APBS  1.5
vpbe.c File Reference

Class Vpbe methods. More...

#include "vpbe.h"
Include dependency graph for vpbe.c:

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Macros

#define MAX_SPLINE_WINDOW   0.5
 

Functions

VPUBLIC ValistVpbe_getValist (Vpbe *thee)
 Get atom list. More...
 
VPUBLIC VaccVpbe_getVacc (Vpbe *thee)
 Get accessibility oracle. More...
 
VPUBLIC double Vpbe_getBulkIonicStrength (Vpbe *thee)
 Get bulk ionic strength. More...
 
VPUBLIC double Vpbe_getTemperature (Vpbe *thee)
 Get temperature. More...
 
VPUBLIC double Vpbe_getSoluteDiel (Vpbe *thee)
 Get solute dielectric constant. More...
 
VPUBLIC double * Vpbe_getSoluteCenter (Vpbe *thee)
 Get coordinates of solute center. More...
 
VPUBLIC double Vpbe_getSolventDiel (Vpbe *thee)
 Get solvent dielectric constant. More...
 
VPUBLIC double Vpbe_getSolventRadius (Vpbe *thee)
 Get solvent molecule radius. More...
 
VPUBLIC double Vpbe_getMaxIonRadius (Vpbe *thee)
 Get maximum radius of ion species. More...
 
VPUBLIC double Vpbe_getXkappa (Vpbe *thee)
 Get Debye-Huckel parameter. More...
 
VPUBLIC double Vpbe_getDeblen (Vpbe *thee)
 Get Debye-Huckel screening length. More...
 
VPUBLIC double Vpbe_getZkappa2 (Vpbe *thee)
 Get modified squared Debye-Huckel parameter. More...
 
VPUBLIC double Vpbe_getZmagic (Vpbe *thee)
 Get charge scaling factor. More...
 
VPUBLIC double Vpbe_getSoluteRadius (Vpbe *thee)
 Get sphere radius which bounds biomolecule. More...
 
VPUBLIC double Vpbe_getSoluteXlen (Vpbe *thee)
 Get length of solute in x dimension. More...
 
VPUBLIC double Vpbe_getSoluteYlen (Vpbe *thee)
 Get length of solute in y dimension. More...
 
VPUBLIC double Vpbe_getSoluteZlen (Vpbe *thee)
 Get length of solute in z dimension. More...
 
VPUBLIC double Vpbe_getSoluteCharge (Vpbe *thee)
 Get total solute charge. More...
 
VPUBLIC double Vpbe_getzmem (Vpbe *thee)
 Get z position of the membrane bottom. More...
 
VPUBLIC double Vpbe_getLmem (Vpbe *thee)
 Get length of the membrane (A)aauthor Michael Grabe. More...
 
VPUBLIC double Vpbe_getmembraneDiel (Vpbe *thee)
 Get membrane dielectric constant. More...
 
VPUBLIC double Vpbe_getmemv (Vpbe *thee)
 Get membrane potential (kT) More...
 
VPUBLIC VpbeVpbe_ctor (Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V)
 Construct Vpbe object. More...
 
VPUBLIC int Vpbe_ctor2 (Vpbe *thee, Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V)
 FORTRAN stub to construct Vpbe objct. More...
 
VPUBLIC void Vpbe_dtor (Vpbe **thee)
 Object destructor. More...
 
VPUBLIC void Vpbe_dtor2 (Vpbe *thee)
 FORTRAN stub object destructor. More...
 
VPUBLIC double Vpbe_getCoulombEnergy1 (Vpbe *thee)
 Calculate coulombic energy of set of charges. More...
 
VPUBLIC unsigned long int Vpbe_memChk (Vpbe *thee)
 Return the memory used by this structure (and its contents) in bytes. More...
 
VPUBLIC int Vpbe_getIons (Vpbe *thee, int *nion, double ionConc[MAXION], double ionRadii[MAXION], double ionQ[MAXION])
 Get information about the counterion species present. More...
 

Detailed Description

Class Vpbe methods.

Author
Nathan Baker
Version
$Id$
Attention
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
*  Nathan A. Baker (nathan.baker@pnnl.gov)
*  Pacific Northwest National Laboratory
*
*  Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the
* Pacific Northwest National Laboratory, operated by Battelle Memorial
* Institute, Pacific Northwest Division for the U.S. Department of Energy.
*
* Portions Copyright (c) 2002-2010, Washington University in St. Louis.
* Portions Copyright (c) 2002-2010, 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 the developer 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.
*
* 

Definition in file vpbe.c.