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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9108 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-11-26 18:29:31 +00:00
parent eb7c94ccef
commit a64357160f
2 changed files with 131 additions and 32 deletions
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159
src/compute_temp_profile.cpp
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@ -27,6 +27,8 @@
using namespace LAMMPS_NS;
enum{TENSOR,BIN};
/* ---------------------------------------------------------------------- */
ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
@ -34,10 +36,8 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 7) error->all(FLERR,"Illegal compute temp/profile command");
scalar_flag = vector_flag = 1;
size_vector = 6;
scalar_flag = 1;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
@ -54,55 +54,95 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
if (zflag) ivz = ncount++;
nbinx = nbiny = nbinz = 1;
int lastarg;
if (strcmp(arg[6],"x") == 0) {
if (narg != 8) error->all(FLERR,"Illegal compute temp/profile command");
nbinx = atoi(arg[7]);
} else if (strcmp(arg[6],"y") == 0) {
if (narg != 8) error->all(FLERR,"Illegal compute temp/profile command");
nbiny = atoi(arg[7]);
} else if (strcmp(arg[6],"z") == 0) {
if (narg != 8) error->all(FLERR,"Illegal compute temp/profile command");
int iarg = 6;
if (strcmp(arg[iarg],"x") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
nbinx = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
nbiny = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
if (domain->dimension == 2)
error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
nbinz = atoi(arg[7]);
} else if (strcmp(arg[6],"xy") == 0) {
if (narg != 9) error->all(FLERR,"Illegal compute temp/profile command");
nbinx = atoi(arg[7]);
nbiny = atoi(arg[8]);
} else if (strcmp(arg[6],"yz") == 0) {
if (narg != 9) error->all(FLERR,"Illegal compute temp/profile command");
nbinz = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
nbinx = atoi(arg[iarg+1]);
nbiny = atoi(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
if (domain->dimension == 2)
error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
nbiny = atoi(arg[7]);
nbinz = atoi(arg[8]);
} else if (strcmp(arg[6],"xz") == 0) {
if (narg != 9) error->all(FLERR,"Illegal compute temp/profile command");
nbiny = atoi(arg[iarg+1]);
nbinz = atoi(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
if (domain->dimension == 2)
error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
nbinx = atoi(arg[7]);
nbinz = atoi(arg[8]);
} else if (strcmp(arg[6],"xyz") == 0) {
if (narg != 10) error->all(FLERR,"Illegal compute temp/profile command");
nbinx = atoi(arg[iarg+1]);
nbinz = atoi(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"xyz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal compute temp/profile command");
if (domain->dimension == 2)
error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
nbinx = atoi(arg[7]);
nbiny = atoi(arg[8]);
nbinz = atoi(arg[9]);
nbinx = atoi(arg[iarg+1]);
nbiny = atoi(arg[iarg+2]);
nbinz = atoi(arg[iarg+3]);
iarg += 4;
} else error->all(FLERR,"Illegal compute temp/profile command");
// optional keywords
outflag = TENSOR;
while (iarg < narg) {
if (strcmp(arg[iarg],"out") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/profile command");
if (strcmp(arg[iarg+1],"tensor") == 0) outflag = TENSOR;
else if (strcmp(arg[iarg+1],"bin") == 0) outflag = BIN;
else error->all(FLERR,"Illegal compute temp/profile command");
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/profile command");
}
// setup
nbins = nbinx*nbiny*nbinz;
if (nbins <= 0) error->all(FLERR,"Illegal compute temp/profile command");
memory->create(vbin,nbins,ncount+1,"temp/profile:vbin");
memory->create(binave,nbins,ncount+1,"temp/profile:binave");
if (outflag == TENSOR) {
vector_flag = 1;
size_vector = 6;
extvector = 1;
vector = new double[size_vector];
} else {
array_flag = 1;
size_array_rows = nbins;
size_array_cols = 2;
extarray = 0;
memory->create(tbin,nbins,"temp/profile:tbin");
memory->create(tbinall,nbins,"temp/profile:tbinall");
memory->create(array,nbins,2,"temp/profile:array");
}
maxatom = 0;
bin = NULL;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
@ -113,7 +153,12 @@ ComputeTempProfile::~ComputeTempProfile()
memory->destroy(binave);
memory->destroy(bin);
memory->destroy(vbiasall);
delete [] vector;
if (outflag == TENSOR) delete [] vector;
else {
memory->destroy(tbin);
memory->destroy(tbinall);
memory->destroy(array);
}
}
/* ---------------------------------------------------------------------- */
@ -244,6 +289,58 @@ void ComputeTempProfile::compute_vector()
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void ComputeTempProfile::compute_array()
{
int i,ibin;
double vthermal[3];
invoked_array = update->ntimestep;
bin_average();
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nbins; i++) tbin[i] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
ibin = bin[i];
if (xflag) vthermal[0] = v[i][0] - binave[ibin][ivx];
else vthermal[0] = v[i][0];
if (yflag) vthermal[1] = v[i][1] - binave[ibin][ivy];
else vthermal[1] = v[i][1];
if (zflag) vthermal[2] = v[i][2] - binave[ibin][ivz];
else vthermal[2] = v[i][2];
if (rmass)
tbin[ibin] += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
tbin[ibin] += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(tbin,tbinall,nbins,MPI_DOUBLE,MPI_SUM,world);
int nper = domain->dimension;
for (i = 0; i < nbins; i++) {
array[i][0] = binave[i][ncount];
if (array[i][0] > 0.0) {
dof = nper*array[i][0] - extra_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
array[i][1] = tfactor*tbinall[i];
} else array[i][1] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */