APBS  1.5
vgrid.h File Reference

Potential oracle for Cartesian mesh data. More...

#include "apbscfg.h"
#include "maloc/maloc.h"
#include "generic/vhal.h"
#include "generic/vstring.h"
Include dependency graph for vgrid.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Data Structures

struct  sVgrid
 Electrostatic potential oracle for Cartesian mesh data. More...
 

Macros

#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

VEXTERNC unsigned long int Vgrid_memChk (Vgrid *thee)
 Return the memory used by this structure (and its contents) in bytes. More...
 
VEXTERNC VgridVgrid_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) More...
 
VEXTERNC 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) More...
 
VEXTERNC int Vgrid_value (Vgrid *thee, double x[3], double *value)
 Get potential value (from mesh or approximation) at a point. More...
 
VEXTERNC void Vgrid_dtor (Vgrid **thee)
 Object destructor. More...
 
VEXTERNC void Vgrid_dtor2 (Vgrid *thee)
 FORTRAN stub object destructor. More...
 
VEXTERNC int Vgrid_curvature (Vgrid *thee, double pt[3], int cflag, double *curv)
 Get second derivative values at a point. More...
 
VEXTERNC int Vgrid_gradient (Vgrid *thee, double pt[3], double grad[3])
 Get first derivative values at a point. More...
 
VEXTERNC int Vgrid_readGZ (Vgrid *thee, const char *fname)
 Read in OpenDX data in GZIP format. More...
 
VEXTERNC void Vgrid_writeGZ (Vgrid *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname, char *title, double *pvec)
 Write out OpenDX data in GZIP format. More...
 
VEXTERNC 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. More...
 
VEXTERNC 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. More...
 
VEXTERNC int Vgrid_readDX (Vgrid *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Read in data in OpenDX grid format. More...
 
VEXTERNC void Vgrid_writeDXBIN (Vgrid *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname, char *title, double *pvec)
 Write out the binary data in OpenDX grid format. More...
 
VEXTERNC int Vgrid_readDXBIN (Vgrid *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Read in binary data in OpenDX grid format. More...
 
VEXTERNC double Vgrid_integrate (Vgrid *thee)
 Get the integral of the data. More...
 
VEXTERNC double Vgrid_normL1 (Vgrid *thee)
 Get the $L_1$ norm of the data. This returns the integral:

\[ \| u \|_{L_1} = \int_\Omega | u(x) | dx \]

. More...

 
VEXTERNC double Vgrid_normL2 (Vgrid *thee)
 Get the $L_2$ norm of the data. This returns the integral:

\[ \| u \|_{L_2} = \left( \int_\Omega | u(x) |^2 dx \right)^{1/2} \]

. More...

 
VEXTERNC double Vgrid_normLinf (Vgrid *thee)
 Get the $L_\infty$ norm of the data. This returns the integral:

\[ \| u \|_{L_\infty} = \sup_{x \in \Omega} | u(x) | \]

. More...

 
VEXTERNC double Vgrid_seminormH1 (Vgrid *thee)
 Get the $H_1$ semi-norm of the data. This returns the integral:

\[ | u |_{H_1} = \left( \int_\Omega |\nabla u(x)|^2 dx \right)^{1/2} \]

. More...

 
VEXTERNC double Vgrid_normH1 (Vgrid *thee)
 Get the $H_1$ norm (or energy norm) of the data. This returns the integral:

\[ \| u \|_{H_1} = \left( \int_\Omega |\nabla u(x)|^2 dx + \int_\Omega |u(x)|^2 dx \right)^{1/2} \]

. More...

 

Detailed Description

Potential oracle for Cartesian mesh data.

Author
Nathan Baker and Steve Bond
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 vgrid.h.

Function Documentation

◆ Vgrid_writeGZ()

VEXTERNC void Vgrid_writeGZ ( Vgrid thee,
const char *  iodev,
const char *  iofmt,
const char *  thost,
const char *  fname,
char *  title,
double *  pvec 
)

Write out OpenDX data in GZIP format.

Author
Dave Gohara
Parameters
theeObject to hold new grid data
iodevI/O device
iofmtI/O format
thostRemote host name
fnameFile name
titleData title
pvecMasking vector (0 = not written)

Definition at line 1011 of file vgrid.c.