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

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) 2010-2020 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) 2002-2020, 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.

Macro Definition Documentation

MAX_SPLINE_WINDOW

#define MAX_SPLINE_WINDOW   0.5

Definition at line 62 of file vpbe.c.