<!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: routines.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>routines.h File Reference</h1>Header file for front end auxiliary routines. <a href="#_details">More...</a> <p> <code>#include "apbscfg.h"</code><br> <code>#include "<a class="el" href="apbs_8h-source.html">apbs/apbs.h</a>"</code><br> <code>#include "<a class="el" href="nosh_8h-source.html">apbs/nosh.h</a>"</code><br> <code>#include "<a class="el" href="mgparm_8h-source.html">apbs/mgparm.h</a>"</code><br> <code>#include "<a class="el" href="pbeparm_8h-source.html">apbs/pbeparm.h</a>"</code><br> <code>#include "<a class="el" href="femparm_8h-source.html">apbs/femparm.h</a>"</code><br> <code>#include "<a class="el" href="vparam_8h-source.html">apbs/vparam.h</a>"</code><br> <code>#include "<a class="el" href="vfetk_8h-source.html">apbs/vfetk.h</a>"</code><br> <p> <div class="dynheader"> Include dependency graph for routines.h:</div> <div class="dynsection"> <p><center><img src="routines_8h__incl.png" border="0" usemap="#routines.h_map" alt=""></center> <map name="routines.h_map"> <area shape="rect" href="apbs_8h.html" title="Top-level header for APBS." alt="" coords="1283,82,1377,109"><area shape="rect" href="femparm_8h.html" title="Contains declarations for class APOLparm." alt="" coords="263,232,383,258"><area shape="rect" href="mgparm_8h.html" title="Contains declarations for class MGparm." alt="" coords="610,306,725,333"><area shape="rect" href="nosh_8h.html" title="Contains declarations for class NOsh." alt="" coords="474,157,570,184"><area shape="rect" href="pbeparm_8h.html" title="Contains declarations for class PBEparm." alt="" coords="1247,232,1365,258"><area shape="rect" href="vparam_8h.html" title="Contains declarations for class Vparam." alt="" coords="762,530,871,557"><area shape="rect" href="vfetk_8h.html" title="Contains declarations for class Vfetk." alt="" coords="2555,157,2649,184"><area shape="rect" href="vhal_8h.html" title="Contains generic macro definitions for APBS." alt="" coords="962,680,1053,706"><area shape="rect" href="vstring_8h.html" title="Contains declarations for class Vstring." alt="" coords="813,605,919,632"><area shape="rect" href="vunit_8h.html" title="Contains a collection of useful constants and conversion factors." alt="" coords="1927,605,2023,632"><area shape="rect" href="valist_8h.html" title="Contains declarations for class Valist." alt="" coords="1674,456,1770,482"><area shape="rect" href="vatom_8h.html" title="Contains declarations for class Vatom." alt="" coords="2137,530,2238,557"><area shape="rect" href="vacc_8h.html" title="Contains declarations for class Vacc." alt="" coords="1897,306,1990,333"><area shape="rect" href="vcap_8h.html" title="Contains declarations for class Vcap." alt="" coords="2471,232,2565,258"><area shape="rect" href="vgreen_8h.html" title="Contains declarations for class Vgreen." alt="" coords="2449,381,2555,408"><area shape="rect" href="vpbe_8h.html" title="Contains declarations for class Vpbe." alt="" coords="1813,232,1906,258"><area shape="rect" href="vgrid_8h.html" title="Potential oracle for Cartesian mesh data." alt="" coords="895,530,991,557"><area shape="rect" href="vmgrid_8h.html" title="Multiresolution oracle for Cartesian mesh data." alt="" coords="991,456,1098,482"><area shape="rect" href="vopot_8h.html" title="Potential oracle for Cartesian mesh data." alt="" coords="1454,157,1553,184"><area shape="rect" href="vpmg_8h.html" title="Contains declarations for class Vpmg." alt="" coords="1110,157,1209,184"><area shape="rect" href="vpmgp_8h.html" title="Contains declarations for class Vpmgp." alt="" coords="863,232,970,258"><area shape="rect" href="vpee_8h.html" title="Contains declarations for class Vpee." alt="" coords="3054,381,3147,408"><area shape="rect" href="apolparm_8h-source.html" title="apbs/apolparm.h" alt="" coords="1122,456,1245,482"><area shape="rect" href="vclist_8h.html" title="Contains declarations for class Vclist." alt="" coords="1895,381,1991,408"><area shape="rect" href="vcsm_8h.html" title="Contains declarations for the Vcsm class." alt="" coords="2883,381,2979,408"></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="routines_8h__dep__incl.png" border="0" usemap="#routines.hdep_map" alt=""></center> <map name="routines.hdep_map"> <area shape="rect" href="main_8c.html" title="APBS "front end" program using formatted input files." alt="" coords="7,82,69,109"><area shape="rect" href="routines_8c.html" title="Supporting routines for APBS front end." alt="" coords="93,82,173,109"></map> </div> <p> <a href="routines_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="structAtomForce.html">AtomForce</a></td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Structure to hold atomic forces. <a href="structAtomForce.html#_details">More...</a><br></td></tr> <tr><td colspan="2"><br><h2>Defines</h2></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="gc8cd79b3347023a8eb7714000fb860f5"></a><!-- doxytag: member="routines.h::APBSRC" ref="gc8cd79b3347023a8eb7714000fb860f5" args="" --> #define </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#gc8cd79b3347023a8eb7714000fb860f5">APBSRC</a> 13</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Return code for APBS during failure. <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="g5cac86051c09ec93d5cd7da30d9132e0"></a><!-- doxytag: member="routines.h::AtomForce" ref="g5cac86051c09ec93d5cd7da30d9132e0" args="" --> typedef struct <a class="el" href="structAtomForce.html">AtomForce</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#g5cac86051c09ec93d5cd7da30d9132e0">AtomForce</a></td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Define <a class="el" href="structAtomForce.html" title="Structure to hold atomic forces.">AtomForce</a> type. <br></td></tr> <tr><td colspan="2"><br><h2>Functions</h2></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structVparam.html">Vparam</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#ge373e54f41b5dc9cb275baef6f6115b3">loadParameter</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Loads and returns parameter object. <a href="group__Frontend.html#ge373e54f41b5dc9cb275baef6f6115b3"></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__Frontend.html#gde48c79ecd7d2bf5838a4e0519b19f9a">loadMolecules</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structVparam.html">Vparam</a> *param, <a class="el" href="structsValist.html">Valist</a> *alist[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Load the molecules given in NOsh into atom lists. <a href="group__Frontend.html#gde48c79ecd7d2bf5838a4e0519b19f9a"></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__Frontend.html#gf15fae1faaacaee69eb1ec79a1d2c0d3">killMolecules</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsValist.html">Valist</a> *alist[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the loaded molecules. <a href="group__Frontend.html#gf15fae1faaacaee69eb1ec79a1d2c0d3"></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__Frontend.html#g0744b51dd1328f9623331b0bd6b2a41e">loadDielMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *dielXMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielYMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielZMap[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Load the dielectric maps given in NOsh into grid objects. <a href="group__Frontend.html#g0744b51dd1328f9623331b0bd6b2a41e"></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__Frontend.html#g8fc9aaea29e0981630c959189125a9a2">killDielMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *dielXMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielYMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielZMap[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the loaded dielectric. <a href="group__Frontend.html#g8fc9aaea29e0981630c959189125a9a2"></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__Frontend.html#g5b70151ac7dbfc3c615a6fed6367390b">loadKappaMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *kappa[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Load the kappa maps given in NOsh into grid objects. <a href="group__Frontend.html#g5b70151ac7dbfc3c615a6fed6367390b"></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__Frontend.html#g903bb83abbd4bb2b9102d782b319e26c">killKappaMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *kappa[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the loaded kappa maps. <a href="group__Frontend.html#g903bb83abbd4bb2b9102d782b319e26c"></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__Frontend.html#g8bfbb3f554c21aaca1e87b59ec7e36c4">loadChargeMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *charge[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Load the charge maps given in NOsh into grid objects. <a href="group__Frontend.html#g8bfbb3f554c21aaca1e87b59ec7e36c4"></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__Frontend.html#gbd66a61c0345b5fb2a1f7cf28eda455f">killChargeMaps</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVgrid.html">Vgrid</a> *charge[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the loaded charge maps. <a href="group__Frontend.html#gbd66a61c0345b5fb2a1f7cf28eda455f"></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__Frontend.html#g52af26682a1da9e8ccd01daee70b7a41">printPBEPARM</a> (<a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Print out generic PBE params loaded from input. <a href="group__Frontend.html#g52af26682a1da9e8ccd01daee70b7a41"></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__Frontend.html#gc204e507188bb0c897a7ddd0e471622b">printMGPARM</a> (<a class="el" href="structsMGparm.html">MGparm</a> *mgparm, double realCenter[3])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Print out MG-specific params loaded from input. <a href="group__Frontend.html#gc204e507188bb0c897a7ddd0e471622b"></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__Frontend.html#g672ad18a84d014f587dcc7c417f16611">initMG</a> (int icalc, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsMGparm.html">MGparm</a> *mgparm, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, double realCenter[3], <a class="el" href="structsVpbe.html">Vpbe</a> *pbe[NOSH_MAXCALC], <a class="el" href="structsValist.html">Valist</a> *alist[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielXMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielYMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *dielZMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *kappaMap[NOSH_MAXMOL], <a class="el" href="structsVgrid.html">Vgrid</a> *chargeMap[NOSH_MAXMOL], <a class="el" href="structsVpmgp.html">Vpmgp</a> *pmgp[NOSH_MAXCALC], <a class="el" href="structsVpmg.html">Vpmg</a> *pmg[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Initialize an MG calculation. <a href="group__Frontend.html#g672ad18a84d014f587dcc7c417f16611"></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__Frontend.html#gb0ce95b1f26075f244714265de179a90">killMG</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVpbe.html">Vpbe</a> *pbe[NOSH_MAXCALC], <a class="el" href="structsVpmgp.html">Vpmgp</a> *pmgp[NOSH_MAXCALC], <a class="el" href="structsVpmg.html">Vpmg</a> *pmg[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Kill structures initialized during an MG calculation. <a href="group__Frontend.html#gb0ce95b1f26075f244714265de179a90"></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__Frontend.html#ge5fef94b530af7a96dc63a3deed97413">solveMG</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg, <a class="el" href="group__MGparm.html#gcf31be9905f8e0ba1e083e1119b7cd1d">MGparm_CalcType</a> type)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Solve the PBE with MG. <a href="group__Frontend.html#ge5fef94b530af7a96dc63a3deed97413"></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__Frontend.html#g38fa11fc3ff3b68abcb0e507e445185c">setPartMG</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsMGparm.html">MGparm</a> *mgparm, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Set MG partitions for calculating observables and performing I/O. <a href="group__Frontend.html#g38fa11fc3ff3b68abcb0e507e445185c"></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__Frontend.html#g2c9c9e4d6c9011d8206cd8e1e9d87426">energyMG</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, int icalc, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate electrostatic energies from MG solution. <a href="group__Frontend.html#g2c9c9e4d6c9011d8206cd8e1e9d87426"></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__Frontend.html#g0d20f0a6407d4ef03e15b5738612381e">killEnergy</a> ()</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Kill arrays allocated for energies. <a href="group__Frontend.html#g0d20f0a6407d4ef03e15b5738612381e"></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__Frontend.html#gfa145c12f55d0efd7fcace66ffde7567">forceMG</a> (Vmem *mem, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsMGparm.html">MGparm</a> *mgparm, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg, int *nforce, <a class="el" href="structAtomForce.html">AtomForce</a> **atomForce, <a class="el" href="structsValist.html">Valist</a> *alist[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate forces from MG solution. <a href="group__Frontend.html#gfa145c12f55d0efd7fcace66ffde7567"></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__Frontend.html#g85261d2d20693fd91564bdadc911dbbb">killForce</a> (Vmem *mem, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Free memory from MG force calculation. <a href="group__Frontend.html#g85261d2d20693fd91564bdadc911dbbb"></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__Frontend.html#g26c23c3a3879a11ebeea23eb271e5bc6">storeAtomEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *pmg, int icalc, double **atomEnergy, int *nenergy)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Store energy in arrays for future use. <a href="group__Frontend.html#g26c23c3a3879a11ebeea23eb271e5bc6"></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__Frontend.html#g0243cce85fc0dd6f64739a905b4742f0">writedataFlat</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Write out information to a flat file. <a href="group__Frontend.html#g0243cce85fc0dd6f64739a905b4742f0"></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__Frontend.html#g969c5202eb71574a7b3823f1e1049795">writedataXML</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Write out information to an XML file. <a href="group__Frontend.html#g969c5202eb71574a7b3823f1e1049795"></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__Frontend.html#g4f37ce55e96d10897a327e3841e0beed">writedataMG</a> (int rank, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Write out observables from MG calculation to file. <a href="group__Frontend.html#g4f37ce55e96d10897a327e3841e0beed"></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__Frontend.html#g12b5e7fa0d0f177f7b1668df0629bc1e">writematMG</a> (int rank, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsVpmg.html">Vpmg</a> *pmg)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Write out operator matrix from MG calculation to file. <a href="group__Frontend.html#g12b5e7fa0d0f177f7b1668df0629bc1e"></a><br></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#g8955a29284f6c8dd7ab3d2843fa5f9f2">returnEnergy</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, double totEnergy[NOSH_MAXCALC], int iprint)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Access net local energy. <a href="group__Frontend.html#g8955a29284f6c8dd7ab3d2843fa5f9f2"></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__Frontend.html#gfb4a43b1ee07988e941f8cb5d54f0f23">printEnergy</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, double totEnergy[NOSH_MAXCALC], int iprint)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print energy data (deprecated...see printElecEnergy). <a href="group__Frontend.html#gfb4a43b1ee07988e941f8cb5d54f0f23"></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__Frontend.html#gad105790d5d821a70c2556d8f678bff9">printElecEnergy</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, double totEnergy[NOSH_MAXCALC], int iprint)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print energy data. <a href="group__Frontend.html#gad105790d5d821a70c2556d8f678bff9"></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__Frontend.html#g3ea91bf9d5a15e204315b2792dffc5c2">printApolEnergy</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, int iprint)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print energy data. <a href="group__Frontend.html#g3ea91bf9d5a15e204315b2792dffc5c2"></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__Frontend.html#g2f661dc633c6c5c8c6ee988dd332a746">printForce</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC], int i)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print force data (deprecated...see printElecForce). <a href="group__Frontend.html#g2f661dc633c6c5c8c6ee988dd332a746"></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__Frontend.html#gd03579d4b8a648e812b748af288a1023">printElecForce</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC], int i)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print force data. <a href="group__Frontend.html#gd03579d4b8a648e812b748af288a1023"></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__Frontend.html#gd34565687f0168cd9fd15b5747ef7084">printApolForce</a> (Vcom *com, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, int nforce[NOSH_MAXCALC], <a class="el" href="structAtomForce.html">AtomForce</a> *atomForce[NOSH_MAXCALC], int i)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Combine and pretty-print force data. <a href="group__Frontend.html#gd34565687f0168cd9fd15b5747ef7084"></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__Frontend.html#g6484d734f8fb04d4f2f2c6ef4541e25a">startVio</a> ()</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Wrapper to start MALOC Vio layer. <a href="group__Frontend.html#g6484d734f8fb04d4f2f2c6ef4541e25a"></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__Frontend.html#g8a9dbdbf57bf8a9e308147abe0e8da34">printFEPARM</a> (int icalc, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Print out FE-specific params loaded from input. <a href="group__Frontend.html#g8a9dbdbf57bf8a9e308147abe0e8da34"></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__Frontend.html#gfb412d6d72af68e499856b6ade594787">energyFE</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, int icalc, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC], int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate electrostatic energies from FE solution. <a href="group__Frontend.html#gfb412d6d72af68e499856b6ade594787"></a><br></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#g2a07181f0b784288233c5b71d53e3e92">initFE</a> (int icalc, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsVpbe.html">Vpbe</a> *pbe[NOSH_MAXCALC], <a class="el" href="structsValist.html">Valist</a> *alist[NOSH_MAXMOL], <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC], Gem *gm[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Initialize FE solver objects. <a href="group__Frontend.html#g2a07181f0b784288233c5b71d53e3e92"></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__Frontend.html#ge90a8d20839ced8a3e7d2caca35cbea0">killFE</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsVpbe.html">Vpbe</a> *pbe[NOSH_MAXCALC], <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Kill structures initialized during an FE calculation. <a href="group__Frontend.html#ge90a8d20839ced8a3e7d2caca35cbea0"></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__Frontend.html#g4263953eaca54df840862f6ca2ee4f26">preRefineFE</a> (int i, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Pre-refine mesh before solve. <a href="group__Frontend.html#g4263953eaca54df840862f6ca2ee4f26"></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__Frontend.html#gd4c2ae8f06b8721031b13ed18631fd48">partFE</a> (int i, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Partition mesh (if applicable). <a href="group__Frontend.html#gd4c2ae8f06b8721031b13ed18631fd48"></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__Frontend.html#gca674b06e3c15fb8c10e39e82096fa67">solveFE</a> (int i, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Solve-estimate-refine. <a href="group__Frontend.html#gca674b06e3c15fb8c10e39e82096fa67"></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__Frontend.html#gf2493d6ed066b920ef8f5e37533b700d">postRefineFE</a> (int icalc, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsFEMparm.html">FEMparm</a> *feparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk[NOSH_MAXCALC])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Estimate error, mark mesh, and refine mesh after solve. <a href="group__Frontend.html#gf2493d6ed066b920ef8f5e37533b700d"></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__Frontend.html#gf4dd79aefdee50f5bddc206e6302fd34">writedataFE</a> (int rank, <a class="el" href="structsNOsh.html">NOsh</a> *nosh, <a class="el" href="structsPBEparm.html">PBEparm</a> *pbeparm, <a class="el" href="structsVfetk.html">Vfetk</a> *fetk)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Write FEM data to files. <a href="group__Frontend.html#gf4dd79aefdee50f5bddc206e6302fd34"></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__Frontend.html#g13242b98c256ee3cf6613c52d194c1f9">energyAPOL</a> (<a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate non-polar energies. <a href="group__Frontend.html#g13242b98c256ee3cf6613c52d194c1f9"></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__Frontend.html#g3a8e8616dbc43a553e8f51939acfeaa8">forceAPOL</a> (<a class="el" href="structsVacc.html">Vacc</a> *acc, Vmem *mem, <a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, int *nforce, <a class="el" href="structAtomForce.html">AtomForce</a> **atomForce, <a class="el" href="structsValist.html">Valist</a> *alist, <a class="el" href="structsVclist.html">Vclist</a> *clist)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate non-polar forces. <a href="group__Frontend.html#g3a8e8616dbc43a553e8f51939acfeaa8"></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__Frontend.html#g777e5bac9e149e6c9b51cbca372cfdfb">initAPOL</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, Vmem *mem, <a class="el" href="structVparam.html">Vparam</a> *param, <a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, int *nforce, <a class="el" href="structAtomForce.html">AtomForce</a> **atomForce, <a class="el" href="structsValist.html">Valist</a> *alist)</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Upperlevel routine to the non-polar energy and force routines. <a href="group__Frontend.html#g777e5bac9e149e6c9b51cbca372cfdfb"></a><br></td></tr> <tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#g26b8b211a2a3049f5e424f773a8207b7">loadMeshes</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, Gem *gm[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Load the meshes given in NOsh into geometry objects. <a href="group__Frontend.html#g26b8b211a2a3049f5e424f773a8207b7"></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__Frontend.html#gddc9fadc54a9e22e8b2b2efc74066273">killMeshes</a> (<a class="el" href="structsNOsh.html">NOsh</a> *nosh, Gem *alist[NOSH_MAXMOL])</td></tr> <tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the loaded meshes. <a href="group__Frontend.html#gddc9fadc54a9e22e8b2b2efc74066273"></a><br></td></tr> </table> <hr><a name="_details"></a><h2>Detailed Description</h2> Header file for front end auxiliary routines. <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="routines_8h.html" title="Header file for front end auxiliary routines.">routines.h</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> </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>