Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/fix_group.cpp
fb6c2b60f942efficient_neuronet

Last Change
Raw File

fix_group.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <string.h>
#include "fix_group.h"
#include "group.h"
#include "update.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "region.h"
#include "modify.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixGroup::FixGroup(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
idregion(NULL), idvar(NULL)
{
// dgroupbit = bitmask of dynamic group
// group ID is last part of fix ID
int n = strlen(id) - strlen("GROUP_") + 1;
char *dgroup = new char[n];
strcpy(dgroup,&id[strlen("GROUP_")]);
gbit = group->bitmask[group->find(dgroup)];
gbitinverse = group->inversemask[group->find(dgroup)];
delete [] dgroup;
// process optional args
regionflag = 0;
varflag = 0;
nevery = 1;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
if (domain->find_region(arg[iarg+1]) < 0)
error->all(FLERR,"Region ID for group dynamic does not exist");
regionflag = 1;
delete [] idregion;
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"var") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
if (input->variable->find(arg[iarg+1]) < 0)
error->all(FLERR,"Variable name for group dynamic does not exist");
varflag = 1;
delete [] idvar;
int n = strlen(arg[iarg+1]) + 1;
idvar = new char[n];
strcpy(idvar,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery <= 0) error->all(FLERR,"Illegal group command");
iarg += 2;
} else error->all(FLERR,"Illegal group command");
}
}
/* ---------------------------------------------------------------------- */
FixGroup::~FixGroup()
{
delete [] idregion;
delete [] idvar;
}
/* ---------------------------------------------------------------------- */
int FixGroup::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGroup::init()
{
// parent group cannot be dynamic
// else order of FixGroup fixes would matter
if (group->dynamic[igroup])
error->all(FLERR,"Group dynamic parent group cannot be dynamic");
// set current indices for region and variable
if (regionflag) {
iregion = domain->find_region(idregion);
if (iregion < 0)
error->all(FLERR,"Region ID for group dynamic does not exist");
region = domain->regions[iregion];
}
if (varflag) {
ivar = input->variable->find(idvar);
if (ivar < 0)
error->all(FLERR,"Variable name for group dynamic does not exist");
if (!input->variable->atomstyle(ivar))
error->all(FLERR,"Variable for group dynamic is invalid style");
}
// warn if any FixGroup is not at tail end of all post_integrate fixes
Fix **fix = modify->fix;
int *fmask = modify->fmask;
int nfix = modify->nfix;
int n = 0;
for (int i = 0; i < nfix; i++) if (POST_INTEGRATE & fmask[i]) n++;
int warn = 0;
for (int i = 0; i < nfix; i++) {
if (POST_INTEGRATE & fmask[i]) {
for (int j = i+1; j < nfix; j++) {
if (POST_INTEGRATE & fmask[j]) {
if (strstr(fix[j]->id,"GROUP_") != fix[j]->id) warn = 1;
}
}
}
}
if (warn && comm->me == 0)
error->warning(FLERR,"One or more dynamic groups may not be "
"updated at correct point in timestep");
}
/* ----------------------------------------------------------------------
assign atoms to group
------------------------------------------------------------------------- */
void FixGroup::setup(int vflag)
{
set_group();
}
/* ---------------------------------------------------------------------- */
void FixGroup::post_integrate()
{
// only assign atoms to group on steps that are multiples of nevery
if (update->ntimestep % nevery == 0) set_group();
}
/* ---------------------------------------------------------------------- */
void FixGroup::set_group()
{
int nlocal = atom->nlocal;
// invoke atom-style variable if defined
double *var = NULL;
if (varflag) {
modify->clearstep_compute();
memory->create(var,nlocal,"fix/group:varvalue");
input->variable->compute_atom(ivar,igroup,var,1,0);
modify->addstep_compute(update->ntimestep + nevery);
}
// update region in case it has a variable dependence or is dynamic
if (regionflag) region->prematch();
// set mask for each atom
// only in group if in parent group, in region, variable is non-zero
// if compute, fix, etc needs updated masks of ghost atoms,
// it must do forward_comm() to update them
double **x = atom->x;
int *mask = atom->mask;
int inflag;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
inflag = 1;
if (regionflag && !region->match(x[i][0],x[i][1],x[i][2])) inflag = 0;
if (varflag && var[i] == 0.0) inflag = 0;
} else inflag = 0;
if (inflag) mask[i] |= gbit;
else mask[i] &= gbitinverse;
}
if (varflag) memory->destroy(var);
}
c4science · Help