Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/CORESHELL/compute_temp_cs.cpp
1ba7f726cce2lammm-master-deprecated

Last Change
Raw File

compute_temp_cs.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (Technical University of Munich)
(hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_store.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
extarray = 0;
// find and define groupbits for core and shell groups
cgroup = group->find(arg[3]);
if (cgroup == -1)
error->all(FLERR,"Cannot find specified group ID for core particles");
groupbit_c = group->bitmask[cgroup];
sgroup = group->find(arg[4]);
if (sgroup == -1)
error->all(FLERR,"Cannot find specified group ID for shell particles");
groupbit_s = group->bitmask[sgroup];
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[6];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "0";
newarg[5] = (char *) "1";
modify->add_fix(6,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called
// skip if resetting from restart file
if (fix->restart_reset) {
fix->restart_reset = 0;
firstflag = 0;
} else {
double *partner = fix->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
firstflag = 1;
}
// allocate memory
vector = new double[6];
maxatom = 0;
vint = NULL;
// set comm size needed by this Compute
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
ComputeTempCS::~ComputeTempCS()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
memory->destroy(vint);
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::init()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::setup()
{
if (firstflag) {
firstflag = 0;
// insure # of core atoms = # of shell atoms
int ncores = group->count(cgroup);
nshells = group->count(sgroup);
if (ncores != nshells)
error->all(FLERR,"Number of core atoms != number of shell atoms");
// for each C/S pair:
// set partner IDs of both atoms if this atom stores bond between them
// will set partner IDs for ghost atoms if needed by another proc
// nall loop insures all ghost atom partner IDs are set before reverse comm
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *partner = fix->vstore;
tagint partnerID;
int nall = nlocal + atom->nghost;
for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
int i,j,m,match;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
for (m = 0; m < num_bond[i]; m++) {
partnerID = bond_atom[i][m];
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
match = 0;
if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
if (match) {
partner[i] = ubuf(partnerID).d;
partner[j] = ubuf(tag[i]).d;
}
}
}
}
// reverse comm to acquire unknown partner IDs from ghost atoms
// only needed if newton_bond = on
if (force->newton_bond) comm->reverse_comm_compute(this);
// check that all C/S partners were found
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
partnerID = (tagint) ubuf(partner[i]).i;
if (partnerID == 0) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Core/shell partners were not all found");
}
// calculate DOF for temperature
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::dof_compute()
{
adjust_dof_fix();
int nper = domain->dimension;
natoms_temp = group->count(igroup);
dof = nper * natoms_temp;
dof -= nper * nshells;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempCS::compute_scalar()
{
double vthermal[3];
invoked_scalar = update->ntimestep;
vcm_pairs();
// calculate thermal scalar in respect to atom velocities as center-of-mass
// velocities of its according core/shell pairs
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::compute_vector()
{
invoked_vector = update->ntimestep;
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massone;
double t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::vcm_pairs()
{
int i,j;
double massone,masstwo;
double vcm[3];
// reallocate vint if necessary
int nlocal = atom->nlocal;
if (atom->nmax > maxatom) {
memory->destroy(vint);
maxatom = atom->nmax;
memory->create(vint,maxatom,3,"temp/cs:vint");
}
// vcm = COM velocity of each CS pair
// vint = internal velocity of each C/S atom, used as bias
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *partner = fix->vstore;
tagint partnerID;
for (i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) &&
(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vcm[0] = v[i][0]*massone;
vcm[1] = v[i][1]*massone;
vcm[2] = v[i][2]*massone;
partnerID = (tagint) ubuf(partner[i]).i;
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
if (rmass) masstwo = rmass[j];
else masstwo = mass[type[j]];
vcm[0] += v[j][0]*masstwo;
vcm[1] += v[j][1]*masstwo;
vcm[2] += v[j][2]*masstwo;
vcm[0] /= (massone + masstwo);
vcm[1] /= (massone + masstwo);
vcm[2] /= (massone + masstwo);
vint[i][0] = v[i][0] - vcm[0];
vint[i][1] = v[i][1] - vcm[1];
vint[i][2] = v[i][2] - vcm[2];
} else vint[i][0] = vint[i][1] = vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias(int i, double *v)
{
v[0] -= vint[i][0];
v[1] -= vint[i][1];
v[2] -= vint[i][2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_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];
}
}
/* ----------------------------------------------------------------------
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;
}
c4science · Help