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vfetk.h File Reference

Contains declarations for class Vfetk. More...

#include "maloc/maloc.h"
#include "mc/mc.h"
#include "apbs/vhal.h"
#include "apbs/vatom.h"
#include "apbs/vcsm.h"
#include "apbs/vpbe.h"
#include "apbs/vunit.h"
#include "apbs/vgreen.h"
#include "apbs/vcap.h"
#include "apbs/pbeparm.h"
#include "apbs/femparm.h"

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Data Structures

struct  sVfetk
 Contains public data members for Vfetk class/module. More...

struct  sVfetk_LocalVar
 Vfetk LocalVar subclass Contains variables used when solving the PDE with FEtk. More...


Typedefs

typedef enum eVfetk_LsolvType Vfetk_LsolvType
 Declare FEMparm_LsolvType type.

typedef enum eVfetk_NsolvType Vfetk_NsolvType
 Declare FEMparm_NsolvType type.

typedef enum eVfetk_GuessType Vfetk_GuessType
 Declare FEMparm_GuessType type.

typedef enum eVfetk_PrecType Vfetk_PrecType
 Declare FEMparm_GuessType type.

typedef sVfetk Vfetk
 Declaration of the Vfetk class as the Vfetk structure.

typedef sVfetk_LocalVar Vfetk_LocalVar
 Declaration of the Vfetk_LocalVar subclass as the Vfetk_LocalVar structure.


Enumerations

enum  eVfetk_LsolvType {
  VLT_SLU = 0,
  VLT_MG = 1,
  VLT_CG = 2,
  VLT_BCG = 3
}
 Linear solver type. More...

enum  eVfetk_NsolvType {
  VNT_NEW = 0,
  VNT_INC = 1,
  VNT_ARC = 2
}
 Non-linear solver type. More...

enum  eVfetk_GuessType {
  VGT_ZERO = 0,
  VGT_DIRI = 1,
  VGT_PREV = 2
}
 Initial guess type. More...

enum  eVfetk_PrecType {
  VPT_IDEN = 0,
  VPT_DIAG = 1,
  VPT_MG = 2
}
 Preconditioner type. More...


Functions

Gem * Vfetk_getGem (Vfetk *thee)
 Get a pointer to the Gem (grid manager) object.

AM * Vfetk_getAM (Vfetk *thee)
 Get a pointer to the AM (algebra manager) object.

VpbeVfetk_getVpbe (Vfetk *thee)
 Get a pointer to the Vpbe (PBE manager) object.

VcsmVfetk_getVcsm (Vfetk *thee)
 Get a pointer to the Vcsm (charge-simplex map) object.

int Vfetk_getAtomColor (Vfetk *thee, int iatom)
 Get the partition information for a particular atom.

VfetkVfetk_ctor (Vpbe *pbe, Vhal_PBEType type)
 Constructor for Vfetk object.

int Vfetk_ctor2 (Vfetk *thee, Vpbe *pbe, Vhal_PBEType type)
 FORTRAN stub constructor for Vfetk object.

void Vfetk_dtor (Vfetk **thee)
 Object destructor.

void Vfetk_dtor2 (Vfetk *thee)
 FORTRAN stub object destructor.

double * Vfetk_getSolution (Vfetk *thee, int *length)
 Create an array containing the solution (electrostatic potential in units of ) at the finest mesh level.

void Vfetk_setParameters (Vfetk *thee, PBEparm *pbeparm, FEMparm *feparm)
 Set the parameter objects.

double Vfetk_energy (Vfetk *thee, int color, int nonlin)
 Return the total electrostatic energy.

double Vfetk_dqmEnergy (Vfetk *thee, int color)
 Get the "mobile charge" and "polarization" contributions to the electrostatic energy.

double Vfetk_qfEnergy (Vfetk *thee, int color)
 Get the "fixed charge" contribution to the electrostatic energy.

double Vfetk_lnDet (Vfetk *thee, int color, int oflag, int mflag)
 Calculate the log determinant of the specified operator.

int Vfetk_memChk (Vfetk *thee)
 Return the memory used by this structure (and its contents) in bytes.

void Vfetk_setAtomColors (Vfetk *thee)
 Transfer color (partition ID) information frmo a partitioned mesh to the atoms.

void Bmat_printHB (Bmat *thee, char *fname)
 Writes a Bmat to disk in Harwell-Boeing sparse matrix format.

int Bmat_choleskyFactor (Bmat *thee, int flag)
 Assembles the Cholesky factorization of a Bmat.

double Mat_lnDetDiag (Mat *thee)
 Returns the log(abs(det(D))) of a diagonal Mat, D.

int Vfetk_genCube (Vfetk *thee, double center[3], double length[3])
 Generates a simple cubic tetrahedral mesh.

PDE * Vfetk_PDE_ctor (Vfetk *fetk)
 Constructs the FEtk PDE object.

int Vfetk_PDE_ctor2 (PDE *thee, Vfetk *fetk)
 Intializes the FEtk PDE object.

void Vfetk_PDE_dtor (PDE **thee)
 Destroys FEtk PDE object.

void Vfetk_PDE_dtor2 (PDE *thee)
 FORTRAN stub: destroys FEtk PDE object.

void Vfetk_PDE_initAssemble (PDE *thee, int ip[], double rp[])
 Do once-per-assembly initialization.

void Vfetk_PDE_initElement (PDE *thee, int elementType, int chart, double tvx[][3], void *data)
 Do once-per-element initialization.

void Vfetk_PDE_initFace (PDE *thee, int faceType, int chart, double tnvec[])
 Do once-per-face initialization.

void Vfetk_PDE_initPoint (PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3])
 Do once-per-point initialization.

void Vfetk_PDE_Fu (PDE *thee, int key, double F[])
 Evaluate strong form of PBE. For interior points, this is:

where is the (possibly nonlinear) mobile ion term and 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:

where 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.

double Vfetk_PDE_Fu_v (PDE *thee, int key, double V[], double dV[][3])
 This is the weak form of the PBE; i.e. the strong form integrated with a test function to give:

where denotes the mobile ion term.

double Vfetk_PDE_DFu_wv (PDE *thee, int key, double W[], double dW[][3], double V[], double dV[][3])
 This is the linearization of the weak form of the PBE; e.g., for use in a Newton iteration. This is the functional linearization of the strong form integrated with a test function to give:

where denotes the functional derivation of the mobile ion term.

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.

void Vfetk_PDE_u_D (PDE *thee, int type, int chart, double txq[], double F[])
 Evaluate the Dirichlet boundary condition at the given point.

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.

void Vfetk_PDE_bisectEdge (int dim, int dimII, int edgeType, int chart[], double vx[][3])
 Define the way manifold edges are bisected.

void Vfetk_PDE_mapBoundary (int dim, int dimII, int vertexType, int chart, double vx[3])
 Map a boundary point to some pre-defined shape.

int Vfetk_PDE_markSimplex (int dim, int dimII, int simplexType, int faceType[4], int vertexType[4], int chart[], double vx[][3], void *simplex)
 User-defined error estimator -- in our case, a geometry-based refinement method; forcing simplex refinement at the dielectric boundary and (for non-regularized PBE) the charges.

void Vfetk_PDE_oneChart (int dim, int dimII, int objType, int chart[], double vx[][3], int dimV)
 Unify the chart for different coordinate systems -- a no-op for us.

double Vfetk_PDE_Ju (PDE *thee, int key)
 Energy functional. This returns the energy (less delta function terms) in the form:

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

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).

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.

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.

void Vfetk_readMesh (Vfetk *thee, int skey, Vio *sock)
 Read in mesh and initialize associated internal structures.

void Vfetk_dumpLocalVar ()
 Debugging routine to print out local variables used by PDE object.

int Vfetk_fillArray (Vfetk *thee, Bvec *vec, Vdata_Type type)
 Fill an array with the specified data.

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.


Detailed Description

Contains declarations for class Vfetk.

Version:
Id:
vfetk.h,v 2.29 2004/01/19 21:01:36 apbs Exp
Author:
Nathan A. Baker
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) 2002-2004.  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
 *
 * 

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