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compute_pressure.cpp
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Mon, Nov 11, 02:14

compute_pressure.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 <string.h>
#include <stdlib.h>
#include "compute_pressure.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute pressure command");
if (igroup) error->all(FLERR,"Compute pressure must use group all");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 0;
pressflag = 1;
timeflag = 1;
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
else {
int n = strlen(arg[3]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
if (modify->compute[icompute]->tempflag == 0)
error->all(FLERR,"Compute pressure temperature ID does not "
"compute temperature");
}
// process optional args
if (narg == 4) {
keflag = 1;
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
} else {
keflag = 0;
pairflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
kspaceflag = fixflag = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else if (strcmp(arg[iarg],"virial") == 0) {
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
} else error->all(FLERR,"Illegal compute pressure command");
iarg++;
}
}
// error check
if (keflag && id_temp == NULL)
error->all(FLERR,"Compute pressure requires temperature ID "
"to include kinetic energy");
vector = new double[6];
nvirial = 0;
vptr = NULL;
}
/* ---------------------------------------------------------------------- */
ComputePressure::~ComputePressure()
{
delete [] id_temp;
delete [] vector;
delete [] vptr;
}
/* ---------------------------------------------------------------------- */
void ComputePressure::init()
{
boltz = force->boltz;
nktv2p = force->nktv2p;
dimension = domain->dimension;
// set temperature compute, must be done in init()
// fixes could have changed or compute_modify could have changed it
if (keflag) {
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
temperature = modify->compute[icompute];
}
// detect contributions to virial
// vptr points to all virial[6] contributions
delete [] vptr;
nvirial = 0;
vptr = NULL;
if (pairflag && force->pair) nvirial++;
if (bondflag && atom->molecular && force->bond) nvirial++;
if (angleflag && atom->molecular && force->angle) nvirial++;
if (dihedralflag && atom->molecular && force->dihedral) nvirial++;
if (improperflag && atom->molecular && force->improper) nvirial++;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag) nvirial++;
if (nvirial) {
vptr = new double*[nvirial];
nvirial = 0;
if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
if (dihedralflag && force->dihedral)
vptr[nvirial++] = force->dihedral->virial;
if (improperflag && force->improper)
vptr[nvirial++] = force->improper->virial;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag)
vptr[nvirial++] = modify->fix[i]->virial;
}
// flag Kspace contribution separately, since not summed across procs
if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial;
else kspace_virial = NULL;
}
/* ----------------------------------------------------------------------
compute total pressure, averaged over Pxx, Pyy, Pzz
------------------------------------------------------------------------- */
double ComputePressure::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (update->vflag_global != invoked_scalar)
error->all(FLERR,"Virial was not tallied on needed timestep");
// invoke temperature if it hasn't been already
double t;
if (keflag) {
if (temperature->invoked_scalar != update->ntimestep)
t = temperature->compute_scalar();
else t = temperature->scalar;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(3,3);
if (keflag)
scalar = (temperature->dof * boltz * t +
virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(2,2);
if (keflag)
scalar = (temperature->dof * boltz * t +
virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
}
return scalar;
}
/* ----------------------------------------------------------------------
compute pressure tensor
assume KE tensor has already been computed
------------------------------------------------------------------------- */
void ComputePressure::compute_vector()
{
invoked_vector = update->ntimestep;
if (update->vflag_global != invoked_vector)
error->all(FLERR,"Virial was not tallied on needed timestep");
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
"tensor components with kspace_style msm");
// invoke temperature if it hasn't been already
double *ke_tensor;
if (keflag) {
if (temperature->invoked_vector != update->ntimestep)
temperature->compute_vector();
ke_tensor = temperature->vector;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(6,3);
if (keflag) {
for (int i = 0; i < 6; i++)
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
} else
for (int i = 0; i < 6; i++)
vector[i] = virial[i] * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(4,2);
if (keflag) {
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
} else {
vector[0] = virial[0] * inv_volume * nktv2p;
vector[1] = virial[1] * inv_volume * nktv2p;
vector[3] = virial[3] * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputePressure::virial_compute(int n, int ndiag)
{
int i,j;
double v[6],*vcomponent;
for (i = 0; i < n; i++) v[i] = 0.0;
// sum contributions to virial from forces and fixes
for (j = 0; j < nvirial; j++) {
vcomponent = vptr[j];
for (i = 0; i < n; i++) v[i] += vcomponent[i];
}
// sum virial across procs
MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world);
// KSpace virial contribution is already summed across procs
if (kspace_virial)
for (i = 0; i < n; i++) virial[i] += kspace_virial[i];
// LJ long-range tail correction, only if pair contributions are included
if (force->pair && pairflag && force->pair->tail_flag)
for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
}
/* ---------------------------------------------------------------------- */
void ComputePressure::reset_extra_compute_fix(const char *id_new)
{
delete [] id_temp;
int n = strlen(id_new) + 1;
id_temp = new char[n];
strcpy(id_temp,id_new);
}

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