git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10367 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_adapt.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "force.h"
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#include "pair.h"
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#include "pair_hybrid.h"
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#include "kspace.h"
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#include "input.h"
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#include "variable.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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using namespace MathConst;
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enum{PAIR,KSPACE,ATOM};
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enum{DIAMETER,CHARGE};
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/* ---------------------------------------------------------------------- */
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FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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if (narg < 5) error->all(FLERR,"Illegal fix adapt command");
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nevery = force->inumeric(FLERR,arg[3]);
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if (nevery < 0) error->all(FLERR,"Illegal fix adapt command");
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// count # of adaptations
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nadapt = 0;
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int iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"pair") == 0) {
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if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 6;
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} else if (strcmp(arg[iarg],"kspace") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 2;
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} else if (strcmp(arg[iarg],"atom") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 3;
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} else break;
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}
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if (nadapt == 0) error->all(FLERR,"Illegal fix adapt command");
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adapt = new Adapt[nadapt];
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// parse keywords
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nadapt = 0;
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diamflag = 0;
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chgflag = 0;
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iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"pair") == 0) {
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if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
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adapt[nadapt].which = PAIR;
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int n = strlen(arg[iarg+1]) + 1;
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adapt[nadapt].pstyle = new char[n];
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strcpy(adapt[nadapt].pstyle,arg[iarg+1]);
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n = strlen(arg[iarg+2]) + 1;
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adapt[nadapt].pparam = new char[n];
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strcpy(adapt[nadapt].pparam,arg[iarg+2]);
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force->bounds(arg[iarg+3],atom->ntypes,
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adapt[nadapt].ilo,adapt[nadapt].ihi);
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force->bounds(arg[iarg+4],atom->ntypes,
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adapt[nadapt].jlo,adapt[nadapt].jhi);
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if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
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n = strlen(&arg[iarg+5][2]) + 1;
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adapt[nadapt].var = new char[n];
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strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
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} else error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 6;
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} else if (strcmp(arg[iarg],"kspace") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
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adapt[nadapt].which = KSPACE;
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if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
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int n = strlen(&arg[iarg+1][2]) + 1;
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adapt[nadapt].var = new char[n];
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strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
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} else error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 2;
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} else if (strcmp(arg[iarg],"atom") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
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adapt[nadapt].which = ATOM;
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if (strcmp(arg[iarg+1],"diameter") == 0) {
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adapt[nadapt].aparam = DIAMETER;
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diamflag = 1;
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} else if (strcmp(arg[iarg+1],"charge") == 0) {
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adapt[nadapt].aparam = CHARGE;
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chgflag = 1;
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} else error->all(FLERR,"Illegal fix adapt command");
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if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
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int n = strlen(&arg[iarg+2][2]) + 1;
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adapt[nadapt].var = new char[n];
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strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
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} else error->all(FLERR,"Illegal fix adapt command");
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nadapt++;
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iarg += 3;
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} else break;
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}
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// optional keywords
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resetflag = 0;
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scaleflag = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"reset") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
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if (strcmp(arg[iarg+1],"no") == 0) resetflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) resetflag = 1;
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else error->all(FLERR,"Illegal fix adapt command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"scale") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
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if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1;
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else error->all(FLERR,"Illegal fix adapt command");
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iarg += 2;
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} else error->all(FLERR,"Illegal fix adapt command");
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}
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// allocate pair style arrays
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int n = atom->ntypes;
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for (int m = 0; m < nadapt; m++)
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if (adapt[m].which == PAIR)
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memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
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}
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/* ---------------------------------------------------------------------- */
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FixAdapt::~FixAdapt()
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{
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for (int m = 0; m < nadapt; m++) {
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delete [] adapt[m].var;
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if (adapt[m].which == PAIR) {
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delete [] adapt[m].pstyle;
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delete [] adapt[m].pparam;
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memory->destroy(adapt[m].array_orig);
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}
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}
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delete [] adapt;
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}
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/* ---------------------------------------------------------------------- */
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int FixAdapt::setmask()
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{
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int mask = 0;
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mask |= PRE_FORCE;
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mask |= POST_RUN;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixAdapt::init()
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{
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int i,j;
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// setup and error checks
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anypair = 0;
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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ad->ivar = input->variable->find(ad->var);
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if (ad->ivar < 0)
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error->all(FLERR,"Variable name for fix adapt does not exist");
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if (!input->variable->equalstyle(ad->ivar))
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error->all(FLERR,"Variable for fix adapt is invalid style");
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if (ad->which == PAIR) {
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anypair = 1;
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Pair *pair = force->pair_match(ad->pstyle,1);
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if (pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
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void *ptr = pair->extract(ad->pparam,ad->pdim);
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if (ptr == NULL)
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error->all(FLERR,"Fix adapt pair style param not supported");
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ad->pdim = 2;
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if (ad->pdim == 0) ad->scalar = (double *) ptr;
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if (ad->pdim == 2) ad->array = (double **) ptr;
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// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
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if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
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strcmp(force->pair_style,"hybrid/overlay") == 0)) {
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PairHybrid *pair = (PairHybrid *) force->pair;
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for (i = ad->ilo; i <= ad->ihi; i++)
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for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
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if (!pair->check_ijtype(i,j,ad->pstyle))
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error->all(FLERR,"Fix adapt type pair range is not valid for "
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"pair hybrid sub-style");
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}
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} else if (ad->which == KSPACE) {
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if (force->kspace == NULL)
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error->all(FLERR,"Fix adapt kspace style does not exist");
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kspace_scale = (double *) force->kspace->extract("scale");
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} else if (ad->which == ATOM) {
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if (ad->aparam == DIAMETER) {
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if (!atom->radius_flag)
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error->all(FLERR,"Fix adapt requires atom attribute diameter");
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}
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if (ad->aparam == CHARGE) {
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if (!atom->q_flag)
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error->all(FLERR,"Fix adapt requires atom attribute charge");
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}
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}
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}
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// make copy of original pair array values
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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if (ad->which == PAIR && ad->pdim == 2) {
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for (i = ad->ilo; i <= ad->ihi; i++)
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for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
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ad->array_orig[i][j] = ad->array[i][j];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixAdapt::setup_pre_force(int vflag)
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{
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change_settings();
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}
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/* ---------------------------------------------------------------------- */
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void FixAdapt::pre_force(int vflag)
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{
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if (nevery == 0) return;
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if (update->ntimestep % nevery) return;
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change_settings();
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}
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/* ---------------------------------------------------------------------- */
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void FixAdapt::post_run()
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{
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if (resetflag) restore_settings();
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}
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/* ----------------------------------------------------------------------
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change pair,kspace,atom parameters based on variable evaluation
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------------------------------------------------------------------------- */
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void FixAdapt::change_settings()
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{
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int i,j;
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// variable evaluation may invoke computes so wrap with clear/add
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modify->clearstep_compute();
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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double value = input->variable->compute_equal(ad->ivar);
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// set global scalar or type pair array values
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if (ad->which == PAIR) {
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if (ad->pdim == 0) {
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if (scaleflag) *ad->scalar = value * ad->scalar_orig;
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else *ad->scalar = value;
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} else if (ad->pdim == 2) {
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if (scaleflag)
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for (i = ad->ilo; i <= ad->ihi; i++)
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for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
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ad->array[i][j] = value*ad->array_orig[i][j];
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else
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for (i = ad->ilo; i <= ad->ihi; i++)
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for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
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ad->array[i][j] = value;
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}
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// set kspace scale factor
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} else if (ad->which == KSPACE) {
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*kspace_scale = value;
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} else if (ad->which == ATOM) {
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// set radius from diameter
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// also scale rmass to new value
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if (ad->aparam == DIAMETER) {
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int mflag = 0;
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if (atom->rmass_flag) mflag = 1;
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double density;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (mflag == 0) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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radius[i] = 0.5*value;
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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density = rmass[i] / (4.0*MY_PI/3.0 *
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radius[i]*radius[i]*radius[i]);
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radius[i] = 0.5*value;
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rmass[i] = 4.0*MY_PI/3.0 *
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radius[i]*radius[i]*radius[i] * density;
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}
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}
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} else if (ad->aparam == CHARGE) {
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double *q = atom->q;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) q[i] = value;
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}
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}
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}
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modify->addstep_compute(update->ntimestep + nevery);
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// re-initialize pair styles if any PAIR settings were changed
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// this resets other coeffs that may depend on changed values,
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// and also offset and tail corrections
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if (anypair) force->pair->reinit();
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}
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/* ----------------------------------------------------------------------
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restore pair,kspace.atom parameters to original values
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------------------------------------------------------------------------- */
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void FixAdapt::restore_settings()
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{
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for (int m = 0; m < nadapt; m++) {
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Adapt *ad = &adapt[m];
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if (ad->which == PAIR) {
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if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
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else if (ad->pdim == 2) {
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for (int i = ad->ilo; i <= ad->ihi; i++)
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for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
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ad->array[i][j] = ad->array_orig[i][j];
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}
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} else if (ad->which == KSPACE) {
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*kspace_scale = 1.0;
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} else if (ad->which == ATOM) {
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}
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}
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if (anypair) force->pair->reinit();
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}
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