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. More... | |
Typedefs | |
| typedef enum eVfetk_LsolvType | Vfetk_LsolvType |
| Declare FEMparm_LsolvType type. | |
| typedef enum eVfetk_MeshLoad | Vfetk_MeshLoad |
| Declare FEMparm_GuessType 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 struct sVfetk | Vfetk |
| Declaration of the Vfetk class as the Vfetk structure. | |
| typedef struct 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_MeshLoad { VML_DIRICUBE, VML_NEUMCUBE, VML_EXTERNAL } |
Mesh loading operation. 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. | |
| Vrc_Codes | Vfetk_genCube (Vfetk *thee, double center[3], double length[3], Vfetk_MeshLoad meshType) |
| Construct a rectangular mesh (in the current Vfetk object). | |
| 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). | |
| 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. | |
| Vrc_Codes | Vfetk_loadGem (Vfetk *thee, Gem *gm) |
| Load a Gem geometry manager object into Vfetk. | |
![\[ -\nabla \cdot \epsilon \nabla u + b(u) - f \]](form_56.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_59.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_61.png)
![\[ \int_\Omega \left[ \epsilon \nabla w \cdot \nabla v + b'(u) w v - f v \right] dx \]](form_62.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_64.png)
is the output from Vpbe_getZmagic. Detailed Description
Contains declarations for class Vfetk.
- Version:
- Id
- vfetk.h 1350 2009-02-12 00:38:48Z yhuang01
- 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 * * 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 Washington University in St. Louis 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. * *
