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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-20 14:53:21 +00:00
parent 848aece2b4
commit ebe2ee9bac
28 changed files with 833 additions and 99 deletions
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147
src/compute_temp_deform.cpp
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@ -26,6 +26,7 @@
#include "fix_deform.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -48,6 +49,8 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
@ -55,6 +58,7 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
ComputeTempDeform::~ComputeTempDeform()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
@ -69,6 +73,12 @@ void ComputeTempDeform::init()
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
// check fix deform remap settings
for (i = 0; i < modify->nfix; i++)
@ -101,6 +111,12 @@ double ComputeTempDeform::compute_scalar()
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -118,35 +134,25 @@ double ComputeTempDeform::compute_scalar()
double t = 0.0;
if (mass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
if (mass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
else
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
}
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= tfactor;
@ -161,6 +167,11 @@ void ComputeTempDeform::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -196,14 +207,20 @@ void ComputeTempDeform::compute_vector()
t[5] += massone * vthermal[1]*vthermal[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempDeform::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
@ -217,3 +234,81 @@ void ComputeTempDeform::remove_bias(int i, double *v)
v[1] -= vbias[1];
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempDeform::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"compute/temp:vbiasall");
}
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(atom->x[i],lamda);
vbiasall[i][0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbiasall[i][1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbiasall[i][2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vbiasall[i][0];
v[i][1] -= vbiasall[i][1];
v[i][2] -= vbiasall[i][2];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempDeform::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempDeform::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */
double ComputeTempDeform::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}