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<h1>High-level front-end routines</h1><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>Files</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="main_8c.html">main.c</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">APBS "front end" program using formatted input files. <br></td></tr>
<p>
<tr><td class="memItemLeft" nowrap align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="routines_8h.html">routines.h</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Header file for front end auxiliary routines. <br></td></tr>
<p>
<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="Frontend::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="Frontend::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">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Frontend.html#g3c04138a5bfe5d72780bb7e82a18e627">main</a> (int argc, char **argv)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">The main APBS function. <a href="#g3c04138a5bfe5d72780bb7e82a18e627"></a><br></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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#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="#gddc9fadc54a9e22e8b2b2efc74066273"></a><br></td></tr>
</table>
<hr><h2>Function Documentation</h2>
<a class="anchor" name="g13242b98c256ee3cf6613c52d194c1f9"></a><!-- doxytag: member="routines.h::energyAPOL" ref="g13242b98c256ee3cf6613c52d194c1f9" args="(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms)" -->
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<td class="memname">int energyAPOL </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>sasa</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>sav</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>atomsasa</em>[], </td>
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<td class="paramkey"></td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>atomwcaEnergy</em>[], </td>
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<td class="paramkey"></td>
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<td class="paramtype">int </td>
<td class="paramname"> <em>numatoms</em></td><td> </td>
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<div class="memdoc">
<p>
Calculate non-polar energies.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>sasa</em> </td><td>
APOLparm object </td></tr>
<tr><td valign="top"><em>sav</em> </td><td>
Solvent accessible surface area </td></tr>
<tr><td valign="top"><em>atomsasa</em> </td><td>
Solvent accessible volume </td></tr>
<tr><td valign="top"><em>atomwcaEnergy</em> </td><td>
Array for SASA per atom * </td></tr>
<tr><td valign="top"><em>numatoms</em> </td><td>
Array for WCA energy per atom * Number of atoms (or size of the above arrays) * </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00077">ACE_COMPS</a>, <a class="el" href="apolparm_8h-source.html#l00075">ACE_NO</a>, <a class="el" href="apolparm_8h-source.html#l00076">ACE_TOTAL</a>, <a class="el" href="apolparm_8h-source.html#l00162">sAPOLparm::calcenergy</a>, <a class="el" href="apolparm_8h-source.html#l00158">sAPOLparm::gamma</a>, <a class="el" href="apolparm_8h-source.html#l00143">sAPOLparm::press</a>, <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>, and <a class="el" href="apolparm_8h-source.html#l00172">sAPOLparm::wcaEnergy</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>.</p>
</div>
</div><p>
<a class="anchor" name="gfb412d6d72af68e499856b6ade594787"></a><!-- doxytag: member="routines.h::energyFE" ref="gfb412d6d72af68e499856b6ade594787" args="(NOsh *nosh, int icalc, Vfetk *fetk[NOSH_MAXCALC], int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)" -->
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<td class="memname">int energyFE </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
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<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC], </td>
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<td class="paramkey"></td>
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<td class="paramtype">int * </td>
<td class="paramname"> <em>nenergy</em>, </td>
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<td class="paramtype">double * </td>
<td class="paramname"> <em>totEnergy</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double * </td>
<td class="paramname"> <em>qfEnergy</em>, </td>
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<td class="paramtype">double * </td>
<td class="paramname"> <em>qmEnergy</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double * </td>
<td class="paramname"> <em>dielEnergy</em></td><td> </td>
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<p>
Calculate electrostatic energies from FE solution.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Object with parsed input file parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>icalc</em> </td><td>Index of calculation </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>FE object array </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nenergy</em> </td><td>Set to number of entries in energy arrays </td></tr>
<tr><td valign="top"></td><td valign="top"><em>totEnergy</em> </td><td>Set to total energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qfEnergy</em> </td><td>Set to charge-potential energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qmEnergy</em> </td><td>Set to mobile ion energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielEnergy</em> </td><td>Set to polarization energy (in kT) </td></tr>
</table>
</dl>
<dl compact><dt><b><a class="el" href="bug.html#_bug000031">Bug:</a></b></dt><dd>"calcenergy 2" does not work </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="nosh_8h-source.html#l00163">sNOsh_calc::femparm</a>, <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00147">PBE_LRPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="vhal_8h-source.html#l00149">PBE_SMPBE</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="pbeparm_8h-source.html#l00081">PCE_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vfetk_8c-source.html#l00666">Vfetk_energy()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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Here is the call graph for this function:</div>
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<p><center><img src="group__Frontend_gfb412d6d72af68e499856b6ade594787_cgraph.png" border="0" usemap="#group__Frontend_gfb412d6d72af68e499856b6ade594787_cgraph_map" alt=""></center>
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<a class="anchor" name="g2c9c9e4d6c9011d8206cd8e1e9d87426"></a><!-- doxytag: member="routines.h::energyMG" ref="g2c9c9e4d6c9011d8206cd8e1e9d87426" args="(NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)" -->
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<td class="memname">int energyMG </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int * </td>
<td class="paramname"> <em>nenergy</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>totEnergy</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>qfEnergy</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>qmEnergy</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dielEnergy</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Calculate electrostatic energies from MG solution.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Object with parsed input file parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>icalc</em> </td><td>Index of calculation </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nenergy</em> </td><td>Set to number of entries in energy arrays </td></tr>
<tr><td valign="top"></td><td valign="top"><em>totEnergy</em> </td><td>Set to total energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qfEnergy</em> </td><td>Set to charge-potential energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qmEnergy</em> </td><td>Set to mobile ion energy (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielEnergy</em> </td><td>Set to polarization energy (in kT) </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vhal_8h-source.html#l00347">APBS_TIMER_ENERGY</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="vpmg_8c-source.html#l02127">extEnergy()</a>, <a class="el" href="nosh_8h-source.html#l00162">sNOsh_calc::mgparm</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00081">PCE_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00080">PCE_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vpmg_8c-source.html#l01165">Vpmg_dielEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l01136">Vpmg_energy()</a>, <a class="el" href="vpmg_8c-source.html#l01592">Vpmg_qfAtomEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l01492">Vpmg_qfEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l01256">Vpmg_qmEnergy()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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<a class="anchor" name="g3a8e8616dbc43a553e8f51939acfeaa8"></a><!-- doxytag: member="routines.h::forceAPOL" ref="g3a8e8616dbc43a553e8f51939acfeaa8" args="(Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist)" -->
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<td class="memname">int forceAPOL </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>acc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int * </td>
<td class="paramname"> <em>nforce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> ** </td>
<td class="paramname"> <em>atomForce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Calculate non-polar forces.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>acc</em> </td><td>
Accessiblity object </td></tr>
<tr><td valign="top"><em>mem</em> </td><td>
Memory manager </td></tr>
<tr><td valign="top"><em>apolparm</em> </td><td>
Apolar calculation parameter object </td></tr>
<tr><td valign="top"><em>nforce</em> </td><td>
Number of atomic forces to calculate statements for </td></tr>
<tr><td valign="top"><em>atomForce</em> </td><td>
Object for storing atom forces </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Atom list </td></tr>
<tr><td valign="top"><em>clist</em> </td><td>
Cell list for accessibility object </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00093">ACF_COMPS</a>, <a class="el" href="apolparm_8h-source.html#l00092">ACF_TOTAL</a>, <a class="el" href="vacc_8h-source.html#l00106">sVacc::alist</a>, <a class="el" href="apolparm_8h-source.html#l00134">sAPOLparm::bconc</a>, <a class="el" href="apolparm_8h-source.html#l00165">sAPOLparm::calcforce</a>, <a class="el" href="apolparm_8h-source.html#l00140">sAPOLparm::dpos</a>, <a class="el" href="apolparm_8h-source.html#l00158">sAPOLparm::gamma</a>, <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>, <a class="el" href="apolparm_8h-source.html#l00143">sAPOLparm::press</a>, <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="apolparm_8h-source.html#l00149">sAPOLparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l01229">Vacc_atomdSASA()</a>, <a class="el" href="vacc_8c-source.html#l01118">Vacc_atomdSAV()</a>, <a class="el" href="vacc_8c-source.html#l00789">Vacc_atomSurf()</a>, <a class="el" href="vacc_8c-source.html#l01655">Vacc_wcaForceAtom()</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>.</p>
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<a class="anchor" name="gfa145c12f55d0efd7fcace66ffde7567"></a><!-- doxytag: member="routines.h::forceMG" ref="gfa145c12f55d0efd7fcace66ffde7567" args="(Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm, Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL])" -->
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<td class="memname">int forceMG </td>
<td>(</td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsMGparm.html">MGparm</a> * </td>
<td class="paramname"> <em>mgparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int * </td>
<td class="paramname"> <em>nforce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> ** </td>
<td class="paramname"> <em>atomForce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Calculate forces from MG solution.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>mem</em> </td><td>Memory management object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>Generic PBE parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>mgparm</em> </td><td>MG-specific parmaeters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nforce</em> </td><td>Set to number of forces in arrays </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomForce</em> </td><td>List of atom forces </td></tr>
<tr><td valign="top"></td><td valign="top"><em>alist</em> </td><td>List of atom lists </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="vhal_8h-source.html#l00353">APBS_TIMER_FORCE</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="mgparm_8h-source.html#l00117">sMGparm::chgm</a>, <a class="el" href="pbeparm_8h-source.html#l00116">sPBEparm::molid</a>, <a class="el" href="pbeparm_8h-source.html#l00097">PCF_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="routines_8h-source.html#l00082">AtomForce::qfForce</a>, <a class="el" href="pbeparm_8h-source.html#l00143">sPBEparm::srfm</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vpmg_8c-source.html#l05211">Vpmg_dbForce()</a>, <a class="el" href="vpmg_8c-source.html#l05047">Vpmg_ibForce()</a>, <a class="el" href="vpmg_8c-source.html#l05465">Vpmg_qfForce()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g777e5bac9e149e6c9b51cbca372cfdfb"></a><!-- doxytag: member="routines.h::initAPOL" ref="g777e5bac9e149e6c9b51cbca372cfdfb" args="(NOsh *nosh, Vmem *mem, Vparam *param, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int initAPOL </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structVparam.html">Vparam</a> * </td>
<td class="paramname"> <em>param</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int * </td>
<td class="paramname"> <em>nforce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> ** </td>
<td class="paramname"> <em>atomForce</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
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<div class="memdoc">
<p>
Upperlevel routine to the non-polar energy and force routines.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Input parameter object </td></tr>
<tr><td valign="top"><em>mem</em> </td><td>
Memory manager </td></tr>
<tr><td valign="top"><em>param</em> </td><td>
Atom parameters </td></tr>
<tr><td valign="top"><em>apolparm</em> </td><td>
Apolar calculation parameters </td></tr>
<tr><td valign="top"><em>nforce</em> </td><td>
Number of force calculations </td></tr>
<tr><td valign="top"><em>atomForce</em> </td><td>
Atom force storage object </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Atom list </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00134">sAPOLparm::bconc</a>, <a class="el" href="apolparm_8h-source.html#l00162">sAPOLparm::calcenergy</a>, <a class="el" href="apolparm_8h-source.html#l00165">sAPOLparm::calcforce</a>, <a class="el" href="vclist_8h-source.html#l00078">CLIST_AUTO_DOMAIN</a>, <a class="el" href="apolparm_8h-source.html#l00140">sAPOLparm::dpos</a>, <a class="el" href="routines_8c-source.html#l03861">energyAPOL()</a>, <a class="el" href="vparam_8h-source.html#l00090">sVparam_AtomData::epsilon</a>, <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>, <a class="el" href="apolparm_8h-source.html#l00158">sAPOLparm::gamma</a>, <a class="el" href="apolparm_8h-source.html#l00143">sAPOLparm::press</a>, <a class="el" href="vparam_8h-source.html#l00089">sVparam_AtomData::radius</a>, <a class="el" href="apolparm_8h-source.html#l00170">sAPOLparm::sasa</a>, <a class="el" href="apolparm_8h-source.html#l00171">sAPOLparm::sav</a>, <a class="el" href="apolparm_8h-source.html#l00137">sAPOLparm::sdens</a>, <a class="el" href="apolparm_8h-source.html#l00175">sAPOLparm::setwat</a>, <a class="el" href="apolparm_8h-source.html#l00149">sAPOLparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="vacc_8c-source.html#l00705">Vacc_atomSASA()</a>, <a class="el" href="vacc_8c-source.html#l00130">Vacc_ctor()</a>, <a class="el" href="vacc_8c-source.html#l00230">Vacc_dtor()</a>, <a class="el" href="vacc_8c-source.html#l00699">Vacc_totalSASA()</a>, <a class="el" href="vacc_8c-source.html#l01402">Vacc_totalSAV()</a>, <a class="el" href="vacc_8c-source.html#l01620">Vacc_wcaEnergy()</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vatom_8c-source.html#l00118">Vatom_getCharge()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vclist_8c-source.html#l00078">Vclist_ctor()</a>, <a class="el" href="vclist_8c-source.html#l00400">Vclist_dtor()</a>, <a class="el" href="vparam_8c-source.html#l00270">Vparam_getAtomData()</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>, <a class="el" href="apolparm_8h-source.html#l00169">sAPOLparm::watepsilon</a>, <a class="el" href="apolparm_8h-source.html#l00168">sAPOLparm::watsigma</a>, and <a class="el" href="apolparm_8h-source.html#l00172">sAPOLparm::wcaEnergy</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<a class="anchor" name="g2a07181f0b784288233c5b71d53e3e92"></a><!-- doxytag: member="routines.h::initFE" ref="g2a07181f0b784288233c5b71d53e3e92" args="(int icalc, NOsh *nosh, FEMparm *feparm, PBEparm *pbeparm, Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vfetk *fetk[NOSH_MAXCALC], Gem *gm[NOSH_MAXCALC])" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">Vrc_Codes initFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpbe.html">Vpbe</a> * </td>
<td class="paramname"> <em>pbe</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL], </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC], </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">Gem * </td>
<td class="paramname"> <em>gm</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Initialize FE solver objects.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b><a class="el" href="bug.html#_bug000032">Bug:</a></b></dt><dd>THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE </dd></dl>
<dl compact><dt><b><a class="el" href="todo.html#_todo000002">Todo:</a></b></dt><dd>THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Index in pb, fetk to initialize (calculation index) </td></tr>
<tr><td valign="top"><em>feparm</em> </td><td>
Master parmaeter object </td></tr>
<tr><td valign="top"><em>pbeparm</em> </td><td>
FE-specific parameters </td></tr>
<tr><td valign="top"><em>pbe</em> </td><td>
Generic PBE parameters </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Array of PBE objects </td></tr>
<tr><td valign="top"><em>fetk</em> </td><td>
Array of atom lists </td></tr>
<tr><td valign="top"><em>gm</em> </td><td>
Array of finite element objects Array of geometry objects </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
</div><p>
<a class="anchor" name="g672ad18a84d014f587dcc7c417f16611"></a><!-- doxytag: member="routines.h::initMG" ref="g672ad18a84d014f587dcc7c417f16611" args="(int icalc, NOsh *nosh, MGparm *mgparm, PBEparm *pbeparm, double realCenter[3], Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL], Vgrid *kappaMap[NOSH_MAXMOL], Vgrid *chargeMap[NOSH_MAXMOL], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC])" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int initMG </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsMGparm.html">MGparm</a> * </td>
<td class="paramname"> <em>mgparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>realCenter</em>[3], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpbe.html">Vpbe</a> * </td>
<td class="paramname"> <em>pbe</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielXMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielYMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielZMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>kappaMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>chargeMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmgp.html">Vpmgp</a> * </td>
<td class="paramname"> <em>pmgp</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Initialize an MG calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if succesful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>icalc</em> </td><td>
Index of calculation in pmg/pmpg arrays </td></tr>
<tr><td valign="top"><em>nosh</em> </td><td>
Object with parsed input file parameters </td></tr>
<tr><td valign="top"><em>mgparm</em> </td><td>
Object with MG-specific parameters </td></tr>
<tr><td valign="top"><em>pbeparm</em> </td><td>
Object with generic PBE parameters </td></tr>
<tr><td valign="top"><em>realCenter</em> </td><td>
The actual center of the current mesh </td></tr>
<tr><td valign="top"><em>pbe</em> </td><td>
Array of Vpbe objects (one for each calc) </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Array of atom lists </td></tr>
<tr><td valign="top"><em>dielXMap</em> </td><td>
Array of x-shifted dielectric maps </td></tr>
<tr><td valign="top"><em>dielYMap</em> </td><td>
Array of y-shifted dielectric maps </td></tr>
<tr><td valign="top"><em>dielZMap</em> </td><td>
Array of z-shifted dielectric maps </td></tr>
<tr><td valign="top"><em>kappaMap</em> </td><td>
Array of kappa maps </td></tr>
<tr><td valign="top"><em>chargeMap</em> </td><td>
Array of charge maps </td></tr>
<tr><td valign="top"><em>pmgp</em> </td><td>
Array of MG parameter objects (one for each calc) </td></tr>
<tr><td valign="top"><em>pmg</em> </td><td>
Array of MG objects (one for each calc) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vhal_8h-source.html#l00335">APBS_TIMER_SETUP</a>, <a class="el" href="pbeparm_8h-source.html#l00129">sPBEparm::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="mgparm_8h-source.html#l00131">sMGparm::center</a>, <a class="el" href="pbeparm_8h-source.html#l00126">sPBEparm::chargeMapID</a>, <a class="el" href="mgparm_8h-source.html#l00117">sMGparm::chgm</a>, <a class="el" href="pbeparm_8h-source.html#l00120">sPBEparm::dielMapID</a>, <a class="el" href="pbeparm_8h-source.html#l00134">sPBEparm::ionc</a>, <a class="el" href="pbeparm_8h-source.html#l00133">sPBEparm::ionq</a>, <a class="el" href="pbeparm_8h-source.html#l00135">sPBEparm::ionr</a>, <a class="el" href="pbeparm_8h-source.html#l00123">sPBEparm::kappaMapID</a>, <a class="el" href="mgparm_8h-source.html#l00185">sMGparm::method</a>, <a class="el" href="pbeparm_8h-source.html#l00116">sPBEparm::molid</a>, <a class="el" href="nosh_8h-source.html#l00235">sNOsh::ncharge</a>, <a class="el" href="nosh_8h-source.html#l00224">sNOsh::ndiel</a>, <a class="el" href="pbeparm_8h-source.html#l00131">sPBEparm::nion</a>, <a class="el" href="nosh_8h-source.html#l00232">sNOsh::nkappa</a>, <a class="el" href="mgparm_8h-source.html#l00182">sMGparm::nonlintype</a>, <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00147">PBE_LRPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="vhal_8h-source.html#l00149">PBE_SMPBE</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="pbeparm_8h-source.html#l00079">PCE_NO</a>, <a class="el" href="pbeparm_8h-source.html#l00137">sPBEparm::pdie</a>, <a class="el" href="pbeparm_8h-source.html#l00139">sPBEparm::sdens</a>, <a class="el" href="pbeparm_8h-source.html#l00141">sPBEparm::sdie</a>, <a class="el" href="pbeparm_8h-source.html#l00152">sPBEparm::smsize</a>, <a class="el" href="pbeparm_8h-source.html#l00155">sPBEparm::smvolume</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00143">sPBEparm::srfm</a>, <a class="el" href="pbeparm_8h-source.html#l00147">sPBEparm::swin</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="mgparm_8h-source.html#l00188">sMGparm::useAqua</a>, <a class="el" href="pbeparm_8h-source.html#l00124">sPBEparm::useChargeMap</a>, <a class="el" href="pbeparm_8h-source.html#l00118">sPBEparm::useDielMap</a>, <a class="el" href="pbeparm_8h-source.html#l00121">sPBEparm::useKappaMap</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vatom_8c-source.html#l00118">Vatom_getCharge()</a>, <a class="el" href="vpbe_8c-source.html#l00196">Vpbe_ctor()</a>, <a class="el" href="vpbe_8c-source.html#l00399">Vpbe_dtor()</a>, <a class="el" href="vpbe_8c-source.html#l00140">Vpbe_getDeblen()</a>, <a class="el" href="vpmg_8c-source.html#l00125">Vpmg_ctor()</a>, <a class="el" href="vpmg_8c-source.html#l00489">Vpmg_dtor()</a>, <a class="el" href="vpmg_8c-source.html#l04885">Vpmg_fillco()</a>, <a class="el" href="vpmgp_8c-source.html#l00076">Vpmgp_ctor()</a>, <a class="el" href="vpmgp_8c-source.html#l00168">Vpmgp_dtor()</a>, and <a class="el" href="vhal_8h-source.html#l00114">VSM_SPLINE</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gbd66a61c0345b5fb2a1f7cf28eda455f"></a><!-- doxytag: member="routines.h::killChargeMaps" ref="gbd66a61c0345b5fb2a1f7cf28eda455f" args="(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])" -->
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<td class="memname">void killChargeMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>charge</em>[NOSH_MAXMOL]</td><td> </td>
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<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Destroy the loaded charge maps.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>charge</em> </td><td>List of charge maps </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00235">sNOsh::ncharge</a>, and <a class="el" href="vgrid_8c-source.html#l00135">Vgrid_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g8fc9aaea29e0981630c959189125a9a2"></a><!-- doxytag: member="routines.h::killDielMaps" ref="g8fc9aaea29e0981630c959189125a9a2" args="(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL])" -->
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<td class="memname">void killDielMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielXMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielYMap</em>[NOSH_MAXMOL], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielZMap</em>[NOSH_MAXMOL]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<div class="memdoc">
<p>
Destroy the loaded dielectric.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielXMap</em> </td><td>List of x-shifted dielectric maps </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielYMap</em> </td><td>List of y-shifted dielectric maps </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielZMap</em> </td><td>List of x-shifted dielectric maps </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00224">sNOsh::ndiel</a>, and <a class="el" href="vgrid_8c-source.html#l00135">Vgrid_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g0d20f0a6407d4ef03e15b5738612381e"></a><!-- doxytag: member="routines.h::killEnergy" ref="g0d20f0a6407d4ef03e15b5738612381e" args="()" -->
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<td class="memname">void killEnergy </td>
<td>(</td>
<td class="paramname"> </td>
<td> ) </td>
<td></td>
</tr>
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<div class="memdoc">
<p>
Kill arrays allocated for energies.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
</div><p>
<a class="anchor" name="ge90a8d20839ced8a3e7d2caca35cbea0"></a><!-- doxytag: member="routines.h::killFE" ref="ge90a8d20839ced8a3e7d2caca35cbea0" args="(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL])" -->
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<td class="memname">void killFE </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpbe.html">Vpbe</a> * </td>
<td class="paramname"> <em>pbe</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Gem * </td>
<td class="paramname"> <em>gem</em>[NOSH_MAXMOL]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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</div>
<div class="memdoc">
<p>
Kill structures initialized during an FE calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>pbe</em> </td><td>
Object with parsed input file parameters </td></tr>
<tr><td valign="top"><em>fetk</em> </td><td>
Array of Vpbe objects for each calc </td></tr>
<tr><td valign="top"><em>gem</em> </td><td>
Array of FEtk objects for each calc Array of geometry manager objects for each calc </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00185">sNOsh::ncalc</a>, <a class="el" href="nosh_8h-source.html#l00238">sNOsh::nmesh</a>, <a class="el" href="vfetk_8c-source.html#l00619">Vfetk_dtor()</a>, and <a class="el" href="vpbe_8c-source.html#l00399">Vpbe_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g85261d2d20693fd91564bdadc911dbbb"></a><!-- doxytag: member="routines.h::killForce" ref="g85261d2d20693fd91564bdadc911dbbb" args="(Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC])" -->
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<td class="memname">void killForce </td>
<td>(</td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<p>
Free memory from MG force calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>mem</em> </td><td>Memory management object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nforce</em> </td><td>Number of forces in arrays </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomForce</em> </td><td>List of atom forces </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00185">sNOsh::ncalc</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
</div><p>
<a class="anchor" name="g903bb83abbd4bb2b9102d782b319e26c"></a><!-- doxytag: member="routines.h::killKappaMaps" ref="g903bb83abbd4bb2b9102d782b319e26c" args="(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])" -->
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<td class="memname">void killKappaMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>kappa</em>[NOSH_MAXMOL]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<div class="memdoc">
<p>
Destroy the loaded kappa maps.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>kappa</em> </td><td>List of kappa maps </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00232">sNOsh::nkappa</a>, and <a class="el" href="vgrid_8c-source.html#l00135">Vgrid_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gddc9fadc54a9e22e8b2b2efc74066273"></a><!-- doxytag: member="routines.h::killMeshes" ref="gddc9fadc54a9e22e8b2b2efc74066273" args="(NOsh *nosh, Gem *alist[NOSH_MAXMOL])" -->
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<td class="memname">void killMeshes </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Gem * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL]</td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Destroy the loaded meshes.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
NOsh object with input file information </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Populated list of geometry objects to be destroyed </td></tr>
</table>
</dl>
</div>
</div><p>
<a class="anchor" name="gb0ce95b1f26075f244714265de179a90"></a><!-- doxytag: member="routines.h::killMG" ref="gb0ce95b1f26075f244714265de179a90" args="(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC])" -->
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<td class="memname">void killMG </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpbe.html">Vpbe</a> * </td>
<td class="paramname"> <em>pbe</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmgp.html">Vpmgp</a> * </td>
<td class="paramname"> <em>pmgp</em>[NOSH_MAXCALC], </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em>[NOSH_MAXCALC]</td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Kill structures initialized during an MG calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>pbe</em> </td><td>
Object with parsed input file parameters </td></tr>
<tr><td valign="top"><em>pmgp</em> </td><td>
Array of Vpbe objects for each calc </td></tr>
<tr><td valign="top"><em>pmg</em> </td><td>
Array of MG parameter objects for each calc Array of MG objects for each calc </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00185">sNOsh::ncalc</a>, <a class="el" href="vpbe_8c-source.html#l00399">Vpbe_dtor()</a>, <a class="el" href="vpmg_8c-source.html#l00489">Vpmg_dtor()</a>, and <a class="el" href="vpmgp_8c-source.html#l00168">Vpmgp_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gf15fae1faaacaee69eb1ec79a1d2c0d3"></a><!-- doxytag: member="routines.h::killMolecules" ref="gf15fae1faaacaee69eb1ec79a1d2c0d3" args="(NOsh *nosh, Valist *alist[NOSH_MAXMOL])" -->
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<td class="memname">void killMolecules </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL]</td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Destroy the loaded molecules.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>alist</em> </td><td>List of atom list objects </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00216">sNOsh::nmol</a>, and <a class="el" href="valist_8c-source.html#l00166">Valist_dtor()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g8bfbb3f554c21aaca1e87b59ec7e36c4"></a><!-- doxytag: member="routines.h::loadChargeMaps" ref="g8bfbb3f554c21aaca1e87b59ec7e36c4" args="(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])" -->
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<td class="memname">int loadChargeMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>charge</em>[NOSH_MAXMOL]</td><td> </td>
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<p>
Load the charge maps given in NOsh into grid objects.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>charge</em> </td><td>List of kappa maps </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00237">sNOsh::chargefmt</a>, <a class="el" href="nosh_8h-source.html#l00236">sNOsh::chargepath</a>, <a class="el" href="nosh_8h-source.html#l00234">sNOsh::kappafmt</a>, <a class="el" href="nosh_8h-source.html#l00235">sNOsh::ncharge</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vgrid_8c-source.html#l00076">Vgrid_ctor()</a>, and <a class="el" href="vgrid_8c-source.html#l00439">Vgrid_readDX()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g0744b51dd1328f9623331b0bd6b2a41e"></a><!-- doxytag: member="routines.h::loadDielMaps" ref="g0744b51dd1328f9623331b0bd6b2a41e" args="(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL])" -->
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<td class="memname">int loadDielMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielXMap</em>[NOSH_MAXMOL], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielYMap</em>[NOSH_MAXMOL], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>dielZMap</em>[NOSH_MAXMOL]</td><td> </td>
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<p>
Load the dielectric maps given in NOsh into grid objects.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielXMap</em> </td><td>List of x-shifted dielectric maps </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielYMap</em> </td><td>List of y-shifted dielectric maps </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielZMap</em> </td><td>List of x-shifted dielectric maps </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00231">sNOsh::dielfmt</a>, <a class="el" href="nosh_8h-source.html#l00225">sNOsh::dielXpath</a>, <a class="el" href="nosh_8h-source.html#l00227">sNOsh::dielYpath</a>, <a class="el" href="nosh_8h-source.html#l00229">sNOsh::dielZpath</a>, <a class="el" href="nosh_8h-source.html#l00224">sNOsh::ndiel</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vgrid_8c-source.html#l00076">Vgrid_ctor()</a>, and <a class="el" href="vgrid_8c-source.html#l00439">Vgrid_readDX()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g5b70151ac7dbfc3c615a6fed6367390b"></a><!-- doxytag: member="routines.h::loadKappaMaps" ref="g5b70151ac7dbfc3c615a6fed6367390b" args="(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])" -->
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<td class="memname">int loadKappaMaps </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVgrid.html">Vgrid</a> * </td>
<td class="paramname"> <em>kappa</em>[NOSH_MAXMOL]</td><td> </td>
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<td></td>
<td>)</td>
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<p>
Load the kappa maps given in NOsh into grid objects.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object with input file information </td></tr>
<tr><td valign="top"></td><td valign="top"><em>kappa</em> </td><td>List of kappa maps </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00234">sNOsh::kappafmt</a>, <a class="el" href="nosh_8h-source.html#l00233">sNOsh::kappapath</a>, <a class="el" href="nosh_8h-source.html#l00232">sNOsh::nkappa</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vgrid_8c-source.html#l00076">Vgrid_ctor()</a>, and <a class="el" href="vgrid_8c-source.html#l00439">Vgrid_readDX()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g26b8b211a2a3049f5e424f773a8207b7"></a><!-- doxytag: member="routines.h::loadMeshes" ref="g26b8b211a2a3049f5e424f773a8207b7" args="(NOsh *nosh, Gem *gm[NOSH_MAXMOL])" -->
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<td class="memname">Vrc_Codes loadMeshes </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">Gem * </td>
<td class="paramname"> <em>gm</em>[NOSH_MAXMOL]</td><td> </td>
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<p>
Load the meshes given in NOsh into geometry objects.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Error code on success/failure </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
NOsh object with input file information </td></tr>
<tr><td valign="top"><em>gm</em> </td><td>
List of geometry objects (to be populated) </td></tr>
</table>
</dl>
</div>
</div><p>
<a class="anchor" name="gde48c79ecd7d2bf5838a4e0519b19f9a"></a><!-- doxytag: member="routines.h::loadMolecules" ref="gde48c79ecd7d2bf5838a4e0519b19f9a" args="(NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL])" -->
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<td class="memname">int loadMolecules </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structVparam.html">Vparam</a> * </td>
<td class="paramname"> <em>param</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>[NOSH_MAXMOL]</td><td> </td>
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<td></td><td></td><td></td>
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<p>
Load the molecules given in NOsh into atom lists.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
NOsh object with input file information </td></tr>
<tr><td valign="top"><em>param</em> </td><td>
NULL (if PQR files only) or pointer to parameter object </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
List of atom list objects (to be populated) </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00221">sNOsh::gotparm</a>, <a class="el" href="nosh_8h-source.html#l00218">sNOsh::molfmt</a>, <a class="el" href="nosh_8h-source.html#l00217">sNOsh::molpath</a>, <a class="el" href="nosh_8h-source.html#l00096">NMF_PDB</a>, <a class="el" href="nosh_8h-source.html#l00095">NMF_PQR</a>, <a class="el" href="nosh_8h-source.html#l00097">NMF_XML</a>, <a class="el" href="nosh_8h-source.html#l00216">sNOsh::nmol</a>, <a class="el" href="nosh_8h-source.html#l00222">sNOsh::parmpath</a>, <a class="el" href="valist_8c-source.html#l00137">Valist_ctor()</a>, <a class="el" href="valist_8c-source.html#l00166">Valist_dtor()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="valist_8c-source.html#l00514">Valist_readPDB()</a>, <a class="el" href="valist_8c-source.html#l00605">Valist_readPQR()</a>, and <a class="el" href="valist_8c-source.html#l00709">Valist_readXML()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="ge373e54f41b5dc9cb275baef6f6115b3"></a><!-- doxytag: member="routines.h::loadParameter" ref="ge373e54f41b5dc9cb275baef6f6115b3" args="(NOsh *nosh)" -->
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<td class="memname"><a class="el" href="structVparam.html">Vparam</a>* loadParameter </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em> </td>
<td> ) </td>
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Loads and returns parameter object.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Pointer to parameter object or NULL </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Pointer to NOsh object with input file information </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00221">sNOsh::gotparm</a>, <a class="el" href="nosh_8h-source.html#l00127">NPF_FLAT</a>, <a class="el" href="nosh_8h-source.html#l00128">NPF_XML</a>, <a class="el" href="nosh_8h-source.html#l00223">sNOsh::parmfmt</a>, <a class="el" href="nosh_8h-source.html#l00222">sNOsh::parmpath</a>, <a class="el" href="vparam_8c-source.html#l00184">Vparam_ctor()</a>, <a class="el" href="vparam_8c-source.html#l00448">Vparam_readFlatFile()</a>, and <a class="el" href="vparam_8c-source.html#l00309">Vparam_readXMLFile()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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<a class="anchor" name="g3c04138a5bfe5d72780bb7e82a18e627"></a><!-- doxytag: member="main.c::main" ref="g3c04138a5bfe5d72780bb7e82a18e627" args="(int argc, char **argv)" -->
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<div class="memproto">
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<td class="memname">int main </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>argc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char ** </td>
<td class="paramname"> <em>argv</em></td><td> </td>
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<td></td>
<td>)</td>
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<div class="memdoc">
<p>
The main APBS function.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Dave Gohara, Todd Dolinsky </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Status code (0 for success) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>argc</em> </td><td>
Number of arguments </td></tr>
<tr><td valign="top"><em>argv</em> </td><td>
Argument strings </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00109">ACD_ERROR</a>, <a class="el" href="vhal_8h-source.html#l00329">APBS_TIMER_WALL_CLOCK</a>, <a class="el" href="routines_8h-source.html#l00074">APBSRC</a>, <a class="el" href="nosh_8h-source.html#l00214">sNOsh::apol2calc</a>, <a class="el" href="nosh_8h-source.html#l00251">sNOsh::apolname</a>, <a class="el" href="nosh_8h-source.html#l00165">sNOsh_calc::apolparm</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="nosh_8h-source.html#l00166">sNOsh_calc::calctype</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="routines_8c-source.html#l03441">energyFE()</a>, <a class="el" href="routines_8c-source.html#l01056">energyMG()</a>, <a class="el" href="nosh_8h-source.html#l00163">sNOsh_calc::femparm</a>, <a class="el" href="routines_8c-source.html#l01120">forceMG()</a>, <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, <a class="el" href="group__Frontend.html#g2a07181f0b784288233c5b71d53e3e92">initFE()</a>, <a class="el" href="routines_8c-source.html#l00762">initMG()</a>, <a class="el" href="routines_8c-source.html#l00555">killChargeMaps()</a>, <a class="el" href="routines_8c-source.html#l00413">killDielMaps()</a>, <a class="el" href="routines_8c-source.html#l01249">killEnergy()</a>, <a class="el" href="routines_8c-source.html#l03016">killFE()</a>, <a class="el" href="routines_8c-source.html#l01257">killForce()</a>, <a class="el" href="routines_8c-source.html#l00488">killKappaMaps()</a>, <a class="el" href="routines_8c-source.html#l00954">killMG()</a>, <a class="el" href="routines_8c-source.html#l00248">killMolecules()</a>, <a class="el" href="routines_8c-source.html#l00502">loadChargeMaps()</a>, <a class="el" href="routines_8c-source.html#l00260">loadDielMaps()</a>, <a class="el" href="routines_8c-source.html#l00435">loadKappaMaps()</a>, <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>, <a class="el" href="routines_8c-source.html#l00077">loadParameter()</a>, <a class="el" href="femparm_8h-source.html#l00160">sFEMparm::maxsolve</a>, <a class="el" href="nosh_8h-source.html#l00162">sNOsh_calc::mgparm</a>, <a class="el" href="apolparm_8h-source.html#l00131">sAPOLparm::molid</a>, <a class="el" href="nosh_8h-source.html#l00196">sNOsh::napol</a>, <a class="el" href="nosh_8h-source.html#l00185">sNOsh::ncalc</a>, <a class="el" href="nosh_8h-source.html#l00113">NCT_APOL</a>, <a class="el" href="nosh_8h-source.html#l00112">NCT_FEM</a>, <a class="el" href="nosh_8h-source.html#l00111">NCT_MG</a>, <a class="el" href="nosh_8h-source.html#l00190">sNOsh::nelec</a>, <a class="el" href="nosh_8c-source.html#l00236">NOsh_ctor()</a>, <a class="el" href="nosh_8c-source.html#l00281">NOsh_dtor()</a>, <a class="el" href="nosh_8h-source.html#l00080">NOSH_MAXCALC</a>, <a class="el" href="nosh_8h-source.html#l00076">NOSH_MAXMOL</a>, <a class="el" href="nosh_8c-source.html#l00399">NOsh_parseInput()</a>, <a class="el" href="nosh_8c-source.html#l01225">NOsh_setupApolCalc()</a>, <a class="el" href="nosh_8c-source.html#l01144">NOsh_setupElecCalc()</a>, <a class="el" href="nosh_8h-source.html#l00241">sNOsh::nprint</a>, <a class="el" href="nosh_8h-source.html#l00146">NPT_APOLENERGY</a>, <a class="el" href="nosh_8h-source.html#l00147">NPT_APOLFORCE</a>, <a class="el" href="nosh_8h-source.html#l00144">NPT_ELECENERGY</a>, <a class="el" href="nosh_8h-source.html#l00145">NPT_ELECFORCE</a>, <a class="el" href="nosh_8h-source.html#l00142">NPT_ENERGY</a>, <a class="el" href="nosh_8h-source.html#l00143">NPT_FORCE</a>, <a class="el" href="vhal_8h-source.html#l00198">OUTPUT_FLAT</a>, <a class="el" href="vhal_8h-source.html#l00197">OUTPUT_NULL</a>, <a class="el" href="vhal_8h-source.html#l00199">OUTPUT_XML</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00081">PCE_COMPS</a>, <a class="el" href="routines_8c-source.html#l03483">postRefineFE()</a>, <a class="el" href="routines_8c-source.html#l03337">preRefineFE()</a>, <a class="el" href="routines_8c-source.html#l02288">printApolEnergy()</a>, <a class="el" href="routines_8c-source.html#l02816">printApolForce()</a>, <a class="el" href="routines_8c-source.html#l02229">printElecEnergy()</a>, <a class="el" href="routines_8c-source.html#l02583">printElecForce()</a>, <a class="el" href="routines_8c-source.html#l02167">printEnergy()</a>, <a class="el" href="routines_8c-source.html#l03197">printFEPARM()</a>, <a class="el" href="routines_8c-source.html#l02347">printForce()</a>, <a class="el" href="routines_8c-source.html#l00732">printMGPARM()</a>, <a class="el" href="routines_8c-source.html#l00571">printPBEPARM()</a>, <a class="el" href="nosh_8h-source.html#l00242">sNOsh::printwhat</a>, <a class="el" href="routines_8c-source.html#l01014">setPartMG()</a>, <a class="el" href="routines_8c-source.html#l03391">solveFE()</a>, <a class="el" href="routines_8c-source.html#l00980">solveMG()</a>, <a class="el" href="routines_8c-source.html#l00075">startVio()</a>, <a class="el" href="routines_8c-source.html#l01344">storeAtomEnergy()</a>, <a class="el" href="mgparm_8h-source.html#l00111">sMGparm::type</a>, <a class="el" href="vparam_8c-source.html#l00216">Vparam_dtor()</a>, <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="routines_8c-source.html#l03538">writedataFE()</a>, <a class="el" href="routines_8c-source.html#l01361">writedataFlat()</a>, <a class="el" href="routines_8c-source.html#l01845">writedataMG()</a>, <a class="el" href="routines_8c-source.html#l01591">writedataXML()</a>, and <a class="el" href="routines_8c-source.html#l01274">writematMG()</a>.</p>
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<a class="anchor" name="gd4c2ae8f06b8721031b13ed18631fd48"></a><!-- doxytag: member="routines.h::partFE" ref="gd4c2ae8f06b8721031b13ed18631fd48" args="(int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])" -->
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<td class="memname">int partFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC]</td><td> </td>
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<p>
Partition mesh (if applicable).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>Calculation index </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Master parameter object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>feparm</em> </td><td>FE-specific parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>Array of FE solver objects </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="vfetk_8c-source.html#l00806">Vfetk_setAtomColors()</a>.</p>
<p>
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<a class="anchor" name="gf2493d6ed066b920ef8f5e37533b700d"></a><!-- doxytag: member="routines.h::postRefineFE" ref="gf2493d6ed066b920ef8f5e37533b700d" args="(int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])" -->
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<td class="memname">int postRefineFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC]</td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Estimate error, mark mesh, and refine mesh after solve.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>icalc</em> </td><td>Calculation index </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Master parameter object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>feparm</em> </td><td>FE-specific parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>Array of FE solver objects </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise -- note that a 0 will likely imply that either the max number of vertices have been met or no vertices were marked for refinement. In either case, this should not be treated as a fatal error. </dd></dl>
<p>References <a class="el" href="femparm_8h-source.html#l00147">sFEMparm::akeySOLVE</a>, <a class="el" href="femparm_8h-source.html#l00140">sFEMparm::ekey</a>, <a class="el" href="femparm_8h-source.html#l00137">sFEMparm::etol</a>, <a class="el" href="femparm_8h-source.html#l00097">FRT_DUAL</a>, <a class="el" href="femparm_8h-source.html#l00095">FRT_GEOM</a>, <a class="el" href="femparm_8h-source.html#l00099">FRT_LOCA</a>, <a class="el" href="femparm_8h-source.html#l00096">FRT_RESI</a>, <a class="el" href="femparm_8h-source.html#l00094">FRT_UNIF</a>, <a class="el" href="femparm_8h-source.html#l00162">sFEMparm::maxvert</a>, and <a class="el" href="femparm_8h-source.html#l00165">sFEMparm::pkey</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
</div><p>
<a class="anchor" name="g4263953eaca54df840862f6ca2ee4f26"></a><!-- doxytag: member="routines.h::preRefineFE" ref="g4263953eaca54df840862f6ca2ee4f26" args="(int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])" -->
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<td class="memname">int preRefineFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
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<div class="memdoc">
<p>
Pre-refine mesh before solve.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>Calculation index </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Master parameter object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>feparm</em> </td><td>FE-specific parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>Array of FE solver objects </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="femparm_8h-source.html#l00143">sFEMparm::akeyPRE</a>, <a class="el" href="femparm_8h-source.html#l00140">sFEMparm::ekey</a>, <a class="el" href="femparm_8h-source.html#l00137">sFEMparm::etol</a>, <a class="el" href="femparm_8h-source.html#l00097">FRT_DUAL</a>, <a class="el" href="femparm_8h-source.html#l00095">FRT_GEOM</a>, <a class="el" href="femparm_8h-source.html#l00099">FRT_LOCA</a>, <a class="el" href="femparm_8h-source.html#l00096">FRT_RESI</a>, <a class="el" href="femparm_8h-source.html#l00094">FRT_UNIF</a>, <a class="el" href="femparm_8h-source.html#l00165">sFEMparm::pkey</a>, <a class="el" href="femparm_8h-source.html#l00150">sFEMparm::targetNum</a>, and <a class="el" href="femparm_8h-source.html#l00155">sFEMparm::targetRes</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
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<a class="anchor" name="g3ea91bf9d5a15e204315b2792dffc5c2"></a><!-- doxytag: member="routines.h::printApolEnergy" ref="g3ea91bf9d5a15e204315b2792dffc5c2" args="(NOsh *nosh, int iprint)" -->
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<td class="memname">int printApolEnergy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>iprint</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Combine and pretty-print energy data.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>iprint</em> </td><td>
Index of energy statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00076">ACE_TOTAL</a>, <a class="el" href="nosh_8h-source.html#l00214">sNOsh::apol2calc</a>, <a class="el" href="nosh_8h-source.html#l00251">sNOsh::apolname</a>, <a class="el" href="nosh_8h-source.html#l00165">sNOsh_calc::apolparm</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="apolparm_8h-source.html#l00162">sAPOLparm::calcenergy</a>, <a class="el" href="apolparm_8h-source.html#l00158">sAPOLparm::gamma</a>, <a class="el" href="apolparm_8h-source.html#l00143">sAPOLparm::press</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="apolparm_8h-source.html#l00170">sAPOLparm::sasa</a>, <a class="el" href="apolparm_8h-source.html#l00171">sAPOLparm::sav</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, and <a class="el" href="apolparm_8h-source.html#l00172">sAPOLparm::wcaEnergy</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gd34565687f0168cd9fd15b5747ef7084"></a><!-- doxytag: member="routines.h::printApolForce" ref="gd34565687f0168cd9fd15b5747ef7084" args="(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)" -->
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<td class="memname">int printApolForce </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<div class="memdoc">
<p>
Combine and pretty-print force data.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Communications object </td></tr>
<tr><td valign="top"><em>nforce</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>atomForce</em> </td><td>
Number of forces calculated </td></tr>
<tr><td valign="top"><em>i</em> </td><td>
Array of force structures Index of force statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00093">ACF_COMPS</a>, <a class="el" href="apolparm_8h-source.html#l00091">ACF_NO</a>, <a class="el" href="apolparm_8h-source.html#l00092">ACF_TOTAL</a>, <a class="el" href="nosh_8h-source.html#l00214">sNOsh::apol2calc</a>, <a class="el" href="nosh_8h-source.html#l00251">sNOsh::apolname</a>, <a class="el" href="nosh_8h-source.html#l00165">sNOsh_calc::apolparm</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="apolparm_8h-source.html#l00165">sAPOLparm::calcforce</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="routines_8h-source.html#l00084">AtomForce::sasaForce</a>, <a class="el" href="routines_8h-source.html#l00085">AtomForce::savForce</a>, <a class="el" href="apolparm_8h-source.html#l00155">sAPOLparm::temp</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, and <a class="el" href="routines_8h-source.html#l00086">AtomForce::wcaForce</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gad105790d5d821a70c2556d8f678bff9"></a><!-- doxytag: member="routines.h::printElecEnergy" ref="gad105790d5d821a70c2556d8f678bff9" args="(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)" -->
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<td class="memname">int printElecEnergy </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>totEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>iprint</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Combine and pretty-print energy data.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Communications object </td></tr>
<tr><td valign="top"><em>totEnergy</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>iprint</em> </td><td>
Array of energies from different calculations Index of energy statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00079">PCE_NO</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gd03579d4b8a648e812b748af288a1023"></a><!-- doxytag: member="routines.h::printElecForce" ref="gd03579d4b8a648e812b748af288a1023" args="(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)" -->
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<td class="memname">int printElecForce </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Combine and pretty-print force data.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Communications object </td></tr>
<tr><td valign="top"><em>nforce</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>atomForce</em> </td><td>
Number of forces calculated </td></tr>
<tr><td valign="top"><em>i</em> </td><td>
Array of force structures Index of force statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="routines_8h-source.html#l00083">AtomForce::dbForce</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="routines_8h-source.html#l00081">AtomForce::ibForce</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00097">PCF_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00095">PCF_NO</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="routines_8h-source.html#l00082">AtomForce::qfForce</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gfb4a43b1ee07988e941f8cb5d54f0f23"></a><!-- doxytag: member="routines.h::printEnergy" ref="gfb4a43b1ee07988e941f8cb5d54f0f23" args="(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)" -->
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<td class="memname">int printEnergy </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>totEnergy</em>[NOSH_MAXCALC], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>iprint</em></td><td> </td>
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<td></td>
<td>)</td>
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<div class="memdoc">
<p>
Combine and pretty-print energy data (deprecated...see printElecEnergy).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Communications object </td></tr>
<tr><td valign="top"><em>totEnergy</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>iprint</em> </td><td>
Array of energies from different calculations Index of energy statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00079">PCE_NO</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g8a9dbdbf57bf8a9e308147abe0e8da34"></a><!-- doxytag: member="routines.h::printFEPARM" ref="g8a9dbdbf57bf8a9e308147abe0e8da34" args="(int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])" -->
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<td class="memname">void printFEPARM </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>icalc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Print out FE-specific params loaded from input.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>icalc</em> </td><td>Calculation index </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Master parameter object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>feparm</em> </td><td>FE-specific parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>Array of FE solver objects </td></tr>
</table>
</dl>
<p>References <a class="el" href="femparm_8h-source.html#l00143">sFEMparm::akeyPRE</a>, <a class="el" href="femparm_8h-source.html#l00147">sFEMparm::akeySOLVE</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="femparm_8h-source.html#l00140">sFEMparm::ekey</a>, <a class="el" href="femparm_8h-source.html#l00137">sFEMparm::etol</a>, <a class="el" href="femparm_8h-source.html#l00077">FET_FRAC</a>, <a class="el" href="femparm_8h-source.html#l00076">FET_GLOB</a>, <a class="el" href="femparm_8h-source.html#l00075">FET_SIMP</a>, <a class="el" href="femparm_8h-source.html#l00097">FRT_DUAL</a>, <a class="el" href="femparm_8h-source.html#l00095">FRT_GEOM</a>, <a class="el" href="femparm_8h-source.html#l00099">FRT_LOCA</a>, <a class="el" href="femparm_8h-source.html#l00096">FRT_RESI</a>, <a class="el" href="femparm_8h-source.html#l00094">FRT_UNIF</a>, <a class="el" href="femparm_8h-source.html#l00135">sFEMparm::glen</a>, <a class="el" href="femparm_8h-source.html#l00160">sFEMparm::maxsolve</a>, <a class="el" href="femparm_8h-source.html#l00162">sFEMparm::maxvert</a>, <a class="el" href="femparm_8h-source.html#l00150">sFEMparm::targetNum</a>, <a class="el" href="femparm_8h-source.html#l00155">sFEMparm::targetRes</a>, <a class="el" href="vfetk_8h-source.html#l00135">VGT_DIRI</a>, <a class="el" href="vfetk_8h-source.html#l00136">VGT_PREV</a>, <a class="el" href="vfetk_8h-source.html#l00134">VGT_ZERO</a>, <a class="el" href="vfetk_8h-source.html#l00085">VLT_BCG</a>, <a class="el" href="vfetk_8h-source.html#l00084">VLT_CG</a>, <a class="el" href="vfetk_8h-source.html#l00083">VLT_MG</a>, <a class="el" href="vfetk_8h-source.html#l00082">VLT_SLU</a>, <a class="el" href="vfetk_8h-source.html#l00119">VNT_ARC</a>, <a class="el" href="vfetk_8h-source.html#l00118">VNT_INC</a>, <a class="el" href="vfetk_8h-source.html#l00117">VNT_NEW</a>, <a class="el" href="vfetk_8h-source.html#l00152">VPT_DIAG</a>, <a class="el" href="vfetk_8h-source.html#l00151">VPT_IDEN</a>, and <a class="el" href="vfetk_8h-source.html#l00153">VPT_MG</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
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<a class="anchor" name="g2f661dc633c6c5c8c6ee988dd332a746"></a><!-- doxytag: member="routines.h::printForce" ref="g2f661dc633c6c5c8c6ee988dd332a746" args="(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)" -->
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<td class="memname">int printForce </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Combine and pretty-print force data (deprecated...see printElecForce).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>nosh</em> </td><td>
Communications object </td></tr>
<tr><td valign="top"><em>nforce</em> </td><td>
Parameters from input file </td></tr>
<tr><td valign="top"><em>atomForce</em> </td><td>
Number of forces calculated </td></tr>
<tr><td valign="top"><em>i</em> </td><td>
Array of force structures Index of force statement to print </td></tr>
</table>
</dl>
<p>References <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="routines_8h-source.html#l00083">AtomForce::dbForce</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="routines_8h-source.html#l00081">AtomForce::ibForce</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00097">PCF_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00095">PCF_NO</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="routines_8h-source.html#l00082">AtomForce::qfForce</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gc204e507188bb0c897a7ddd0e471622b"></a><!-- doxytag: member="routines.h::printMGPARM" ref="gc204e507188bb0c897a7ddd0e471622b" args="(MGparm *mgparm, double realCenter[3])" -->
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<td class="memname">void printMGPARM </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsMGparm.html">MGparm</a> * </td>
<td class="paramname"> <em>mgparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>realCenter</em>[3]</td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Print out MG-specific params loaded from input.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>realCenter</em> </td><td>Center of mesh for actual calculation </td></tr>
<tr><td valign="top"></td><td valign="top"><em>mgparm</em> </td><td>MGparm object </td></tr>
</table>
</dl>
<p>References <a class="el" href="mgparm_8h-source.html#l00117">sMGparm::chgm</a>, <a class="el" href="mgparm_8h-source.html#l00115">sMGparm::dime</a>, <a class="el" href="mgparm_8h-source.html#l00128">sMGparm::glen</a>, <a class="el" href="mgparm_8h-source.html#l00126">sMGparm::grid</a>, <a class="el" href="mgparm_8h-source.html#l00075">MCT_PARALLEL</a>, <a class="el" href="mgparm_8h-source.html#l00123">sMGparm::nlev</a>, <a class="el" href="mgparm_8h-source.html#l00177">sMGparm::ofrac</a>, <a class="el" href="mgparm_8h-source.html#l00171">sMGparm::pdime</a>, and <a class="el" href="mgparm_8h-source.html#l00111">sMGparm::type</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
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<a class="anchor" name="g52af26682a1da9e8ccd01daee70b7a41"></a><!-- doxytag: member="routines.h::printPBEPARM" ref="g52af26682a1da9e8ccd01daee70b7a41" args="(PBEparm *pbeparm)" -->
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<td class="memname">void printPBEPARM </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Print out generic PBE params loaded from input.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>PBEparm object </td></tr>
</table>
</dl>
<p>References <a class="el" href="pbeparm_8h-source.html#l00129">sPBEparm::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vhal_8h-source.html#l00217">BCFL_MDH</a>, <a class="el" href="vhal_8h-source.html#l00215">BCFL_SDH</a>, <a class="el" href="vhal_8h-source.html#l00214">BCFL_ZERO</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="pbeparm_8h-source.html#l00134">sPBEparm::ionc</a>, <a class="el" href="pbeparm_8h-source.html#l00133">sPBEparm::ionq</a>, <a class="el" href="pbeparm_8h-source.html#l00135">sPBEparm::ionr</a>, <a class="el" href="pbeparm_8h-source.html#l00116">sPBEparm::molid</a>, <a class="el" href="pbeparm_8h-source.html#l00131">sPBEparm::nion</a>, <a class="el" href="pbeparm_8h-source.html#l00162">sPBEparm::numwrite</a>, <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00147">PBE_LRPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="vhal_8h-source.html#l00149">PBE_SMPBE</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="pbeparm_8h-source.html#l00079">PCE_NO</a>, <a class="el" href="pbeparm_8h-source.html#l00097">PCF_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00137">sPBEparm::pdie</a>, <a class="el" href="pbeparm_8h-source.html#l00141">sPBEparm::sdie</a>, <a class="el" href="pbeparm_8h-source.html#l00152">sPBEparm::smsize</a>, <a class="el" href="pbeparm_8h-source.html#l00155">sPBEparm::smvolume</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00143">sPBEparm::srfm</a>, <a class="el" href="pbeparm_8h-source.html#l00147">sPBEparm::swin</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vhal_8h-source.html#l00274">VDT_CHARGE</a>, <a class="el" href="vhal_8h-source.html#l00291">VDT_DIELX</a>, <a class="el" href="vhal_8h-source.html#l00293">VDT_DIELY</a>, <a class="el" href="vhal_8h-source.html#l00295">VDT_DIELZ</a>, <a class="el" href="vhal_8h-source.html#l00285">VDT_EDENS</a>, <a class="el" href="vhal_8h-source.html#l00282">VDT_IVDW</a>, <a class="el" href="vhal_8h-source.html#l00297">VDT_KAPPA</a>, <a class="el" href="vhal_8h-source.html#l00284">VDT_LAP</a>, <a class="el" href="vhal_8h-source.html#l00287">VDT_NDENS</a>, <a class="el" href="vhal_8h-source.html#l00275">VDT_POT</a>, <a class="el" href="vhal_8h-source.html#l00289">VDT_QDENS</a>, <a class="el" href="vhal_8h-source.html#l00276">VDT_SMOL</a>, <a class="el" href="vhal_8h-source.html#l00278">VDT_SSPL</a>, <a class="el" href="vhal_8h-source.html#l00280">VDT_VDW</a>, <a class="el" href="pbeparm_8h-source.html#l00166">sPBEparm::writefmt</a>, <a class="el" href="pbeparm_8h-source.html#l00163">sPBEparm::writestem</a>, and <a class="el" href="pbeparm_8h-source.html#l00165">sPBEparm::writetype</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
</div><p>
<a class="anchor" name="g8955a29284f6c8dd7ab3d2843fa5f9f2"></a><!-- doxytag: member="routines.h::returnEnergy" ref="g8955a29284f6c8dd7ab3d2843fa5f9f2" args="(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)" -->
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<td class="memname">double returnEnergy </td>
<td>(</td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>totEnergy</em>[NOSH_MAXCALC], </td>
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<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>iprint</em></td><td> </td>
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<p>
Access net local energy.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Justin Xiang </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>com</em> </td><td>Communications object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>totEnergy</em> </td><td>Array of energies from different calculations </td></tr>
<tr><td valign="top"></td><td valign="top"><em>iprint</em> </td><td>Index of energy statement to print </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Net local energy </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00079">PCE_NO</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
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<a class="anchor" name="g38fa11fc3ff3b68abcb0e507e445185c"></a><!-- doxytag: member="routines.h::setPartMG" ref="g38fa11fc3ff3b68abcb0e507e445185c" args="(NOsh *nosh, MGparm *mgparm, Vpmg *pmg)" -->
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<td class="memname">int setPartMG </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsMGparm.html">MGparm</a> * </td>
<td class="paramname"> <em>mgparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em></td><td> </td>
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<p>
Set MG partitions for calculating observables and performing I/O.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Object with parsed input file parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>mgparm</em> </td><td>MG parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG object </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="mgparm_8h-source.html#l00131">sMGparm::center</a>, <a class="el" href="mgparm_8h-source.html#l00128">sMGparm::glen</a>, <a class="el" href="mgparm_8h-source.html#l00075">MCT_PARALLEL</a>, <a class="el" href="mgparm_8h-source.html#l00164">sMGparm::partDisjCenter</a>, <a class="el" href="mgparm_8h-source.html#l00166">sMGparm::partDisjLength</a>, <a class="el" href="mgparm_8h-source.html#l00168">sMGparm::partDisjOwnSide</a>, <a class="el" href="mgparm_8h-source.html#l00111">sMGparm::type</a>, and <a class="el" href="vpmg_8c-source.html#l00553">Vpmg_setPart()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="gca674b06e3c15fb8c10e39e82096fa67"></a><!-- doxytag: member="routines.h::solveFE" ref="gca674b06e3c15fb8c10e39e82096fa67" args="(int i, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])" -->
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<td class="memname">int solveFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>i</em>, </td>
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<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsFEMparm.html">FEMparm</a> * </td>
<td class="paramname"> <em>feparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em>[NOSH_MAXCALC]</td><td> </td>
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<p>
Solve-estimate-refine.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>Calculation index </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Master parameter object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>feparm</em> </td><td>FE-specific parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>Generic PBE parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>Array of FE solver objects </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>
< AM_hPcg<p>
< Coarse-grid solver; 0 = SLU, 1 = MG, 2 = CG, 3 = BCG, 4 = PCG, 5 = PBCG<p>
< Primal problem<p>
< Preconditioner; 0 = identity.
<p>References <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00147">PBE_LRPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="vhal_8h-source.html#l00149">PBE_SMPBE</a>, and <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
</div>
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<a class="anchor" name="ge5fef94b530af7a96dc63a3deed97413"></a><!-- doxytag: member="routines.h::solveMG" ref="ge5fef94b530af7a96dc63a3deed97413" args="(NOsh *nosh, Vpmg *pmg, MGparm_CalcType type)" -->
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<td class="memname">int solveMG </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__MGparm.html#gcf31be9905f8e0ba1e083e1119b7cd1d">MGparm_CalcType</a> </td>
<td class="paramname"> <em>type</em></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<p>
Solve the PBE with MG.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Object with parsed input file parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG objects for this calculation </td></tr>
<tr><td valign="top"></td><td valign="top"><em>type</em> </td><td>Type of MG calculation </td></tr>
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</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="vhal_8h-source.html#l00341">APBS_TIMER_SOLVER</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="mgparm_8h-source.html#l00076">MCT_DUMMY</a>, <a class="el" href="vpmgp_8h-source.html#l00079">sVpmgp::nx</a>, <a class="el" href="vpmgp_8h-source.html#l00080">sVpmgp::ny</a>, <a class="el" href="vpmgp_8h-source.html#l00081">sVpmgp::nz</a>, <a class="el" href="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</a>, and <a class="el" href="vpmg_8c-source.html#l00360">Vpmg_solve()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g6484d734f8fb04d4f2f2c6ef4541e25a"></a><!-- doxytag: member="routines.h::startVio" ref="g6484d734f8fb04d4f2f2c6ef4541e25a" args="()" -->
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<td class="memname">void startVio </td>
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<p>
Wrapper to start MALOC Vio layer.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker and Robert Konecny </dd></dl>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<a class="anchor" name="g26c23c3a3879a11ebeea23eb271e5bc6"></a><!-- doxytag: member="routines.h::storeAtomEnergy" ref="g26c23c3a3879a11ebeea23eb271e5bc6" args="(Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy)" -->
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<td>(</td>
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<td class="paramname"> <em>atomEnergy</em>, </td>
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<p>
Store energy in arrays for future use.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Todd Dolinsky </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>pmg</em> </td><td>
MG object </td></tr>
<tr><td valign="top"><em>icalc</em> </td><td>
Calculation number </td></tr>
<tr><td valign="top"><em>atomEnergy</em> </td><td>
Pointer to storage array of doubles </td></tr>
<tr><td valign="top"><em>nenergy</em> </td><td>
Stores number of atoms per calc </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vpmg_8h-source.html#l00096">sVpmg::vmem</a>, and <a class="el" href="vpmg_8c-source.html#l01592">Vpmg_qfAtomEnergy()</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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<area shape="rect" href="group__Valist.html#g6e228909b1e2c178ee292ae97c5bce62" title="Get pointer to particular atom in list." alt="" coords="212,7,324,34"><area shape="rect" href="group__Valist.html#g2aea567c031963b275f4e6e31f9c3e74" title="Get number of atoms in the list." alt="" coords="184,58,352,85"><area shape="rect" href="group__Vpmg.html#g0491b8552abe33bd484bc731437c51bf" title="Get the per-atom "fixed charge" contribution to the electrostatic energy..." alt="" coords="193,109,342,135"><area shape="rect" href="group__Vatom.html#g6123ac049c637301d5aa730c18c94756" title="Get atomic charge." alt="" coords="402,83,533,110"><area shape="rect" href="group__Vatom.html#gbe19ed4ab35365a2e8f7505bcbb6bca2" title="Get atomic position." alt="" coords="400,134,536,161"></map>
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<a class="anchor" name="gf4dd79aefdee50f5bddc206e6302fd34"></a><!-- doxytag: member="routines.h::writedataFE" ref="gf4dd79aefdee50f5bddc206e6302fd34" args="(int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int writedataFE </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>rank</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVfetk.html">Vfetk</a> * </td>
<td class="paramname"> <em>fetk</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Write FEM data to files.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>rank</em> </td><td>Rank of processor (for parallel runs) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>NOsh object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>PBEparm object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fetk</em> </td><td>FEtk object (with solution) </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="vfetk_8h-source.html#l00177">sVfetk::am</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00199">sNOsh::ispara</a>, <a class="el" href="pbeparm_8h-source.html#l00162">sPBEparm::numwrite</a>, <a class="el" href="nosh_8h-source.html#l00200">sNOsh::proc_rank</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vhal_8h-source.html#l00274">VDT_CHARGE</a>, <a class="el" href="vhal_8h-source.html#l00291">VDT_DIELX</a>, <a class="el" href="vhal_8h-source.html#l00293">VDT_DIELY</a>, <a class="el" href="vhal_8h-source.html#l00295">VDT_DIELZ</a>, <a class="el" href="vhal_8h-source.html#l00285">VDT_EDENS</a>, <a class="el" href="vhal_8h-source.html#l00282">VDT_IVDW</a>, <a class="el" href="vhal_8h-source.html#l00297">VDT_KAPPA</a>, <a class="el" href="vhal_8h-source.html#l00284">VDT_LAP</a>, <a class="el" href="vhal_8h-source.html#l00287">VDT_NDENS</a>, <a class="el" href="vhal_8h-source.html#l00275">VDT_POT</a>, <a class="el" href="vhal_8h-source.html#l00289">VDT_QDENS</a>, <a class="el" href="vhal_8h-source.html#l00276">VDT_SMOL</a>, <a class="el" href="vhal_8h-source.html#l00278">VDT_SSPL</a>, <a class="el" href="vhal_8h-source.html#l00280">VDT_VDW</a>, <a class="el" href="vfetk_8c-source.html#l02215">Vfetk_fillArray()</a>, <a class="el" href="vfetk_8c-source.html#l02380">Vfetk_write()</a>, <a class="el" href="pbeparm_8h-source.html#l00166">sPBEparm::writefmt</a>, <a class="el" href="pbeparm_8h-source.html#l00163">sPBEparm::writestem</a>, and <a class="el" href="pbeparm_8h-source.html#l00165">sPBEparm::writetype</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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<p><center><img src="group__Frontend_gf4dd79aefdee50f5bddc206e6302fd34_cgraph.png" border="0" usemap="#group__Frontend_gf4dd79aefdee50f5bddc206e6302fd34_cgraph_map" alt=""></center>
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<a class="anchor" name="g0243cce85fc0dd6f64739a905b4742f0"></a><!-- doxytag: member="routines.h::writedataFlat" ref="g0243cce85fc0dd6f64739a905b4742f0" args="(NOsh *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], AtomForce *atomForce[NOSH_MAXCALC])" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int writedataFlat </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char * </td>
<td class="paramname"> <em>fname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>totEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>qfEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>qmEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>dielEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nenergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>atomEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Write out information to a flat file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Todd Dolinsky </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>com</em> </td><td>The communications object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fname</em> </td><td>The target XML file name </td></tr>
<tr><td valign="top"></td><td valign="top"><em>totEnergy</em> </td><td>An array with per-calc total energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qfEnergy</em> </td><td>An array with per-calc charge-potential energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qmEnergy</em> </td><td>An array with per-calc mobile energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielEnergy</em> </td><td>An array with per-calc polarization energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nenergy</em> </td><td>An array containing the number of atoms per-calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomEnergy</em> </td><td>An array containing per-atom energies (in KT) per calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nforce</em> </td><td>An array containing the number of forces calculated per-calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomForce</em> </td><td>An array containing per-atom forces per calc </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="pbeparm_8h-source.html#l00129">sPBEparm::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vhal_8h-source.html#l00217">BCFL_MDH</a>, <a class="el" href="vhal_8h-source.html#l00215">BCFL_SDH</a>, <a class="el" href="vhal_8h-source.html#l00214">BCFL_ZERO</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="mgparm_8h-source.html#l00115">sMGparm::dime</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="mgparm_8h-source.html#l00128">sMGparm::glen</a>, <a class="el" href="mgparm_8h-source.html#l00126">sMGparm::grid</a>, <a class="el" href="pbeparm_8h-source.html#l00134">sPBEparm::ionc</a>, <a class="el" href="pbeparm_8h-source.html#l00133">sPBEparm::ionq</a>, <a class="el" href="pbeparm_8h-source.html#l00135">sPBEparm::ionr</a>, <a class="el" href="mgparm_8h-source.html#l00074">MCT_AUTO</a>, <a class="el" href="mgparm_8h-source.html#l00076">MCT_DUMMY</a>, <a class="el" href="mgparm_8h-source.html#l00073">MCT_MANUAL</a>, <a class="el" href="mgparm_8h-source.html#l00075">MCT_PARALLEL</a>, <a class="el" href="nosh_8h-source.html#l00162">sNOsh_calc::mgparm</a>, <a class="el" href="pbeparm_8h-source.html#l00116">sPBEparm::molid</a>, <a class="el" href="nosh_8h-source.html#l00190">sNOsh::nelec</a>, <a class="el" href="pbeparm_8h-source.html#l00131">sPBEparm::nion</a>, <a class="el" href="nosh_8h-source.html#l00241">sNOsh::nprint</a>, <a class="el" href="nosh_8h-source.html#l00142">NPT_ENERGY</a>, <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="pbeparm_8h-source.html#l00081">PCE_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00080">PCE_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00137">sPBEparm::pdie</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="nosh_8h-source.html#l00242">sNOsh::printwhat</a>, <a class="el" href="pbeparm_8h-source.html#l00141">sPBEparm::sdie</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00143">sPBEparm::srfm</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="mgparm_8h-source.html#l00111">sMGparm::type</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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<a class="anchor" name="g4f37ce55e96d10897a327e3841e0beed"></a><!-- doxytag: member="routines.h::writedataMG" ref="g4f37ce55e96d10897a327e3841e0beed" args="(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">int writedataMG </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>rank</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Write out observables from MG calculation to file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>rank</em> </td><td>Processor rank (if parallel calculation) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>Generic PBE parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG object </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="vpmgp_8h-source.html#l00083">sVpmgp::hx</a>, <a class="el" href="vpmgp_8h-source.html#l00084">sVpmgp::hy</a>, <a class="el" href="vpmgp_8h-source.html#l00085">sVpmgp::hzed</a>, <a class="el" href="nosh_8h-source.html#l00199">sNOsh::ispara</a>, <a class="el" href="vpbe_8h-source.html#l00098">sVpbe::maxIonRadius</a>, <a class="el" href="pbeparm_8h-source.html#l00162">sPBEparm::numwrite</a>, <a class="el" href="vpmgp_8h-source.html#l00079">sVpmgp::nx</a>, <a class="el" href="vpmgp_8h-source.html#l00080">sVpmgp::ny</a>, <a class="el" href="vpmgp_8h-source.html#l00081">sVpmgp::nz</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="nosh_8h-source.html#l00200">sNOsh::proc_rank</a>, <a class="el" href="vpmg_8h-source.html#l00126">sVpmg::pvec</a>, <a class="el" href="vpmg_8h-source.html#l00109">sVpmg::rwork</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00147">sPBEparm::swin</a>, <a class="el" href="vhal_8h-source.html#l00315">VDF_AVS</a>, <a class="el" href="vhal_8h-source.html#l00313">VDF_DX</a>, <a class="el" href="vhal_8h-source.html#l00316">VDF_MCSF</a>, <a class="el" href="vhal_8h-source.html#l00314">VDF_UHBD</a>, <a class="el" href="vhal_8h-source.html#l00274">VDT_CHARGE</a>, <a class="el" href="vhal_8h-source.html#l00291">VDT_DIELX</a>, <a class="el" href="vhal_8h-source.html#l00293">VDT_DIELY</a>, <a class="el" href="vhal_8h-source.html#l00295">VDT_DIELZ</a>, <a class="el" href="vhal_8h-source.html#l00285">VDT_EDENS</a>, <a class="el" href="vhal_8h-source.html#l00282">VDT_IVDW</a>, <a class="el" href="vhal_8h-source.html#l00297">VDT_KAPPA</a>, <a class="el" href="vhal_8h-source.html#l00284">VDT_LAP</a>, <a class="el" href="vhal_8h-source.html#l00287">VDT_NDENS</a>, <a class="el" href="vhal_8h-source.html#l00275">VDT_POT</a>, <a class="el" href="vhal_8h-source.html#l00289">VDT_QDENS</a>, <a class="el" href="vhal_8h-source.html#l00276">VDT_SMOL</a>, <a class="el" href="vhal_8h-source.html#l00278">VDT_SSPL</a>, <a class="el" href="vhal_8h-source.html#l00280">VDT_VDW</a>, <a class="el" href="vgrid_8c-source.html#l00076">Vgrid_ctor()</a>, <a class="el" href="vgrid_8c-source.html#l00135">Vgrid_dtor()</a>, <a class="el" href="vgrid_8c-source.html#l00663">Vgrid_writeDX()</a>, <a class="el" href="vgrid_8c-source.html#l00913">Vgrid_writeUHBD()</a>, <a class="el" href="vpmg_8c-source.html#l00818">Vpmg_fillArray()</a>, <a class="el" href="pbeparm_8h-source.html#l00166">sPBEparm::writefmt</a>, <a class="el" href="pbeparm_8h-source.html#l00163">sPBEparm::writestem</a>, <a class="el" href="pbeparm_8h-source.html#l00165">sPBEparm::writetype</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, and <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<a class="anchor" name="g969c5202eb71574a7b3823f1e1049795"></a><!-- doxytag: member="routines.h::writedataXML" ref="g969c5202eb71574a7b3823f1e1049795" args="(NOsh *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], AtomForce *atomForce[NOSH_MAXCALC])" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int writedataXML </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vcom * </td>
<td class="paramname"> <em>com</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char * </td>
<td class="paramname"> <em>fname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>totEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>qfEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>qmEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>dielEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nenergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>atomEnergy</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nforce</em>[NOSH_MAXCALC], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structAtomForce.html">AtomForce</a> * </td>
<td class="paramname"> <em>atomForce</em>[NOSH_MAXCALC]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Write out information to an XML file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Todd Dolinsky </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>com</em> </td><td>The communications object </td></tr>
<tr><td valign="top"></td><td valign="top"><em>fname</em> </td><td>The target XML file name </td></tr>
<tr><td valign="top"></td><td valign="top"><em>totEnergy</em> </td><td>An array with per-calc total energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qfEnergy</em> </td><td>An array with per-calc charge-potential energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>qmEnergy</em> </td><td>An array with per-calc mobile energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>dielEnergy</em> </td><td>An array with per-calc polarization energies (in kT) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nenergy</em> </td><td>An array containing the number of atoms per-calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomEnergy</em> </td><td>An array containing per-atom energies (in KT) per calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nforce</em> </td><td>An array containing the number of forces calculated per-calc </td></tr>
<tr><td valign="top"></td><td valign="top"><em>atomForce</em> </td><td>An array containing per-atom forces per calc </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="pbeparm_8h-source.html#l00129">sPBEparm::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vhal_8h-source.html#l00217">BCFL_MDH</a>, <a class="el" href="vhal_8h-source.html#l00215">BCFL_SDH</a>, <a class="el" href="vhal_8h-source.html#l00214">BCFL_ZERO</a>, <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00182">sNOsh::calc</a>, <a class="el" href="pbeparm_8h-source.html#l00158">sPBEparm::calcenergy</a>, <a class="el" href="pbeparm_8h-source.html#l00160">sPBEparm::calcforce</a>, <a class="el" href="mgparm_8h-source.html#l00115">sMGparm::dime</a>, <a class="el" href="nosh_8h-source.html#l00206">sNOsh::elec2calc</a>, <a class="el" href="nosh_8h-source.html#l00249">sNOsh::elecname</a>, <a class="el" href="mgparm_8h-source.html#l00128">sMGparm::glen</a>, <a class="el" href="mgparm_8h-source.html#l00126">sMGparm::grid</a>, <a class="el" href="pbeparm_8h-source.html#l00134">sPBEparm::ionc</a>, <a class="el" href="pbeparm_8h-source.html#l00133">sPBEparm::ionq</a>, <a class="el" href="pbeparm_8h-source.html#l00135">sPBEparm::ionr</a>, <a class="el" href="mgparm_8h-source.html#l00074">MCT_AUTO</a>, <a class="el" href="mgparm_8h-source.html#l00076">MCT_DUMMY</a>, <a class="el" href="mgparm_8h-source.html#l00073">MCT_MANUAL</a>, <a class="el" href="mgparm_8h-source.html#l00075">MCT_PARALLEL</a>, <a class="el" href="nosh_8h-source.html#l00162">sNOsh_calc::mgparm</a>, <a class="el" href="pbeparm_8h-source.html#l00116">sPBEparm::molid</a>, <a class="el" href="nosh_8h-source.html#l00190">sNOsh::nelec</a>, <a class="el" href="pbeparm_8h-source.html#l00131">sPBEparm::nion</a>, <a class="el" href="nosh_8h-source.html#l00241">sNOsh::nprint</a>, <a class="el" href="nosh_8h-source.html#l00142">NPT_ENERGY</a>, <a class="el" href="vhal_8h-source.html#l00145">PBE_LPBE</a>, <a class="el" href="vhal_8h-source.html#l00146">PBE_NPBE</a>, <a class="el" href="nosh_8h-source.html#l00164">sNOsh_calc::pbeparm</a>, <a class="el" href="pbeparm_8h-source.html#l00127">sPBEparm::pbetype</a>, <a class="el" href="pbeparm_8h-source.html#l00081">PCE_COMPS</a>, <a class="el" href="pbeparm_8h-source.html#l00080">PCE_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00096">PCF_TOTAL</a>, <a class="el" href="pbeparm_8h-source.html#l00137">sPBEparm::pdie</a>, <a class="el" href="nosh_8h-source.html#l00245">sNOsh::printcalc</a>, <a class="el" href="nosh_8h-source.html#l00244">sNOsh::printnarg</a>, <a class="el" href="nosh_8h-source.html#l00246">sNOsh::printop</a>, <a class="el" href="nosh_8h-source.html#l00242">sNOsh::printwhat</a>, <a class="el" href="pbeparm_8h-source.html#l00141">sPBEparm::sdie</a>, <a class="el" href="pbeparm_8h-source.html#l00145">sPBEparm::srad</a>, <a class="el" href="pbeparm_8h-source.html#l00143">sPBEparm::srfm</a>, <a class="el" href="pbeparm_8h-source.html#l00149">sPBEparm::temp</a>, <a class="el" href="mgparm_8h-source.html#l00111">sMGparm::type</a>, <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, and <a class="el" href="vunit_8h-source.html#l00098">Vunit_Na</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<a class="anchor" name="g12b5e7fa0d0f177f7b1668df0629bc1e"></a><!-- doxytag: member="routines.h::writematMG" ref="g12b5e7fa0d0f177f7b1668df0629bc1e" args="(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int writematMG </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>rank</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsNOsh.html">NOsh</a> * </td>
<td class="paramname"> <em>nosh</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsPBEparm.html">PBEparm</a> * </td>
<td class="paramname"> <em>pbeparm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>pmg</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Write out operator matrix from MG calculation to file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>rank</em> </td><td>Processor rank (if parallel calculation) </td></tr>
<tr><td valign="top"></td><td valign="top"><em>nosh</em> </td><td>Parameters from input file </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pbeparm</em> </td><td>Generic PBE parameters </td></tr>
<tr><td valign="top"></td><td valign="top"><em>pmg</em> </td><td>MG object </td></tr>
</table>
</dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>1 if successful, 0 otherwise </dd></dl>
<p>References <a class="el" href="nosh_8h-source.html#l00202">sNOsh::bogus</a>, <a class="el" href="nosh_8h-source.html#l00199">sNOsh::ispara</a>, <a class="el" href="nosh_8h-source.html#l00200">sNOsh::proc_rank</a>, <a class="el" href="vpmg_8c-source.html#l00072">Vpmg_printColComp()</a>, <a class="el" href="pbeparm_8h-source.html#l00168">sPBEparm::writemat</a>, <a class="el" href="pbeparm_8h-source.html#l00173">sPBEparm::writematflag</a>, and <a class="el" href="pbeparm_8h-source.html#l00172">sPBEparm::writematstem</a>.</p>
<p>Referenced by <a class="el" href="main_8c-source.html#l00084">main()</a>.</p>
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