git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13197 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
503
src/CORESHELL/compute_temp_cs.cpp
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503
src/CORESHELL/compute_temp_cs.cpp
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@ -0,0 +1,503 @@
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/* ----------------------------------------------------------------------
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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: Hendrik Heenen (Technical University of Munich)
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(hendrik.heenen at mytum.com)
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "stdlib.h"
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#include "string.h"
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#include "math.h"
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#include "compute_temp_cs.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "domain.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 "modify.h"
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#include "fix.h"
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#include "fix_store.h"
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#include "comm.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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ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
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if (atom->avec->bonds_allow == 0)
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error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
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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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extarray = 0;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// find and define groupbits for core and shell groups
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cgroup = group->find(arg[3]);
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if (cgroup == -1)
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error->all(FLERR,"Could not find specified group ID for core particles");
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groupbit_c = group->bitmask[cgroup];
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sgroup = group->find(arg[4]);
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if (sgroup == -1)
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error->all(FLERR,"Could not find specified group ID for shell particles");
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groupbit_s = group->bitmask[sgroup];
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// create a new fix STORE style
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// id = compute-ID + COMPUTE_STORE, fix group = compute group
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int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
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id_fix = new char[n];
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strcpy(id_fix,id);
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strcat(id_fix,"_COMPUTE_STORE");
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char **newarg = new char*[5];
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newarg[0] = id_fix;
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newarg[1] = group->names[igroup];
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newarg[2] = (char *) "STORE";
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newarg[3] = (char *) "0";
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newarg[4] = (char *) "1";
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modify->add_fix(5,newarg);
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fix = (FixStore *) modify->fix[modify->nfix-1];
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delete [] newarg;
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// set fix store values = 0 for now
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// fill them in via setup() once Comm::borders() has been called
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// skip if resetting from restart file
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if (fix->restart_reset) {
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fix->restart_reset = 0;
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firstflag = 0;
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} else {
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double *partner = fix->vstore;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
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firstflag = 1;
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}
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// allocate memory
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vector = new double[6];
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maxatom = 0;
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vint = NULL;
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// set comm size needed by this Compute
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comm_reverse = 1;
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempCS::~ComputeTempCS()
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{
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// check nfix in case all fixes have already been deleted
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if (modify->nfix) modify->delete_fix(id_fix);
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delete [] id_fix;
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delete [] vector;
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memory->destroy(vint);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempCS::init()
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{
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if (comm->ghost_velocity == 0)
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error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempCS::setup()
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{
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if (firstflag) {
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firstflag = 0;
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// insure # of core atoms = # of shell atoms
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int ncores = group->count(cgroup);
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nshells = group->count(sgroup);
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if (ncores != nshells)
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error->all(FLERR,"Number of core atoms != number of shell atoms");
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// for each C/S pair:
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// set partner IDs of both atoms if this atom stores bond between them
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// will set partner IDs for ghost atoms if needed by another proc
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// nall loop insures all ghost atom partner IDs are set before reverse comm
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int *num_bond = atom->num_bond;
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tagint **bond_atom = atom->bond_atom;
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tagint *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *partner = fix->vstore;
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tagint partnerID;
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int nall = nlocal + atom->nghost;
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for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
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int i,j,m,match;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
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for (m = 0; m < num_bond[i]; m++) {
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partnerID = bond_atom[i][m];
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j = atom->map(partnerID);
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if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
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match = 0;
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if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
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if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
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if (match) {
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partner[i] = ubuf(partnerID).d;
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partner[j] = ubuf(tag[i]).d;
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}
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}
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}
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}
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// reverse comm to acquire unknown partner IDs from ghost atoms
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// only needed if newton_bond = on
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if (force->newton_bond) comm->reverse_comm_compute(this);
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// check that all C/S partners were found
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int flag = 0;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
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partnerID = (tagint) ubuf(partner[i]).i;
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if (partnerID == 0) flag = 1;
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}
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}
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int flagall;
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
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if (flagall) error->all(FLERR,"Core/shell partners were not all found");
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}
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// calculate DOF for temperature
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fix_dof = -1;
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dof_compute();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempCS::dof_compute()
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{
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if (fix_dof) adjust_dof_fix();
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int nper = domain->dimension;
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double natoms = group->count(igroup);
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dof = nper * natoms;
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dof -= nper * nshells;
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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 ComputeTempCS::compute_scalar()
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{
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int i;
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double vthermal[3];
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invoked_scalar = update->ntimestep;
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vcm_pairs();
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// calculate thermal scalar in respect to atom velocities as center-of-mass
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// velocities of its according core/shell pairs
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double **v = atom->v;
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int *mask = atom->mask;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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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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vthermal[0] = v[i][0] - vint[i][0];
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vthermal[1] = v[i][1] - vint[i][1];
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vthermal[2] = v[i][2] - vint[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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}
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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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scalar *= tfactor;
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempCS::compute_vector()
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{
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double vthermal[3];
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invoked_vector = update->ntimestep;
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vcm_pairs();
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// calculate thermal vector in respect to atom velocities as center-of-mass
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// velocities of its according C/S pairs
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double **v = atom->v;
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int *mask = atom->mask;
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tagint *molecule = atom->molecule;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double massone;
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double 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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vthermal[0] = v[i][0] - vint[i][0];
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vthermal[1] = v[i][1] - vint[i][1];
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vthermal[2] = v[i][2] - vint[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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}
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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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void ComputeTempCS::vcm_pairs()
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{
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int i,j;
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double massone,masstwo;
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double vcm[3];
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// reallocate vint if necessary
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int nlocal = atom->nlocal;
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if (nlocal > maxatom) {
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memory->destroy(vint);
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maxatom = atom->nmax;
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memory->create(vint,maxatom,3,"temp/cs:vint");
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}
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// vcm = COM velocity of each CS pair
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// vint = internal velocity of each C/S atom, used as bias
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double **v = atom->v;
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int *mask = atom->mask;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double *partner = fix->vstore;
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tagint partnerID;
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for (int i = 0; i < nlocal; i++) {
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if ((mask[i] & groupbit) &&
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(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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vcm[0] = v[i][0]*massone;
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vcm[1] = v[i][1]*massone;
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vcm[2] = v[i][2]*massone;
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partnerID = (tagint) ubuf(partner[i]).i;
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j = atom->map(partnerID);
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if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
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if (rmass) masstwo = rmass[j];
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else masstwo = mass[type[j]];
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vcm[0] += v[j][0]*masstwo;
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vcm[1] += v[j][1]*masstwo;
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vcm[2] += v[j][2]*masstwo;
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vcm[0] /= (massone + masstwo);
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vcm[1] /= (massone + masstwo);
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vcm[2] /= (massone + masstwo);
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vint[i][0] = v[i][0] - vcm[0];
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vint[i][1] = v[i][1] - vcm[1];
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vint[i][2] = v[i][2] - vcm[2];
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} else vint[i][0] = vint[i][1] = vint[i][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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thermal velocity in this case is COM velocity of C/S pair
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------------------------------------------------------------------------- */
|
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void ComputeTempCS::remove_bias(int i, double *v)
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{
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v[0] -= vint[i][0];
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v[1] -= vint[i][1];
|
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v[2] -= vint[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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thermal velocity in this case is COM velocity of C/S pair
|
||||
------------------------------------------------------------------------- */
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void ComputeTempCS::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;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
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||||
v[i][0] -= vint[i][0];
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||||
v[i][1] -= vint[i][1];
|
||||
v[i][2] -= vint[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reset thermal velocity of all atoms to be consistent with bias
|
||||
called from velocity command after it creates thermal velocities
|
||||
this resets each atom's velocity to COM velocity of C/S pair
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeTempCS::reapply_bias_all()
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// recalculate current COM velocities
|
||||
|
||||
vcm_pairs();
|
||||
|
||||
// zero vint after using ti so that Velocity call to restore_bias_all()
|
||||
// will not further alter the velocities within a C/S pair
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
v[i][0] -= vint[i][0];
|
||||
v[i][1] -= vint[i][1];
|
||||
v[i][2] -= vint[i][2];
|
||||
vint[i][0] = 0.0;
|
||||
vint[i][1] = 0.0;
|
||||
vint[i][2] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add back in velocity bias to atom I removed by remove_bias()
|
||||
assume remove_bias() was previously called
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeTempCS::restore_bias(int i, double *v)
|
||||
{
|
||||
v[0] += vint[i][0];
|
||||
v[1] += vint[i][1];
|
||||
v[2] += vint[i][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add back in velocity bias to all atoms removed by remove_bias_all()
|
||||
assume remove_bias_all() was previously called
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeTempCS::restore_bias_all()
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
v[i][0] += vint[i][0];
|
||||
v[i][1] += vint[i][1];
|
||||
v[i][2] += vint[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int ComputeTempCS::pack_reverse_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i,m,last;
|
||||
|
||||
double *partner = fix->vstore;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) buf[m++] = partner[i];
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeTempCS::unpack_reverse_comm(int n, int *list, double *buf)
|
||||
{
|
||||
int i,j,m;
|
||||
|
||||
double *partner = fix->vstore;
|
||||
tagint partnerID;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
partnerID = (tagint) ubuf(buf[m++]).i;
|
||||
if (partnerID) partner[j] = ubuf(partnerID).d;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeTempCS::memory_usage()
|
||||
{
|
||||
double bytes = (bigint) maxatom * 3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
Reference in New Issue
Block a user