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compute_temp_body.cpp
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Thu, Oct 31, 15:32

compute_temp_body.cpp
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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: Trung Dac Nguyen (ndactrung@gmail.com)
based on ComputeTempAsphere
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include "compute_temp_body.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ROTATE,ALL};
/* ---------------------------------------------------------------------- */
ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), id_bias(NULL), tbias(NULL), avec(NULL)
{
if (narg < 3) error->all(FLERR,"Illegal compute temp/body command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 0;
id_bias = NULL;
mode = ALL;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/body command");
tempbias = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/body command");
if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
else error->all(FLERR,"Illegal compute temp/body command");
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/body command");
}
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempBody::~ComputeTempBody()
{
delete [] id_bias;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempBody::init()
{
// error check
avec = (AtomVecBody *) atom->style_match("body");
if (!avec)
error->all(FLERR,"Compute temp/body requires atom style body");
// check that all particles are finite-size, no point particles allowed
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (body[i] < 0)
error->one(FLERR,"Compute temp/body requires bodies");
if (tempbias) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
if (tbias->igroup != igroup)
error->all(FLERR,"Bias compute group does not match compute group");
if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
else tempbias = 1;
// init and setup bias compute because
// this compute's setup()->dof_compute() may be called first
tbias->init();
tbias->setup();
}
}
/* ---------------------------------------------------------------------- */
void ComputeTempBody::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempBody::dof_compute()
{
adjust_dof_fix();
// 6 dof for 3d, 3 dof for 2d
// which dof are included also depends on mode
// assume full rotation of extended particles
// user should correct this via compute_modify if needed
natoms_temp = group->count(igroup);
int nper;
if (domain->dimension == 3) {
if (mode == ALL) nper = 6;
else nper = 3;
} else {
if (mode == ALL) nper = 3;
else nper = 1;
}
dof = nper*natoms_temp;
// additional adjustments to dof
if (tempbias == 1) {
if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp;
} else if (tempbias == 2) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
tbias->dof_remove_pre();
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tbias->dof_remove(i)) count++;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= nper*count_all;
}
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempBody::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
AtomVecBody::Bonus *bonus = avec->bonus;
double **v = atom->v;
double **angmom = atom->angmom;
double *rmass = atom->rmass;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *inertia,*quat;
double wbody[3];
double rot[3][3];
// sum translational and rotational energy for each particle
double t = 0.0;
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
// principal moments of inertia
inertia = bonus[body[i]].inertia;
quat = bonus[body[i]].quat;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// principal moments of inertia
inertia = bonus[body[i]].inertia;
quat = bonus[body[i]].quat;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tempbias == 2) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempBody::compute_vector()
{
int i;
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
tbias->remove_bias_all();
}
AtomVecBody::Bonus *bonus = avec->bonus;
double **v = atom->v;
double **angmom = atom->angmom;
double *rmass = atom->rmass;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *inertia,*quat;
double wbody[3],t[6];
double rot[3][3];
double massone;
// sum translational and rotational energy for each particle
for (i = 0; i < 6; i++) t[i] = 0.0;
if (mode == ALL) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
// principal moments of inertia
inertia = bonus[body[i]].inertia;
quat = bonus[body[i]].quat;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// principal moments of inertia
inertia = bonus[body[i]].inertia;
quat = bonus[body[i]].quat;
massone = rmass[i];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
}
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempBody::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempBody::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(i,v);
}

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