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VPRIVATE void | polyEval (int numP, double p[], double c[][VMAXP], double xv[]) |
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VPUBLIC Gem * | Vfetk_getGem (Vfetk *thee) |
| Get a pointer to the Gem (grid manager) object. More...
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VPUBLIC AM * | Vfetk_getAM (Vfetk *thee) |
| Get a pointer to the AM (algebra manager) object. More...
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VPUBLIC Vpbe * | Vfetk_getVpbe (Vfetk *thee) |
| Get a pointer to the Vpbe (PBE manager) object. More...
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VPUBLIC Vcsm * | Vfetk_getVcsm (Vfetk *thee) |
| Get a pointer to the Vcsm (charge-simplex map) object. More...
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VPUBLIC int | Vfetk_getAtomColor (Vfetk *thee, int iatom) |
| Get the partition information for a particular atom. More...
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VPUBLIC Vfetk * | Vfetk_ctor (Vpbe *pbe, Vhal_PBEType type) |
| Constructor for Vfetk object. More...
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VPUBLIC int | Vfetk_ctor2 (Vfetk *thee, Vpbe *pbe, Vhal_PBEType type) |
| FORTRAN stub constructor for Vfetk object. More...
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VPUBLIC void | Vfetk_setParameters (Vfetk *thee, PBEparm *pbeparm, FEMparm *feparm) |
| Set the parameter objects. More...
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VPUBLIC void | Vfetk_dtor (Vfetk **thee) |
| Object destructor. More...
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VPUBLIC void | Vfetk_dtor2 (Vfetk *thee) |
| FORTRAN stub object destructor. More...
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VPUBLIC double * | Vfetk_getSolution (Vfetk *thee, int *length) |
| Create an array containing the solution (electrostatic potential in units of ) at the finest mesh level. More...
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VPUBLIC double | Vfetk_energy (Vfetk *thee, int color, int nonlin) |
| Return the total electrostatic energy. More...
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VPUBLIC double | Vfetk_qfEnergy (Vfetk *thee, int color) |
| Get the "fixed charge" contribution to the electrostatic energy. More...
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VPUBLIC double | Vfetk_dqmEnergy (Vfetk *thee, int color) |
| Get the "mobile charge" and "polarization" contributions to the electrostatic energy. More...
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VPUBLIC void | Vfetk_setAtomColors (Vfetk *thee) |
| Transfer color (partition ID) information frmo a partitioned mesh to the atoms. More...
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VPUBLIC unsigned long int | Vfetk_memChk (Vfetk *thee) |
| Return the memory used by this structure (and its contents) in bytes. More...
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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...
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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...
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VPUBLIC void | Bmat_printHB (Bmat *thee, char *fname) |
| Writes a Bmat to disk in Harwell-Boeing sparse matrix format. More...
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VPUBLIC PDE * | Vfetk_PDE_ctor (Vfetk *fetk) |
| Constructs the FEtk PDE object. More...
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VPUBLIC int | Vfetk_PDE_ctor2 (PDE *thee, Vfetk *fetk) |
| Intializes the FEtk PDE object. More...
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VPUBLIC void | Vfetk_PDE_dtor (PDE **thee) |
| Destroys FEtk PDE object. More...
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VPUBLIC void | Vfetk_PDE_dtor2 (PDE *thee) |
| FORTRAN stub: destroys FEtk PDE object. More...
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VPUBLIC void | Vfetk_PDE_initAssemble (PDE *thee, int ip[], double rp[]) |
| Do once-per-assembly initialization. More...
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VPUBLIC void | Vfetk_PDE_initElement (PDE *thee, int elementType, int chart, double tvx[][3], void *data) |
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VPUBLIC void | Vfetk_PDE_initFace (PDE *thee, int faceType, int chart, double tnvec[]) |
| Do once-per-face initialization. More...
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VPUBLIC void | Vfetk_PDE_initPoint (PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) |
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VPUBLIC void | Vfetk_PDE_Fu (PDE *thee, int key, double F[]) |
| Evaluate strong form of PBE. For interior points, this is: More...
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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: More...
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VPUBLIC double | Vfetk_PDE_DFu_wv (PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) |
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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...
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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...
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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...
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VPUBLIC void | Vfetk_PDE_bisectEdge (int dim, int dimII, int edgeType, int chart[], double vx[][3]) |
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VPUBLIC void | Vfetk_PDE_mapBoundary (int dim, int dimII, int vertexType, int chart, double vx[3]) |
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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) |
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VPUBLIC void | Vfetk_PDE_oneChart (int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) |
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VPUBLIC double | Vfetk_PDE_Ju (PDE *thee, int key) |
| Energy functional. This returns the energy (less delta function terms) in the form: More...
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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...
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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...
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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...
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VPUBLIC void | Vfetk_dumpLocalVar () |
| Debugging routine to print out local variables used by PDE object. More...
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VPUBLIC int | Vfetk_fillArray (Vfetk *thee, Bvec *vec, Vdata_Type type) |
| Fill an array with the specified data. More...
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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...
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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) 2010-2020 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) 2002-2020, 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.