>
0113</pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_vector_plot.html
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......@@ -194,6 +194,6 @@ This function is called by:
0120 delete(Plots(plotOPTS.figure).handles(:))
0121 <span class="keyword">end</span>
0122 <span class="keyword">end</span></pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_vector_plot_MatlabMap.html
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......@@ -238,6 +238,6 @@ This function is called by:
0164 <span class="comment">% delete(Plots(plotOPTS.figure).handles(:))</span>
0165 <span class="comment">% end</span>
0166 <span class="comment">% end</span></pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/do_vector_plot_MatlabMapC.html
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......@@ -224,6 +224,6 @@ This function is called by:
0150 <span class="comment">% delete(Plots(plotOPTS.figure).handles(:))</span>
0151 <span class="comment">% end</span>
0152 <span class="comment">% end</span></pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/example_surface_plot.html
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......@@ -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=<a href="do_vector_plot.html" class="code" title="function [Plots]=do_vector_plot(plotOPTS,FVCOM)">do_vector_plot</a>(plotOPTS,FVCOM)</pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_postproc/graph.dot
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......@@ -16,4 +16,5 @@ digraph m2html {
do_vector_plot_MatlabMap [URL="do_vector_plot_MatlabMap.html"];
do_vector_plot_MatlabMapC [URL="do_vector_plot_MatlabMapC.html"];
example_surface_plot [URL="example_surface_plot.html"];
show_max_CFL [URL="show_max_CFL.html"];
}
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doc/fvcom_postproc/graph.html
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......@@ -34,6 +34,6 @@
</map>
</center>
<hr><address>Generated on Thu 01-Feb-2018 09:48:59 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 Wed 20-Feb-2019 16:06:00 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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doc/fvcom_postproc/index.html
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......@@ -19,7 +19,7 @@
<h2>Matlab files in this directory:</h2>
<table>
<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="README.html">README</a></td><td>README for FVCOM_postproc </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_residual.html">do_residual</a></td><td>DO_RESIDUAL Takes the u and v vectors of a model output and calculates </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_residual_plot.html">do_residual_plot</a></td><td>Take the output of do_residual and plot as a vector figure. Summarises a </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plot.html">do_surface_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotMatlabMap.html">do_surface_plotMatlabMap</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotVel.html">do_surface_plotVel</a></td><td>reads image and plots tracks or stations </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotVelMatlabMap.html">do_surface_plotVelMatlabMap</a></td><td>reads image and plots tracks or stations </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_transect_plot.html">do_transect_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot.html">do_vector_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot_MatlabMap.html">do_vector_plot_MatlabMap</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot_MatlabMapC.html">do_vector_plot_MatlabMapC</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="example_surface_plot.html">example_surface_plot</a></td><td>Sample script to extract and generate m_map contours of tracer variables </td></tr></table>
<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="README.html">README</a></td><td>README for FVCOM_postproc </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_residual.html">do_residual</a></td><td>DO_RESIDUAL Takes the u and v vectors of a model output and calculates </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_residual_plot.html">do_residual_plot</a></td><td>Take the output of do_residual and plot as a vector figure. Summarises a </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plot.html">do_surface_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotMatlabMap.html">do_surface_plotMatlabMap</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotVel.html">do_surface_plotVel</a></td><td>reads image and plots tracks or stations </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_surface_plotVelMatlabMap.html">do_surface_plotVelMatlabMap</a></td><td>reads image and plots tracks or stations </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_transect_plot.html">do_transect_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot.html">do_vector_plot</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot_MatlabMap.html">do_vector_plot_MatlabMap</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="do_vector_plot_MatlabMapC.html">do_vector_plot_MatlabMapC</a></td><td> </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="example_surface_plot.html">example_surface_plot</a></td><td>Sample script to extract and generate m_map contours of tracer variables </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="show_max_CFL.html">show_max_CFL</a></td><td>SHOW_MAX-CFL Function to find the max CFL encountered in each mesh element during an FVCOM model </td></tr></table>
<h2>Subsequent directories:</h2>
......@@ -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 Thu 01-Feb-2018 09:48:59 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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doc/fvcom_prepro/README.html
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......@@ -83,6 +83,6 @@ This function is called by:
0019 <span class="comment">% Revision history</span>
0020 <span class="comment">%</span>
0021 <span class="comment">%==============================================================================</span></pre></div>
<hr><address>Generated on Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_prepro/add_coriolis.html
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......@@ -144,6 +144,6 @@ This function is called by:
0074
0075
0076</pre></div>
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<hr><address>Generated on Wed 20-Feb-2019 16:06:01 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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doc/fvcom_prepro/add_obc_nodes_graphic.html
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......@@ -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>
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doc/fvcom_prepro/add_obc_nodes_list.html
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......@@ -149,7 +149,7 @@ This function is called by:
0062 [~, Nidx] = unique(Nodelist);
0063 Nodelist = Nodelist(sort(Nidx));
0064
0065 assert(max(Nodelist) &lt; Mobj.nVerts, <span class="string">'Your open boundary node number exceed the total number of nodes in the domain\n'</span>)
0065 assert(max(Nodelist) &lt;= Mobj.nVerts, <span class="string">'Your open boundary node number (%d) exceeds the total number of nodes in the domain (%d)'</span>, max(Nodelist), Mobj.nVerts)
0066
0067 <span class="comment">%--------------------------------------------------------------------------</span>
0068 <span class="comment">% Plot the mesh</span>
......@@ -189,6 +189,6 @@ This function is called by:
0102 fprintf(<span class="string">'\nend : %s\n'</span>, subname)
0103 <span class="keyword">end</span>
0104</pre></div>
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doc/fvcom_prepro/add_river_nodes_graphic.html
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......@@ -166,6 +166,6 @@ 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 Thu 01-Feb-2018 09:49:00 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 Wed 20-Feb-2019 16:06:01 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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doc/fvcom_prepro/add_river_nodes_list.html
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......@@ -175,6 +175,6 @@ This function is called by:
0096 fprintf([<span class="string">'end : '</span> subname <span class="string">'\n'</span>])
0097 <span class="keyword">end</span>
0098</pre></div>
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<hr><address>Generated on Wed 20-Feb-2019 16:06:01 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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doc/fvcom_prepro/add_sigma_forDT.html
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......@@ -91,6 +91,6 @@ This function is called by:
0045 nc = close(nc);
0046
0047</pre></div>
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doc/fvcom_prepro/add_sponge_nodes.html
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......@@ -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>
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doc/fvcom_prepro/add_sponge_nodes_list.html
View file @ 3ac27449
......@@ -111,7 +111,7 @@ This function is called by:
0036
0037 <span class="keyword">global</span> ftbverbose
0038 <span class="keyword">if</span> ftbverbose
0039 fprintf(<span class="string">'\nbegin : %s\m'</span>, subname)
0039 fprintf(<span class="string">'\nbegin : %s\n'</span>, subname)
0040 <span class="keyword">end</span>
0041
0042 <span class="comment">% Do we want a figure showing how we're getting along?</span>
......@@ -133,11 +133,11 @@ This function is called by:
0058 <span class="keyword">end</span>
0059
0060 figure
0061 patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
0062 <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>);
0063 hold on;
0064 plot(x(SpongeList),y(SpongeList),<span class="string">'wx'</span>)
0065 axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
0061 patch(<span class="string">'Vertices'</span>, [x, y], <span class="string">'Faces'</span>, Mobj.tri, <span class="keyword">...</span>
0062 <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>);
0063 hold on
0064 plot(x(SpongeList), y(SpongeList), <span class="string">'wx'</span>)
0065 axis(<span class="string">'equal'</span>, <span class="string">'tight'</span>)
0066 <span class="keyword">end</span>
0067
0068 npts = length(SpongeList);
......@@ -162,13 +162,13 @@ This function is called by:
0087 <span class="keyword">if</span> numel(unique(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;
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 : %s\n'</span>, subname)
0095 <span class="keyword">end</span>
0096</pre></div>
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doc/fvcom_prepro/add_stations_list.html
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......@@ -206,6 +206,6 @@ This function is called by:
0114 <span class="keyword">if</span> ftbverbose
0115 fprintf(<span class="string">'end : %s\n'</span>, subname)
0116 <span class="keyword">end</span></pre></div>
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doc/fvcom_prepro/add_var_FVCOM_river.html
View file @ 3ac27449
......@@ -182,6 +182,6 @@ This function is called by:
0106 fprintf(<span class="string">'end : %s\n'</span>, subname)
0107 <span class="keyword">end</span>
0108</pre></div>
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doc/fvcom_prepro/add_weights_FVCOM_nested_forcing.html
View file @ 3ac27449
......@@ -222,7 +222,7 @@ This function is called by:
0141
0142
0143 netcdf.putVar(nc2read, cweights_varid, nest.weight_cell);
0144 netcdf.putVar(nc2read, nweights_varid, nest.weight_node');
0144 netcdf.putVar(nc2read, nweights_varid, nest.weight_node);
0145 <span class="keyword">catch</span> e
0146 fprintf(e.message)
0147 error(<span class="string">'Adding variable %s failed - does the variable already exist?'</span>, <span class="string">'weight_cell'</span>)
......@@ -235,6 +235,6 @@ This function is called by:
0154 <span class="keyword">if</span> ftbverbose
0155 fprintf(<span class="string">'end : %s\n'</span>, subname)
0156 <span class="keyword">end</span></pre></div>
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doc/fvcom_prepro/calc_sponge_radius.html
View file @ 3ac27449
......@@ -170,6 +170,6 @@ 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>
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doc/fvcom_prepro/change_shallow_bathy.html 0 → 100644
View file @ 3ac27449
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<h1>change_shallow_bathy
</h1>
<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>Deepens shallow nodes by setting a minimum depth and making nodes that</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 M = change_shallow_bathy(M, min_depth) </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"> Deepens shallow nodes by setting a minimum depth and making nodes that
are too shallow the mean of the surrouding deep nodes. Loop until all
nodes are deeper than the minuimum depth required.
function [M]=change_shallow_bathy(M, min_depth)
DESCRIPTION:
INPUT:
M = Mesh object
min_depth = the minimum depth of nodes
OUTPUT:
Nested Mesh object with altered bathymetry.
EXAMPLE USAGE:
Author(s):
Rory O'Hara Murray (Marine Scotland Science)
Revision history:
2014 sometime - 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 M = change_shallow_bathy(M, min_depth)</a>
0002 <span class="comment">% Deepens shallow nodes by setting a minimum depth and making nodes that</span>
0003 <span class="comment">% are too shallow the mean of the surrouding deep nodes. Loop until all</span>
0004 <span class="comment">% nodes are deeper than the minuimum depth required.</span>
0005 <span class="comment">%</span>
0006 <span class="comment">% function [M]=change_shallow_bathy(M, min_depth)</span>
0007 <span class="comment">%</span>
0008 <span class="comment">% DESCRIPTION:</span>
0009 <span class="comment">%</span>
0010 <span class="comment">% INPUT:</span>
0011 <span class="comment">% M = Mesh object</span>
0012 <span class="comment">% min_depth = the minimum depth of nodes</span>
0013 <span class="comment">%</span>
0014 <span class="comment">% OUTPUT:</span>
0015 <span class="comment">% Nested Mesh object with altered bathymetry.</span>
0016 <span class="comment">%</span>
0017 <span class="comment">% EXAMPLE USAGE:</span>
0018 <span class="comment">%</span>
0019 <span class="comment">%</span>
0020 <span class="comment">% Author(s):</span>
0021 <span class="comment">% Rory O'Hara Murray (Marine Scotland Science)</span>
0022 <span class="comment">%</span>
0023 <span class="comment">% Revision history:</span>
0024 <span class="comment">% 2014 sometime - first version</span>
0025 <span class="comment">%</span>
0026 <span class="comment">%==========================================================================</span>
0027
0028 count = 0;
0029 h=-99; <span class="comment">% just to start</span>
0030
0031 <span class="keyword">while</span> sum(h==-99)&gt;0
0032 count=count+1;
0033 disp([<span class="string">'iteration # '</span> num2str(count)])
0034 I = M.h&lt;=min_depth; <span class="comment">% find shallow nodes as depth is +ve down.</span>
0035 If = find(I);
0036 h = [];
0037
0038 <span class="comment">% loop through all shallow nodes with depth&lt;=min_depth</span>
0039 <span class="keyword">for</span> ii=1:length(If)
0040
0041 <span class="comment">% find elements surrounding the shallow node</span>
0042 test = [];
0043 <span class="keyword">for</span> jj=1:3
0044 test = [test; find(M.tri(:,jj)==If(ii))];
0045 <span class="keyword">end</span>
0046 <span class="comment">% find nodes for all these elements surrounding the shallow node</span>
0047 <span class="comment">% (the surrounding nodes)</span>
0048 nodes = unique(M.tri(test,:));
0049
0050 htmp = M.h(nodes);
0051 bla = htmp&gt;min_depth; <span class="comment">% find the nodes that are deeper than min_depth</span>
0052 <span class="keyword">if</span> sum(bla)&gt;0
0053 h(ii) = mean(htmp(bla));<span class="comment">% make the shallow node the mean of the surrounding nodes deeper than min_depth</span>
0054 <span class="keyword">else</span>
0055 h(ii) = -99; <span class="comment">% id no deep surroundign nodes then make it -99 and try again.</span>
0056 <span class="keyword">end</span>
0057 <span class="keyword">end</span>
0058 M.h(I) = h; <span class="comment">% save changes to the Mobj array.</span>
0059 <span class="keyword">end</span>
0060
0061 <span class="keyword">end</span></pre></div>
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doc/fvcom_prepro/create_nesting_nodes.html
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......@@ -202,6 +202,6 @@ This function is called by:
0131 fclose(fid);
0132
0133 disp(<span class="string">'finished creating nesting file'</span>);</pre></div>
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doc/fvcom_prepro/elems2nodes.html
View file @ 3ac27449
......@@ -123,6 +123,6 @@ This function is called by:
0057
0058 <span class="comment">%fprintf(['end : ' subname '\n'])</span>
0059</pre></div>
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doc/fvcom_prepro/estimate_ts.html
View file @ 3ac27449
......@@ -180,6 +180,6 @@ This function is called by:
0105 c = 2 * atan2(sqrt(a), sqrt(1-a));
0106 km = R * c; <span class="comment">% distance in metres</span>
0107</pre></div>
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doc/fvcom_prepro/extract_mesoscale.html
View file @ 3ac27449
......@@ -138,6 +138,6 @@ This function is called by:
0069 <span class="comment">% end</span>
0070
0071</pre></div>
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