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lammps/src/fix_heat.cpp
Axel Kohlmeyer 0034d2db35 apply the rigid body checks to some more example codes
2017-06-05 16:30:30 -04:00

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_heat.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
idregion(NULL), hstr(NULL), vheat(NULL), vscale(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix heat command");
scalar_flag = 1;
global_freq = 1;
extscalar = 0;
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix heat command");
hstr = NULL;
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(&arg[4][2]) + 1;
hstr = new char[n];
strcpy(hstr,&arg[4][2]);
} else {
heat_input = force->numeric(FLERR,arg[4]);
hstyle = CONSTANT;
}
// optional args
iregion = -1;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix heat command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix heat does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix heat command");
}
scale = 1.0;
maxatom = 0;
}
/* ---------------------------------------------------------------------- */
FixHeat::~FixHeat()
{
delete [] hstr;
delete [] idregion;
memory->destroy(vheat);
memory->destroy(vscale);
}
/* ---------------------------------------------------------------------- */
int FixHeat::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixHeat::init()
{
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix heat does not exist");
}
// check variable
if (hstr) {
hvar = input->variable->find(hstr);
if (hvar < 0)
error->all(FLERR,"Variable name for fix heat does not exist");
if (input->variable->equalstyle(hvar)) hstyle = EQUAL;
else if (input->variable->atomstyle(hvar)) hstyle = ATOM;
else error->all(FLERR,"Variable for fix heat is invalid style");
}
// check for rigid bodies in region (done here for performance reasons)
if (modify->check_rigid_region_overlap(groupbit,domain->regions[iregion]))
error->warning(FLERR,"Cannot apply fix heat to atoms in rigid bodies");
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Fix heat group has no atoms");
masstotal = group->mass(igroup);
if (masstotal <= 0.0)
error->all(FLERR,"Fix heat group has invalid mass");
}
/* ---------------------------------------------------------------------- */
void FixHeat::end_of_step()
{
int i;
double heat,ke,massone;
double vsub[3],vcm[3];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
// reallocate per-atom arrays if necessary
if (hstyle == ATOM && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(vheat);
memory->destroy(vscale);
memory->create(vheat,maxatom,"heat:vheat");
memory->create(vscale,maxatom,"heat:vscale");
}
// evaluate variable
if (hstyle != CONSTANT) {
modify->clearstep_compute();
if (hstyle == EQUAL) heat_input = input->variable->compute_equal(hvar);
else input->variable->compute_atom(hvar,igroup,vheat,1,0);
modify->addstep_compute(update->ntimestep + nevery);
}
// vcm = center-of-mass velocity of scaled atoms
if (iregion < 0) {
ke = group->ke(igroup)*force->ftm2v;
group->vcm(igroup,masstotal,vcm);
} else {
masstotal = group->mass(igroup,iregion);
if (masstotal == 0.0) error->all(FLERR,"Fix heat group has no atoms");
ke = group->ke(igroup,iregion)*force->ftm2v;
group->vcm(igroup,masstotal,vcm,iregion);
}
double vcmsq = vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2];
// add heat via scale factor on velocities for CONSTANT and EQUAL cases
// scale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// overall KE cannot go negative
Region *region = NULL;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
if (hstyle != ATOM) {
heat = heat_input*nevery*update->dt*force->ftm2v;
double escale =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (escale < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(escale);
vsub[0] = (scale-1.0) * vcm[0];
vsub[1] = (scale-1.0) * vcm[1];
vsub[2] = (scale-1.0) * vcm[2];
if (iregion < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];
}
}
// add heat via per-atom scale factor on velocities for ATOM case
// vscale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// KE of an atom cannot go negative
} else {
vsub[0] = vsub[1] = vsub[2] = 0.0;
if (iregion < 0) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
heat = vheat[i]*nevery*update->dt*force->ftm2v;
vscale[i] =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (vscale[i] < 0.0)
error->all(FLERR,
"Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vsub[0] += (scale-1.0) * v[i][0]*massone;
vsub[1] += (scale-1.0) * v[i][1]*massone;
vsub[2] += (scale-1.0) * v[i][2]*massone;
}
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
scale = sqrt(vscale[i]);
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];
}
} else {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
heat = vheat[i]*nevery*update->dt*force->ftm2v;
vscale[i] =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (vscale[i] < 0.0)
error->all(FLERR,
"Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vsub[0] += (scale-1.0) * v[i][0]*massone;
vsub[1] += (scale-1.0) * v[i][1]*massone;
vsub[2] += (scale-1.0) * v[i][2]*massone;
}
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
scale = sqrt(vscale[i]);
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];
}
}
}
}
/* ---------------------------------------------------------------------- */
double FixHeat::compute_scalar()
{
double average_scale = scale;
if (hstyle == ATOM) {
double scale_sum = 0.0;
int ncount = 0;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
if (iregion < 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
scale_sum += sqrt(vscale[i]);
ncount++;
}
}
} else {
Region *region = domain->regions[iregion];
region->prematch();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
scale_sum += sqrt(vscale[i]);
ncount++;
}
}
}
double scale_sum_all = 0.0;
int ncount_all = 0;
MPI_Allreduce(&scale_sum,&scale_sum_all,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&ncount,&ncount_all,1,MPI_INT,MPI_SUM,world);
if (ncount_all == 0) average_scale = 0.0;
else average_scale = scale_sum_all/static_cast<double>(ncount_all);
}
return average_scale;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixHeat::memory_usage()
{
double bytes = 0.0;
if (hstyle == ATOM) bytes = atom->nmax*2 * sizeof(double);
return bytes;
}
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