vfetk.c File Reference

Class Vfetk methods. More...

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

Defines

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

Functions

VPUBLIC Gem * Vfetk_getGem (Vfetk *thee)
 Get a pointer to the Gem (grid manager) object.
VPUBLIC AM * Vfetk_getAM (Vfetk *thee)
 Get a pointer to the AM (algebra manager) object.
VPUBLIC Vpbe * Vfetk_getVpbe (Vfetk *thee)
 Get a pointer to the Vpbe (PBE manager) object.
VPUBLIC Vcsm * Vfetk_getVcsm (Vfetk *thee)
 Get a pointer to the Vcsm (charge-simplex map) object.
VPUBLIC int Vfetk_getAtomColor (Vfetk *thee, int iatom)
 Get the partition information for a particular atom.
VPUBLIC Vfetk * Vfetk_ctor (Vpbe *pbe, Vhal_PBEType type)
 Constructor for Vfetk object.
VPUBLIC int Vfetk_ctor2 (Vfetk *thee, Vpbe *pbe, Vhal_PBEType type)
 FORTRAN stub constructor for Vfetk object.
VPUBLIC void Vfetk_setParameters (Vfetk *thee, PBEparm *pbeparm, FEMparm *feparm)
 Set the parameter objects.
VPUBLIC void Vfetk_dtor (Vfetk **thee)
 Object destructor.
VPUBLIC void Vfetk_dtor2 (Vfetk *thee)
 FORTRAN stub object destructor.
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.
VPUBLIC double Vfetk_energy (Vfetk *thee, int color, int nonlin)
 Return the total electrostatic energy.
VPUBLIC double Vfetk_qfEnergy (Vfetk *thee, int color)
 Get the "fixed charge" contribution to the electrostatic energy.
VPUBLIC double Vfetk_dqmEnergy (Vfetk *thee, int color)
 Get the "mobile charge" and "polarization" contributions to the electrostatic energy.
VPUBLIC void Vfetk_setAtomColors (Vfetk *thee)
 Transfer color (partition ID) information frmo a partitioned mesh to the atoms.
VPUBLIC unsigned long int Vfetk_memChk (Vfetk *thee)
 Return the memory used by this structure (and its contents) in bytes.
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).
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).
VPUBLIC void Bmat_printHB (Bmat *thee, char *fname)
 Writes a Bmat to disk in Harwell-Boeing sparse matrix format.
VPUBLIC PDE * Vfetk_PDE_ctor (Vfetk *fetk)
 Constructs the FEtk PDE object.
VPUBLIC int Vfetk_PDE_ctor2 (PDE *thee, Vfetk *fetk)
 Intializes the FEtk PDE object.
VPUBLIC void Vfetk_PDE_dtor (PDE **thee)
 Destroys FEtk PDE object.
VPUBLIC void Vfetk_PDE_dtor2 (PDE *thee)
 FORTRAN stub: destroys FEtk PDE object.
VPUBLIC void Vfetk_PDE_initAssemble (PDE *thee, int ip[], double rp[])
 Do once-per-assembly initialization.
VPUBLIC void Vfetk_PDE_initFace (PDE *thee, int faceType, int chart, double tnvec[])
 Do once-per-face initialization.
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.

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.

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.
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.
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.
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.

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).
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.
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.
VPUBLIC void Vfetk_dumpLocalVar ()
 Debugging routine to print out local variables used by PDE object.
VPUBLIC int Vfetk_fillArray (Vfetk *thee, Bvec *vec, Vdata_Type type)
 Fill an array with the specified data.
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.

Detailed Description

Class Vfetk methods.

Author:
Nathan Baker
Version:
Id
vfetk.c 1490 2009-12-01 14:17:28Z sdg0919
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) 2002-2009, Washington University in St. Louis.
 * Portions Copyright (c) 2002-2009.  Nathan A. Baker
 * Portions Copyright (c) 1999-2002.  The Regents of the University of California.
 * Portions Copyright (c) 1995.  Michael Holst
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