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lammps/src/compute_temp_ramp.cpp
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compute_temp_ramp.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.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdlib.h>
#include <string.h>
#include "compute_temp_ramp.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 9) error->all(FLERR,"Illegal compute temp command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
// parse optional args
scaleflag = 1;
int iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/ramp command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal compute temp/ramp command");
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/ramp command");
}
// setup scaling
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// read standard args and apply scaling
if (strcmp(arg[3],"vx") == 0) v_dim = 0;
else if (strcmp(arg[3],"vy") == 0) v_dim = 1;
else if (strcmp(arg[3],"vz") == 0) v_dim = 2;
else error->all(FLERR,"Illegal compute temp/ramp command");
if (v_dim == 0) {
v_lo = xscale*force->numeric(FLERR,arg[4]);
v_hi = xscale*force->numeric(FLERR,arg[5]);
} else if (v_dim == 1) {
v_lo = yscale*force->numeric(FLERR,arg[4]);
v_hi = yscale*force->numeric(FLERR,arg[5]);
} else if (v_dim == 2) {
v_lo = zscale*force->numeric(FLERR,arg[4]);
v_hi = zscale*force->numeric(FLERR,arg[5]);
}
if (strcmp(arg[6],"x") == 0) coord_dim = 0;
else if (strcmp(arg[6],"y") == 0) coord_dim = 1;
else if (strcmp(arg[6],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal compute temp/ramp command");
if (coord_dim == 0) {
coord_lo = xscale*force->numeric(FLERR,arg[7]);
coord_hi = xscale*force->numeric(FLERR,arg[8]);
} else if (coord_dim == 1) {
coord_lo = yscale*force->numeric(FLERR,arg[7]);
coord_hi = yscale*force->numeric(FLERR,arg[8]);
} else if (coord_dim == 2) {
coord_lo = zscale*force->numeric(FLERR,arg[7]);
coord_hi = zscale*force->numeric(FLERR,arg[8]);
}
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempRamp::~ComputeTempRamp()
{
memory->destroy(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::dof_compute()
{
adjust_dof_fix();
natoms_temp = group->count(igroup);
dof = domain->dimension * natoms_temp;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempRamp::compute_scalar()
{
double fraction,vramp,vthermal[3];
invoked_scalar = update->ntimestep;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vramp = v_lo + fraction*(v_hi - v_lo);
vthermal[0] = v[i][0];
vthermal[1] = v[i][1];
vthermal[2] = v[i][2];
vthermal[v_dim] -= vramp;
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::compute_vector()
{
int i;
double fraction,vramp,vthermal[3];
invoked_vector = update->ntimestep;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double massone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vramp = v_lo + fraction*(v_hi - v_lo);
vthermal[0] = v[i][0];
vthermal[1] = v[i][1];
vthermal[2] = v[i][2];
vthermal[v_dim] -= vramp;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * vthermal[0]*vthermal[0];
t[1] += massone * vthermal[1]*vthermal[1];
t[2] += massone * vthermal[2]*vthermal[2];
t[3] += massone * vthermal[0]*vthermal[1];
t[4] += massone * vthermal[0]*vthermal[2];
t[5] += massone * vthermal[1]*vthermal[2];
}
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 ComputeTempRamp::remove_bias(int i, double *v)
{
double fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vbias[v_dim] = v_lo + fraction*(v_hi - v_lo);
v[v_dim] -= vbias[v_dim];
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRamp::remove_bias_thr(int i, double *v, double *b)
{
double fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
b[v_dim] = v_lo + fraction*(v_hi - v_lo);
v[v_dim] -= b[v_dim];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRamp::remove_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (atom->nmax > maxbias) {
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/ramp:vbiasall");
}
double fraction;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vbiasall[i][v_dim] = v_lo + fraction*(v_hi - v_lo);
v[i][v_dim] -= vbiasall[i][v_dim];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias(int i, double *v)
{
v[v_dim] += vbias[v_dim];
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias_thr()
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias_thr(int i, double *v, double *b)
{
v[v_dim] += b[v_dim];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRamp::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][v_dim] += vbiasall[i][v_dim];
}
/* ---------------------------------------------------------------------- */
double ComputeTempRamp::memory_usage()
{
double bytes = 3*maxbias * sizeof(double);
return bytes;
}
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