vgrid.h File Reference

Potential oracle for Cartesian mesh data. More...

#include "maloc/maloc.h"
#include "apbs/vhal.h"
#include "apbs/vstring.h"

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Data Structures
struct	sVgrid
	Electrostatic potential oracle for Cartesian mesh data. More...
Defines
#define	VGRID_DIGITS 6
	Number of decimal places for comparisons and formatting.
Typedefs
typedef struct sVgrid	Vgrid
	Declaration of the Vgrid class as the sVgrid structure.
Functions
unsigned long int	Vgrid_memChk (Vgrid *thee)
	Return the memory used by this structure (and its contents) in bytes.
Vgrid *	Vgrid_ctor (int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *data)
	Construct Vgrid object with values obtained from Vpmg_readDX (for example).
int	Vgrid_ctor2 (Vgrid thee, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double data)
	Initialize Vgrid object with values obtained from Vpmg_readDX (for example).
int	Vgrid_value (Vgrid thee, double x[3], double value)
	Get potential value (from mesh or approximation) at a point.
void	Vgrid_dtor (Vgrid **thee)
	Object destructor.
void	Vgrid_dtor2 (Vgrid *thee)
	FORTRAN stub object destructor.
int	Vgrid_curvature (Vgrid thee, double pt[3], int cflag, double curv)
	Get second derivative values at a point.
int	Vgrid_gradient (Vgrid *thee, double pt[3], double grad[3])
	Get first derivative values at a point.
void	Vgrid_writeUHBD (Vgrid thee, const char iodev, const char iofmt, const char thost, const char fname, char title, double *pvec)
	Write out the data in UHBD grid format.
void	Vgrid_writeDX (Vgrid thee, const char iodev, const char iofmt, const char thost, const char fname, char title, double *pvec)
	Write out the data in OpenDX grid format.
int	Vgrid_readDX (Vgrid thee, const char iodev, const char iofmt, const char thost, const char *fname)
	Read in data in OpenDX grid format.
double	Vgrid_integrate (Vgrid *thee)
	Get the integral of the data.
double	Vgrid_normL1 (Vgrid *thee)
	Get the norm of the data. This returns the integral: $\\| u \\|_{L_1} = \int_\Omega \| u(x) \| dx$ .
double	Vgrid_normL2 (Vgrid *thee)
	Get the norm of the data. This returns the integral: $\\| u \\|_{L_2} = \left( \int_\Omega \| u(x) \|^2 dx \right)^{1/2}$ .
double	Vgrid_normLinf (Vgrid *thee)
	Get the $L_\infty$ norm of the data. This returns the integral: $\\| u \\|_{L_\infty} = \sup_{x \in \Omega} \| u(x) \|$ .
double	Vgrid_seminormH1 (Vgrid *thee)
	Get the semi-norm of the data. This returns the integral: $\| u \|_{H_1} = \left( \int_\Omega \|\nabla u(x)\|^2 dx \right)^{1/2}$ .
double	Vgrid_normH1 (Vgrid *thee)
	Get the norm (or energy norm) of the data. This returns the integral: $\\| u \\|_{H_1} = \left( \int_\Omega \|\nabla u(x)\|^2 dx + \int_\Omega \|u(x)\|^2 dx \right)^{1/2}$ .

Detailed Description

Potential oracle for Cartesian mesh data.

Author:: Nathan Baker and Steve Bond

Version:

Id: vgrid.h 1350 2009-02-12 00:38:48Z yhuang01

Attention:

 *
 * 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.
 *
 *

vgrid.h File Reference

Data Structures

Defines

Typedefs

Functions

Detailed Description