303 lines
8.9 KiB
C++
303 lines
8.9 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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/* ----------------------------------------------------------------------
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Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <cstdlib>
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#include <cstring>
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#include "compute_temp_rotate.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 "group.h"
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#include "domain.h"
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#include "lattice.h"
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#include "error.h"
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#include "memory.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeTempRotate::ComputeTempRotate(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(FLERR,"Illegal compute temp/rotate 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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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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ComputeTempRotate::~ComputeTempRotate()
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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 ComputeTempRotate::init()
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{
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masstotal = group->mass(igroup);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempRotate::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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void ComputeTempRotate::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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dof = domain->dimension * natoms_temp;
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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 ComputeTempRotate::compute_scalar()
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{
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double vthermal[3];
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double vcm[3],xcm[3],inertia[3][3],angmom[3],omega[3];
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double dx,dy,dz;
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double unwrap[3];
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invoked_scalar = update->ntimestep;
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if (dynamic) masstotal = group->mass(igroup);
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group->vcm(igroup,masstotal,vcm);
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group->xcm(igroup,masstotal,xcm);
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group->inertia(igroup,xcm,inertia);
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group->angmom(igroup,xcm,angmom);
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group->omega(angmom,inertia,omega);
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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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imageint *image = atom->image;
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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/rotate:vbiasall");
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}
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double t = 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->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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vbiasall[i][0] = vcm[0] + dz*omega[1]-dy*omega[2];
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vbiasall[i][1] = vcm[1] + dx*omega[2]-dz*omega[0];
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vbiasall[i][2] = vcm[2] + dy*omega[0]-dx*omega[1];
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vthermal[0] = v[i][0] - vbiasall[i][0];
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vthermal[1] = v[i][1] - vbiasall[i][1];
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vthermal[2] = v[i][2] - vbiasall[i][2];
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if (rmass)
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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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else
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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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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 ComputeTempRotate::compute_vector()
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{
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double vthermal[3];
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double vcm[3],xcm[3],inertia[3][3],angmom[3],omega[3];
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double dx,dy,dz;
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double unwrap[3];
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invoked_vector = update->ntimestep;
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if (dynamic) masstotal = group->mass(igroup);
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group->vcm(igroup,masstotal,vcm);
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group->xcm(igroup,masstotal,xcm);
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group->inertia(igroup,xcm,inertia);
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group->angmom(igroup,xcm,angmom);
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group->omega(angmom,inertia,omega);
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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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imageint *image = atom->image;
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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/rotate:vbiasall");
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}
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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->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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vbiasall[i][0] = vcm[0] + dz*omega[1]-dy*omega[2];
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vbiasall[i][1] = vcm[1] + dx*omega[2]-dz*omega[0];
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vbiasall[i][2] = vcm[2] + dy*omega[0]-dx*omega[1];
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vthermal[0] = v[i][0] - vbiasall[i][0];
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vthermal[1] = v[i][1] - vbiasall[i][1];
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vthermal[2] = v[i][2] - vbiasall[i][2];
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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 * 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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/* ----------------------------------------------------------------------
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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempRotate::remove_bias(int i, double *v)
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{
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v[0] -= vbiasall[i][0];
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v[1] -= vbiasall[i][1];
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v[2] -= vbiasall[i][2];
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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 ComputeTempRotate::remove_bias_thr(int i, double *v, double *)
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{
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v[0] -= vbiasall[i][0];
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v[1] -= vbiasall[i][1];
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v[2] -= vbiasall[i][2];
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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 ComputeTempRotate::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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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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v[i][1] -= vbiasall[i][1];
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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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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 ComputeTempRotate::restore_bias(int i, double *v)
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{
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v[0] += vbiasall[i][0];
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v[1] += vbiasall[i][1];
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v[2] += vbiasall[i][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
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------------------------------------------------------------------------- */
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void ComputeTempRotate::restore_bias_thr(int i, double *v, double *)
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{
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v[0] += vbiasall[i][0];
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v[1] += vbiasall[i][1];
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v[2] += vbiasall[i][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 ComputeTempRotate::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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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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v[i][1] += vbiasall[i][1];
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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 ComputeTempRotate::memory_usage()
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{
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double bytes = maxbias * sizeof(double);
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return bytes;
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}
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