APBS
1.5
|
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 Valist * | Vgreen_getValist (Vgreen *thee) |
Get the atom list associated with this Green's function object. More... | |
VEXTERNC unsigned long int | Vgreen_memChk (Vgreen *thee) |
Return the memory used by this structure (and its contents) in bytes. More... | |
VEXTERNC Vgreen * | Vgreen_ctor (Valist *alist) |
Construct the Green's function oracle. More... | |
VEXTERNC int | Vgreen_ctor2 (Vgreen *thee, Valist *alist) |
FORTRAN stub to construct the Green's function oracle. More... | |
VEXTERNC void | Vgreen_dtor (Vgreen **thee) |
Destruct the Green's function oracle. More... | |
VEXTERNC void | Vgreen_dtor2 (Vgreen *thee) |
FORTRAN stub to destruct the Green's function oracle. More... | |
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. More... | |
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. More... | |
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. More... | |
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) More... | |
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. More... | |
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) More... | |
Provides capabilities for pointwise evaluation of free space Green's function for point charges in a uniform dielectric.
* * 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. * *
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 defined by
where is the atomic charge (in e) and
is the distance to the observation point
. The potential is scaled to units of V.
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 |
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 defined by
where is the atomic charge (in e) and
is the distance to the observation point
. The potential is scaled to units of V.
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 |
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 defined by
where is the atomic charge (in e) and
is the distance to the observation point
. The field is scaled to units of V/Å.
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 |
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 defined by
where is the atomic charge (in e) and
is the distance to the observation point
. The field is scaled to units of V/Å.
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 |
VEXTERNC void Vgreen_dtor | ( | Vgreen ** | thee | ) |
VEXTERNC void Vgreen_dtor2 | ( | Vgreen * | thee | ) |
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 defined by
where is the inverse screening length (in Å)
is the atomic charge (in e), and
r_i is the distance from atom
to the observation point
. The potential is scaled to units of V.
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 ![]() |
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 defined by
where is the inverse screening length (in Å).
is the atomic charge (in e), and
r_i is the distance from atom
to the observation point
. The potential is scaled to units of V/Å.
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 ![]() |