myroutines.c File Reference

Class myroutines methods. More...

#include "mypde.h"
#include "mysolv.c"
#include "tsolve.c"
#include "mygrid.c"

Defines
#define	COULOM_COEF(TEMP, CHG, RAD, COEF)   COEF = 1.67149e+5*CHG/(80*TEMP*RAD)
#define	len_w   15
	define a brief formula for analytical calculations. swtich for debug . swtich for analytical calculation .
Functions
VPUBLIC void	MY_assemR (AM *thee, Bvec *u)
VPUBLIC void	MY_assem (AM *thee, int evalKey, Bvec *u, Bvec *f, int ip[], double rp[], double energies[], int ekeytol)
VPUBLIC int	MY_Solve (AM *am, Bvec *u, Bvec *w[], Vlparam *lparam)
VPUBLIC void	MY_lSolve (AM *thee, Vlparam *lparam)
VPUBLIC void	MY_write (AM *thee, Vlparam *lparam)
VPRIVATE void	PDE_readMesh (AM *am, char path[])
VPRIVATE Vatom *	Valist_getAtomStorage (Valist *thee, Vatom **plist, int *pnlist, int *pnatoms)
VPRIVATE int	Valist_setAtomArray (Valist *thee, Vatom **plist, int nlist, int natoms)
VPUBLIC int	PQR_input (AM *am, Valist *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
	Input the PQR file of a molecule.
VPUBLIC int	dPMF_input (AM *am, const char *iofil, const char *iofor, const char *thost, const char *filnam)
VPUBLIC void	dPMF_mapping (AM *am)
VPUBLIC int	PDE_input (AM *am, Vgrid *grid[], Vlparam *lparam)
VPUBLIC Vlparam *	lparam_ctor ()
VPUBLIC void	lparam_dtor (Vlparam *thee)
Variables
VPRIVATE Bvec *	w [len_w]
	the number of the temporary vectors for solving Au=f.
VPRIVATE int	winuse

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Detailed Description

Class myroutines methods.

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

Author:

Yuhui Cheng, modified after Michael Holst, Nathan Baker, Kaihsu Tai & Jason Suen.

Version:

Id

myroutines.c 1046 2007-07-10 16:58:40Z sobolevnrm

Attention:

 *
 * 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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Function Documentation

VPUBLIC void MY_assemR (  AM *  thee, Bvec *  u )

User-provided surface and volume integrals.

VPUBLIC void MY_lSolve (  AM *  thee, Vlparam *  lparam )

*************************************************************************** Routine: MY_lSolve Purpose: Modified linear solver. Author: Jason Suen, followed Michael Holst *************************************************************************** assembly parameters some i/o make sure we have structure setup for assembling either primal or dual problem < forward (primal) problem (linearized about 0) < backward (dual) problem (linearized about 0) initial guess clear the matrix, rhs, residual assemble the stiffness matrix and load vector return with no errors

VPUBLIC int MY_Solve (  AM *  am, Bvec *  u, Bvec *  w[], Vlparam *  lparam )

the subroutine to solve Au=f. method choice (0=slu,1=mg,2=cg,3=bcg,4=bcg,5=bcgstab,6=continuation) primary methods

VPUBLIC void MY_write (  AM *  thee, Vlparam *  lparam )

output control which allows the use to write the vector u(x) in the desired format. format choice (1=GV,2=GMV,3=DX,4=UCD,5=TEC)

VPUBLIC int PQR_input (  AM *  am, Valist *  thee, const char *  iodev, const char *  iofmt, const char *  thost, const char *  fname )

Input the PQR file of a molecule. Author: Yuhui Cheng < PQR file pointer < To hold lines from the PQR file Counters Information to be gleaned from PQR file Make sure we're reading in an ASCII file Open data files Now we read some lines and count the atoms. Check to see if we got an ATOM line Allocate the necessary space for the atom array Rewind the file pointer (use rewind to clear the error indicator, too) Check to see if we got an ATOM line Try to parse a line without chain IDs and with a string residue ID Get pointer to next available atom position Put it in the atom list Have we gotten all the entries? Assign charges and radii to atom vertices

VPRIVATE Vatom* Valist_getAtomStorage (  Valist *  thee, Vatom **  plist, int *  pnlist, int *  pnatoms )

See if we need more space Double the storage space Check the allocation Copy the atoms over Get the next available spot and increment counters Parameters: plist  Pointer to existing list of atoms pnlist  Size of existing list, may be changed pnatoms  Existing number of atoms in list; incremented before exit

VPRIVATE int Valist_setAtomArray (  Valist *  thee, Vatom **  plist, int  nlist, int  natoms )

Copy over data Free old array Parameters: plist  Pointer to list of atoms to store nlist  Length of list natoms  Number of real atom entries in list

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