APBS  1.5
vfetk.c File Reference

Class Vfetk methods. More...

#include "vfetk.h"
Include dependency graph for vfetk.c:

Go to the source code of this file.

Macros

#define VRINGMAX   1000
 Maximum number of simplices in a simplex ring.
 
#define VATOMMAX   1000000
 Maximum number of atoms associated with a vertex.
 

Functions

VPRIVATE void polyEval (int numP, double p[], double c[][VMAXP], double xv[])
 
VPUBLIC Gem * Vfetk_getGem (Vfetk *thee)
 Get a pointer to the Gem (grid manager) object. More...
 
VPUBLIC AM * Vfetk_getAM (Vfetk *thee)
 Get a pointer to the AM (algebra manager) object. More...
 
VPUBLIC VpbeVfetk_getVpbe (Vfetk *thee)
 Get a pointer to the Vpbe (PBE manager) object. More...
 
VPUBLIC VcsmVfetk_getVcsm (Vfetk *thee)
 Get a pointer to the Vcsm (charge-simplex map) object. More...
 
VPUBLIC int Vfetk_getAtomColor (Vfetk *thee, int iatom)
 Get the partition information for a particular atom. More...
 
VPUBLIC VfetkVfetk_ctor (Vpbe *pbe, Vhal_PBEType type)
 Constructor for Vfetk object. More...
 
VPUBLIC int Vfetk_ctor2 (Vfetk *thee, Vpbe *pbe, Vhal_PBEType type)
 FORTRAN stub constructor for Vfetk object. More...
 
VPUBLIC void Vfetk_setParameters (Vfetk *thee, PBEparm *pbeparm, FEMparm *feparm)
 Set the parameter objects. More...
 
VPUBLIC void Vfetk_dtor (Vfetk **thee)
 Object destructor. More...
 
VPUBLIC void Vfetk_dtor2 (Vfetk *thee)
 FORTRAN stub object destructor. More...
 
VPUBLIC double * Vfetk_getSolution (Vfetk *thee, int *length)
 Create an array containing the solution (electrostatic potential in units of $k_B T/e$) at the finest mesh level. More...
 
VPUBLIC double Vfetk_energy (Vfetk *thee, int color, int nonlin)
 Return the total electrostatic energy. More...
 
VPUBLIC double Vfetk_qfEnergy (Vfetk *thee, int color)
 Get the "fixed charge" contribution to the electrostatic energy. More...
 
VPUBLIC double Vfetk_dqmEnergy (Vfetk *thee, int color)
 Get the "mobile charge" and "polarization" contributions to the electrostatic energy. More...
 
VPUBLIC void Vfetk_setAtomColors (Vfetk *thee)
 Transfer color (partition ID) information frmo a partitioned mesh to the atoms. More...
 
VPUBLIC unsigned long int Vfetk_memChk (Vfetk *thee)
 Return the memory used by this structure (and its contents) in bytes. More...
 
VPUBLIC Vrc_Codes Vfetk_genCube (Vfetk *thee, double center[3], double length[3], Vfetk_MeshLoad meshType)
 Construct a rectangular mesh (in the current Vfetk object) More...
 
VPUBLIC Vrc_Codes Vfetk_loadMesh (Vfetk *thee, double center[3], double length[3], Vfetk_MeshLoad meshType, Vio *sock)
 Loads a mesh into the Vfetk (and associated) object(s). More...
 
VPUBLIC void Bmat_printHB (Bmat *thee, char *fname)
 Writes a Bmat to disk in Harwell-Boeing sparse matrix format. More...
 
VPUBLIC PDE * Vfetk_PDE_ctor (Vfetk *fetk)
 Constructs the FEtk PDE object. More...
 
VPUBLIC int Vfetk_PDE_ctor2 (PDE *thee, Vfetk *fetk)
 Intializes the FEtk PDE object. More...
 
VPUBLIC void Vfetk_PDE_dtor (PDE **thee)
 Destroys FEtk PDE object. More...
 
VPUBLIC void Vfetk_PDE_dtor2 (PDE *thee)
 FORTRAN stub: destroys FEtk PDE object. More...
 
VPUBLIC void Vfetk_PDE_initAssemble (PDE *thee, int ip[], double rp[])
 Do once-per-assembly initialization. More...
 
VPUBLIC void Vfetk_PDE_initElement (PDE *thee, int elementType, int chart, double tvx[][3], void *data)
 
VPUBLIC void Vfetk_PDE_initFace (PDE *thee, int faceType, int chart, double tnvec[])
 Do once-per-face initialization. More...
 
VPUBLIC void Vfetk_PDE_initPoint (PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3])
 
VPUBLIC void Vfetk_PDE_Fu (PDE *thee, int key, double F[])
 Evaluate strong form of PBE. For interior points, this is:

\[ -\nabla \cdot \epsilon \nabla u + b(u) - f \]

where $b(u)$ is the (possibly nonlinear) mobile ion term and $f$ is the source charge distribution term (for PBE) or the induced surface charge distribution (for RPBE). For an interior-boundary (simplex face) point, this is:

\[ [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^+} - [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^-} \]

where $n(x)$ is the normal to the simplex face and the term represents the jump in dielectric displacement across the face. There is no outer-boundary contribution for this problem. More...

 
VPUBLIC double Vfetk_PDE_Fu_v (PDE *thee, int key, double V[], double dV[][VAPBS_DIM])
 This is the weak form of the PBE; i.e. the strong form integrated with a test function to give:

\[ \int_\Omega \left[ \epsilon \nabla u \cdot \nabla v + b(u) v - f v \right] dx \]

where $b(u)$ denotes the mobile ion term. More...

 
VPUBLIC double Vfetk_PDE_DFu_wv (PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3])
 
VPUBLIC void Vfetk_PDE_delta (PDE *thee, int type, int chart, double txq[], void *user, double F[])
 Evaluate a (discretized) delta function source term at the given point. More...
 
VPUBLIC void Vfetk_PDE_u_D (PDE *thee, int type, int chart, double txq[], double F[])
 Evaluate the Dirichlet boundary condition at the given point. More...
 
VPUBLIC void Vfetk_PDE_u_T (PDE *thee, int type, int chart, double txq[], double F[])
 Evaluate the "true solution" at the given point for comparison with the numerical solution. More...
 
VPUBLIC void Vfetk_PDE_bisectEdge (int dim, int dimII, int edgeType, int chart[], double vx[][3])
 
VPUBLIC void Vfetk_PDE_mapBoundary (int dim, int dimII, int vertexType, int chart, double vx[3])
 
VPUBLIC int Vfetk_PDE_markSimplex (int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex)
 
VPUBLIC void Vfetk_PDE_oneChart (int dim, int dimII, int objType, int chart[], double vx[][3], int dimV)
 
VPUBLIC double Vfetk_PDE_Ju (PDE *thee, int key)
 Energy functional. This returns the energy (less delta function terms) in the form:

\[ c^{-1}/2 \int (\epsilon (\nabla u)^2 + \kappa^2 (cosh u - 1)) dx \]

for a 1:1 electrolyte where $c$ is the output from Vpbe_getZmagic. More...

 
VPUBLIC void Vfetk_externalUpdateFunction (SS **simps, int num)
 External hook to simplex subdivision routines in Gem. Called each time a simplex is subdivided (we use it to update the charge-simplex map) More...
 
VPUBLIC int Vfetk_PDE_simplexBasisInit (int key, int dim, int comp, int *ndof, int dof[])
 Initialize the bases for the trial or the test space, for a particular component of the system, at all quadrature points on the master simplex element. More...
 
VPUBLIC void Vfetk_PDE_simplexBasisForm (int key, int dim, int comp, int pdkey, double xq[], double basis[])
 Evaluate the bases for the trial or test space, for a particular component of the system, at all quadrature points on the master simplex element. More...
 
VPUBLIC void Vfetk_dumpLocalVar ()
 Debugging routine to print out local variables used by PDE object. More...
 
VPUBLIC int Vfetk_fillArray (Vfetk *thee, Bvec *vec, Vdata_Type type)
 Fill an array with the specified data. More...
 
VPUBLIC int Vfetk_write (Vfetk *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname, Bvec *vec, Vdata_Format format)
 Write out data. More...
 

Variables

VPRIVATE Vfetk_LocalVar var
 
VPRIVATE char * diriCubeString
 
VPRIVATE char * neumCubeString
 
VPRIVATE int dim_2DP1 = 3
 
VPRIVATE int lgr_2DP1 [3][VMAXP]
 
VPRIVATE int lgr_2DP1x [3][VMAXP]
 
VPRIVATE int lgr_2DP1y [3][VMAXP]
 
VPRIVATE int lgr_2DP1z [3][VMAXP]
 
VPRIVATE int dim_3DP1 = VAPBS_NVS
 
VPRIVATE int lgr_3DP1 [VAPBS_NVS][VMAXP]
 
VPRIVATE int lgr_3DP1x [VAPBS_NVS][VMAXP]
 
VPRIVATE int lgr_3DP1y [VAPBS_NVS][VMAXP]
 
VPRIVATE int lgr_3DP1z [VAPBS_NVS][VMAXP]
 
VPRIVATE const int P_DEG =1
 
VPRIVATE int numP
 
VPRIVATE double c [VMAXP][VMAXP]
 
VPRIVATE double cx [VMAXP][VMAXP]
 
VPRIVATE double cy [VMAXP][VMAXP]
 
VPRIVATE double cz [VMAXP][VMAXP]
 

Detailed Description

Class Vfetk methods.

Author
Nathan Baker
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 vfetk.c.

Variable Documentation

◆ lgr_2DP1

VPRIVATE int lgr_2DP1[3][VMAXP]
Initial value:
= {
{ 2, -2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 386 of file vfetk.c.

◆ lgr_2DP1x

VPRIVATE int lgr_2DP1x[3][VMAXP]
Initial value:
= {
{ -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 395 of file vfetk.c.

◆ lgr_2DP1y

VPRIVATE int lgr_2DP1y[3][VMAXP]
Initial value:
= {
{ -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 402 of file vfetk.c.

◆ lgr_2DP1z

VPRIVATE int lgr_2DP1z[3][VMAXP]
Initial value:
= {
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 409 of file vfetk.c.

◆ lgr_3DP1

VPRIVATE int lgr_3DP1[VAPBS_NVS][VMAXP]
Initial value:
= {
{ 2, -2, -2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 438 of file vfetk.c.

◆ lgr_3DP1x

VPRIVATE int lgr_3DP1x[VAPBS_NVS][VMAXP]
Initial value:
= {
{ -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 446 of file vfetk.c.

◆ lgr_3DP1y

VPRIVATE int lgr_3DP1y[VAPBS_NVS][VMAXP]
Initial value:
= {
{ -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
}

Definition at line 454 of file vfetk.c.

◆ lgr_3DP1z

VPRIVATE int lgr_3DP1z[VAPBS_NVS][VMAXP]
Initial value:
= {
{ -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
{ 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
}

Definition at line 462 of file vfetk.c.