Data Structures | Files | Typedefs | Functions

Vgreen class

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

Data Structures

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

Files

file  vgreen.h
 

Contains declarations for class Vgreen.


file  vgreen.c
 

Class Vgreen methods.


Typedefs

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

Functions

VEXTERNC ValistVgreen_getValist (Vgreen *thee)
 Get the atom list associated with this Green's function object.
VEXTERNC unsigned long int Vgreen_memChk (Vgreen *thee)
 Return the memory used by this structure (and its contents) in bytes.
VEXTERNC VgreenVgreen_ctor (Valist *alist)
 Construct the Green's function oracle.
VEXTERNC int Vgreen_ctor2 (Vgreen *thee, Valist *alist)
 FORTRAN stub to construct the Green's function oracle.
VEXTERNC void Vgreen_dtor (Vgreen **thee)
 Destruct the Green's function oracle.
VEXTERNC void Vgreen_dtor2 (Vgreen *thee)
 FORTRAN stub to destruct the Green's function oracle.
VEXTERNC 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.
VEXTERNC 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.
VEXTERNC 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.
VEXTERNC 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)
VEXTERNC 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.
VEXTERNC 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 (nathan.baker@pnl.gov)
 * Pacific Northwest National Laboratory
 *
 * Additional contributing authors listed in the code documentation.
 *
 * Copyright (c) 2010, Pacific Northwest National Laboratory.  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 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.
 *
 * 

Function Documentation

VEXTERNC 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:
theeVgreen object
nposThe number of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
valThe npos values
Returns:
1 if successful, 0 otherwise

Definition at line 251 of file vgreen.c.

Here is the call graph for this function:

VEXTERNC 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:
theeVgreen object
nposThe number of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
valThe npos values
Returns:
1 if successful, 0 otherwise

Definition at line 217 of file vgreen.c.

Here is the call graph for this function:

Here is the caller graph for this function:

VEXTERNC 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:
theeVgreen object
nposThe number of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
potThe npos potential values
gradxThe npos gradient x-components
gradyThe npos gradient y-components
gradzThe npos gradient z-components
Returns:
1 if successful, 0 otherwise

Definition at line 355 of file vgreen.c.

Here is the call graph for this function:

VEXTERNC 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:
theeVgreen object
nposThe number of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
potThe npos potential values
gradxThe npos gradient x-components
gradyThe npos gradient y-components
gradzThe npos gradient z-components
Returns:
1 if successful, 0 otherwise

Definition at line 303 of file vgreen.c.

Here is the call graph for this function:

Here is the caller graph for this function:

VEXTERNC Vgreen* Vgreen_ctor ( Valist alist )

Construct the Green's function oracle.

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

Definition at line 149 of file vgreen.c.

Here is the call graph for this function:

Here is the caller graph for this function:

VEXTERNC int Vgreen_ctor2 ( Vgreen thee,
Valist alist 
)

FORTRAN stub to construct the Green's function oracle.

Author:
Nathan Baker
Parameters:
theePointer to memory allocated for object
alistAtom (charge) list associated with object
Returns:
1 if successful, 0 otherwise

Definition at line 160 of file vgreen.c.

Here is the caller graph for this function:

VEXTERNC void Vgreen_dtor ( Vgreen **  thee )

Destruct the Green's function oracle.

Author:
Nathan Baker
Parameters:
theePointer to memory location for object

Definition at line 185 of file vgreen.c.

Here is the call graph for this function:

Here is the caller graph for this function:

VEXTERNC void Vgreen_dtor2 ( Vgreen thee )

FORTRAN stub to destruct the Green's function oracle.

Author:
Nathan Baker
Parameters:
theePointer to object

Definition at line 193 of file vgreen.c.

Here is the caller graph for this function:

VEXTERNC Valist* Vgreen_getValist ( Vgreen thee )

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

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

Definition at line 135 of file vgreen.c.

VEXTERNC 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:
theeVgreen object
nposNumber of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
valThe npos values
kappaThe value of $\kappa$ (see above)
Returns:
1 if successful, 0 otherwise

Definition at line 202 of file vgreen.c.

VEXTERNC 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:
theeVgreen object
nposThe number of positions to evaluate
xThe npos x-coordinates
yThe npos y-coordinates
zThe npos z-coordinates
gradxThe npos gradient x-components
gradyThe npos gradient y-components
gradzThe npos gradient z-components
kappaThe value of $\kappa$ (see above)
Returns:
int 1 if sucessful, 0 otherwise

Definition at line 209 of file vgreen.c.

VEXTERNC unsigned long int Vgreen_memChk ( Vgreen thee )

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

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

Definition at line 142 of file vgreen.c.