Defines | |
| #define | VGRID_DIGITS 6 |
| Number of decimal places for comparisons and formatting. | |
| #define | IJK(i, j, k) (((k)*(nx)*(ny))+((j)*(nx))+(i)) |
Functions | |
| VPRIVATE int | Vgrid_buildBasis (double x, double x0, double hx, int imax, int loc[3], double phi[3], double phix[3], double phixx[3]) |
| VPRIVATE int | Vgrid_eval (Vgrid *thee, double pt[3], double *value, double grad[3], double curv[3]) |
| VPUBLIC int | Vmgrid_eval (Vmgrid *thee, double pt[3], double *value, double grad[3], double curv[3]) |
| VPRIVATE int | Vgrid_val (Vgrid *thee, double pt[3], double *value) |
| Get potential value (from mesh or approximation) at a point. | |
| VPRIVATE int | Vgrid_curv (Vgrid *thee, double pt[3], double curv[3]) |
| Get potential gradient (from mesh or approximation) at a point. | |
| VPUBLIC int | Vmgrid_curv (Vmgrid *thee, double pt[3], double curv[3]) |
Variables | |
| VPRIVATE double | Vcompare |
Problem type: time-dependent, Diffusion-reaction Spatial dimension: 2 or 3 Product dimension: 1 Differential operator: Linear or nonlinear potential equation with symmetric or nonsymmetric linear part Boundary conditions: zero or nonzero Dirichlet conditions nonzero or zero Neumann/Robin conditions
Note: Equation for component i is defined as
sum(del(A_ij del(u_j))) = B_i in omega -n dot sum(A_ij del(u_j)) = C_i along natural boundaries
_____ \ ____ ____ \ \ /. A_ij \ / u_j = B_i in omega / \/ \/ /____ j
____ \ ____ \ -n . A_ij \ / u_j = C_i along natural boundaries / \/ /___ j
* * SMOL -- Adaptive Smoluchowski Solver * * Yuhui Cheng (ycheng@mccammon.ucsd.edu) * Dept. of Chemistry and Biochemistry * University of California, San Diego * * Additional contributing authors listed in the code documentation. * * * Copyright (c) 2006-2007. University of California, San Diego * All Rights Reserved. * Portions Copyright (c) 1995. Michael Holst. * * This file is part of SMOL. * * SMOL 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. * * SMOL 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 SMOL; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 * USA * * * Linking SMOL statically or dynamically with other modules is making a * combined work based on SMOL. Thus, the terms and conditions of the * GNU * General Public License cover the whole combination. * * SPECIAL GPL EXCEPTION * In addition, as a special exception, the copyright holders of SMOL * give you permission to combine the SMOL program with free software * programs and libraries that are released under the GNU LGPL or with * code included in releases of ISIM, Ion Simulator Interface, PMV, * PyMOL * VMD, and Vision. Such combined software may be linked with SMOL * and * redistributed together in original or modified form as mere * aggregation * without requirement that the entire work be under the scope of the * GNU * General Public License. This special exception permission is also * extended * to any software listed in the SPECIAL GPL EXCEPTION clauses by the * FEtk, MC, or MALOC libraries. * * Note that people who make modified versions of SMOL are not obligated * to grant this special exception for their modified versions; it is * their choice whether to do so. The GNU General Public License gives * permission to release a modified version without this exception; this * exception also makes it possible to release a modified version which * carries forward this exception. * *
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Get potential gradient (from mesh or approximation) at a point.
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Get potential value (from mesh or approximation) at a point.
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1.3.9.1