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<h1>vpmg.c File Reference</h1>Class Vpmg methods.
<a href="#_details">More...</a>
<p>
<code>#include "apbscfg.h"</code><br>
<code>#include "<a class="el" href="vpmg-private_8h-source.html">vpmg-private.h</a>"</code><br>
<code>#include "<a class="el" href="vpmg_8h-source.html">apbs/vpmg.h</a>"</code><br>
<code>#include "<a class="el" href="vhal_8h-source.html">apbs/vhal.h</a>"</code><br>
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Include dependency graph for vpmg.c:</div>
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<p><center><img src="vpmg_8c__incl.png" border="0" usemap="#vpmg.c_map" alt=""></center>
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<area shape="rect" href="vpmg-private_8h.html" title="Class Vpmg private method declaration." alt="" coords="842,98,954,125"><area shape="rect" href="vpmg_8h.html" title="Contains declarations for class Vpmg." alt="" coords="942,173,1041,200"><area shape="rect" href="vhal_8h.html" title="Contains generic macro definitions for APBS." alt="" coords="482,696,573,722"><area shape="rect" href="vpmgp_8h.html" title="Contains declarations for class Vpmgp." alt="" coords="1346,546,1453,573"><area shape="rect" href="mgparm_8h.html" title="Contains declarations for class MGparm." alt="" coords="1344,621,1458,648"><area shape="rect" href="vacc_8h.html" title="Contains declarations for class Vacc." alt="" coords="512,322,605,349"><area shape="rect" href="vcap_8h.html" title="Contains declarations for class Vcap." alt="" coords="1634,322,1728,349"><area shape="rect" href="vpbe_8h.html" title="Contains declarations for class Vpbe." alt="" coords="426,248,520,274"><area shape="rect" href="vgrid_8h.html" title="Potential oracle for Cartesian mesh data." alt="" coords="829,546,925,573"><area shape="rect" href="pbeparm_8h.html" title="Contains declarations for class PBEparm." alt="" coords="1000,621,1117,648"><area shape="rect" href="valist_8h.html" title="Contains declarations for class Valist." alt="" coords="592,472,688,498"><area shape="rect" href="vatom_8h.html" title="Contains declarations for class Vatom." alt="" coords="413,546,514,573"><area shape="rect" href="vunit_8h.html" title="Contains a collection of useful constants and conversion factors." alt="" coords="242,621,338,648"><area shape="rect" href="vclist_8h.html" title="Contains declarations for class Vclist." alt="" coords="425,397,521,424"><area shape="rect" href="apolparm_8h-source.html" title="apbs/apolparm.h" alt="" coords="712,472,834,498"><area shape="rect" href="vparam_8h.html" title="Contains declarations for class Vparam." alt="" coords="640,546,749,573"><area shape="rect" href="vstring_8h.html" title="Contains declarations for class Vstring." alt="" coords="717,621,824,648"></map>
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<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC unsigned long int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g7969f056027cc7b05b0c6630b52be213">Vpmg_memChk</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the memory used by this structure (and its contents) in bytes. <a href="group__Vpmg.html#g7969f056027cc7b05b0c6630b52be213"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g74856c08e25f851236e0e9fdb2efe4e9">Vpmg_printColComp</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, char path[72], char title[72], char mxtype[3], int flag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Print out a column-compressed sparse matrix in Harwell-Boeing format. <a href="group__Vpmg.html#g74856c08e25f851236e0e9fdb2efe4e9"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC <a class="el" href="structsVpmg.html">Vpmg</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#geab43b3987ea7c67176960f3d7cc1d38">Vpmg_ctor</a> (<a class="el" href="structsVpmgp.html">Vpmgp</a> *pmgp, <a class="el" href="structsVpbe.html">Vpbe</a> *pbe, int focusFlag, <a class="el" href="structsVpmg.html">Vpmg</a> *pmgOLD, <a class="el" href="structsMGparm.html">MGparm</a> *mgparm, <a class="el" href="group__PBEparm.html#g8cc295f42b2029944d85402f93190603">PBEparm_calcEnergy</a> energyFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Constructor for the Vpmg class (allocates new memory). <a href="group__Vpmg.html#geab43b3987ea7c67176960f3d7cc1d38"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#ge3a3587bfb6c15342890a2dada846d4f">Vpmg_ctor2</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, <a class="el" href="structsVpmgp.html">Vpmgp</a> *pmgp, <a class="el" href="structsVpbe.html">Vpbe</a> *pbe, int focusFlag, <a class="el" href="structsVpmg.html">Vpmg</a> *pmgOLD, <a class="el" href="structsMGparm.html">MGparm</a> *mgparm, <a class="el" href="group__PBEparm.html#g8cc295f42b2029944d85402f93190603">PBEparm_calcEnergy</a> energyFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory). <a href="group__Vpmg.html#ge3a3587bfb6c15342890a2dada846d4f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g5ff93c6726088e1e33034f218d761017">Vpmg_solve</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Solve the PBE using PMG. <a href="group__Vpmg.html#g5ff93c6726088e1e33034f218d761017"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g54c8a69f4055041178cc4cd7a7c346ec">Vpmg_dtor</a> (<a class="el" href="structsVpmg.html">Vpmg</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Object destructor. <a href="group__Vpmg.html#g54c8a69f4055041178cc4cd7a7c346ec"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g3cde6b7c8ed033476ff517348567213c">Vpmg_dtor2</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub object destructor. <a href="group__Vpmg.html#g3cde6b7c8ed033476ff517348567213c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#gaef73d86f87bb23134c669f6a0dc571e">Vpmg_setPart</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double lowerCorner[3], double upperCorner[3], int bflags[6])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain. <a href="group__Vpmg.html#gaef73d86f87bb23134c669f6a0dc571e"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g7b7c6cbfc1c468da596efff1d51fd28a">Vpmg_unsetPart</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Remove partition restrictions. <a href="group__Vpmg.html#g7b7c6cbfc1c468da596efff1d51fd28a"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g83b3ab07ffeff693e2519db3a9bebf91">Vpmg_fillArray</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *vec, <a class="el" href="group__Vhal.html#gdfc214425db779e6548c11fab04ab043">Vdata_Type</a> type, double parm, <a class="el" href="group__Vhal.html#ga0aabb1579af98f26effe7796b2d0a0c">Vhal_PBEType</a> pbetype)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill the specified array with accessibility values. <a href="group__Vpmg.html#g83b3ab07ffeff693e2519db3a9bebf91"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#e22a67401cf36cc85b0bd58938587913">Vpmg_polarizEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Determines energy from polarizeable charge and interaction with fixed charges according to Rocchia et al. <a href="#e22a67401cf36cc85b0bd58938587913"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g6f841d1daa341cac487a28bb31dde47d">Vpmg_energy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the total electrostatic energy. <a href="group__Vpmg.html#g6f841d1daa341cac487a28bb31dde47d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g0718ba16e1357ce4ad27c15e960ca8cd">Vpmg_dielEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the "polarization" contribution to the electrostatic energy. <a href="group__Vpmg.html#g0718ba16e1357ce4ad27c15e960ca8cd"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g356d8ee320ee8264f3473583f329abc2">Vpmg_dielGradNorm</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the integral of the gradient of the dielectric function. <a href="group__Vpmg.html#g356d8ee320ee8264f3473583f329abc2"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g72773d2eb289d3bf2d06ab23e198e926">Vpmg_qmEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the "mobile charge" contribution to the electrostatic energy. <a href="group__Vpmg.html#g72773d2eb289d3bf2d06ab23e198e926"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#ff52adddfe50ff4e6282f3bcf05f3dd5">Vpmg_qmEnergySMPBE</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Vpmg_qmEnergy for SMPBE. <a href="#ff52adddfe50ff4e6282f3bcf05f3dd5"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#gbc99a910a365aa8c0e0efce577abb9af">Vpmg_qfEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the "fixed charge" contribution to the electrostatic energy. <a href="group__Vpmg.html#gbc99a910a365aa8c0e0efce577abb9af"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#0876512b1ee9f93ee0378334b886938c">Vpmg_qfEnergyPoint</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculates charge-potential energy using summation over delta function positions (i.e. something like an Linf norm). <a href="#0876512b1ee9f93ee0378334b886938c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g0491b8552abe33bd484bc731437c51bf">Vpmg_qfAtomEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, <a class="el" href="structsVatom.html">Vatom</a> *atom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the per-atom "fixed charge" contribution to the electrostatic energy. <a href="group__Vpmg.html#g0491b8552abe33bd484bc731437c51bf"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#78687d08a4040d18d46337e1345b6dac">Vpmg_qfEnergyVolume</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, int extFlag)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculates charge-potential energy as integral over a volume. <a href="#78687d08a4040d18d46337e1345b6dac"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#1271687db8aa07b73c4ce3316943b72c">Vpmg_splineSelect</a> (int srfm, <a class="el" href="structsVacc.html">Vacc</a> *acc, double *gpos, double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Selects a spline based surface method from either VSM_SPLINE, VSM_SPLINE5 or VSM_SPLINE7. <a href="#1271687db8aa07b73c4ce3316943b72c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#d55928ed41b43f65ba1c494b2c577353">focusFillBound</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, <a class="el" href="structsVpmg.html">Vpmg</a> *pmgOLD)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">For focusing, fill in the boundaries of the new mesh based on the potential values in the old mesh. <a href="#d55928ed41b43f65ba1c494b2c577353"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#f0c2a5754fbe7a35b083ef600dab299d">extEnergy</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, <a class="el" href="structsVpmg.html">Vpmg</a> *pmgOLD, <a class="el" href="group__PBEparm.html#g8cc295f42b2029944d85402f93190603">PBEparm_calcEnergy</a> extFlag, double partMin[3], double partMax[3], int bflags[6])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">For focusing, set external energy data members in new Vpmg object based on energy calculations on old Vpmg object from regions outside the indicated partition. <a href="#f0c2a5754fbe7a35b083ef600dab299d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#1c36249103e072eefcadd4332d8b6855">bcfl1sp</a> (double size, double *apos, double charge, double xkappa, double pre1, double *pos)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) due to a specific ion at a specific point. <a href="#1c36249103e072eefcadd4332d8b6855"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#787e4bcc6b7ec8a87aed577535268eb3">bcfl1</a> (double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Increment all boundary points by pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) to add the effect of the Debye-Huckel potential due to a single charge. <a href="#787e4bcc6b7ec8a87aed577535268eb3"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#2ef3b09ecf0404038dabf01cc0c3dbaf">bcfl2</a> (double size, double *apos, double charge, double *dipole, double *quad, double xkappa, double eps_p, double eps_w, double T, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Increment all boundary points to include the Debye-Huckel potential due to a single multipole site. (truncated at quadrupole). <a href="#2ef3b09ecf0404038dabf01cc0c3dbaf"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#0f71bb1c4fe48352092a82c88c5eac3e">multipolebc</a> (double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">This routine serves bcfl2. It returns (in tsr) the contraction independent portion of the Debye-Huckel potential tensor for a spherical ion with a central charge, dipole and quadrupole. See the code for an in depth description. <a href="#0f71bb1c4fe48352092a82c88c5eac3e"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#9803b64d96685d27923d899ef6f4c5cd">bcCalc</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill boundary condition arrays. <a href="#9803b64d96685d27923d899ef6f4c5cd"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#35949511a7f2779c8ac7e7c88bdca001">fillcoCoefMap</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill operator coefficient arrays from pre-calculated maps. <a href="#35949511a7f2779c8ac7e7c88bdca001"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#62617829770eaed11c159947453e457c">fillcoCoefMol</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill operator coefficient arrays from a molecular surface calculation. <a href="#62617829770eaed11c159947453e457c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#9217fdfc8737424d5e5ccc1193f9c3b0">fillcoCoefMolIon</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill ion (nonlinear) operator coefficient array from a molecular surface calculation. <a href="#9217fdfc8737424d5e5ccc1193f9c3b0"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#34484f0f2f254b954abf20c5a98ab9d4">fillcoCoefMolDiel</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill differential operator coefficient arrays from a molecular surface calculation. <a href="#34484f0f2f254b954abf20c5a98ab9d4"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#df9fff114eed3d5d94f3adbbf9527483">fillcoCoefMolDielNoSmooth</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill differential operator coefficient arrays from a molecular surface calculation without smoothing. <a href="#df9fff114eed3d5d94f3adbbf9527483"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#afab27ad33274047911bd2ec092eb265">fillcoCoefMolDielSmooth</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill differential operator coefficient arrays from a molecular surface calculation with smoothing. <a href="#afab27ad33274047911bd2ec092eb265"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#61365ff4cedaf084ea6d960d432a3d03">fillcoCoefSpline</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill operator coefficient arrays from a spline-based surface calculation. <a href="#61365ff4cedaf084ea6d960d432a3d03"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#169088d2631112390e9699d0ff25ab0a">fillcoCoef</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Top-level driver to fill all operator coefficient arrays. <a href="#169088d2631112390e9699d0ff25ab0a"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#da65af06c9af5bf4ee593cb051bd0b0d">fillcoCharge</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Top-level driver to fill source term charge array. <a href="#da65af06c9af5bf4ee593cb051bd0b0d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#2fe0074cd016170f829d76a856409185">fillcoChargeMap</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill source term charge array from a pre-calculated map. <a href="#2fe0074cd016170f829d76a856409185"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#7e7a2991c9f8b5e9a4a06843aecd38ae">fillcoChargeSpline1</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill source term charge array from linear interpolation. <a href="#7e7a2991c9f8b5e9a4a06843aecd38ae"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#50d8ef438d4a7a76d869fb256b24d372">bspline2</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate a cubic B-spline. <a href="#50d8ef438d4a7a76d869fb256b24d372"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#8a4a959a2448c20bfc3660f04077892e">dbspline2</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate a cubic B-spline derivative. <a href="#8a4a959a2448c20bfc3660f04077892e"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#6074122271a6957f5d463aa95c90f61c">fillcoChargeSpline2</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill source term charge array from cubic spline interpolation. <a href="#6074122271a6957f5d463aa95c90f61c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g6c39de37132c2eddd3dc62776c95963c">Vpmg_fillco</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, <a class="el" href="group__Vhal.html#g5ccf1935e3604af8c42bc644b3979304">Vsurf_Meth</a> surfMeth, double splineWin, <a class="el" href="group__Vhal.html#gdd887856f01d4328b9a028110a5488a6">Vchrg_Meth</a> chargeMeth, int useDielXMap, <a class="el" href="structsVgrid.html">Vgrid</a> *dielXMap, int useDielYMap, <a class="el" href="structsVgrid.html">Vgrid</a> *dielYMap, int useDielZMap, <a class="el" href="structsVgrid.html">Vgrid</a> *dielZMap, int useKappaMap, <a class="el" href="structsVgrid.html">Vgrid</a> *kappaMap, int useChargeMap, <a class="el" href="structsVgrid.html">Vgrid</a> *chargeMap)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill the coefficient arrays prior to solving the equation. <a href="group__Vpmg.html#g6c39de37132c2eddd3dc62776c95963c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g103f45f00534437713ff979d6277addf">Vpmg_force</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID, <a class="el" href="group__Vhal.html#g5ccf1935e3604af8c42bc644b3979304">Vsurf_Meth</a> srfm, <a class="el" href="group__Vhal.html#gdd887856f01d4328b9a028110a5488a6">Vchrg_Meth</a> chgm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the total force on the specified atom in units of k_B T/AA. <a href="group__Vpmg.html#g103f45f00534437713ff979d6277addf"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g882e62e37d397bcccb791133ddf73696">Vpmg_ibForce</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID, <a class="el" href="group__Vhal.html#g5ccf1935e3604af8c42bc644b3979304">Vsurf_Meth</a> srfm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the osmotic pressure on the specified atom in units of k_B T/AA. <a href="group__Vpmg.html#g882e62e37d397bcccb791133ddf73696"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#gf6feff0d911fcb17703591f70a3fa099">Vpmg_dbForce</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *dbForce, int atomID, <a class="el" href="group__Vhal.html#g5ccf1935e3604af8c42bc644b3979304">Vsurf_Meth</a> srfm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the dielectric boundary forces on the specified atom in units of k_B T/AA. <a href="group__Vpmg.html#gf6feff0d911fcb17703591f70a3fa099"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#g2f6aafdc5ea2bf2fd1a5175231976732">Vpmg_qfForce</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID, <a class="el" href="group__Vhal.html#gdd887856f01d4328b9a028110a5488a6">Vchrg_Meth</a> chgm)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the "charge-field" force on the specified atom in units of k_B T/AA. <a href="group__Vpmg.html#g2f6aafdc5ea2bf2fd1a5175231976732"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#68e3819e4049a4b0c194289a2afb32ea">qfForceSpline1</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Charge-field force due to a linear spline charge function. <a href="#68e3819e4049a4b0c194289a2afb32ea"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#c55adeb810c3e971ebe1bf9b3a137246">qfForceSpline2</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Charge-field force due to a cubic spline charge function. <a href="#c55adeb810c3e971ebe1bf9b3a137246"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#682bb08f7ef2b312b9da1c2ba6e0a25b">qfForceSpline4</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double *force, int atomID)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Charge-field force due to a quintic spline charge function. <a href="#682bb08f7ef2b312b9da1c2ba6e0a25b"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#f4f11e78d20500aa43167eab5e52752f">markSphere</a> (double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hz, double xmin, double ymin, double zmin, double *array, double markVal)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Mark the grid points inside a sphere with a particular value. This marks by resetting the the grid points inside the sphere to the specified value. <a href="#f4f11e78d20500aa43167eab5e52752f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#3667719ad7b6d35bb4ac587513be8b5c">zlapSolve</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee, double **solution, double **source, double **work1)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the solution to Poisson's equation with a simple Laplacian operator and zero-valued Dirichlet boundary conditions. Store the solution in thee->u. <a href="#3667719ad7b6d35bb4ac587513be8b5c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vpmg.html#gc46c3028f8a1b5940afcf6df39e4e2c3">Vpmg_solveLaplace</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Solve Poisson's equation with a homogeneous Laplacian operator using the solvent dielectric constant. This solution is performed by a sine wave decomposition. <a href="group__Vpmg.html#gc46c3028f8a1b5940afcf6df39e4e2c3"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#fcf864c3b65f0d536a2985d931dc4692">VFCHI4</a> (int i, double f)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return 2.5 plus difference of i - f. <a href="#fcf864c3b65f0d536a2985d931dc4692"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#c953c7091df8e4a1df53463baf8fe7ee">bspline4</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate a 5th Order B-Spline (4th order polynomial). <a href="#c953c7091df8e4a1df53463baf8fe7ee"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#aefa250362d354e032dd1d104cfea094">dbspline4</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate a 5th Order B-Spline derivative (4th order polynomial). <a href="#aefa250362d354e032dd1d104cfea094"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#9e0486c0940668c5db8b56f165c474b6">d2bspline4</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate the 2nd derivative of a 5th Order B-Spline. <a href="#9e0486c0940668c5db8b56f165c474b6"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC double </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#ddf938597bc4a997f8766856d8d59de1">d3bspline4</a> (double x)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Evaluate the 3rd derivative of a 5th Order B-Spline. <a href="#ddf938597bc4a997f8766856d8d59de1"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#45c2c05ddfc0c4e4aea3be668137d2e0">fillcoPermanentMultipole</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill source term charge array for the use of permanent multipoles. <a href="#45c2c05ddfc0c4e4aea3be668137d2e0"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#be8b2056b56093552215f2e97c8f5c1b">fillcoCoefSpline4</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill operator coefficient arrays from a 7th order polynomial based surface calculation. <a href="#be8b2056b56093552215f2e97c8f5c1b"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPRIVATE void </td><td class="memItemRight" valign="bottom"><a class="el" href="vpmg_8c.html#b7b5543b591c9433e7190a2fe45b4ca2">fillcoCoefSpline3</a> (<a class="el" href="structsVpmg.html">Vpmg</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill operator coefficient arrays from a 5th order polynomial based surface calculation. <a href="#b7b5543b591c9433e7190a2fe45b4ca2"></a><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
Class Vpmg methods.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="version" compact><dt><b>Version:</b></dt><dd></dd></dl>
<dl class="rcs" compact><dt><b>Id</b></dt><dd><a class="el" href="vpmg_8c.html" title="Class Vpmg methods.">vpmg.c</a> 1350 2009-02-12 00:38:48Z yhuang01 </dd></dl>
<dl class="attention" compact><dt><b>Attention:</b></dt><dd><div class="fragment"><pre class="fragment">
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (baker@biochem.wustl.edu)
* Dept. of Biochemistry and Molecular Biophysics
* Center for Computational Biology
* Washington University in St. Louis
*
* Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2002-2009, Washington University in St. Louis.
* Portions Copyright (c) 2002-2009. Nathan A. Baker
* Portions Copyright (c) 1999-2002. The Regents of the University of California.
* Portions Copyright (c) 1995. Michael Holst
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* - Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* - Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* - Neither the name of Washington University in St. Louis nor the names of its
* contributors may be used to endorse or promote products derived from this
* software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* </pre></div> </dd></dl>
<hr><h2>Function Documentation</h2>
<a class="anchor" name="9803b64d96685d27923d899ef6f4c5cd"></a><!-- doxytag: member="vpmg.c::bcCalc" ref="9803b64d96685d27923d899ef6f4c5cd" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void bcCalc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
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<div class="memdoc">
<p>
Fill boundary condition arrays.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::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#l00219">BCFL_UNUSED</a>, <a class="el" href="vhal_8h-source.html#l00214">BCFL_ZERO</a>, <a class="el" href="vpmg_8h-source.html#l00123">sVpmg::gxcf</a>, <a class="el" href="vpmg_8h-source.html#l00124">sVpmg::gycf</a>, <a class="el" href="vpmg_8h-source.html#l00125">sVpmg::gzcf</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>, and <a class="el" href="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04885">Vpmg_fillco()</a>.</p>
</div>
</div><p>
<a class="anchor" name="787e4bcc6b7ec8a87aed577535268eb3"></a><!-- doxytag: member="vpmg.c::bcfl1" ref="787e4bcc6b7ec8a87aed577535268eb3" args="(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz)" -->
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<td class="memname">VPRIVATE void bcfl1 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>size</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>apos</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>charge</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>xkappa</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>pre1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gxcf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gycf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gzcf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>xf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>yf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>zf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nx</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>ny</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nz</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Increment all boundary points by pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) to add the effect of the Debye-Huckel potential due to a single charge.
<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>apos</em> </td><td>
Size of the ion </td></tr>
<tr><td valign="top"><em>charge</em> </td><td>
Position of the ion </td></tr>
<tr><td valign="top"><em>xkappa</em> </td><td>
Charge of the ion </td></tr>
<tr><td valign="top"><em>pre1</em> </td><td>
Exponential screening factor </td></tr>
<tr><td valign="top"><em>gxcf</em> </td><td>
Unit- and dielectric-dependent prefactor </td></tr>
<tr><td valign="top"><em>gycf</em> </td><td>
Set to x-boundary values </td></tr>
<tr><td valign="top"><em>gzcf</em> </td><td>
Set to y-boundary values </td></tr>
<tr><td valign="top"><em>xf</em> </td><td>
Set to z-boundary values </td></tr>
<tr><td valign="top"><em>yf</em> </td><td>
Boundary point x-coordinates </td></tr>
<tr><td valign="top"><em>zf</em> </td><td>
Boundary point y-coordinates </td></tr>
<tr><td valign="top"><em>nx</em> </td><td>
Boundary point z-coordinates </td></tr>
<tr><td valign="top"><em>ny</em> </td><td>
Number of grid points in x-direction </td></tr>
<tr><td valign="top"><em>nz</em> </td><td>
Number of grid points in y-direction Number of grid points in y-direction </td></tr>
</table>
</dl>
</div>
</div><p>
<a class="anchor" name="1c36249103e072eefcadd4332d8b6855"></a><!-- doxytag: member="vpmg.c::bcfl1sp" ref="1c36249103e072eefcadd4332d8b6855" args="(double size, double *apos, double charge, double xkappa, double pre1, double *pos)" -->
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<td class="memname">VPRIVATE double bcfl1sp </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>size</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>apos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>charge</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>xkappa</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>pre1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>pos</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Calculate pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) due to a specific ion at a specific point.
<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>Value of above function in arbitrary units (dependent on pre-factor) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>apos</em> </td><td>
Atom size </td></tr>
<tr><td valign="top"><em>charge</em> </td><td>
Atom position </td></tr>
<tr><td valign="top"><em>xkappa</em> </td><td>
Atom charge </td></tr>
<tr><td valign="top"><em>pre1</em> </td><td>
Exponential screening factor </td></tr>
<tr><td valign="top"><em>pos</em> </td><td>
Unit- and dielectric-dependent prefactor Function evaluation position </td></tr>
</table>
</dl>
</div>
</div><p>
<a class="anchor" name="2ef3b09ecf0404038dabf01cc0c3dbaf"></a><!-- doxytag: member="vpmg.c::bcfl2" ref="2ef3b09ecf0404038dabf01cc0c3dbaf" args="(double size, double *apos, double charge, double *dipole, double *quad, double xkappa, double eps_p, double eps_w, double T, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz)" -->
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<td class="memname">VPRIVATE void bcfl2 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>size</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>apos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>charge</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dipole</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>quad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>xkappa</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>eps_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>eps_w</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>T</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gxcf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gycf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>gzcf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>xf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>yf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>zf</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nx</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>ny</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nz</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Increment all boundary points to include the Debye-Huckel potential due to a single multipole site. (truncated at quadrupole).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>apos</em> </td><td>
Size of the ion </td></tr>
<tr><td valign="top"><em>charge</em> </td><td>
Position of the ion </td></tr>
<tr><td valign="top"><em>dipole</em> </td><td>
Charge of the ion </td></tr>
<tr><td valign="top"><em>quad</em> </td><td>
Dipole of the ion </td></tr>
<tr><td valign="top"><em>xkappa</em> </td><td>
Traceless Quadrupole of the ion </td></tr>
<tr><td valign="top"><em>eps_p</em> </td><td>
Exponential screening factor </td></tr>
<tr><td valign="top"><em>eps_w</em> </td><td>
Solute dielectric </td></tr>
<tr><td valign="top"><em>T</em> </td><td>
Solvent dielectric </td></tr>
<tr><td valign="top"><em>gxcf</em> </td><td>
Temperature </td></tr>
<tr><td valign="top"><em>gycf</em> </td><td>
Set to x-boundary values </td></tr>
<tr><td valign="top"><em>gzcf</em> </td><td>
Set to y-boundary values </td></tr>
<tr><td valign="top"><em>xf</em> </td><td>
Set to z-boundary values </td></tr>
<tr><td valign="top"><em>yf</em> </td><td>
Boundary point x-coordinates </td></tr>
<tr><td valign="top"><em>zf</em> </td><td>
Boundary point y-coordinates </td></tr>
<tr><td valign="top"><em>nx</em> </td><td>
Boundary point z-coordinates </td></tr>
<tr><td valign="top"><em>ny</em> </td><td>
Number of grid points in x-direction </td></tr>
<tr><td valign="top"><em>nz</em> </td><td>
Number of grid points in y-direction Number of grid points in y-direction </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpmg_8c-source.html#l03022">multipolebc()</a>, <a class="el" href="vunit_8h-source.html#l00090">Vunit_ec</a>, <a class="el" href="vunit_8h-source.html#l00106">Vunit_eps0</a>, and <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<p><center><img src="vpmg_8c_2ef3b09ecf0404038dabf01cc0c3dbaf_cgraph.png" border="0" usemap="#vpmg_8c_2ef3b09ecf0404038dabf01cc0c3dbaf_cgraph_map" alt=""></center>
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<area shape="rect" href="vpmg-private_8h.html#0f71bb1c4fe48352092a82c88c5eac3e" title="This routine serves bcfl2. It returns (in tsr) the contraction independent portion..." alt="" coords="106,8,197,34"></map>
</div>
</div>
</div><p>
<a class="anchor" name="50d8ef438d4a7a76d869fb256b24d372"></a><!-- doxytag: member="vpmg.c::bspline2" ref="50d8ef438d4a7a76d869fb256b24d372" args="(double x)" -->
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<td class="memname">VPRIVATE double bspline2 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate a cubic B-spline.
<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>Cubic B-spline value </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04759">fillcoChargeSpline2()</a>, and <a class="el" href="vpmg_8c-source.html#l05645">qfForceSpline2()</a>.</p>
</div>
</div><p>
<a class="anchor" name="c953c7091df8e4a1df53463baf8fe7ee"></a><!-- doxytag: member="vpmg.c::bspline4" ref="c953c7091df8e4a1df53463baf8fe7ee" args="(double x)" -->
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<td class="memname">VPRIVATE double bspline4 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate a 5th Order B-Spline (4th order polynomial).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>: Michael Schnieders </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>5th Order B-Spline </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, and <a class="el" href="vpmg_8c-source.html#l05757">qfForceSpline4()</a>.</p>
</div>
</div><p>
<a class="anchor" name="9e0486c0940668c5db8b56f165c474b6"></a><!-- doxytag: member="vpmg.c::d2bspline4" ref="9e0486c0940668c5db8b56f165c474b6" args="(double x)" -->
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<td class="memname">VPUBLIC double d2bspline4 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate the 2nd derivative of a 5th Order B-Spline.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>: Michael Schnieders </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>2nd derivative of a 5th Order B-Spline </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>.</p>
</div>
</div><p>
<a class="anchor" name="ddf938597bc4a997f8766856d8d59de1"></a><!-- doxytag: member="vpmg.c::d3bspline4" ref="ddf938597bc4a997f8766856d8d59de1" args="(double x)" -->
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<td class="memname">VPUBLIC double d3bspline4 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate the 3rd derivative of a 5th Order B-Spline.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>: Michael Schnieders </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>3rd derivative of a 5th Order B-Spline </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
</div>
</div><p>
<a class="anchor" name="8a4a959a2448c20bfc3660f04077892e"></a><!-- doxytag: member="vpmg.c::dbspline2" ref="8a4a959a2448c20bfc3660f04077892e" args="(double x)" -->
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<td class="memname">VPRIVATE double dbspline2 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate a cubic B-spline derivative.
<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>Cubic B-spline derivative </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l05645">qfForceSpline2()</a>.</p>
</div>
</div><p>
<a class="anchor" name="aefa250362d354e032dd1d104cfea094"></a><!-- doxytag: member="vpmg.c::dbspline4" ref="aefa250362d354e032dd1d104cfea094" args="(double x)" -->
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<td class="memname">VPUBLIC double dbspline4 </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Evaluate a 5th Order B-Spline derivative (4th order polynomial).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>: Michael Schnieders </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>5th Order B-Spline derivative </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>x</em> </td><td>
Position </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, and <a class="el" href="vpmg_8c-source.html#l05757">qfForceSpline4()</a>.</p>
</div>
</div><p>
<a class="anchor" name="f0c2a5754fbe7a35b083ef600dab299d"></a><!-- doxytag: member="vpmg.c::extEnergy" ref="f0c2a5754fbe7a35b083ef600dab299d" args="(Vpmg *thee, Vpmg *pmgOLD, PBEparm_calcEnergy extFlag, double partMin[3], double partMax[3], int bflags[6])" -->
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<td class="memname">VPRIVATE void extEnergy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </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>pmgOLD</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__PBEparm.html#g8cc295f42b2029944d85402f93190603">PBEparm_calcEnergy</a> </td>
<td class="paramname"> <em>extFlag</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>partMin</em>[3], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>partMax</em>[3], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>bflags</em>[6]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
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<p>
For focusing, set external energy data members in new Vpmg object based on energy calculations on old Vpmg object from regions outside the indicated partition.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Todd Dolinsky </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>pmgOLD</em> </td><td>
Newly created PMG manager </td></tr>
<tr><td valign="top"><em>extFlag</em> </td><td>
Old PMG manager, source of energies </td></tr>
<tr><td valign="top"><em>partMin</em> </td><td>
Energy calculation flag </td></tr>
<tr><td valign="top"><em>partMax</em> </td><td>
Partition lower corner </td></tr>
<tr><td valign="top"><em>bflags</em> </td><td>
Partition upper corner Which boundaries to include the calculation </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#l00127">sVpmg::extDiEnergy</a>, <a class="el" href="vpmg_8h-source.html#l00131">sVpmg::extQfEnergy</a>, <a class="el" href="vpmg_8h-source.html#l00129">sVpmg::extQmEnergy</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="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="vatom_8h-source.html#l00078">sVatom::partID</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</a>, <a class="el" href="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vatom_8h-source.html#l00075">sVatom::position</a>, <a class="el" href="vpmg_8h-source.html#l00126">sVpmg::pvec</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="vhal_8h-source.html#l00432">VAPBS_BACK</a>, <a class="el" href="vhal_8h-source.html#l00438">VAPBS_DOWN</a>, <a class="el" href="vhal_8h-source.html#l00414">VAPBS_FRONT</a>, <a class="el" href="vhal_8h-source.html#l00426">VAPBS_LEFT</a>, <a class="el" href="vhal_8h-source.html#l00408">VAPBS_RIGHT</a>, <a class="el" href="vhal_8h-source.html#l00420">VAPBS_UP</a>, <a class="el" href="vpmg_8c-source.html#l01165">Vpmg_dielEnergy()</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="vpmg_8c-source.html#l00553">Vpmg_setPart()</a>, <a class="el" href="vpmg_8c-source.html#l00798">Vpmg_unsetPart()</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="routines_8c-source.html#l01056">energyMG()</a>, and <a class="el" href="vpmg_8c-source.html#l00137">Vpmg_ctor2()</a>.</p>
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<a class="anchor" name="da65af06c9af5bf4ee593cb051bd0b0d"></a><!-- doxytag: member="vpmg.c::fillcoCharge" ref="da65af06c9af5bf4ee593cb051bd0b0d" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE Vrc_Codes fillcoCharge </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Top-level driver to fill source term charge array.
<p>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success/failure status </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00137">sVpmg::chargeMeth</a>, <a class="el" href="vpmg_8h-source.html#l00138">sVpmg::chargeSrc</a>, <a class="el" href="vpmg_8c-source.html#l04575">fillcoChargeMap()</a>, <a class="el" href="vpmg_8c-source.html#l04623">fillcoChargeSpline1()</a>, <a class="el" href="vpmg_8c-source.html#l04759">fillcoChargeSpline2()</a>, <a class="el" href="vpmg-private_8h.html#e84de46101d6abe2046ae860b55832a0">fillcoInducedDipole()</a>, <a class="el" href="vpmg-private_8h.html#6139befcbac10d86518d7b4cd397204a">fillcoNLInducedDipole()</a>, <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, <a class="el" href="vpmg_8h-source.html#l00154">sVpmg::useChargeMap</a>, <a class="el" href="vhal_8h-source.html#l00238">VCM_BSPL2</a>, <a class="el" href="vhal_8h-source.html#l00241">VCM_BSPL4</a>, <a class="el" href="vhal_8h-source.html#l00256">VCM_CHARGE</a>, <a class="el" href="vhal_8h-source.html#l00258">VCM_INDUCED</a>, <a class="el" href="vhal_8h-source.html#l00259">VCM_NLINDUCED</a>, <a class="el" href="vhal_8h-source.html#l00257">VCM_PERMANENT</a>, <a class="el" href="vhal_8h-source.html#l00235">VCM_TRIL</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, and <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04885">Vpmg_fillco()</a>.</p>
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<a class="anchor" name="2fe0074cd016170f829d76a856409185"></a><!-- doxytag: member="vpmg.c::fillcoChargeMap" ref="2fe0074cd016170f829d76a856409185" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE Vrc_Codes fillcoChargeMap </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
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<p>
Fill source term charge array from a pre-calculated map.
<p>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success/failure status </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00104">sVpmg::charge</a>, <a class="el" href="vpmg_8h-source.html#l00156">sVpmg::chargeMap</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vgrid_8c-source.html#l00162">Vgrid_value()</a>, <a class="el" href="vpbe_8c-source.html#l00154">Vpbe_getZmagic()</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="vpmg_8h-source.html#l00120">sVpmg::xf</a>, <a class="el" href="vpmg_8h-source.html#l00121">sVpmg::yf</a>, and <a class="el" href="vpmg_8h-source.html#l00122">sVpmg::zf</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04519">fillcoCharge()</a>.</p>
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<a class="anchor" name="7e7a2991c9f8b5e9a4a06843aecd38ae"></a><!-- doxytag: member="vpmg.c::fillcoChargeSpline1" ref="7e7a2991c9f8b5e9a4a06843aecd38ae" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoChargeSpline1 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Fill source term charge array from linear interpolation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00104">sVpmg::charge</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</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="vpbe_8c-source.html#l00154">Vpbe_getZmagic()</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04519">fillcoCharge()</a>.</p>
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<a class="anchor" name="6074122271a6957f5d463aa95c90f61c"></a><!-- doxytag: member="vpmg.c::fillcoChargeSpline2" ref="6074122271a6957f5d463aa95c90f61c" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoChargeSpline2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Fill source term charge array from cubic spline interpolation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8c-source.html#l04727">bspline2()</a>, <a class="el" href="vpmg_8h-source.html#l00104">sVpmg::charge</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</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="vpbe_8c-source.html#l00154">Vpbe_getZmagic()</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04519">fillcoCharge()</a>.</p>
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<a class="anchor" name="169088d2631112390e9699d0ff25ab0a"></a><!-- doxytag: member="vpmg.c::fillcoCoef" ref="169088d2631112390e9699d0ff25ab0a" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoef </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Top-level driver to fill all operator coefficient arrays.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8c-source.html#l03729">fillcoCoefMap()</a>, <a class="el" href="vpmg_8c-source.html#l03852">fillcoCoefMol()</a>, <a class="el" href="vpmg_8c-source.html#l04255">fillcoCoefSpline()</a>, <a class="el" href="vpmg_8c-source.html#l09624">fillcoCoefSpline3()</a>, <a class="el" href="vpmg_8c-source.html#l09134">fillcoCoefSpline4()</a>, <a class="el" href="vpmg_8h-source.html#l00135">sVpmg::surfMeth</a>, <a class="el" href="vpmg_8h-source.html#l00142">sVpmg::useDielXMap</a>, <a class="el" href="vpmg_8h-source.html#l00145">sVpmg::useDielYMap</a>, <a class="el" href="vpmg_8h-source.html#l00148">sVpmg::useDielZMap</a>, <a class="el" href="vpmg_8h-source.html#l00151">sVpmg::useKappaMap</a>, <a class="el" href="vhal_8h-source.html#l00108">VSM_MOL</a>, <a class="el" href="vhal_8h-source.html#l00112">VSM_MOLSMOOTH</a>, <a class="el" href="vhal_8h-source.html#l00114">VSM_SPLINE</a>, <a class="el" href="vhal_8h-source.html#l00124">VSM_SPLINE3</a>, and <a class="el" href="vhal_8h-source.html#l00128">VSM_SPLINE4</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04885">Vpmg_fillco()</a>.</p>
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<a class="anchor" name="35949511a7f2779c8ac7e7c88bdca001"></a><!-- doxytag: member="vpmg.c::fillcoCoefMap" ref="35949511a7f2779c8ac7e7c88bdca001" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMap </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
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<p>
Fill operator coefficient arrays from pre-calculated maps.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00144">sVpmg::dielXMap</a>, <a class="el" href="vpmg_8h-source.html#l00147">sVpmg::dielYMap</a>, <a class="el" href="vpmg_8h-source.html#l00150">sVpmg::dielZMap</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8h-source.html#l00103">sVpmg::kappa</a>, <a class="el" href="vpmg_8h-source.html#l00153">sVpmg::kappaMap</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00142">sVpmg::useDielXMap</a>, <a class="el" href="vpmg_8h-source.html#l00145">sVpmg::useDielYMap</a>, <a class="el" href="vpmg_8h-source.html#l00148">sVpmg::useDielZMap</a>, <a class="el" href="vpmg_8h-source.html#l00151">sVpmg::useKappaMap</a>, <a class="el" href="vgrid_8c-source.html#l00162">Vgrid_value()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmg_8h-source.html#l00120">sVpmg::xf</a>, <a class="el" href="vpmg_8h-source.html#l00121">sVpmg::yf</a>, and <a class="el" href="vpmg_8h-source.html#l00122">sVpmg::zf</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04479">fillcoCoef()</a>, and <a class="el" href="vpmg_8c-source.html#l03852">fillcoCoefMol()</a>.</p>
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<p><center><img src="vpmg_8c_35949511a7f2779c8ac7e7c88bdca001_cgraph.png" border="0" usemap="#vpmg_8c_35949511a7f2779c8ac7e7c88bdca001_cgraph_map" alt=""></center>
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<a class="anchor" name="62617829770eaed11c159947453e457c"></a><!-- doxytag: member="vpmg.c::fillcoCoefMol" ref="62617829770eaed11c159947453e457c" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMol </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
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<div class="memdoc">
<p>
Fill operator coefficient arrays from a molecular surface calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8c-source.html#l03729">fillcoCoefMap()</a>, <a class="el" href="vpmg_8c-source.html#l03965">fillcoCoefMolDiel()</a>, <a class="el" href="vpmg_8c-source.html#l03868">fillcoCoefMolIon()</a>, <a class="el" href="vpmg_8h-source.html#l00142">sVpmg::useDielXMap</a>, <a class="el" href="vpmg_8h-source.html#l00145">sVpmg::useDielYMap</a>, <a class="el" href="vpmg_8h-source.html#l00148">sVpmg::useDielZMap</a>, and <a class="el" href="vpmg_8h-source.html#l00151">sVpmg::useKappaMap</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04479">fillcoCoef()</a>.</p>
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<a class="anchor" name="34484f0f2f254b954abf20c5a98ab9d4"></a><!-- doxytag: member="vpmg.c::fillcoCoefMolDiel" ref="34484f0f2f254b954abf20c5a98ab9d4" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMolDiel </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Fill differential operator coefficient arrays from a molecular surface calculation.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>, <a class="el" href="vpmg_8c-source.html#l04124">fillcoCoefMolDielSmooth()</a>, <a class="el" href="vpmg_8h-source.html#l00135">sVpmg::surfMeth</a>, and <a class="el" href="vhal_8h-source.html#l00112">VSM_MOLSMOOTH</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03852">fillcoCoefMol()</a>.</p>
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<a class="anchor" name="df9fff114eed3d5d94f3adbbf9527483"></a><!-- doxytag: member="vpmg.c::fillcoCoefMolDielNoSmooth" ref="df9fff114eed3d5d94f3adbbf9527483" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMolDielNoSmooth </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Fill differential operator coefficient arrays from a molecular surface calculation without smoothing.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00088">sVpbe::acc</a>, <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8c-source.html#l06045">markSphere()</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vacc_8c-source.html#l00705">Vacc_atomSASA()</a>, <a class="el" href="vacc_8c-source.html#l00900">Vacc_atomSASPoints()</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>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00098">Vpbe_getSoluteDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00119">Vpbe_getSolventRadius()</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03965">fillcoCoefMolDiel()</a>.</p>
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<a class="anchor" name="afab27ad33274047911bd2ec092eb265"></a><!-- doxytag: member="vpmg.c::fillcoCoefMolDielSmooth" ref="afab27ad33274047911bd2ec092eb265" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMolDielSmooth </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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Fill differential operator coefficient arrays from a molecular surface calculation with smoothing.
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Molecular surface, dielectric smoothing following an implementation of Bruccoleri, et al. J Comput Chem 18 268-276 (1997).<p>
This algorithm uses a 9 point harmonic smoothing technique - the point in question and all grid points 1/sqrt(2) grid spacings away.<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>This uses thee->a1cf, thee->a2cf, thee->a3cf as temporary storage. </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Todd Dolinsky </dd></dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00110">sVpmg::a1cf</a>, <a class="el" href="vpmg_8h-source.html#l00112">sVpmg::a2cf</a>, <a class="el" href="vpmg_8h-source.html#l00114">sVpmg::a3cf</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, and <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03965">fillcoCoefMolDiel()</a>.</p>
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<a class="anchor" name="9217fdfc8737424d5e5ccc1193f9c3b0"></a><!-- doxytag: member="vpmg.c::fillcoCoefMolIon" ref="9217fdfc8737424d5e5ccc1193f9c3b0" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefMolIon </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Fill ion (nonlinear) operator coefficient array from a molecular surface calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00088">sVpbe::acc</a>, <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</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="vpmg_8h-source.html#l00103">sVpmg::kappa</a>, <a class="el" href="vpmg_8c-source.html#l06045">markSphere()</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00135">sVpmg::surfMeth</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>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vpbe_8c-source.html#l00126">Vpbe_getMaxIonRadius()</a>, <a class="el" href="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03852">fillcoCoefMol()</a>.</p>
<p>
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<p><center><img src="vpmg_8c_9217fdfc8737424d5e5ccc1193f9c3b0_cgraph.png" border="0" usemap="#vpmg_8c_9217fdfc8737424d5e5ccc1193f9c3b0_cgraph_map" alt=""></center>
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<a class="anchor" name="61365ff4cedaf084ea6d960d432a3d03"></a><!-- doxytag: member="vpmg.c::fillcoCoefSpline" ref="61365ff4cedaf084ea6d960d432a3d03" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefSpline </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Fill operator coefficient arrays from a spline-based surface calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8h-source.html#l00103">sVpmg::kappa</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00136">sVpmg::splineWin</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>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vpbe_8c-source.html#l00126">Vpbe_getMaxIonRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00098">Vpbe_getSoluteDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04479">fillcoCoef()</a>.</p>
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<p><center><img src="vpmg_8c_61365ff4cedaf084ea6d960d432a3d03_cgraph.png" border="0" usemap="#vpmg_8c_61365ff4cedaf084ea6d960d432a3d03_cgraph_map" alt=""></center>
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<a class="anchor" name="b7b5543b591c9433e7190a2fe45b4ca2"></a><!-- doxytag: member="vpmg.c::fillcoCoefSpline3" ref="b7b5543b591c9433e7190a2fe45b4ca2" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefSpline3 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Fill operator coefficient arrays from a 5th order polynomial based surface calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8h-source.html#l00103">sVpmg::kappa</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00136">sVpmg::splineWin</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>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vpbe_8c-source.html#l00126">Vpbe_getMaxIonRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00098">Vpbe_getSoluteDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04479">fillcoCoef()</a>.</p>
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<p><center><img src="vpmg_8c_b7b5543b591c9433e7190a2fe45b4ca2_cgraph.png" border="0" usemap="#vpmg_8c_b7b5543b591c9433e7190a2fe45b4ca2_cgraph_map" alt=""></center>
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<a class="anchor" name="be8b2056b56093552215f2e97c8f5c1b"></a><!-- doxytag: member="vpmg.c::fillcoCoefSpline4" ref="be8b2056b56093552215f2e97c8f5c1b" args="(Vpmg *thee)" -->
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<td class="memname">VPRIVATE void fillcoCoefSpline4 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Fill operator coefficient arrays from a 7th order polynomial based surface calculation.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00100">sVpmg::epsx</a>, <a class="el" href="vpmg_8h-source.html#l00101">sVpmg::epsy</a>, <a class="el" href="vpmg_8h-source.html#l00102">sVpmg::epsz</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="vpmg_8h-source.html#l00103">sVpmg::kappa</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00136">sVpmg::splineWin</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>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vpbe_8c-source.html#l00126">Vpbe_getMaxIonRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00098">Vpbe_getSoluteDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04479">fillcoCoef()</a>.</p>
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Here is the call graph for this function:</div>
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<p><center><img src="vpmg_8c_be8b2056b56093552215f2e97c8f5c1b_cgraph.png" border="0" usemap="#vpmg_8c_be8b2056b56093552215f2e97c8f5c1b_cgraph_map" alt=""></center>
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<a class="anchor" name="45c2c05ddfc0c4e4aea3be668137d2e0"></a><!-- doxytag: member="vpmg.c::fillcoPermanentMultipole" ref="45c2c05ddfc0c4e4aea3be668137d2e0" args="(Vpmg *thee)" -->
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<td class="memname">VPUBLIC void fillcoPermanentMultipole </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Fill source term charge array for the use of permanent multipoles.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmg_8c-source.html#l06331">bspline4()</a>, <a class="el" href="vpmg_8h-source.html#l00104">sVpmg::charge</a>, <a class="el" href="vpmg_8c-source.html#l06397">d2bspline4()</a>, <a class="el" href="vpmg_8c-source.html#l06365">dbspline4()</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</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="vpmg_8c-source.html#l06327">VFCHI4()</a>, <a class="el" href="vpbe_8c-source.html#l00154">Vpbe_getZmagic()</a>, <a class="el" href="vpmgp_8h-source.html#l00114">sVpmgp::xcent</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00115">sVpmgp::ycent</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00116">sVpmgp::zcent</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l04519">fillcoCharge()</a>.</p>
<p>
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<p><center><img src="vpmg_8c_45c2c05ddfc0c4e4aea3be668137d2e0_cgraph.png" border="0" usemap="#vpmg_8c_45c2c05ddfc0c4e4aea3be668137d2e0_cgraph_map" alt=""></center>
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</div>
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</div><p>
<a class="anchor" name="d55928ed41b43f65ba1c494b2c577353"></a><!-- doxytag: member="vpmg.c::focusFillBound" ref="d55928ed41b43f65ba1c494b2c577353" args="(Vpmg *thee, Vpmg *pmgOLD)" -->
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<td class="memname">VPRIVATE void focusFillBound </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</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>
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<td></td>
<td>)</td>
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<div class="memdoc">
<p>
For focusing, fill in the boundaries of the new mesh based on the potential values in the old mesh.
<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>pmgOLD</em> </td><td>
New PMG object (the one just created) Old PMG object </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00123">sVpmg::gxcf</a>, <a class="el" href="vpmg_8h-source.html#l00124">sVpmg::gycf</a>, <a class="el" href="vpmg_8h-source.html#l00125">sVpmg::gzcf</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</a>, <a class="el" href="vpbe_8c-source.html#l00106">Vpbe_getSoluteCenter()</a>, <a class="el" href="vpbe_8c-source.html#l00185">Vpbe_getSoluteCharge()</a>, <a class="el" href="vpbe_8c-source.html#l00161">Vpbe_getSoluteRadius()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00090">Vpbe_getTemperature()</a>, <a class="el" href="vpbe_8c-source.html#l00133">Vpbe_getXkappa()</a>, <a class="el" href="vunit_8h-source.html#l00090">Vunit_ec</a>, <a class="el" href="vunit_8h-source.html#l00106">Vunit_eps0</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</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="vpmg_8c-source.html#l00137">Vpmg_ctor2()</a>.</p>
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<a class="anchor" name="f4f11e78d20500aa43167eab5e52752f"></a><!-- doxytag: member="vpmg.c::markSphere" ref="f4f11e78d20500aa43167eab5e52752f" args="(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hz, double xmin, double ymin, double zmin, double *array, double markVal)" -->
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<td class="memname">VPRIVATE void markSphere </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>rtot</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>tpos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nx</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>ny</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nz</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>hx</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>hy</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>hzed</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>xmin</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>ymin</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>zmin</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>array</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>markVal</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<p>
Mark the grid points inside a sphere with a particular value. This marks by resetting the the grid points inside the sphere to the specified value.
<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>tpos</em> </td><td>
Sphere radius </td></tr>
<tr><td valign="top"><em>nx</em> </td><td>
Sphere position </td></tr>
<tr><td valign="top"><em>ny</em> </td><td>
Number of grid points </td></tr>
<tr><td valign="top"><em>nz</em> </td><td>
Number of grid points </td></tr>
<tr><td valign="top"><em>hx</em> </td><td>
Number of grid points </td></tr>
<tr><td valign="top"><em>hy</em> </td><td>
Grid spacing </td></tr>
<tr><td valign="top"><em>hz</em> </td><td>
Grid spacing </td></tr>
<tr><td valign="top"><em>xmin</em> </td><td>
Grid spacing </td></tr>
<tr><td valign="top"><em>ymin</em> </td><td>
Grid lower corner </td></tr>
<tr><td valign="top"><em>zmin</em> </td><td>
Grid lower corner </td></tr>
<tr><td valign="top"><em>array</em> </td><td>
Grid lower corner </td></tr>
<tr><td valign="top"><em>markVal</em> </td><td>
Grid values Value to mark with </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>, and <a class="el" href="vpmg_8c-source.html#l03868">fillcoCoefMolIon()</a>.</p>
</div>
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<a class="anchor" name="0f71bb1c4fe48352092a82c88c5eac3e"></a><!-- doxytag: member="vpmg.c::multipolebc" ref="0f71bb1c4fe48352092a82c88c5eac3e" args="(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3])" -->
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<td class="memname">VPRIVATE void multipolebc </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>r</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>kappa</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>eps_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>eps_w</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>rad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>tsr</em>[3]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<p>
This routine serves bcfl2. It returns (in tsr) the contraction independent portion of the Debye-Huckel potential tensor for a spherical ion with a central charge, dipole and quadrupole. See the code for an in depth description.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>kappa</em> </td><td>
Distance to the boundary </td></tr>
<tr><td valign="top"><em>eps_p</em> </td><td>
Exponential screening factor </td></tr>
<tr><td valign="top"><em>eps_w</em> </td><td>
Solute dielectric </td></tr>
<tr><td valign="top"><em>rad</em> </td><td>
Solvent dielectric </td></tr>
<tr><td valign="top"><em>tsr</em> </td><td>
Radius of the sphere Contraction-independent portion of each tensor </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l02368">bcfl2()</a>.</p>
</div>
</div><p>
<a class="anchor" name="68e3819e4049a4b0c194289a2afb32ea"></a><!-- doxytag: member="vpmg.c::qfForceSpline1" ref="68e3819e4049a4b0c194289a2afb32ea" args="(Vpmg *thee, double *force, int atomID)" -->
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<td class="memname">VPRIVATE void qfForceSpline1 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>atomID</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
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<p>
Charge-field force due to a linear spline charge function.
<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>atomID</em> </td><td>
Set to force Valist atom ID </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</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="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="vatom_8h-source.html#l00078">sVatom::partID</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</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>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</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="vhal_8h-source.html#l00444">VPMGSMALL</a>, <a class="el" href="vpmgp_8h-source.html#l00191">sVpmgp::xmax</a>, <a class="el" href="vpmgp_8h-source.html#l00188">sVpmgp::xmin</a>, <a class="el" href="vpmgp_8h-source.html#l00192">sVpmgp::ymax</a>, <a class="el" href="vpmgp_8h-source.html#l00189">sVpmgp::ymin</a>, <a class="el" href="vpmgp_8h-source.html#l00193">sVpmgp::zmax</a>, and <a class="el" href="vpmgp_8h-source.html#l00190">sVpmgp::zmin</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l05465">Vpmg_qfForce()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<p><center><img src="vpmg_8c_68e3819e4049a4b0c194289a2afb32ea_cgraph.png" border="0" usemap="#vpmg_8c_68e3819e4049a4b0c194289a2afb32ea_cgraph_map" alt=""></center>
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<area shape="rect" href="group__Valist.html#g6e228909b1e2c178ee292ae97c5bce62" title="Get pointer to particular atom in list." alt="" coords="182,8,294,34"><area shape="rect" href="group__Vatom.html#g6123ac049c637301d5aa730c18c94756" title="Get atomic charge." alt="" coords="173,58,304,85"><area shape="rect" href="group__Vatom.html#gbe19ed4ab35365a2e8f7505bcbb6bca2" title="Get atomic position." alt="" coords="170,109,306,136"></map>
</div>
</div>
</div><p>
<a class="anchor" name="c55adeb810c3e971ebe1bf9b3a137246"></a><!-- doxytag: member="vpmg.c::qfForceSpline2" ref="c55adeb810c3e971ebe1bf9b3a137246" args="(Vpmg *thee, double *force, int atomID)" -->
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<td class="memname">VPRIVATE void qfForceSpline2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>atomID</em></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>
Charge-field force due to a cubic spline charge function.
<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>atomID</em> </td><td>
Set to force Valist atom ID </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8c-source.html#l04727">bspline2()</a>, <a class="el" href="vpmg_8c-source.html#l04743">dbspline2()</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="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="vatom_8h-source.html#l00078">sVatom::partID</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</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>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</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="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00191">sVpmgp::xmax</a>, <a class="el" href="vpmgp_8h-source.html#l00188">sVpmgp::xmin</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00192">sVpmgp::ymax</a>, <a class="el" href="vpmgp_8h-source.html#l00189">sVpmgp::ymin</a>, <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>, <a class="el" href="vpmgp_8h-source.html#l00193">sVpmgp::zmax</a>, and <a class="el" href="vpmgp_8h-source.html#l00190">sVpmgp::zmin</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l05465">Vpmg_qfForce()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<p><center><img src="vpmg_8c_c55adeb810c3e971ebe1bf9b3a137246_cgraph.png" border="0" usemap="#vpmg_8c_c55adeb810c3e971ebe1bf9b3a137246_cgraph_map" alt=""></center>
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<a class="anchor" name="682bb08f7ef2b312b9da1c2ba6e0a25b"></a><!-- doxytag: member="vpmg.c::qfForceSpline4" ref="682bb08f7ef2b312b9da1c2ba6e0a25b" args="(Vpmg *thee, double *force, int atomID)" -->
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<td class="memname">VPRIVATE void qfForceSpline4 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>atomID</em></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>
Charge-field force due to a quintic spline charge function.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>atomID</em> </td><td>
Set to force Valist atom ID </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmg_8c-source.html#l06331">bspline4()</a>, <a class="el" href="vpmg_8c-source.html#l06365">dbspline4()</a>, <a class="el" href="vpmg_8h-source.html#l00140">sVpmg::filled</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</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="vpmg_8c-source.html#l06327">VFCHI4()</a>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00191">sVpmgp::xmax</a>, <a class="el" href="vpmgp_8h-source.html#l00188">sVpmgp::xmin</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, <a class="el" href="vpmgp_8h-source.html#l00192">sVpmgp::ymax</a>, <a class="el" href="vpmgp_8h-source.html#l00189">sVpmgp::ymin</a>, <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>, <a class="el" href="vpmgp_8h-source.html#l00193">sVpmgp::zmax</a>, and <a class="el" href="vpmgp_8h-source.html#l00190">sVpmgp::zmin</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l05465">Vpmg_qfForce()</a>.</p>
<p>
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<p><center><img src="vpmg_8c_682bb08f7ef2b312b9da1c2ba6e0a25b_cgraph.png" border="0" usemap="#vpmg_8c_682bb08f7ef2b312b9da1c2ba6e0a25b_cgraph_map" alt=""></center>
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<area shape="rect" href="vpmg-private_8h.html#c953c7091df8e4a1df53463baf8fe7ee" title="Evaluate a 5th Order B-Spline (4th order polynomial)." alt="" coords="202,8,274,34"><area shape="rect" href="vpmg-private_8h.html#91d1557ecff0ea7809aface06c0c179e" title="Evaluate a 5th Order B-Spline derivative (4th order polynomial)." alt="" coords="198,58,278,85"><area shape="rect" href="group__Valist.html#g6e228909b1e2c178ee292ae97c5bce62" title="Get pointer to particular atom in list." alt="" coords="182,109,294,136"><area shape="rect" href="group__Vatom.html#g6123ac049c637301d5aa730c18c94756" title="Get atomic charge." alt="" coords="173,160,304,186"><area shape="rect" href="group__Vatom.html#gbe19ed4ab35365a2e8f7505bcbb6bca2" title="Get atomic position." alt="" coords="170,210,306,237"><area shape="rect" href="vpmg-private_8h.html#fcf864c3b65f0d536a2985d931dc4692" title="Return 2.5 plus difference of i - f." alt="" coords="204,261,273,288"></map>
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<a class="anchor" name="fcf864c3b65f0d536a2985d931dc4692"></a><!-- doxytag: member="vpmg.c::VFCHI4" ref="fcf864c3b65f0d536a2985d931dc4692" args="(int i, double f)" -->
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<td class="memname">VPRIVATE double VFCHI4 </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">double </td>
<td class="paramname"> <em>f</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Return 2.5 plus difference of i - f.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>(2.5+((double)(i)-(f))) </dd></dl>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, and <a class="el" href="vpmg_8c-source.html#l05757">qfForceSpline4()</a>.</p>
</div>
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<a class="anchor" name="e22a67401cf36cc85b0bd58938587913"></a><!-- doxytag: member="vpmg.c::Vpmg_polarizEnergy" ref="e22a67401cf36cc85b0bd58938587913" args="(Vpmg *thee, int extFlag)" -->
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<td class="memname">VPRIVATE double Vpmg_polarizEnergy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>extFlag</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<div class="memdoc">
<p>
Determines energy from polarizeable charge and interaction with fixed charges according to Rocchia et al.
<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>Energy in kT </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>extFlag</em> </td><td>
If 1, add external energy contributions to result </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#l00104">sVpmg::charge</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</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="vgrid_8c-source.html#l00076">Vgrid_ctor()</a>, <a class="el" href="vgrid_8c-source.html#l00280">Vgrid_curvature()</a>, <a class="el" href="vpbe_8c-source.html#l00098">Vpbe_getSoluteDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00112">Vpbe_getSolventDiel()</a>, <a class="el" href="vpbe_8c-source.html#l00090">Vpbe_getTemperature()</a>, <a class="el" href="vunit_8h-source.html#l00090">Vunit_ec</a>, <a class="el" href="vunit_8h-source.html#l00106">Vunit_eps0</a>, <a class="el" href="vunit_8h-source.html#l00094">Vunit_kb</a>, <a class="el" href="vpmgp_8h-source.html#l00188">sVpmgp::xmin</a>, and <a class="el" href="vpmgp_8h-source.html#l00189">sVpmgp::ymin</a>.</p>
<p>
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<p><center><img src="vpmg_8c_e22a67401cf36cc85b0bd58938587913_cgraph.png" border="0" usemap="#vpmg_8c_e22a67401cf36cc85b0bd58938587913_cgraph_map" alt=""></center>
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<a class="anchor" name="0876512b1ee9f93ee0378334b886938c"></a><!-- doxytag: member="vpmg.c::Vpmg_qfEnergyPoint" ref="0876512b1ee9f93ee0378334b886938c" args="(Vpmg *thee, int extFlag)" -->
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<td class="memname">VPRIVATE double Vpmg_qfEnergyPoint </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>extFlag</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Calculates charge-potential energy using summation over delta function positions (i.e. something like an Linf norm).
<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>Energy in kT </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>extFlag</em> </td><td>
If 1, add external energy contributions to result </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpbe_8h-source.html#l00086">sVpbe::alist</a>, <a class="el" href="vpmgp_8h-source.html#l00131">sVpmgp::bcfl</a>, <a class="el" href="vhal_8h-source.html#l00220">BCFL_FOCUS</a>, <a class="el" href="vpmg_8h-source.html#l00131">sVpmg::extQfEnergy</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="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="vatom_8h-source.html#l00078">sVatom::partID</a>, <a class="el" href="vpmg_8h-source.html#l00098">sVpmg::pbe</a>, <a class="el" href="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00126">sVpmg::pvec</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</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="vpmgp_8h-source.html#l00191">sVpmgp::xmax</a>, <a class="el" href="vpmgp_8h-source.html#l00188">sVpmgp::xmin</a>, <a class="el" href="vpmgp_8h-source.html#l00192">sVpmgp::ymax</a>, <a class="el" href="vpmgp_8h-source.html#l00189">sVpmgp::ymin</a>, <a class="el" href="vpmgp_8h-source.html#l00193">sVpmgp::zmax</a>, and <a class="el" href="vpmgp_8h-source.html#l00190">sVpmgp::zmin</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l01492">Vpmg_qfEnergy()</a>.</p>
<p>
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<p><center><img src="vpmg_8c_0876512b1ee9f93ee0378334b886938c_cgraph.png" border="0" usemap="#vpmg_8c_0876512b1ee9f93ee0378334b886938c_cgraph_map" alt=""></center>
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<a class="anchor" name="78687d08a4040d18d46337e1345b6dac"></a><!-- doxytag: member="vpmg.c::Vpmg_qfEnergyVolume" ref="78687d08a4040d18d46337e1345b6dac" args="(Vpmg *thee, int extFlag)" -->
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<td class="memname">VPRIVATE double Vpmg_qfEnergyVolume </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>extFlag</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Calculates charge-potential energy as integral over a volume.
<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>Energy in kT </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>extFlag</em> </td><td>
If 1, add external energy contributions to result </td></tr>
</table>
</dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00104">sVpmg::charge</a>, <a class="el" href="vpmg_8h-source.html#l00131">sVpmg::extQfEnergy</a>, <a class="el" href="vpmg_8h-source.html#l00140">sVpmg::filled</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="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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00126">sVpmg::pvec</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</a>, and <a class="el" href="vpbe_8c-source.html#l00154">Vpbe_getZmagic()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l01492">Vpmg_qfEnergy()</a>.</p>
<p>
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<p><center><img src="vpmg_8c_78687d08a4040d18d46337e1345b6dac_cgraph.png" border="0" usemap="#vpmg_8c_78687d08a4040d18d46337e1345b6dac_cgraph_map" alt=""></center>
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<a class="anchor" name="ff52adddfe50ff4e6282f3bcf05f3dd5"></a><!-- doxytag: member="vpmg.c::Vpmg_qmEnergySMPBE" ref="ff52adddfe50ff4e6282f3bcf05f3dd5" args="(Vpmg *thee, int extFlag)" -->
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<td class="memname">VPUBLIC double Vpmg_qmEnergySMPBE </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>extFlag</em></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>
Vpmg_qmEnergy for SMPBE.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Vincent Chu </dd></dl>
<p>References <a class="el" href="vpmg_8h-source.html#l00129">sVpmg::extQmEnergy</a>, <a class="el" href="vpmg_8h-source.html#l00140">sVpmg::filled</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="vpmg_8h-source.html#l00103">sVpmg::kappa</a>, <a class="el" href="vhal_8h-source.html#l00377">MAXION</a>, <a class="el" href="vpmgp_8h-source.html#l00086">sVpmgp::nonlin</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="vpmg_8h-source.html#l00097">sVpmg::pmgp</a>, <a class="el" href="vpmg_8h-source.html#l00126">sVpmg::pvec</a>, <a class="el" href="vpbe_8h-source.html#l00119">sVpbe::smsize</a>, <a class="el" href="vpbe_8h-source.html#l00118">sVpbe::smvolume</a>, <a class="el" href="vpmg_8h-source.html#l00119">sVpmg::u</a>, <a class="el" href="vcap_8c-source.html#l00058">Vcap_exp()</a>, <a class="el" href="vpbe_8c-source.html#l00083">Vpbe_getBulkIonicStrength()</a>, <a class="el" href="vpbe_8c-source.html#l00467">Vpbe_getIons()</a>, and <a class="el" href="vpbe_8c-source.html#l00147">Vpbe_getZkappa2()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l01256">Vpmg_qmEnergy()</a>.</p>
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<p><center><img src="vpmg_8c_ff52adddfe50ff4e6282f3bcf05f3dd5_cgraph.png" border="0" usemap="#vpmg_8c_ff52adddfe50ff4e6282f3bcf05f3dd5_cgraph_map" alt=""></center>
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<a class="anchor" name="1271687db8aa07b73c4ce3316943b72c"></a><!-- doxytag: member="vpmg.c::Vpmg_splineSelect" ref="1271687db8aa07b73c4ce3316943b72c" args="(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force)" -->
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<td class="memname">VPRIVATE void Vpmg_splineSelect </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>srfm</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>acc</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double * </td>
<td class="paramname"> <em>gpos</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em></td><td> </td>
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<td>)</td>
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<p>
Selects a spline based surface method from either VSM_SPLINE, VSM_SPLINE5 or VSM_SPLINE7.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </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>
Surface method, currently VSM_SPLINE, VSM_SPLINE5, or VSM_SPLINE7 </td></tr>
<tr><td valign="top"><em>gpos</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Position array -> array[3] </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Atom object Force array -> array[3] </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00295">Vacc_splineAccGradAtomNorm()</a>, <a class="el" href="vacc_8c-source.html#l01017">Vacc_splineAccGradAtomNorm3()</a>, <a class="el" href="vacc_8c-source.html#l00924">Vacc_splineAccGradAtomNorm4()</a>, <a class="el" href="vhal_8h-source.html#l00114">VSM_SPLINE</a>, <a class="el" href="vhal_8h-source.html#l00124">VSM_SPLINE3</a>, and <a class="el" href="vhal_8h-source.html#l00128">VSM_SPLINE4</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l05211">Vpmg_dbForce()</a>, and <a class="el" href="vpmg_8c-source.html#l05047">Vpmg_ibForce()</a>.</p>
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<a class="anchor" name="3667719ad7b6d35bb4ac587513be8b5c"></a><!-- doxytag: member="vpmg.c::zlapSolve" ref="3667719ad7b6d35bb4ac587513be8b5c" args="(Vpmg *thee, double **solution, double **source, double **work1)" -->
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<td class="memname">VPRIVATE void zlapSolve </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVpmg.html">Vpmg</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double ** </td>
<td class="paramname"> <em>solution</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double ** </td>
<td class="paramname"> <em>source</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double ** </td>
<td class="paramname"> <em>work1</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
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<p>
Calculate the solution to Poisson's equation with a simple Laplacian operator and zero-valued Dirichlet boundary conditions. Store the solution in thee->u.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="note" compact><dt><b>Note:</b></dt><dd>Vpmg_fillco must be called first </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>source</em> </td><td>
Solution term vector </td></tr>
<tr><td valign="top"><em>work1</em> </td><td>
Source term vector Work vector </td></tr>
</table>
</dl>
<p>References <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="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>, <a class="el" href="vpmgp_8h-source.html#l00185">sVpmgp::xlen</a>, <a class="el" href="vpmgp_8h-source.html#l00186">sVpmgp::ylen</a>, and <a class="el" href="vpmgp_8h-source.html#l00187">sVpmgp::zlen</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l06238">Vpmg_solveLaplace()</a>.</p>
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