<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html><head><meta http-equiv="Content-Type" content="text/html;charset=UTF-8"> <title>APBS: vcsm.h File Reference</title> <link href="apbs.css" rel="stylesheet" type="text/css"> <link href="tabs.css" rel="stylesheet" type="text/css"> </head><body> <!-- Generated by Doxygen 1.5.7.1 --> <div class="navigation" id="top"> <div class="tabs"> <ul> <li><a href="index.html"><span>Main Page</span></a></li> <li><a href="pages.html"><span>Related Pages</span></a></li> <li><a href="modules.html"><span>Modules</span></a></li> <li><a href="annotated.html"><span>Data Structures</span></a></li> <li class="current"><a href="files.html"><span>Files</span></a></li> </ul> </div> <div class="tabs"> <ul> <li><a href="files.html"><span>File List</span></a></li> <li><a href="globals.html"><span>Globals</span></a></li> </ul> </div> </div> <div class="contents"> <h1>vcsm.h File Reference</h1>Contains declarations for the Vcsm class. <a href="#_details">More...</a> <p> <code>#include "maloc/maloc.h"</code><br> <code>#include "<a class="el" href="vhal_8h-source.html">apbs/vhal.h</a>"</code><br> <code>#include "<a class="el" href="valist_8h-source.html">apbs/valist.h</a>"</code><br> <code>#include "mc/mc.h"</code><br> <p> <div class="dynheader"> Include dependency graph for vcsm.h:</div> <div class="dynsection"> <p><center><img src="vcsm_8h__incl.png" border="0" usemap="#vcsm.h_map" alt=""></center> <map name="vcsm.h_map"> <area shape="rect" href="vhal_8h.html" title="Contains generic macro definitions for APBS." alt="" coords="504,306,594,333"><area shape="rect" href="valist_8h.html" title="Contains declarations for class Valist." alt="" coords="348,82,444,109"><area shape="rect" href="vatom_8h.html" title="Contains declarations for class Vatom." alt="" coords="109,231,210,258"><area shape="rect" href="vparam_8h.html" title="Contains declarations for class Vparam." alt="" coords="341,157,450,183"><area shape="rect" href="vunit_8h.html" title="Contains a collection of useful constants and conversion factors." alt="" coords="285,231,381,258"><area shape="rect" href="vstring_8h.html" title="Contains declarations for class Vstring." alt="" coords="405,231,512,258"></map> </div> <p> <div class="dynheader"> This graph shows which files directly or indirectly include this file:</div> <div class="dynsection"> <p><center><img src="vcsm_8h__dep__incl.png" border="0" usemap="#vcsm.hdep_map" alt=""></center> <map name="vcsm.hdep_map"> <area shape="rect" href="vfetk_8h.html" title="Contains declarations for class Vfetk." alt="" coords="108,82,172,109"><area shape="rect" href="vcsm_8c.html" title="Class Vcsm methods." alt="" coords="196,82,260,109"><area shape="rect" href="vfetk_8c.html" title="Class Vfetk methods." alt="" coords="8,157,69,183"><area shape="rect" href="apbs_8h.html" title="Top-level header for APBS." alt="" coords="144,157,205,183"><area shape="rect" href="routines_8h.html" title="Header file for front end auxiliary routines." alt="" coords="16,231,98,258"><area shape="rect" href="routines_8c.html" title="Supporting routines for APBS front end." alt="" coords="250,306,330,333"><area shape="rect" href="mgparm_8c.html" title="Class MGparm methods." alt="" coords="173,231,253,258"><area shape="rect" href="main_8c.html" title="APBS "front end" program using formatted input files." alt="" coords="66,306,128,333"></map> </div> <p> <a href="vcsm_8h-source.html">Go to the source code of this file.</a><table border="0" cellpadding="0" cellspacing="0"> <tr><td></td></tr> <tr><td colspan="2"><br><h2>Data Structures</h2></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top">struct </td><td class="memItemRight" valign="bottom"><a class="el" href="structsVcsm.html">sVcsm</a></td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Charge-simplex map class. <a href="structsVcsm.html#_details">More...</a><br></td></tr> <tr><td colspan="2"><br><h2>Typedefs</h2></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="g03db177f1f93081210039a71717ae1aa"></a><!-- doxytag: member="vcsm.h::Vcsm" ref="g03db177f1f93081210039a71717ae1aa" args="" --> typedef struct <a class="el" href="structsVcsm.html">sVcsm</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g03db177f1f93081210039a71717ae1aa">Vcsm</a></td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Declaration of the Vcsm class as the Vcsm structure. <br></td></tr> <tr><td colspan="2"><br><h2>Functions</h2></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vcsm.html#g8b61bc1d195da9bf2019d131e4e76043">Gem_setExternalUpdateFunction</a> (Gem *thee, void(*externalUpdate)(SS **simps, int num))</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">External function for FEtk Gem class to use during mesh refinement. <a href="group__Vcsm.html#g8b61bc1d195da9bf2019d131e4e76043"></a><br></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top"><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">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"><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">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">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">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">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">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"><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">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">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">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">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">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> Contains declarations for the Vcsm class. <p> <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_8h.html" title="Contains declarations for the Vcsm class.">vcsm.h</a> 1350 2009-02-12 00:38:48Z yhuang01 </dd></dl> <dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan A. Baker</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> </div> <hr size="1"><address style="text-align: right;"><small>Generated on Thu Feb 12 06:23:50 2009 for APBS by <a href="http://www.doxygen.org/index.html"> <img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.7.1 </small></address> </body> </html>