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Vgreen class

Provides capabilities for pointwise evaluation of free space Green's function for point charges in a uniform dielectric. More...


Files

file  vgreen.h
 Contains declarations for class Vgreen.


Data Structures

struct  sVgreen
 Contains public data members for Vgreen class/module. More...


Typedefs

typedef sVgreen Vgreen
 Declaration of the Vgreen class as the Vgreen structure.


Functions

Valist * Vgreen_getValist (Vgreen *thee)
 Get the atom list associated with this Green's function object.

unsigned long int Vgreen_memChk (Vgreen *thee)
 Return the memory used by this structure (and its contents) in bytes.

Vgreen * Vgreen_ctor (Valist *alist)
 Construct the Green's function oracle.

int Vgreen_ctor2 (Vgreen *thee, Valist *alist)
 FORTRAN stub to construct the Green's function oracle.

void Vgreen_dtor (Vgreen **thee)
 Destruct the Green's function oracle.

void Vgreen_dtor2 (Vgreen *thee)
 FORTRAN stub to destruct the Green's function oracle.

int Vgreen_helmholtz (Vgreen *thee, int npos, double *x, double *y, double *z, double *val, double kappa)
 Get the Green's function for Helmholtz's equation integrated over the atomic point charges.

int Vgreen_helmholtzD (Vgreen *thee, int npos, double *x, double *y, double *z, double *gradx, double *grady, double *gradz, double kappa)
 Get the gradient of Green's function for Helmholtz's equation integrated over the atomic point charges.

int Vgreen_coulomb_direct (Vgreen *thee, int npos, double *x, double *y, double *z, double *val)
 Get the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation.

int Vgreen_coulomb (Vgreen *thee, int npos, double *x, double *y, double *z, double *val)
 Get the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation or H. E. Johnston, R. Krasny FMM library (if available).

int Vgreen_coulombD_direct (Vgreen *thee, int npos, double *x, double *y, double *z, double *pot, double *gradx, double *grady, double *gradz)
 Get gradient of the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation.

int Vgreen_coulombD (Vgreen *thee, int npos, double *x, double *y, double *z, double *pot, double *gradx, double *grady, double *gradz)
 Get gradient of the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using either direct summation or H. E. Johnston/R. Krasny FMM library (if available).

Detailed Description

Provides capabilities for pointwise evaluation of free space Green's function for point charges in a uniform dielectric.

Note:
Right now, these are very slow methods without any fast multipole acceleration.
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) 2002-2005.  Washington University in St. Louis.
 * All Rights Reserved.
 * Portions Copyright (c) 1999-2002.  The Regents of the University of
 * California.  
 * Portions Copyright (c) 1995.  Michael Holst.
 *
 * This file is part of APBS.
 *
 * APBS is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * APBS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with APBS; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
 *
 *

Function Documentation

int Vgreen_coulomb (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  val
) 
 

Get the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation or H. E. Johnston, R. Krasny FMM library (if available).

Returns the potential $\phi$ defined by

\[ \phi(r) = \sum_i \frac{q_i}{r_i} \]

where $q_i$ is the atomic charge (in e) and $r_i$ is the distance to the observation point $r$. The potential is scaled to units of V.

Author:
Nathan Baker
Parameters:
thee Vgreen object
npos The number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
val The npos values
Returns:
1 if successful, 0 otherwise

int Vgreen_coulomb_direct (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  val
) 
 

Get the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation.

Returns the potential $\phi$ defined by

\[ \phi(r) = \sum_i \frac{q_i}{r_i} \]

where $q_i$ is the atomic charge (in e) and $r_i$ is the distance to the observation point $r$. The potential is scaled to units of V.

Author:
Nathan Baker
Parameters:
thee Vgreen object
npos The number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
val The npos values
Returns:
1 if successful, 0 otherwise

int Vgreen_coulombD (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  pot,
double *  gradx,
double *  grady,
double *  gradz
) 
 

Get gradient of the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using either direct summation or H. E. Johnston/R. Krasny FMM library (if available).

Returns the field $\nabla \phi$ defined by

\[ \nabla \phi(r) = \sum_i \frac{q_i}{r_i} \]

where $q_i$ is the atomic charge (in e) and $r_i$ is the distance to the observation point $r$. The field is scaled to units of V/Å.

Author:
Nathan Baker
Parameters:
thee Vgreen object
npos The number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
pot The npos potential values
gradx The npos gradient x-components
grady The npos gradient y-components
gradz The npos gradient z-components
Returns:
1 if successful, 0 otherwise

int Vgreen_coulombD_direct (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  pot,
double *  gradx,
double *  grady,
double *  gradz
) 
 

Get gradient of the Coulomb's Law Green's function (solution to Laplace's equation) integrated over the atomic point charges using direct summation.

Returns the field $\nabla \phi$ defined by

\[ \nabla \phi(r) = \sum_i \frac{q_i}{r_i} \]

where $q_i$ is the atomic charge (in e) and $r_i$ is the distance to the observation point $r$. The field is scaled to units of V/Å.

Author:
Nathan Baker
Parameters:
thee Vgreen object
npos The number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
pot The npos potential values
gradx The npos gradient x-components
grady The npos gradient y-components
gradz The npos gradient z-components
Returns:
1 if successful, 0 otherwise

Vgreen* Vgreen_ctor (  Valist *  alist  ) 
 

Construct the Green's function oracle.

Author:
Nathan Baker
Parameters:
alist Atom (charge) list associated with object
Returns:
Pointer to newly allocated Green's function oracle

int Vgreen_ctor2 (  Vgreen *  thee,
Valist *  alist
) 
 

FORTRAN stub to construct the Green's function oracle.

Author:
Nathan Baker
Parameters:
thee Pointer to memory allocated for object
alist Atom (charge) list associated with object
Returns:
1 if successful, 0 otherwise

void Vgreen_dtor (  Vgreen **  thee  ) 
 

Destruct the Green's function oracle.

Author:
Nathan Baker
Parameters:
thee Pointer to memory location for object

void Vgreen_dtor2 (  Vgreen *  thee  ) 
 

FORTRAN stub to destruct the Green's function oracle.

Author:
Nathan Baker
Parameters:
thee Pointer to object

Valist* Vgreen_getValist (  Vgreen *  thee  ) 
 

Get the atom list associated with this Green's function object.

Author:
Nathan Baker
Parameters:
thee Vgreen object
Returns:
Pointer to Valist object associated with this Green's function object

int Vgreen_helmholtz (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  val,
double  kappa
) 
 

Get the Green's function for Helmholtz's equation integrated over the atomic point charges.

Returns the potential $\phi$ defined by

\[ \phi(r) = \sum_i \frac{q_i e^{-\kappa r_i}}{r_i} \]

where $\kappa$ is the inverse screening length (in Å) $q_i$ is the atomic charge (in e), and $r_i$ r_i is the distance from atom $i$ to the observation point $r$. The potential is scaled to units of V.

Author:
Nathan Baker
Bug:
Not implemented yet
Note:
Not implemented yet
Parameters:
thee Vgreen object
npos Number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
val The npos values
kappa The value of $\kappa$ (see above)
Returns:
1 if successful, 0 otherwise

int Vgreen_helmholtzD (  Vgreen *  thee,
int  npos,
double *  x,
double *  y,
double *  z,
double *  gradx,
double *  grady,
double *  gradz,
double  kappa
) 
 

Get the gradient of Green's function for Helmholtz's equation integrated over the atomic point charges.

Returns the field $\nabla \phi$ defined by

\[ \nabla \phi(r) = \nabla \sum_i \frac{q_i e^{-\kappa r_i}}{r_i} \]

where $\kappa$ is the inverse screening length (in Å). $q_i$ is the atomic charge (in e), and $r_i$ r_i is the distance from atom $i$ to the observation point $r$. The potential is scaled to units of V/Å.

Author:
Nathan Baker
Bug:
Not implemented yet
Note:
Not implemented yet
Parameters:
thee Vgreen object
npos The number of positions to evaluate
x The npos x-coordinates
y The npos y-coordinates
z The npos z-coordinates
gradx The npos gradient x-components
grady The npos gradient y-components
gradz The npos gradient z-components
kappa The value of $\kappa$ (see above)
Returns:
int 1 if sucessful, 0 otherwise

unsigned long int Vgreen_memChk (  Vgreen *  thee  ) 
 

Return the memory used by this structure (and its contents) in bytes.

Author:
Nathan Baker
Parameters:
thee Vgreen object
Returns:
The memory used by this structure and its contents in bytes

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