forked from lijiext/lammps
332 lines
9.1 KiB
C++
332 lines
9.1 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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#include <mpi.h>
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#include <stdlib.h>
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#include "compute_temp_partial.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "domain.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 6) error->all(FLERR,"Illegal compute temp/partial command");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extscalar = 0;
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extvector = 1;
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tempflag = 1;
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tempbias = 1;
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xflag = force->inumeric(FLERR,arg[3]);
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yflag = force->inumeric(FLERR,arg[4]);
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zflag = force->inumeric(FLERR,arg[5]);
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if ((xflag != 0 && xflag != 1) || (yflag != 0 && yflag != 1)
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|| (zflag != 0 && zflag != 1))
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error->all(FLERR,"Illegal compute temp/partial command");
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if (zflag && domain->dimension == 2)
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error->all(FLERR,"Compute temp/partial cannot use vz for 2d systemx");
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maxbias = 0;
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vbiasall = NULL;
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vector = new double[6];
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempPartial::~ComputeTempPartial()
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{
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memory->destroy(vbiasall);
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempPartial::setup()
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{
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dynamic = 0;
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if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
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dof_compute();
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}
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/* ----------------------------------------------------------------------
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DOF for a body of N atoms with S constraints (e.g. from SHAKE)
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DOF = nper/dim (dim*N - S), where dim = dimensionality = 2 or 3
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------------------------------------------------------------------------- */
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void ComputeTempPartial::dof_compute()
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{
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adjust_dof_fix();
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natoms_temp = group->count(igroup);
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int nper = xflag+yflag+zflag;
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dof = nper * natoms_temp;
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// distribute extra dofs evenly across active dimensions
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dof -= (1.0*nper/domain->dimension)*(fix_dof + extra_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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int ComputeTempPartial::dof_remove(int i)
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{
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int nper = xflag+yflag+zflag;
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return (domain->dimension - nper);
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempPartial::compute_scalar()
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{
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invoked_scalar = update->ntimestep;
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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 t = 0.0;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
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zflag*v[i][2]*v[i][2]) * rmass[i];
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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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t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
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zflag*v[i][2]*v[i][2]) * mass[type[i]];
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}
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MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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if (dynamic) dof_compute();
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if (dof < 0.0 && natoms_temp > 0.0)
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error->all(FLERR,"Temperature compute degrees of freedom < 0");
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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 ComputeTempPartial::compute_vector()
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{
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int i;
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invoked_vector = update->ntimestep;
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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 massone,t[6];
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for (i = 0; i < 6; i++) t[i] = 0.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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t[0] += massone * xflag*v[i][0]*v[i][0];
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t[1] += massone * yflag*v[i][1]*v[i][1];
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t[2] += massone * zflag*v[i][2]*v[i][2];
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t[3] += massone * xflag*yflag*v[i][0]*v[i][1];
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t[4] += massone * xflag*zflag*v[i][0]*v[i][2];
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t[5] += massone * yflag*zflag*v[i][1]*v[i][2];
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}
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MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
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}
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/* ----------------------------------------------------------------------
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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempPartial::remove_bias(int i, double *v)
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{
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if (!xflag) {
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vbias[0] = v[0];
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v[0] = 0.0;
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}
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if (!yflag) {
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vbias[1] = v[1];
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v[1] = 0.0;
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}
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if (!zflag) {
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vbias[2] = v[2];
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v[2] = 0.0;
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}
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}
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/* ----------------------------------------------------------------------
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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempPartial::remove_bias_thr(int i, double *v, double *b)
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{
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if (!xflag) {
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b[0] = v[0];
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v[0] = 0.0;
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}
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if (!yflag) {
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b[1] = v[1];
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v[1] = 0.0;
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}
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if (!zflag) {
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b[2] = v[2];
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v[2] = 0.0;
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}
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}
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/* ----------------------------------------------------------------------
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remove velocity bias from all atoms to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempPartial::remove_bias_all()
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{
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (atom->nmax > maxbias) {
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memory->destroy(vbiasall);
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maxbias = atom->nmax;
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memory->create(vbiasall,maxbias,3,"temp/partial:vbiasall");
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}
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if (!xflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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vbiasall[i][0] = v[i][0];
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v[i][0] = 0.0;
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}
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}
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if (!yflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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vbiasall[i][1] = v[i][1];
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v[i][1] = 0.0;
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}
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}
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if (!zflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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vbiasall[i][2] = v[i][2];
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v[i][2] = 0.0;
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}
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}
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}
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/* ----------------------------------------------------------------------
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reset thermal velocity of all atoms to be consistent with bias
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called from velocity command after it creates thermal velocities
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this re-zero components that should stay zero
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------------------------------------------------------------------------- */
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void ComputeTempPartial::reapply_bias_all()
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{
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (!xflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) v[i][0] = 0.0;
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}
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if (!yflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) v[i][1] = 0.0;
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}
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if (!zflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) v[i][2] = 0.0;
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}
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}
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/* ----------------------------------------------------------------------
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add back in velocity bias to atom I removed by remove_bias()
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assume remove_bias() was previously called
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------------------------------------------------------------------------- */
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void ComputeTempPartial::restore_bias(int i, double *v)
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{
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if (!xflag) v[0] += vbias[0];
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if (!yflag) v[1] += vbias[1];
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if (!zflag) v[2] += vbias[2];
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}
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/* ----------------------------------------------------------------------
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add back in velocity bias to atom I removed by remove_bias_thr()
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assume remove_bias_thr() was previously called with the same buffer b
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------------------------------------------------------------------------- */
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void ComputeTempPartial::restore_bias_thr(int i, double *v, double *b)
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{
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if (!xflag) v[0] += b[0];
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if (!yflag) v[1] += b[1];
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if (!zflag) v[2] += b[2];
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}
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/* ----------------------------------------------------------------------
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add back in velocity bias to all atoms removed by remove_bias_all()
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assume remove_bias_all() was previously called
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------------------------------------------------------------------------- */
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void ComputeTempPartial::restore_bias_all()
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{
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (!xflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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v[i][0] += vbiasall[i][0];
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}
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if (!yflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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v[i][1] += vbiasall[i][1];
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}
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if (!zflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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v[i][2] += vbiasall[i][2];
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}
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempPartial::memory_usage()
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{
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double bytes = 3*maxbias * sizeof(double);
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return bytes;
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}
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