APBS 3.0.0
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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.c
 Class Vgreen methods.
 
file  vgreen.h
 Contains declarations for class Vgreen.
 

Data Structures

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

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@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) 2002-2010, 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.
*
* 

Typedef Documentation

◆ Vgreen

typedef struct sVgreen Vgreen

Declaration of the Vgreen class as the Vgreen structure.

Definition at line 101 of file vgreen.h.

Function Documentation

◆ Vgreen_coulomb()

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 258 of file vgreen.c.

◆ Vgreen_coulomb_direct()

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 224 of file vgreen.c.

◆ Vgreen_coulombD()

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 362 of file vgreen.c.

◆ Vgreen_coulombD_direct()

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 310 of file vgreen.c.

◆ Vgreen_ctor()

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 156 of file vgreen.c.

◆ Vgreen_ctor2()

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 167 of file vgreen.c.

◆ Vgreen_dtor()

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 192 of file vgreen.c.

◆ Vgreen_dtor2()

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 200 of file vgreen.c.

◆ Vgreen_getValist()

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 142 of file vgreen.c.

◆ Vgreen_helmholtz()

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 209 of file vgreen.c.

◆ Vgreen_helmholtzD()

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 216 of file vgreen.c.

◆ Vgreen_memChk()

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 149 of file vgreen.c.