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fix_atom_swap.cpp
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Fri, Apr 4, 02:44

fix_atom_swap.cpp
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/* ----------------------------------------------------------------------
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 authors: Paul Crozier (SNL)
Alexander Stukowski
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdlib.h>
#include <string.h>
#include "fix_atom_swap.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "compute.h"
#include "group.h"
#include "domain.h"
#include "region.h"
#include "random_park.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "thermo.h"
#include "output.h"
#include "neighbor.h"
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
idregion(NULL), type_list(NULL), mu(NULL), qtype(NULL), sqrt_mass_ratio(NULL), random_equal(NULL), random_unequal(NULL)
{
if (narg < 10) error->all(FLERR,"Illegal fix atom/swap command");
dynamic_group_allow = 1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
restart_global = 1;
time_depend = 1;
// required args
nevery = force->inumeric(FLERR,arg[3]);
ncycles = force->inumeric(FLERR,arg[4]);
seed = force->inumeric(FLERR,arg[5]);
double temperature = force->numeric(FLERR,arg[6]);
beta = 1.0/(force->boltz*temperature);
if (nevery <= 0) error->all(FLERR,"Illegal fix atom/swap command");
if (ncycles < 0) error->all(FLERR,"Illegal fix atom/swap command");
if (seed <= 0) error->all(FLERR,"Illegal fix atom/swap command");
memory->create(type_list,atom->ntypes,"atom/swap:type_list");
memory->create(mu,atom->ntypes+1,"atom/swap:mu");
for (int i = 1; i <= atom->ntypes; i++) mu[i] = 0.0;
// read options from end of input line
options(narg-7,&arg[7]);
// random number generator, same for all procs
random_equal = new RanPark(lmp,seed);
// random number generator, not the same for all procs
random_unequal = new RanPark(lmp,seed);
// set up reneighboring
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
// zero out counters
nswap_attempts = 0.0;
nswap_successes = 0.0;
atom_swap_nmax = 0;
local_swap_atom_list = NULL;
local_swap_iatom_list = NULL;
local_swap_jatom_list = NULL;
// set comm size needed by this Fix
if (atom->q_flag) comm_forward = 2;
else comm_forward = 1;
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixAtomSwap::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix atom/swap command");
regionflag = 0;
conserve_ke_flag = 1;
semi_grand_flag = 0;
nswaptypes = 0;
nmutypes = 0;
iregion = -1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix atom/swap command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix atom/swap does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"ke") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix atom/swap command");
if (strcmp(arg[iarg+1],"no") == 0) conserve_ke_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) conserve_ke_flag = 1;
else error->all(FLERR,"Illegal fix atom/swap command");
iarg += 2;
} else if (strcmp(arg[iarg],"semi-grand") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix atom/swap command");
if (strcmp(arg[iarg+1],"no") == 0) semi_grand_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) semi_grand_flag = 1;
else error->all(FLERR,"Illegal fix atom/swap command");
iarg += 2;
} else if (strcmp(arg[iarg],"types") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix atom/swap command");
iarg++;
while (iarg < narg) {
if (isalpha(arg[iarg][0])) break;
if (nswaptypes >= atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
type_list[nswaptypes] = force->numeric(FLERR,arg[iarg]);
nswaptypes++;
iarg++;
}
} else if (strcmp(arg[iarg],"mu") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix atom/swap command");
iarg++;
while (iarg < narg) {
if (isalpha(arg[iarg][0])) break;
nmutypes++;
if (nmutypes > atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
mu[nmutypes] = force->numeric(FLERR,arg[iarg]);
iarg++;
}
} else error->all(FLERR,"Illegal fix atom/swap command");
}
}
/* ---------------------------------------------------------------------- */
FixAtomSwap::~FixAtomSwap()
{
memory->destroy(type_list);
memory->destroy(mu);
memory->destroy(qtype);
memory->destroy(sqrt_mass_ratio);
if (regionflag) delete [] idregion;
delete random_equal;
delete random_unequal;
}
/* ---------------------------------------------------------------------- */
int FixAtomSwap::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAtomSwap::init()
{
char *id_pe = (char *) "thermo_pe";
int ipe = modify->find_compute(id_pe);
c_pe = modify->compute[ipe];
int *type = atom->type;
if (nswaptypes < 2)
error->all(FLERR,"Must specify at least 2 types in fix atom/swap command");
if (semi_grand_flag) {
if (nswaptypes != nmutypes)
error->all(FLERR,"Need nswaptypes mu values in fix atom/swap command");
} else {
if (nswaptypes != 2)
error->all(FLERR,"Only 2 types allowed when not using semi-grand in fix atom/swap command");
if (nmutypes != 0)
error->all(FLERR,"Mu not allowed when not using semi-grand in fix atom/swap command");
}
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
if (type_list[iswaptype] <= 0 || type_list[iswaptype] > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix atom/swap command");
// this is only required for non-semi-grand
// in which case, nswaptypes = 2
if (atom->q_flag && !semi_grand_flag) {
double qmax,qmin;
int firstall,first;
memory->create(qtype,nswaptypes,"atom/swap:qtype");
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++) {
first = 1;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->mask[i] & groupbit) {
if (type[i] == type_list[iswaptype]) {
if (first) {
qtype[iswaptype] = atom->q[i];
first = 0;
} else if (qtype[iswaptype] != atom->q[i])
error->one(FLERR,"All atoms of a swapped type must have the same charge.");
}
}
}
MPI_Allreduce(&first,&firstall,1,MPI_INT,MPI_MIN,world);
if (firstall) error->all(FLERR,"At least one atom of each swapped type must be present to define charges.");
if (first) qtype[iswaptype] = -DBL_MAX;
MPI_Allreduce(&qtype[iswaptype],&qmax,1,MPI_DOUBLE,MPI_MAX,world);
if (first) qtype[iswaptype] = DBL_MAX;
MPI_Allreduce(&qtype[iswaptype],&qmin,1,MPI_DOUBLE,MPI_MIN,world);
if (qmax != qmin) error->all(FLERR,"All atoms of a swapped type must have same charge.");
}
}
memory->create(sqrt_mass_ratio,atom->ntypes+1,atom->ntypes+1,"atom/swap:sqrt_mass_ratio");
for (int itype = 1; itype <= atom->ntypes; itype++)
for (int jtype = 1; jtype <= atom->ntypes; jtype++)
sqrt_mass_ratio[itype][jtype] = sqrt(atom->mass[itype]/atom->mass[jtype]);
// check to see if itype and jtype cutoffs are the same
// if not, reneighboring will be needed between swaps
double **cutsq = force->pair->cutsq;
unequal_cutoffs = false;
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
for (int jswaptype = 0; jswaptype < nswaptypes; jswaptype++)
for (int ktype = 1; ktype <= atom->ntypes; ktype++)
if (cutsq[type_list[iswaptype]][ktype] != cutsq[type_list[jswaptype]][ktype])
unequal_cutoffs = true;
// check that no swappable atoms are in atom->firstgroup
// swapping such an atom might not leave firstgroup atoms first
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int firstgroupbit = group->bitmask[atom->firstgroup];
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Cannot do atom/swap on atoms in atom_modify first group");
}
}
/* ----------------------------------------------------------------------
attempt Monte Carlo swaps
------------------------------------------------------------------------- */
void FixAtomSwap::pre_exchange()
{
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
energy_stored = energy_full();
int nsuccess = 0;
if (semi_grand_flag) {
update_semi_grand_atoms_list();
for (int i = 0; i < ncycles; i++) nsuccess += attempt_semi_grand();
} else {
update_swap_atoms_list();
for (int i = 0; i < ncycles; i++) nsuccess += attempt_swap();
}
nswap_attempts += ncycles;
nswap_successes += nsuccess;
energy_full();
next_reneighbor = update->ntimestep + nevery;
}
/* ----------------------------------------------------------------------
Note: atom charges are assumed equal and so are not updated
------------------------------------------------------------------------- */
int FixAtomSwap::attempt_semi_grand()
{
if (nswap == 0) return 0;
double energy_before = energy_stored;
int itype,jtype,jswaptype;
int i = pick_semi_grand_atom();
if (i >= 0) {
jswaptype = static_cast<int> (nswaptypes*random_unequal->uniform());
jtype = type_list[jswaptype];
itype = atom->type[i];
while (itype == jtype) {
jswaptype = static_cast<int> (nswaptypes*random_unequal->uniform());
jtype = type_list[jswaptype];
}
atom->type[i] = jtype;
}
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
} else {
comm->forward_comm_fix(this);
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
int success = 0;
if (i >= 0)
if (random_unequal->uniform() <
exp(-beta*(energy_after - energy_before
+ mu[jtype] - mu[itype]))) success = 1;
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
update_semi_grand_atoms_list();
energy_stored = energy_after;
if (conserve_ke_flag) {
if (i >= 0) {
atom->v[i][0] *= sqrt_mass_ratio[itype][jtype];
atom->v[i][1] *= sqrt_mass_ratio[itype][jtype];
atom->v[i][2] *= sqrt_mass_ratio[itype][jtype];
}
}
return 1;
} else {
if (i >= 0) {
atom->type[i] = itype;
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
} else {
comm->forward_comm_fix(this);
}
}
return 0;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixAtomSwap::attempt_swap()
{
if ((niswap == 0) || (njswap == 0)) return 0;
double energy_before = energy_stored;
int i = pick_i_swap_atom();
int j = pick_j_swap_atom();
int itype = type_list[0];
int jtype = type_list[1];
if (i >= 0) {
atom->type[i] = jtype;
if (atom->q_flag) atom->q[i] = qtype[1];
}
if (j >= 0) {
atom->type[j] = itype;
if (atom->q_flag) atom->q[j] = qtype[0];
}
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
} else {
comm->forward_comm_fix(this);
}
double energy_after = energy_full();
if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
update_swap_atoms_list();
energy_stored = energy_after;
if (conserve_ke_flag) {
if (i >= 0) {
atom->v[i][0] *= sqrt_mass_ratio[itype][jtype];
atom->v[i][1] *= sqrt_mass_ratio[itype][jtype];
atom->v[i][2] *= sqrt_mass_ratio[itype][jtype];
}
if (j >= 0) {
atom->v[j][0] *= sqrt_mass_ratio[jtype][itype];
atom->v[j][1] *= sqrt_mass_ratio[jtype][itype];
atom->v[j][2] *= sqrt_mass_ratio[jtype][itype];
}
}
return 1;
} else {
if (i >= 0) {
atom->type[i] = type_list[0];
if (atom->q_flag) atom->q[i] = qtype[0];
}
if (j >= 0) {
atom->type[j] = type_list[1];
if (atom->q_flag) atom->q[j] = qtype[1];
}
energy_stored = energy_before;
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
} else {
comm->forward_comm_fix(this);
}
}
return 0;
}
/* ----------------------------------------------------------------------
compute system potential energy
------------------------------------------------------------------------- */
double FixAtomSwap::energy_full()
{
int eflag = 1;
int vflag = 0;
if (modify->n_pre_neighbor) modify->pre_neighbor();
if (modify->n_pre_force) modify->pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) force->kspace->compute(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();
return total_energy;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixAtomSwap::pick_semi_grand_atom()
{
int i = -1;
int iwhichglobal = static_cast<int> (nswap*random_equal->uniform());
if ((iwhichglobal >= nswap_before) &&
(iwhichglobal < nswap_before + nswap_local)) {
int iwhichlocal = iwhichglobal - nswap_before;
i = local_swap_atom_list[iwhichlocal];
}
return i;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixAtomSwap::pick_i_swap_atom()
{
int i = -1;
int iwhichglobal = static_cast<int> (niswap*random_equal->uniform());
if ((iwhichglobal >= niswap_before) &&
(iwhichglobal < niswap_before + niswap_local)) {
int iwhichlocal = iwhichglobal - niswap_before;
i = local_swap_iatom_list[iwhichlocal];
}
return i;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixAtomSwap::pick_j_swap_atom()
{
int j = -1;
int jwhichglobal = static_cast<int> (njswap*random_equal->uniform());
if ((jwhichglobal >= njswap_before) &&
(jwhichglobal < njswap_before + njswap_local)) {
int jwhichlocal = jwhichglobal - njswap_before;
j = local_swap_jatom_list[jwhichlocal];
}
return j;
}
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */
void FixAtomSwap::update_semi_grand_atoms_list()
{
int nlocal = atom->nlocal;
double **x = atom->x;
if (atom->nmax > atom_swap_nmax) {
memory->sfree(local_swap_atom_list);
atom_swap_nmax = atom->nmax;
local_swap_atom_list = (int *) memory->smalloc(atom_swap_nmax*sizeof(int),
"MCSWAP:local_swap_atom_list");
}
nswap_local = 0;
if (regionflag) {
for (int i = 0; i < nlocal; i++) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 1) {
if (atom->mask[i] & groupbit) {
int itype = atom->type[i];
int iswaptype;
for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
if (itype == type_list[iswaptype]) break;
if (iswaptype == nswaptypes) continue;
local_swap_atom_list[nswap_local] = i;
nswap_local++;
}
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
int itype = atom->type[i];
int iswaptype;
for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
if (itype == type_list[iswaptype]) break;
if (iswaptype == nswaptypes) continue;
local_swap_atom_list[nswap_local] = i;
nswap_local++;
}
}
}
MPI_Allreduce(&nswap_local,&nswap,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&nswap_local,&nswap_before,1,MPI_INT,MPI_SUM,world);
nswap_before -= nswap_local;
}
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */
void FixAtomSwap::update_swap_atoms_list()
{
int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
if (atom->nmax > atom_swap_nmax) {
memory->sfree(local_swap_iatom_list);
memory->sfree(local_swap_jatom_list);
atom_swap_nmax = atom->nmax;
local_swap_iatom_list = (int *) memory->smalloc(atom_swap_nmax*sizeof(int),
"MCSWAP:local_swap_iatom_list");
local_swap_jatom_list = (int *) memory->smalloc(atom_swap_nmax*sizeof(int),
"MCSWAP:local_swap_jatom_list");
}
niswap_local = 0;
njswap_local = 0;
if (regionflag) {
for (int i = 0; i < nlocal; i++) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 1) {
if (atom->mask[i] & groupbit) {
if (type[i] == type_list[0]) {
local_swap_iatom_list[niswap_local] = i;
niswap_local++;
} else if (type[i] == type_list[1]) {
local_swap_jatom_list[njswap_local] = i;
njswap_local++;
}
}
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
if (type[i] == type_list[0]) {
local_swap_iatom_list[niswap_local] = i;
niswap_local++;
} else if (type[i] == type_list[1]) {
local_swap_jatom_list[njswap_local] = i;
njswap_local++;
}
}
}
}
MPI_Allreduce(&niswap_local,&niswap,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&niswap_local,&niswap_before,1,MPI_INT,MPI_SUM,world);
niswap_before -= niswap_local;
MPI_Allreduce(&njswap_local,&njswap,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&njswap_local,&njswap_before,1,MPI_INT,MPI_SUM,world);
njswap_before -= njswap_local;
}
/* ---------------------------------------------------------------------- */
int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
int *type = atom->type;
double *q = atom->q;
m = 0;
if (atom->q_flag) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = type[j];
buf[m++] = q[j];
}
} else {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = type[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixAtomSwap::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
int *type = atom->type;
double *q = atom->q;
m = 0;
last = first + n;
if (atom->q_flag) {
for (i = first; i < last; i++) {
type[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
}
} else {
for (i = first; i < last; i++)
type[i] = static_cast<int> (buf[m++]);
}
}
/* ----------------------------------------------------------------------
return acceptance ratio
------------------------------------------------------------------------- */
double FixAtomSwap::compute_vector(int n)
{
if (n == 0) return nswap_attempts;
if (n == 1) return nswap_successes;
return 0.0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixAtomSwap::memory_usage()
{
double bytes = atom_swap_nmax * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixAtomSwap::write_restart(FILE *fp)
{
int n = 0;
double list[4];
list[n++] = random_equal->state();
list[n++] = random_unequal->state();
list[n++] = next_reneighbor;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixAtomSwap::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
seed = static_cast<int> (list[n++]);
random_equal->reset(seed);
seed = static_cast<int> (list[n++]);
random_unequal->reset(seed);
next_reneighbor = static_cast<int> (list[n++]);
}

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