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fix_bond_break.cpp
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Thu, Oct 3, 03:14

fix_bond_break.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.
------------------------------------------------------------------------- */
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "fix_bond_break.h"
#include "update.h"
#include "respa.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix bond/break command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix bond/break command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
btype = atoi(arg[4]);
double cutoff = atof(arg[5]);
if (btype < 1 || btype > atom->nbondtypes)
error->all("Invalid bond type in fix bond/break command");
if (cutoff < 0.0) error->all("Illegal fix bond/break command");
cutsq = cutoff*cutoff;
// optional keywords
fraction = 1.0;
int seed = 12345;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all("Illegal fix bond/break command");
fraction = atof(arg[iarg+1]);
seed = atoi(arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
error->all("Illegal fix bond/break command");
if (seed <= 0) error->all("Illegal fix bond/break command");
iarg += 3;
} else error->all("Illegal fix bond/break command");
}
// error check
if (atom->molecular == 0)
error->all("Cannot use fix bond/break with non-molecular systems");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + me);
// set comm sizes needed by this fix
comm_forward = 2;
comm_reverse = 2;
// allocate arrays local to this fix
nmax = 0;
partner = NULL;
distsq = NULL;
// zero out stats
breakcount = 0;
breakcounttotal = 0;
}
/* ---------------------------------------------------------------------- */
FixBondBreak::~FixBondBreak()
{
delete random;
// delete locally stored arrays
memory->destroy(partner);
memory->destroy(distsq);
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::init()
{
// require special bonds = 0,1,1
int flag = 0;
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0) flag = 1;
if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0) flag = 1;
if (flag) error->all("Fix bond/break requires special_bonds = 0,1,1");
// warn if angles, dihedrals, impropers are being used
if (force->angle || force->dihedral || force->improper) {
if (me == 0)
error->warning("Broken bonds will not alter angles, "
"dihedrals, or impropers");
}
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::post_integrate()
{
int i,j,k,m,n,i1,i2,n1,n3,possible,type;
double delx,dely,delz,rsq,min,max;
int *slist;
if (update->ntimestep % nevery) return;
// need updated ghost atom positions
comm->forward_comm();
// resize bond partner list and initialize it
// probability array overlays distsq array
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(partner);
memory->destroy(distsq);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/break:partner");
memory->create(distsq,nmax,"bond/break:distsq");
probability = distsq;
}
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
for (i = 0; i < nall; i++) {
partner[i] = 0;
distsq[i] = 0.0;
}
// loop over bond list
// setup possible partner list of bonds to break
double **x = atom->x;
int *tag = atom->tag;
int *mask = atom->mask;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
if (!(mask[i1] & groupbit)) continue;
if (!(mask[i2] & groupbit)) continue;
if (type != btype) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutsq) continue;
if (rsq > distsq[i1]) {
partner[i1] = tag[i2];
distsq[i1] = rsq;
}
if (rsq > distsq[i2]) {
partner[i2] = tag[i1];
distsq[i2] = rsq;
}
}
// reverse comm of partner info
if (force->newton_bond) comm->reverse_comm_fix(this);
// each atom now knows its winning partner
// for prob check, generate random value for each atom with a bond partner
// forward comm of partner and random value, so ghosts have it
if (fraction < 1.0) {
for (i = 0; i < nlocal; i++)
if (partner[i]) probability[i] = random->uniform();
}
comm->forward_comm_fix(this);
// break bonds
// if both atoms list each other as winning bond partner
// and probability constraint is satisfied
int **bond_type = atom->bond_type;
int **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
int **special = atom->special;
int nbreak = 0;
for (i = 0; i < nlocal; i++) {
if (partner[i] == 0) continue;
j = atom->map(partner[i]);
if (partner[j] != tag[i]) continue;
// apply probability constraint
// MIN,MAX insures values are added in same order on different procs
if (fraction < 1.0) {
min = MIN(probability[i],probability[j]);
max = MAX(probability[i],probability[j]);
if (0.5*(min+max) >= fraction) continue;
}
// delete bond from atom I if I stores it
// atom J will also do this
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == partner[i]) {
for (k = m; k < num_bond[i]-1; k++) {
bond_atom[i][k] = bond_atom[i][k+1];
bond_type[i][k] = bond_type[i][k+1];
}
num_bond[i]--;
break;
}
}
// remove J from special bond list for atom I
// atom J will also do this
slist = atom->special[i];
n1 = nspecial[i][0];
n3 = nspecial[i][2];
for (m = 0; m < n1; m++)
if (slist[m] == partner[i]) break;
for (; m < n3-1; m++) slist[m] = slist[m+1];
nspecial[i][0]--;
nspecial[i][1]--;
nspecial[i][2]--;
// count the broken bond once
if (tag[i] < tag[j]) nbreak++;
}
// tally stats
MPI_Allreduce(&nbreak,&breakcount,1,MPI_INT,MPI_SUM,world);
breakcounttotal += breakcount;
atom->nbonds -= breakcount;
// trigger reneighboring if any bonds were formed
if (breakcount) next_reneighbor = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = partner[j];
buf[m++] = probability[j];
}
return 2;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
partner[i] = static_cast<int> (buf[m++]);
probability[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = partner[i];
buf[m++] = distsq[i];
}
return 2;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m+1] > distsq[j]) {
partner[j] = static_cast<int> (buf[m++]);
distsq[j] = buf[m++];
} else m += 2;
}
}
/* ---------------------------------------------------------------------- */
double FixBondBreak::compute_vector(int n)
{
if (n == 1) return (double) breakcount;
return (double) breakcounttotal;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondBreak::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax * sizeof(double);
return bytes;
}

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