Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F118893207
compute_temp_ramp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Jun 22, 19:24
Size
8 KB
Mime Type
text/x-c
Expires
Tue, Jun 24, 19:24 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
26924879
Attached To
rLAMMPS lammps
compute_temp_ramp.cpp
View Options
/* ----------------------------------------------------------------------
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 "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 9) error->all("Illegal compute temp command");
// parse optional args
scaleflag = 1;
int iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("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("Illegal compute temp/ramp command");
iarg += 2;
} else error->all("Illegal compute temp/ramp command");
}
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of compute temp/ramp with undefined lattice");
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("Illegal compute temp/ramp command");
if (v_dim == 0) {
v_lo = xscale*atof(arg[4]);
v_hi = xscale*atof(arg[5]);
} else if (v_dim == 1) {
v_lo = yscale*atof(arg[4]);
v_hi = yscale*atof(arg[5]);
} else if (v_dim == 2) {
v_lo = zscale*atof(arg[4]);
v_hi = zscale*atof(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("Illegal compute temp/ramp command");
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[7]);
coord_hi = xscale*atof(arg[8]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[7]);
coord_hi = yscale*atof(arg[8]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[7]);
coord_hi = zscale*atof(arg[8]);
}
// settings
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempRamp::~ComputeTempRamp()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::init()
{
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::dof_compute()
{
double natoms = group->count(igroup);
int nper = domain->dimension;
dof = nper * natoms;
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 (mass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
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 (mass) massone = mass[type[i]];
else massone = rmass[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 all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRamp::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 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 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 = maxbias * sizeof(double);
return bytes;
}
Event Timeline
Log In to Comment