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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 "string.h"
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#include "fix_group.h"
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#include "group.h"
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#include "update.h"
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#include "atom.h"
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#include "force.h"
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#include "comm.h"
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#include "domain.h"
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#include "region.h"
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#include "modify.h"
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#include "input.h"
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#include "variable.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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/* ---------------------------------------------------------------------- */
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FixGroup::FixGroup(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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// dgroupbit = bitmask of dynamic group
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// group ID is last part of fix ID
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int n = strlen(id) - strlen("GROUP_") + 1;
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char *dgroup = new char[n];
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strcpy(dgroup,&id[strlen("GROUP_")]);
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gbit = group->bitmask[group->find(dgroup)];
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gbitinverse = group->inversemask[group->find(dgroup)];
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delete [] dgroup;
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// process optional args
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regionflag = 0;
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idregion = NULL;
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varflag = 0;
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idvar = NULL;
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nevery = 1;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
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if (domain->find_region(arg[iarg+1]) < 0)
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error->all(FLERR,"Region ID for group dynamic does not exist");
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regionflag = 1;
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delete [] idregion;
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int n = strlen(arg[iarg+1]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"var") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
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if (input->variable->find(arg[iarg+1]) < 0)
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error->all(FLERR,"Variable name for group dynamic does not exist");
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varflag = 1;
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delete [] idvar;
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int n = strlen(arg[iarg+1]) + 1;
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idvar = new char[n];
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strcpy(idvar,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"every") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
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nevery = force->inumeric(FLERR,arg[iarg+1]);
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if (nevery <= 0) error->all(FLERR,"Illegal group command");
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iarg += 2;
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} else error->all(FLERR,"Illegal group command");
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}
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}
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/* ---------------------------------------------------------------------- */
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FixGroup::~FixGroup()
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{
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delete [] idregion;
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delete [] idvar;
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}
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/* ---------------------------------------------------------------------- */
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int FixGroup::setmask()
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{
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int mask = 0;
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mask |= POST_INTEGRATE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixGroup::init()
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{
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// parent group cannot be dynamic
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// else order of FixGroup fixes would matter
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if (group->dynamic[igroup])
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error->all(FLERR,"Group dynamic parent group cannot be dynamic");
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// set current indices for region and variable
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if (regionflag) {
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iregion = domain->find_region(idregion);
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if (iregion < 0)
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error->all(FLERR,"Region ID for group dynamic does not exist");
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region = domain->regions[iregion];
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}
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if (varflag) {
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ivar = input->variable->find(idvar);
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if (ivar < 0)
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error->all(FLERR,"Variable name for group dynamic does not exist");
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if (!input->variable->atomstyle(ivar))
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error->all(FLERR,"Variable for group dynamic is invalid style");
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}
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// warn if any FixGroup is not at tail end of all post_integrate fixes
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Fix **fix = modify->fix;
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int *fmask = modify->fmask;
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int nfix = modify->nfix;
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int n = 0;
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for (int i = 0; i < nfix; i++) if (POST_INTEGRATE & fmask[i]) n++;
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int warn = 0;
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for (int i = 0; i < nfix; i++) {
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if (POST_INTEGRATE & fmask[i]) {
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for (int j = i+1; j < nfix; j++) {
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if (POST_INTEGRATE & fmask[j]) {
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if (strstr(fix[j]->id,"GROUP_") != fix[j]->id) warn = 1;
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}
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}
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}
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}
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if (warn && comm->me == 0)
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error->warning(FLERR,"One or more dynamic groups may not be "
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"updated at correct point in timestep");
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}
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/* ----------------------------------------------------------------------
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assign atoms to group
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------------------------------------------------------------------------- */
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void FixGroup::setup(int vflag)
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{
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set_group();
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}
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/* ---------------------------------------------------------------------- */
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void FixGroup::post_integrate()
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{
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// only assign atoms to group on steps that are multiples of nevery
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if (update->ntimestep % nevery == 0) set_group();
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}
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/* ---------------------------------------------------------------------- */
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void FixGroup::set_group()
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{
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int nlocal = atom->nlocal;
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// invoke atom-style variable if defined
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double *var = NULL;
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if (varflag) {
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modify->clearstep_compute();
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memory->create(var,nlocal,"fix/group:varvalue");
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input->variable->compute_atom(ivar,igroup,var,1,0);
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modify->addstep_compute(update->ntimestep + nevery);
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}
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// set mask for each atom
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// only in group if in parent group, in region, variable is non-zero
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double **x = atom->x;
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int *mask = atom->mask;
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int inflag;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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inflag = 1;
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if (regionflag && !region->match(x[i][0],x[i][1],x[i][2])) inflag = 0;
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if (varflag && var[i] == 0.0) inflag = 0;
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} else inflag = 0;
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if (inflag) mask[i] |= gbit;
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else mask[i] &= gbitinverse;
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}
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if (varflag) memory->destroy(var);
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}
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@ -0,0 +1,53 @@
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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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#ifdef FIX_CLASS
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FixStyle(GROUP,FixGroup)
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#else
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#ifndef LMP_FIX_GROUP_H
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#define LMP_FIX_GROUP_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixGroup : public Fix {
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public:
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FixGroup(class LAMMPS *, int, char **);
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~FixGroup();
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int setmask();
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void init();
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void setup(int);
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void post_integrate();
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private:
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int gbit,gbitinverse;
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int regionflag,varflag;
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int iregion,ivar;
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char *idregion,*idvar;
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class Region *region;
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void set_group();
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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*/
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