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<h1>vcsm.c File Reference</h1>Class Vcsm methods.
<a href="#_details">More...</a>
<p>
<code>#include "apbscfg.h"</code><br>
<code>#include "<a class="el" href="vcsm_8h-source.html">apbs/vcsm.h</a>"</code><br>
<p>
<div class="dynheader">
Include dependency graph for vcsm.c:</div>
<div class="dynsection">
<p><center><img src="vcsm_8c__incl.png" border="0" usemap="#vcsm.c_map" alt=""></center>
<map name="vcsm.c_map">
<area shape="rect" href="vcsm_8h.html" title="Contains declarations for the Vcsm class." alt="" coords="480,82,576,109"><area shape="rect" href="vhal_8h.html" title="Contains generic macro definitions for APBS." alt="" coords="504,381,594,408"><area shape="rect" href="valist_8h.html" title="Contains declarations for class Valist." alt="" coords="358,157,454,184"><area shape="rect" href="vatom_8h.html" title="Contains declarations for class Vatom." alt="" coords="109,306,210,333"><area shape="rect" href="vparam_8h.html" title="Contains declarations for class Vparam." alt="" coords="352,232,461,258"><area shape="rect" href="vunit_8h.html" title="Contains a collection of useful constants and conversion factors." alt="" coords="285,306,381,333"><area shape="rect" href="vstring_8h.html" title="Contains declarations for class Vstring." alt="" coords="405,306,512,333"></map>
</div>
<table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC <a class="el" href="structsValist.html">Valist</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g1fbb8a489885b17a1cde685082ca0d2f">Vcsm_getValist</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atom list. <a href="group__Vcsm.html#g1fbb8a489885b17a1cde685082ca0d2f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g66a9b72b572a2e69ecbf31d756739a30">Vcsm_getNumberAtoms</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int isimp)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get number of atoms associated with a simplex. <a href="group__Vcsm.html#g66a9b72b572a2e69ecbf31d756739a30"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC <a class="el" href="structsVatom.html">Vatom</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g9fb0ff4858be085d6698bd1a1bac8d0d">Vcsm_getAtom</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int iatom, int isimp)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get particular atom associated with a simplex. <a href="group__Vcsm.html#g9fb0ff4858be085d6698bd1a1bac8d0d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g0e64a5068f0bb54b5c0603ff87b47d55">Vcsm_getAtomIndex</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int iatom, int isimp)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get ID of particular atom in a simplex. <a href="group__Vcsm.html#g0e64a5068f0bb54b5c0603ff87b47d55"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g701eb998730985130ba77005d7c55b22">Vcsm_getNumberSimplices</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int iatom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get number of simplices associated with an atom. <a href="group__Vcsm.html#g701eb998730985130ba77005d7c55b22"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC SS * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g9caeb8476cc7827c595d531c8ac1d004">Vcsm_getSimplex</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int isimp, int iatom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get particular simplex associated with an atom. <a href="group__Vcsm.html#g9caeb8476cc7827c595d531c8ac1d004"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g8df5e4cef201f28ec5fad361c205b47f">Vcsm_getSimplexIndex</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, int isimp, int iatom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get index particular simplex associated with an atom. <a href="group__Vcsm.html#g8df5e4cef201f28ec5fad361c205b47f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC unsigned long int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#gde3d06b69f9a830c2a801cea8576eddb">Vcsm_memChk</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the memory used by this structure (and its contents) in bytes. <a href="group__Vcsm.html#gde3d06b69f9a830c2a801cea8576eddb"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC <a class="el" href="structsVcsm.html">Vcsm</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g9d6d4cd551a393c05dab3022a8eb401b">Vcsm_ctor</a> (<a class="el" href="structsValist.html">Valist</a> *alist, Gem *gm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Construct Vcsm object. <a href="group__Vcsm.html#g9d6d4cd551a393c05dab3022a8eb401b"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g9e2eed4344b173d8cf5125bfdb8be8fb">Vcsm_ctor2</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, <a class="el" href="structsValist.html">Valist</a> *alist, Gem *gm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to construct Vcsm object. <a href="group__Vcsm.html#g9e2eed4344b173d8cf5125bfdb8be8fb"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#ge1506d49d6faaf810fa884c18f9c3bba">Vcsm_init</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Initialize charge-simplex map with mesh and atom data. <a href="group__Vcsm.html#ge1506d49d6faaf810fa884c18f9c3bba"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g2bc0fee3715143539faf899297555398">Vcsm_dtor</a> (<a class="el" href="structsVcsm.html">Vcsm</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy Vcsm object. <a href="group__Vcsm.html#g2bc0fee3715143539faf899297555398"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g3c31f8010c42b53a7454bdac94aa9acf">Vcsm_dtor2</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to destroy Vcsm object. <a href="group__Vcsm.html#g3c31f8010c42b53a7454bdac94aa9acf"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g23ba96a1f619c002a84a96d09c66205a">Vcsm_update</a> (<a class="el" href="structsVcsm.html">Vcsm</a> *thee, SS **simps, int num)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Update the charge-simplex and simplex-charge maps after refinement. <a href="group__Vcsm.html#g23ba96a1f619c002a84a96d09c66205a"></a><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
Class Vcsm methods.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="version" compact><dt><b>Version:</b></dt><dd></dd></dl>
<dl class="rcs" compact><dt><b>Id</b></dt><dd><a class="el" href="vcsm_8c.html" title="Class Vcsm methods.">vcsm.c</a> 1350 2009-02-12 00:38:48Z yhuang01 </dd></dl>
<dl class="attention" compact><dt><b>Attention:</b></dt><dd><div class="fragment"><pre class="fragment">
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (baker@biochem.wustl.edu)
* Dept. of Biochemistry and Molecular Biophysics
* Center for Computational Biology
* Washington University in St. Louis
*
* Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2002-2009, Washington University in St. Louis.
* Portions Copyright (c) 2002-2009. Nathan A. Baker
* Portions Copyright (c) 1999-2002. The Regents of the University of California.
* Portions Copyright (c) 1995. Michael Holst
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* - Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* - Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* - Neither the name of Washington University in St. Louis nor the names of its
* contributors may be used to endorse or promote products derived from this
* software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* </pre></div> </dd></dl>
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