git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@624 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/compute_temp_deform.cpp
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193
src/compute_temp_deform.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Pieter in 't Veld (SNL)
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "string.h"
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#include "compute_temp_deform.h"
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#include "domain.h"
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#include "atom.h"
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#include "force.h"
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#include "modify.h"
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#include "fix.h"
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#include "fix_deform.h"
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#include "group.h"
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#include "comm.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
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/* ---------------------------------------------------------------------- */
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ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute temp/deform command");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extensive = 0;
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tempflag = 1;
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vector = new double[6];
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempDeform::~ComputeTempDeform()
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{
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDeform::init()
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{
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int i;
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fix_dof = 0;
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for (i = 0; i < modify->nfix; i++)
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fix_dof += modify->fix[i]->dof(igroup);
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recount();
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// check fix deform remap settings
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for (i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"deform") == 0) {
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if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP &&
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comm->me == 0)
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error->warning("Using fix nvt/sllod with inconsistent fix deform remapping");
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break;
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}
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if (i == modify->nfix && comm->me == 0)
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error->warning("Using fix nvt/sllod with no fix deform defined");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDeform::recount()
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{
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double natoms = group->count(igroup);
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dof = force->dimension * natoms;
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dof -= extra_dof + fix_dof;
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if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
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else tfactor = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempDeform::compute_scalar()
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{
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double lamda[3],vstream[3],vthermal[3];
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double **x = atom->x;
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double **v = atom->v;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// lamda = 0-1 triclinic lamda coords
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// vstream = streaming velocity = Hrate*lamda + Hratelo
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// vthermal = thermal velocity = v - vstream
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double *h_rate = domain->h_rate;
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double *h_ratelo = domain->h_ratelo;
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double t = 0.0;
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if (mass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
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vthermal[2]*vthermal[2]) * mass[type[i]];
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}
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}
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else
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
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vthermal[2]*vthermal[2]) * rmass[i];
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}
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MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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scalar *= tfactor;
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDeform::compute_vector()
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{
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double lamda[3],vstream[3],vthermal[3];
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double **x = atom->x;
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double **v = atom->v;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *h_rate = domain->h_rate;
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double *h_ratelo = domain->h_ratelo;
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double massone,t[6];
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for (int i = 0; i < 6; i++) t[i] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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if (mass) massone = mass[type[i]];
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else massone = rmass[i];
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t[0] += massone * vthermal[0]*vthermal[0];
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t[1] += massone * vthermal[1]*vthermal[1];
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t[2] += massone * vthermal[2]*vthermal[2];
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t[3] += massone * vthermal[0]*vthermal[1];
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t[4] += massone * vthermal[0]*vthermal[2];
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t[5] += massone * vthermal[1]*vthermal[2];
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}
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MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
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for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
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}
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