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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10319 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-07-24 14:15:39 +00:00
parent 6884feef2c
commit 8bcd618af1
1 changed files with 43 additions and 21 deletions
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56
src/compute_temp_profile.cpp
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@ -52,6 +52,7 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
if (xflag) ivx = ncount++; if (xflag) ivx = ncount++;
if (yflag) ivy = ncount++; if (yflag) ivy = ncount++;
if (zflag) ivz = ncount++; if (zflag) ivz = ncount++;
ncount += 2;
nbinx = nbiny = nbinz = 1; nbinx = nbiny = nbinz = 1;
int lastarg; int lastarg;
@ -120,8 +121,8 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
nbins = nbinx*nbiny*nbinz; nbins = nbinx*nbiny*nbinz;
if (nbins <= 0) error->all(FLERR,"Illegal compute temp/profile command"); if (nbins <= 0) error->all(FLERR,"Illegal compute temp/profile command");
memory->create(vbin,nbins,ncount+1,"temp/profile:vbin"); memory->create(vbin,nbins,ncount,"temp/profile:vbin");
memory->create(binave,nbins,ncount+1,"temp/profile:binave"); memory->create(binave,nbins,ncount,"temp/profile:binave");
if (outflag == TENSOR) { if (outflag == TENSOR) {
vector_flag = 1; vector_flag = 1;
@ -337,7 +338,7 @@ void ComputeTempProfile::compute_array()
int nper = domain->dimension; int nper = domain->dimension;
for (i = 0; i < nbins; i++) { for (i = 0; i < nbins; i++) {
array[i][0] = binave[i][ncount]; array[i][0] = binave[i][ncount-1];
if (array[i][0] > 0.0) { if (array[i][0] > 0.0) {
dof = nper*array[i][0] - extra_dof; dof = nper*array[i][0] - extra_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
@ -414,7 +415,7 @@ void ComputeTempProfile::restore_bias_all()
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
compute average velocity in each bin compute average COM velocity in each bin
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void ComputeTempProfile::bin_average() void ComputeTempProfile::bin_average()
@ -424,37 +425,58 @@ void ComputeTempProfile::bin_average()
if (box_change) bin_setup(); if (box_change) bin_setup();
bin_assign(); bin_assign();
// clear bins, including particle count // clear bins, including particle mass and count
for (i = 0; i < nbins; i++) for (i = 0; i < nbins; i++)
for (j = 0; j <= ncount; j++) for (j = 0; j < ncount; j++)
vbin[i][j] = 0.0; vbin[i][j] = 0.0;
// sum each particle's velocity to appropriate bin // sum each particle's mass-weighted velocity, mass, count to appropriate bin
double **v = atom->v; double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask; int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int nc2 = ncount-2;
int nc1 = ncount-1;
if (rmass) {
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
ibin = bin[i]; ibin = bin[i];
if (xflag) vbin[ibin][ivx] += v[i][0]; if (xflag) vbin[ibin][ivx] += rmass[i]*v[i][0];
if (yflag) vbin[ibin][ivy] += v[i][1]; if (yflag) vbin[ibin][ivy] += rmass[i]*v[i][1];
if (zflag) vbin[ibin][ivz] += v[i][2]; if (zflag) vbin[ibin][ivz] += rmass[i]*v[i][2];
vbin[ibin][ncount] += 1.0; vbin[ibin][nc2] += rmass[i];
vbin[ibin][nc1] += 1.0;
}
} else {
double onemass;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
ibin = bin[i];
onemass = mass[type[i]];
if (xflag) vbin[ibin][ivx] += onemass*v[i][0];
if (yflag) vbin[ibin][ivy] += onemass*v[i][1];
if (zflag) vbin[ibin][ivz] += onemass*v[i][2];
vbin[ibin][nc2] += onemass;
vbin[ibin][nc1] += 1.0;
}
} }
// sum bins across processors // sum bins across processors
MPI_Allreduce(vbin[0],binave[0],nbins*(ncount+1),MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(vbin[0],binave[0],nbins*ncount,MPI_DOUBLE,MPI_SUM,world);
// compute ave velocity in each bin, checking for no particles // compute ave COM velocity in each bin, checking for no particles
for (i = 0; i < nbins; i++) for (i = 0; i < nbins; i++)
if (binave[i][ncount] > 0.0) if (binave[i][nc1] > 0.0)
for (j = 0; j < ncount; j++) for (j = 0; j < nc2; j++)
binave[i][j] /= binave[i][ncount]; binave[i][j] /= binave[i][nc2];
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -540,6 +562,6 @@ void ComputeTempProfile::bin_assign()
double ComputeTempProfile::memory_usage() double ComputeTempProfile::memory_usage()
{ {
double bytes = maxatom * sizeof(int); double bytes = maxatom * sizeof(int);
bytes += nbins*(ncount+1) * sizeof(double); bytes += nbins*ncount * sizeof(double);
return bytes; return bytes;
} }