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fix_bond_create.cpp
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Mon, Nov 4, 22:16

fix_bond_create.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_create.h"
#include "update.h"
#include "respa.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all("Illegal fix bond/create command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix bond/create command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
iatomtype = atoi(arg[4]);
jatomtype = atoi(arg[5]);
double cutoff = atof(arg[6]);
btype = atoi(arg[7]);
if (iatomtype < 1 || iatomtype > atom->ntypes ||
jatomtype < 1 || jatomtype > atom->ntypes)
error->all("Invalid atom type in fix bond/create command");
if (cutoff < 0.0) error->all("Illegal fix bond/create command");
if (btype < 1 || btype > atom->nbondtypes)
error->all("Invalid bond type in fix bond/create command");
cutsq = cutoff*cutoff;
// optional keywords
imaxbond = 0;
inewtype = iatomtype;
jmaxbond = 0;
jnewtype = jatomtype;
fraction = 1.0;
int seed = 12345;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"iparam") == 0) {
if (iarg+3 > narg) error->all("Illegal fix bond/create command");
imaxbond = atoi(arg[iarg+1]);
inewtype = atoi(arg[iarg+2]);
if (imaxbond < 0) error->all("Illegal fix bond/create command");
if (inewtype < 1 || inewtype > atom->ntypes)
error->all("Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"jparam") == 0) {
if (iarg+3 > narg) error->all("Illegal fix bond/create command");
jmaxbond = atoi(arg[iarg+1]);
jnewtype = atoi(arg[iarg+2]);
if (jmaxbond < 0) error->all("Illegal fix bond/create command");
if (jnewtype < 1 || jnewtype > atom->ntypes)
error->all("Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all("Illegal fix bond/create command");
fraction = atof(arg[iarg+1]);
seed = atoi(arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
error->all("Illegal fix bond/create command");
if (seed <= 0) error->all("Illegal fix bond/create command");
iarg += 3;
} else error->all("Illegal fix bond/create command");
}
// error check
if (atom->molecular == 0)
error->all("Cannot use fix bond/create with non-molecular systems");
if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all("Inconsistent iparam/jparam values in fix bond/create command");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + me);
// perform initial allocation of atom-based arrays
// register with Atom class
// bondcount values will be initialized in setup()
bondcount = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
countflag = 0;
// 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
createcount = 0;
createcounttotal = 0;
}
/* ---------------------------------------------------------------------- */
FixBondCreate::~FixBondCreate()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
delete random;
// delete locally stored arrays
memory->destroy(bondcount);
memory->destroy(partner);
memory->destroy(distsq);
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::init()
{
// check cutoff for iatomtype,jatomtype
if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all("Fix bond/create cutoff is longer than pairwise cutoff");
// require special bonds = 0,1,1
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0)
error->all("Fix bond/create requires special_bonds lj = 0,1,1");
if (atom->q_flag)
if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0)
error->all("Fix bond/create requires special_bonds coul = 0,1,1");
// warn if angles, dihedrals, impropers are being used
if (force->angle || force->dihedral || force->improper) {
if (me == 0)
error->warning("Created bonds will not create angles, "
"dihedrals, or impropers");
}
// need a half neighbor list, built when ever re-neighboring occurs
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::setup(int vflag)
{
int i,j,m;
// compute initial bondcount if this is first run
// can't do this earlier, like in constructor or init, b/c need ghost info
if (countflag) return;
countflag = 1;
// count bonds stored with each bond I own
// if newton bond is not set, just increment count on atom I
// if newton bond is set, also increment count on atom J even if ghost
// bondcount is long enough to tally ghost atom counts
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
int **bond_atom = atom->bond_atom;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;
int newton_bond = force->newton_bond;
for (i = 0; i < nall; i++) bondcount[i] = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
if (bond_type[i][j] == btype) {
bondcount[i]++;
if (newton_bond) {
m = atom->map(bond_atom[i][j]);
if (m < 0)
error->one("Could not count initial bonds in fix bond/create");
bondcount[m]++;
}
}
}
// if newton_bond is set, need to sum bondcount
commflag = 0;
if (newton_bond) comm->reverse_comm_fix(this);
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::post_integrate()
{
int i,j,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,min,max;
int *ilist,*jlist,*numneigh,**firstneigh,*slist;
if (update->ntimestep % nevery) return;
// need updated ghost atom positions
comm->forward_comm();
// forward comm of bondcount, so ghosts have it
commflag = 0;
comm->forward_comm_fix(this);
// 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/create:partner");
memory->create(distsq,nmax,"bond/create:distsq");
probability = distsq;
}
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
for (i = 0; i < nall; i++) {
partner[i] = 0;
distsq[i] = BIG;
}
// loop over neighbors of my atoms
// each atom sets one closest eligible partner atom ID to bond with
double **x = atom->x;
int *tag = atom->tag;
int *mask = atom->mask;
int *type = atom->type;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (!(mask[j] & groupbit)) continue;
jtype = type[j];
possible = 0;
if (itype == iatomtype && jtype == jatomtype) {
if ((imaxbond == 0 || bondcount[i] < imaxbond) &&
(jmaxbond == 0 || bondcount[j] < jmaxbond))
possible = 1;
} else if (itype == jatomtype && jtype == iatomtype) {
if ((jmaxbond == 0 || bondcount[i] < jmaxbond) &&
(imaxbond == 0 || bondcount[j] < imaxbond))
possible = 1;
}
if (!possible) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
if (rsq < distsq[i]) {
partner[i] = tag[j];
distsq[i] = rsq;
}
if (rsq < distsq[j]) {
partner[j] = tag[i];
distsq[j] = rsq;
}
}
}
// reverse comm of distsq and partner
// not needed if newton_pair off since I,J pair was seen by both procs
commflag = 1;
if (force->newton_pair) 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);
// create bonds for atoms I own
// if other atom is owned by another proc, it should create same bond
// 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 newton_bond = force->newton_bond;
int ncreate = 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;
}
// if newton_bond is set, only store with I or J
// if not newton_bond, store bond with both I and J
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one("New bond exceeded bonds per atom in fix bond/create");
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
}
// add a 1-2 neighbor to special bond list for atom I
// atom J will also do this
slist = atom->special[i];
n1 = nspecial[i][0];
n3 = nspecial[i][2];
if (n3 == atom->maxspecial)
error->one("New bond exceeded special list size in fix bond/create");
for (m = n3; m > n1; m--) slist[m+1] = slist[m];
slist[n1] = tag[j];
nspecial[i][0]++;
nspecial[i][1]++;
nspecial[i][2]++;
// increment bondcount, convert atom to new type if limit reached
bondcount[i]++;
if (type[i] == iatomtype) {
if (bondcount[i] == imaxbond) type[i] = inewtype;
} else {
if (bondcount[i] == jmaxbond) type[i] = jnewtype;
}
// count the created bond once
if (tag[i] < tag[j]) ncreate++;
}
// tally stats
MPI_Allreduce(&ncreate,&createcount,1,MPI_INT,MPI_SUM,world);
createcounttotal += createcount;
atom->nbonds += createcount;
// trigger reneighboring if any bonds were formed
if (createcount) next_reneighbor = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
if (commflag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = bondcount[j];
}
return 1;
} else {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = partner[j];
buf[m++] = probability[j];
}
return 2;
}
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (commflag == 0) {
for (i = first; i < last; i++)
bondcount[i] = static_cast<int> (buf[m++]);
} else {
for (i = first; i < last; i++) {
partner[i] = static_cast<int> (buf[m++]);
probability[i] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (commflag == 0) {
for (i = first; i < last; i++)
buf[m++] = bondcount[i];
return 1;
} else {
for (i = first; i < last; i++) {
buf[m++] = distsq[i];
buf[m++] = partner[i];
}
return 2;
}
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
if (commflag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
bondcount[j] += static_cast<int> (buf[m++]);
}
} else {
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m] < distsq[j]) {
distsq[j] = buf[m++];
partner[j] = static_cast<int> (buf[m++]);
} else m += 2;
}
}
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::grow_arrays(int nmax)
{
memory->grow(bondcount,nmax,"bond/create:bondcount");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::copy_arrays(int i, int j)
{
bondcount[j] = bondcount[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::pack_exchange(int i, double *buf)
{
buf[0] = bondcount[i];
return 1;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::unpack_exchange(int nlocal, double *buf)
{
bondcount[nlocal] = static_cast<int> (buf[0]);
return 1;
}
/* ---------------------------------------------------------------------- */
double FixBondCreate::compute_vector(int n)
{
if (n == 1) return (double) createcount;
return (double) createcounttotal;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondCreate::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax*2 * sizeof(int);
bytes += nmax * sizeof(double);
return bytes;
}

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