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fix_bond_break.cpp
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Wed, Nov 6, 06:14

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 "atom_vec.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;
using namespace FixConst;
#define DELTA 16
/* ---------------------------------------------------------------------- */
FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/break command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
btype = force->inumeric(FLERR,arg[4]);
cutoff = force->numeric(FLERR,arg[5]);
if (btype < 1 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in fix bond/break command");
if (cutoff < 0.0) error->all(FLERR,"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(FLERR,"Illegal fix bond/break command");
fraction = force->numeric(FLERR,arg[iarg+1]);
seed = force->inumeric(FLERR,arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR,"Illegal fix bond/break command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/break command");
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/break command");
}
// error check
if (atom->molecular != 1)
error->all(FLERR,"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
// forward is big due to comm of broken bonds and 1-2 neighbors
comm_forward = MAX(2,2+atom->maxspecial);
comm_reverse = 2;
// allocate arrays local to this fix
nmax = 0;
partner = finalpartner = NULL;
distsq = NULL;
maxbreak = 0;
broken = NULL;
maxinfluenced = 0;
influenced = NULL;
// copy = special list for one atom
// may contain 1-2 neighs of all 1-3 neighs before dedup() shrinks it
int maxspecial = atom->maxspecial;
copy = new tagint[maxspecial*maxspecial + maxspecial];
// zero out stats
breakcount = 0;
breakcounttotal = 0;
}
/* ---------------------------------------------------------------------- */
FixBondBreak::~FixBondBreak()
{
delete random;
// delete locally stored arrays
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
memory->destroy(broken);
memory->destroy(influenced);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
if (force->improper) {
if (force->improper_match("class2") || force->improper_match("ring"))
error->all(FLERR,"Cannot yet use fix bond/break with this "
"improper style");
}
lastcheck = -1;
// DEBUG
// print_bb();
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::post_integrate()
{
int i,j,k,m,n,i1,i2,n1,n3,type;
double delx,dely,delz,rsq;
tagint *slist;
if (update->ntimestep % nevery) return;
// check that all procs have needed ghost atoms within ghost cutoff
// only if neighbor list has changed since last check
if (lastcheck < neighbor->lastcall) check_ghosts();
// acquire updated ghost atom positions
// necessary b/c are calling this after integrate, but before Verlet comm
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(finalpartner);
memory->destroy(distsq);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/break:partner");
memory->create(finalpartner,nmax,"bond/break:finalpartner");
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;
finalpartner[i] = 0;
distsq[i] = 0.0;
}
// loop over bond list
// setup possible partner list of bonds to break
double **x = atom->x;
tagint *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];
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();
}
commflag = 1;
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;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
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 using RN for atom with smallest ID
if (fraction < 1.0) {
if (tag[i] < tag[j]) {
if (probability[i] >= fraction) continue;
} else {
if (probability[j] >= 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, whatever proc it is on
slist = special[i];
n1 = nspecial[i][0];
for (m = 0; m < n1; m++)
if (slist[m] == partner[i]) break;
n3 = nspecial[i][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
nspecial[i][0]--;
nspecial[i][1]--;
nspecial[i][2]--;
// store final broken bond partners and count the broken bond once
finalpartner[i] = tag[j];
finalpartner[j] = tag[i];
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 broken
// this insures neigh lists will immediately reflect the topology changes
// done if no bonds broken
if (breakcount) next_reneighbor = update->ntimestep;
if (!breakcount) return;
// communicate final partner and 1-2 special neighbors
// 1-2 neighs already reflect broken bonds
commflag = 2;
comm->forward_comm_variable_fix(this);
// create list of broken bonds that influence my owned atoms
// even if between owned-ghost or ghost-ghost atoms
// finalpartner is now set for owned and ghost atoms so loop over nall
// OK if duplicates in broken list due to ghosts duplicating owned atoms
// check J < 0 to insure a broken bond to unknown atom is included
// i.e. bond partner outside of cutoff length
nbreak = 0;
for (i = 0; i < nall; i++) {
if (finalpartner[i] == 0) continue;
j = atom->map(finalpartner[i]);
if (j < 0 || tag[i] < tag[j]) {
if (nbreak == maxbreak) {
maxbreak += DELTA;
memory->grow(broken,maxbreak,2,"bond/break:broken");
}
broken[nbreak][0] = tag[i];
broken[nbreak][1] = finalpartner[i];
nbreak++;
}
}
// update special neigh lists of all atoms affected by any broken bond
// also remove angles/dihedrals/impropers broken by broken bonds
update_topology();
// DEBUG
// print_bb();
}
/* ----------------------------------------------------------------------
insure all atoms 2 hops away from owned atoms are in ghost list
this allows dihedral 1-2-3-4 to be properly deleted
and special list of 1 to be properly updated
if I own atom 1, but not 2,3,4, and bond 3-4 is deleted
then 2,3 will be ghosts and 3 will store 4 as its finalpartner
------------------------------------------------------------------------- */
void FixBondBreak::check_ghosts()
{
int i,j,n;
tagint *slist;
int **nspecial = atom->nspecial;
int **special = atom->special;
int nlocal = atom->nlocal;
int flag = 0;
for (i = 0; i < nlocal; i++) {
slist = special[i];
n = nspecial[i][1];
for (j = 0; j < n; j++)
if (atom->map(slist[j]) < 0) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix bond/break needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
/* ----------------------------------------------------------------------
double loop over my atoms and broken bonds
influenced = 1 if atom's topology is affected by any broken bond
yes if is one of 2 atoms in bond
yes if both atom IDs appear in atom's special list
else no
if influenced:
check for angles/dihedrals/impropers to break due to broken bond
rebuild the atom's special list of 1-2,1-3,1-4 neighs
------------------------------------------------------------------------- */
void FixBondBreak::update_topology()
{
int i,j,k,n,influence,found;
tagint id1,id2;
tagint *slist;
int angles_allow = atom->avec->angles_allow;
int dihedrals_allow = atom->avec->dihedrals_allow;
int impropers_allow = atom->avec->impropers_allow;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
if (nlocal > maxinfluenced) {
maxinfluenced = atom->nmax;
memory->destroy(influenced);
memory->create(influenced,maxinfluenced,"bond/break:influenced");
}
nangles = 0;
ndihedrals = 0;
nimpropers = 0;
for (i = 0; i < nlocal; i++) {
influenced[i] = 0;
slist = special[i];
for (j = 0; j < nbreak; j++) {
id1 = broken[j][0];
id2 = broken[j][1];
influence = 0;
if (tag[i] == id1 || tag[i] == id2) influence = 1;
else {
n = nspecial[i][2];
found = 0;
for (k = 0; k < n; k++)
if (slist[k] == id1 || slist[k] == id2) found++;
if (found == 2) influence = 1;
}
if (!influence) continue;
influenced[i] = 1;
if (angles_allow) break_angles(i,id1,id2);
if (dihedrals_allow) break_dihedrals(i,id1,id2);
if (impropers_allow) break_impropers(i,id1,id2);
}
}
int newton_bond = force->newton_bond;
int all;
if (angles_allow) {
MPI_Allreduce(&nangles,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 3;
atom->nangles -= all;
}
if (dihedrals_allow) {
MPI_Allreduce(&ndihedrals,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->ndihedrals -= all;
}
if (impropers_allow) {
MPI_Allreduce(&nimpropers,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->nimpropers -= all;
}
for (i = 0; i < nlocal; i++)
if (influenced[i]) rebuild_special(i,id1,id2);
}
/* ----------------------------------------------------------------------
break any angles owned by atom M that include atom IDs 1 and 2
angle is broken if ID1-ID2 is one of 2 bonds in linear angle
------------------------------------------------------------------------- */
void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
{
int j,found;
int num_angle = atom->num_angle[m];
int *angle_type = atom->angle_type[m];
tagint *angle_atom1 = atom->angle_atom1[m];
tagint *angle_atom2 = atom->angle_atom2[m];
tagint *angle_atom3 = atom->angle_atom3[m];
int i = 0;
while (i < num_angle) {
found = 0;
if (angle_atom1[i] == id1 && angle_atom2[i] == id2) found = 1;
else if (angle_atom2[i] == id1 && angle_atom3[i] == id2) found = 1;
else if (angle_atom1[i] == id2 && angle_atom2[i] == id1) found = 1;
else if (angle_atom2[i] == id2 && angle_atom3[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_angle-1; j++) {
angle_type[j] = angle_type[j+1];
angle_atom1[j] = angle_atom1[j+1];
angle_atom2[j] = angle_atom2[j+1];
angle_atom3[j] = angle_atom3[j+1];
}
num_angle--;
nangles++;
}
}
atom->num_angle[m] = num_angle;
}
/* ----------------------------------------------------------------------
break any dihedrals owned by atom M that include atom IDs 1,2,3
dihedral is broken if ID1-ID2 is one of 3 bonds in linear dihedral
------------------------------------------------------------------------- */
void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
{
int j,found;
int num_dihedral = atom->num_dihedral[m];
int *dihedral_type = atom->dihedral_type[m];
tagint *dihedral_atom1 = atom->dihedral_atom1[m];
tagint *dihedral_atom2 = atom->dihedral_atom2[m];
tagint *dihedral_atom3 = atom->dihedral_atom3[m];
tagint *dihedral_atom4 = atom->dihedral_atom4[m];
int i = 0;
while (i < num_dihedral) {
found = 0;
if (dihedral_atom1[i] == id1 && dihedral_atom2[i] == id2) found = 1;
else if (dihedral_atom2[i] == id1 && dihedral_atom3[i] == id2) found = 1;
else if (dihedral_atom3[i] == id1 && dihedral_atom4[i] == id2) found = 1;
else if (dihedral_atom1[i] == id2 && dihedral_atom2[i] == id1) found = 1;
else if (dihedral_atom2[i] == id2 && dihedral_atom3[i] == id1) found = 1;
else if (dihedral_atom3[i] == id2 && dihedral_atom4[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_dihedral-1; j++) {
dihedral_type[j] = dihedral_type[j+1];
dihedral_atom1[j] = dihedral_atom1[j+1];
dihedral_atom2[j] = dihedral_atom2[j+1];
dihedral_atom3[j] = dihedral_atom3[j+1];
dihedral_atom4[j] = dihedral_atom4[j+1];
}
num_dihedral--;
ndihedrals++;
}
}
atom->num_dihedral[m] = num_dihedral;
}
/* ----------------------------------------------------------------------
break any impropers owned by atom M that include atom IDs 1,2,3
improper is broken if ID1-ID2 is one of 3 bonds in improper (I-J,I-K,I-L)
------------------------------------------------------------------------- */
void FixBondBreak::break_impropers(int m, tagint id1, tagint id2)
{
int j,found;
int num_improper = atom->num_improper[m];
int *improper_type = atom->improper_type[m];
tagint *improper_atom1 = atom->improper_atom1[m];
tagint *improper_atom2 = atom->improper_atom2[m];
tagint *improper_atom3 = atom->improper_atom3[m];
tagint *improper_atom4 = atom->improper_atom4[m];
int i = 0;
while (i < num_improper) {
found = 0;
if (improper_atom1[i] == id1 && improper_atom2[i] == id2) found = 1;
else if (improper_atom1[i] == id1 && improper_atom3[i] == id2) found = 1;
else if (improper_atom1[i] == id1 && improper_atom4[i] == id2) found = 1;
else if (improper_atom1[i] == id2 && improper_atom2[i] == id1) found = 1;
else if (improper_atom1[i] == id2 && improper_atom3[i] == id1) found = 1;
else if (improper_atom1[i] == id2 && improper_atom4[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_improper-1; j++) {
improper_type[j] = improper_type[j+1];
improper_atom1[j] = improper_atom1[j+1];
improper_atom2[j] = improper_atom2[j+1];
improper_atom3[j] = improper_atom3[j+1];
improper_atom4[j] = improper_atom4[j+1];
}
num_improper--;
nimpropers++;
}
}
atom->num_improper[m] = num_improper;
}
/* ----------------------------------------------------------------------
re-build special list of atom M due to bond ID1-ID2 being formed
does not affect 1-2 neighs (already include effects of new bond)
may affect 1-3 and 1-4 bonds
------------------------------------------------------------------------- */
void FixBondBreak::rebuild_special(int m, tagint id1, tagint id2)
{
int i,j,n,n1,cn1,cn2,cn3;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
// new 1-2 neighs of atom M
slist = special[m];
n1 = nspecial[m][0];
cn1 = 0;
for (i = 0; i < n1; i++)
copy[cn1++] = slist[i];
// new 1-3 neighs of atom M, based on 1-2 neighs of 1-2 neighs
// exclude self
// remove duplicates after adding all possible 1-3 neighs
cn2 = cn1;
for (i = 0; i < cn1; i++) {
n = atom->map(copy[i]);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn2++] = slist[j];
}
cn2 = dedup(cn1,cn2,copy);
// new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
// exclude self
// remove duplicates after adding all possible 1-4 neighs
cn3 = cn2;
for (i = cn1; i < cn2; i++) {
n = atom->map(copy[i]);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn3++] = slist[j];
}
cn3 = dedup(cn2,cn3,copy);
// store new special list with atom M
nspecial[m][0] = cn1;
nspecial[m][1] = cn2;
nspecial[m][2] = cn3;
memcpy(special[m],copy,cn3*sizeof(int));
}
/* ----------------------------------------------------------------------
remove all ID duplicates in copy from Nstart:Nstop-1
compare to all previous values in copy
return N decremented by any discarded duplicates
------------------------------------------------------------------------- */
int FixBondBreak::dedup(int nstart, int nstop, tagint *copy)
{
int i;
int m = nstart;
while (m < nstop) {
for (i = 0; i < m; i++)
if (copy[i] == copy[m]) {
copy[m] = copy[nstop-1];
nstop--;
break;
}
if (i == m) m++;
}
return nstop;
}
/* ---------------------------------------------------------------------- */
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,k,m,ns;
if (commflag == 1) {
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(partner[j]).d;
buf[m++] = probability[j];
}
return 2;
}
int **nspecial = atom->nspecial;
int **special = atom->special;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(finalpartner[j]).d;
ns = nspecial[j][0];
buf[m++] = ubuf(ns).d;
for (k = 0; k < ns; k++)
buf[m++] = ubuf(special[j][k]).d;
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::unpack_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
if (commflag == 1) {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
partner[i] = (tagint) ubuf(buf[m++]).i;
probability[i] = buf[m++];
}
} else {
int **nspecial = atom->nspecial;
int **special = atom->special;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
finalpartner[i] = (tagint) ubuf(buf[m++]).i;
ns = (int) ubuf(buf[m++]).i;
nspecial[i][0] = ns;
for (j = 0; j < ns; j++)
special[i][j] = (tagint) ubuf(buf[m++]).i;
}
}
}
/* ---------------------------------------------------------------------- */
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++] = ubuf(partner[i]).d;
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] = (tagint) ubuf(buf[m++]).i;
distsq[j] = buf[m++];
} else m += 2;
}
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::print_bb()
{
for (int i = 0; i < atom->nlocal; i++) {
printf("TAG %i: %d nbonds: ",atom->tag[i],atom->num_bond[i]);
for (int j = 0; j < atom->num_bond[i]; j++) {
printf(" %d",atom->bond_atom[i][j]);
}
printf("\n");
printf("TAG %i: %d nangles: ",atom->tag[i],atom->num_angle[i]);
for (int j = 0; j < atom->num_angle[i]; j++) {
printf(" %d %d %d,",atom->angle_atom1[i][j],
atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
}
printf("\n");
printf("TAG %i: %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
for (int j = 0; j < atom->num_dihedral[i]; j++) {
printf(" %d %d %d %d,",atom->dihedral_atom1[i][j],
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
atom->dihedral_atom4[i][j]);
}
printf("\n");
printf("TAG %i: %d %d %d nspecial: ",atom->tag[i],
atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) {
printf(" %d",atom->special[i][j]);
}
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s %i: %d %d %d nspecial: ",str,m,n1,n2,n3);
for (int j = 0; j < n3; j++) printf(" %d",v[j]);
printf("\n");
}
/* ---------------------------------------------------------------------- */
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 = 2*nmax * sizeof(tagint);
bytes += nmax * sizeof(double);
bytes += maxinfluenced * sizeof(int);
return bytes;
}

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