#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. | |
| Vpbe * | Vfetk_getVpbe (Vfetk *thee) |
| Get a pointer to the Vpbe (PBE manager) object. | |
| Vcsm * | Vfetk_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. | |
| Vfetk * | Vfetk_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. | |
| unsigned long 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 | Vfetk_genCube (Vfetk *thee, double center[VAPBS_DIM], double length[VAPBS_DIM]) |
| 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[][VAPBS_DIM], 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[][VAPBS_DIM]) |
| 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
where | |
| 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:
| |
| double | Vfetk_PDE_DFu_wv (PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][VAPBS_DIM]) |
| 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 | |
| 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[][VAPBS_DIM]) |
| Define the way manifold edges are bisected. | |
| void | Vfetk_PDE_mapBoundary (int dim, int dimII, int vertexType, int chart, double vx[VAPBS_DIM]) |
| Map a boundary point to some pre-defined shape. | |
| int | Vfetk_PDE_markSimplex (int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][VAPBS_DIM], 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[][VAPBS_DIM], 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 | |
| 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. | |
* * 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) 2002-2005. 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 * *
1.3.5
![\[ -\nabla \cdot \epsilon \nabla u + b(u) - f \]](form_61.png)
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: ![\[ [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^+} - [\epsilon(x) \nabla u(x) \cdot n(x)]_{x=0^-} \]](form_64.png)
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. ![\[ \int_\Omega \left[ \epsilon \nabla u \cdot \nabla v + b(u) v - f v \right] dx \]](form_66.png)
![\[ \int_\Omega \left[ \epsilon \nabla w \cdot \nabla v + b'(u) w v - f v \right] dx \]](form_67.png)
denotes the functional derivation of the mobile ion term. ![\[ c^{-1}/2 \int (\epsilon (\nabla u)^2 + \kappa^2 (cosh u - 1)) dx \]](form_69.png)
is the output from Vpbe_getZmagic.