diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp
index 46934f96e..af173115e 100644
--- a/src/fix_heat.cpp
+++ b/src/fix_heat.cpp
@@ -1,194 +1,259 @@
/* ----------------------------------------------------------------------
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};
+enum{CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal fix heat command");
scalar_flag = 1;
global_freq = 1;
extscalar = 0;
nevery = atoi(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]);
- hstyle = EQUAL;
} else {
heat_input = atof(arg[4]);
hstyle = CONSTANT;
}
// optional args
iregion = -1;
idregion = NULL;
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;
+ vheat = NULL;
}
/* ---------------------------------------------------------------------- */
FixHeat::~FixHeat()
{
delete [] hstr;
delete [] idregion;
+ memory->destroy(vheat);
}
/* ---------------------------------------------------------------------- */
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))
- error->all(FLERR,"Variable for fix heat is invalid style");
+ if (input->variable->equalstyle(hvar)) hstyle = EQUAL;
+ else if (input->variable->equalstyle(hvar)) hstyle = ATOM;
+ else error->all(FLERR,"Variable for fix heat is invalid style");
}
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Fix heat group has no atoms");
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void FixHeat::end_of_step()
{
+ int i;
double heat,ke;
double vsub[3],vcm[3];
- Region *region = NULL;
- if (iregion >= 0) region = domain->regions[iregion];
+ Region *region;
+
+ double **x = atom->x;
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- if (hstyle == EQUAL) {
+ // reallocate vheat array if necessary
+
+ if (hstyle == ATOM && atom->nlocal > maxatom) {
+ maxatom = atom->nmax;
+ memory->destroy(vheat);
+ memory->create(vheat,maxatom,"heat:vheat");
+ }
+
+ if (hstyle != CONSTANT) {
modify->clearstep_compute();
- heat_input = input->variable->compute_equal(hvar);
+
+ if (hstyle == EQUAL) heat_input = input->variable->compute_equal(hvar);
+ else {
+ input->variable->compute_atom(hvar,igroup,vheat,1,0);
+
+ double mine = 0.0;
+ if (iregion < 0) {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) mine += vheat[i];
+ } else {
+ region = domain->regions[iregion];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ mine += vheat[i];
+ }
+ MPI_Allreduce(&mine,&heat_input,1,MPI_DOUBLE,MPI_SUM,world);
+ }
+
modify->addstep_compute(update->ntimestep + nevery);
}
+ // vcm = center-of-mass velocity of scaled atoms
+ // scale = velocity scale factor to accomplish eflux change in energy
+ // vsub = ??? // NOTE: document this?
+
if (iregion < 0) {
heat = heat_input*nevery*update->dt*force->ftm2v;
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");
heat = heat_input*nevery*update->dt*force->ftm2v;
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];
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);
+ // NOTE: if hstyle = ATOM, do something different to compute vsub ??
+
vsub[0] = (scale-1.0) * vcm[0];
vsub[1] = (scale-1.0) * vcm[1];
vsub[2] = (scale-1.0) * vcm[2];
- double **x = atom->x;
- double **v = atom->v;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- if (iregion < 0) {
- for (int 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];
- }
+ // add heat via scale factor on velocities for CONSTANT and EQUAL cases
+
+ if (hstyle != ATOM) {
+ 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 {
+ region = domain->regions[iregion];
+ 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
+
} 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];
- }
+ if (iregion < 0) {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ scale = 0.0; // NOTE: set to per-atom value
+ 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 {
+ region = domain->regions[iregion];
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
+ scale = 0.0; // NOTE: set to per-atom value
+ 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()
{
+ // NOTE: what should this be for per-atom case?
+
return scale;
}
diff --git a/src/fix_heat.h b/src/fix_heat.h
index 4562ac9a9..35884704f 100644
--- a/src/fix_heat.h
+++ b/src/fix_heat.h
@@ -1,72 +1,75 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(heat,FixHeat)
#else
#ifndef LMP_FIX_HEAT_H
#define LMP_FIX_HEAT_H
#include "fix.h"
namespace LAMMPS_NS {
class FixHeat : public Fix {
public:
FixHeat(class LAMMPS *, int, char **);
~FixHeat();
int setmask();
void init();
void end_of_step();
double compute_scalar();
private:
int iregion;
double heat_input;
double masstotal;
double scale;
char *idregion;
char *hstr;
int hstyle,hvar;
+
+ int maxatom;
+ double *vheat;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Region ID for fix heat does not exist
Self-explanatory.
E: Fix heat group has no atoms
Self-explanatory.
E: Fix heat kinetic energy went negative
This will cause the velocity rescaling about to be performed by fix
heat to be invalid.
*/