293 lines
8.6 KiB
C++
293 lines
8.6 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://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 "fix_momentum_chunk.h"
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#include "atom.h"
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#include "compute.h"
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#include "compute_chunk_atom.h"
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#include "compute_com_chunk.h"
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#include "domain.h"
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#include "error.h"
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#include "group.h"
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#include "modify.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ----------------------------------------------------------------------
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Contributing author: Jiang Xiao (Hong Kong Polytechnic University)
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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FixMomentumChunk::FixMomentumChunk(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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cchunk(nullptr), ccom(nullptr), cvcm(nullptr), comega(nullptr)
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{
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if (narg < 5) error->all(FLERR,"Illegal fix momentum/chunk command");
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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if (nevery <= 0) error->all(FLERR,"Illegal fix momentum/chunk command");
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id_chunk = arg[4];
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int icompute = modify->find_compute(id_chunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for fix momentum/chunk");
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id_com.clear();
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id_vcm.clear();
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id_omega.clear();
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linear = angular = rescale = 0;
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int iarg = 5;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"linear") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal fix momentum command");
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linear = 1;
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xflag = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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yflag = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
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zflag = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
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iarg += 4;
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} else if (strcmp(arg[iarg],"angular") == 0) {
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angular = 1;
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iarg += 1;
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} else if (strcmp(arg[iarg],"rescale") == 0) {
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rescale = 1;
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iarg += 1;
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} else error->all(FLERR,"Illegal fix momentum/chunk command");
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}
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if (linear == 0 && angular == 0)
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error->all(FLERR,"Illegal fix momentum/chunk command");
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if (linear)
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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 fix momentum/chunk command");
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dynamic_group_allow = 0;
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}
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FixMomentumChunk::~FixMomentumChunk()
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{
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if (!id_com.empty()) modify->delete_compute(id_com);
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if (!id_vcm.empty()) modify->delete_compute(id_vcm);
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if (!id_omega.empty()) modify->delete_compute(id_omega);
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}
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/* ---------------------------------------------------------------------- */
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int FixMomentumChunk::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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mask |= POST_RUN;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixMomentumChunk::init()
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{
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// current indices for idchunk and idcom
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int icompute = modify->find_compute(id_chunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for fix momentum/chunk");
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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if (strcmp(cchunk->style,"chunk/atom") != 0)
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error->all(FLERR,"Fix momentum/chunk does not use chunk/atom compute");
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// create computes dependent on chunks
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id_com = id + id_chunk + "_com";
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icompute = modify->find_compute(id_com);
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if (icompute >= 0) modify->delete_compute(id_com);
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auto cmd = fmt::format("{} {} com/chunk {}",id_com,group->names[igroup],id_chunk);
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modify->add_compute(cmd);
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icompute = modify->find_compute(id_com);
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ccom = (ComputeCOMChunk *) modify->compute[icompute];
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id_vcm = id + id_chunk + "_vcm";
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icompute = modify->find_compute(id_vcm);
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if (icompute >= 0) modify->delete_compute(id_vcm);
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cmd = fmt::format("{} {} vcm/chunk {}",id_vcm,group->names[igroup],id_chunk);
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modify->add_compute(cmd);
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icompute = modify->find_compute(id_vcm);
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cvcm = modify->compute[icompute];
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id_omega = id + id_chunk + "_omega";
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icompute = modify->find_compute(id_omega);
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if (icompute >= 0) modify->delete_compute(id_omega);
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cmd = fmt::format("{} {} omega/chunk {}",id_omega,group->names[igroup],id_chunk);
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modify->add_compute(cmd);
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icompute = modify->find_compute(id_omega);
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comega = modify->compute[icompute];
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}
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/* ---------------------------------------------------------------------- */
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void FixMomentumChunk::end_of_step()
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{
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// calculate per-chunk properties.
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// this will also trigger a compute/update of the chunks if needed.
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ccom->compute_array();
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cvcm->compute_array();
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comega->compute_array();
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nchunk = cchunk->nchunk;
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int *ichunk = cchunk->ichunk;
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double **com = ccom->array;
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double **vcm = cvcm->array;
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double **omega = comega->array;
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// apply removing translational and rotational velocity from atoms in each chunk
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double **v = atom->v;
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int *mask = atom->mask;
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const int nlocal = atom->nlocal;
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// compute per-chunk kinetic energy before momentum removal, if needed
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double *ke_chunk_old,*ke_chunk_new,*ke_chunk_local,*factor;
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if (rescale) {
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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ke_chunk_old = new double[nchunk];
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ke_chunk_local = new double[nchunk];
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memset(ke_chunk_local,0,nchunk*sizeof(double));
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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int m = ichunk[i]-1;
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if (m < 0) continue;
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if (rmass)
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ke_chunk_local[m] += rmass[i] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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else
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ke_chunk_local[m] += mass[type[i]] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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}
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}
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MPI_Allreduce(ke_chunk_local,ke_chunk_old,nchunk,MPI_DOUBLE,MPI_SUM,world);
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}
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if (linear) {
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// adjust velocities by vcm to zero linear momentum
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// only adjust a component if flag is set
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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int m = ichunk[i]-1;
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if (m < 0) continue;
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if (xflag) v[i][0] -= vcm[m][0];
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if (yflag) v[i][1] -= vcm[m][1];
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if (zflag) v[i][2] -= vcm[m][2];
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}
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}
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}
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if (angular) {
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// adjust velocities to zero omega
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// vnew_i = v_i - w x r_i
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// must use unwrapped coords to compute r_i correctly
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double **x = atom->x;
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imageint *image = atom->image;
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double dx,dy,dz;
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double unwrap[3];
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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int m = ichunk[i]-1;
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if (m < 0) continue;
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - com[m][0];
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dy = unwrap[1] - com[m][1];
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dz = unwrap[2] - com[m][2];
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v[i][0] -= omega[m][1]*dz - omega[m][2]*dy;
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v[i][1] -= omega[m][2]*dx - omega[m][0]*dz;
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v[i][2] -= omega[m][0]*dy - omega[m][1]*dx;
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}
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}
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}
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// compute kinetic energy after momentum removal, if needed
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if (rescale) {
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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ke_chunk_new = new double[nchunk];
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factor = new double[nchunk];
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memset(ke_chunk_local,0,nchunk*sizeof(double));
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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int m = ichunk[i]-1;
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if (m < 0) continue;
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if (rmass)
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ke_chunk_local[m] += rmass[i] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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else
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ke_chunk_local[m] += mass[type[i]] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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}
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}
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MPI_Allreduce(ke_chunk_local,ke_chunk_new,nchunk,MPI_DOUBLE,MPI_SUM,world);
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// get scaling factors
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for (int m = 0; m < nchunk; ++m)
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factor[m] = (ke_chunk_new[0] > 0.0) ? sqrt(ke_chunk_old[m]/ke_chunk_new[m]) : 1.0;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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int m = ichunk[i]-1;
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if (m < 0) continue;
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v[i][0] *= factor[m];
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v[i][1] *= factor[m];
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v[i][2] *= factor[m];
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}
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}
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delete[] factor;
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delete[] ke_chunk_local;
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delete[] ke_chunk_old;
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delete[] ke_chunk_new;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixMomentumChunk::post_run()
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{
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modify->delete_compute(id_com);
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modify->delete_compute(id_vcm);
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modify->delete_compute(id_omega);
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id_com.clear();
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id_vcm.clear();
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id_omega.clear();
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}
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