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fix_bond_create.cpp
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Sun, Nov 10, 01:23

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 "atom_vec.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;
using namespace FixConst;
#define BIG 1.0e20
#define DELTA 16
/* ---------------------------------------------------------------------- */
FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
bondcount(NULL), partner(NULL), finalpartner(NULL), distsq(NULL), created(NULL), copy(NULL), random(NULL)
{
if (narg < 8) error->all(FLERR,"Illegal fix bond/create command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/create command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
iatomtype = force->inumeric(FLERR,arg[4]);
jatomtype = force->inumeric(FLERR,arg[5]);
double cutoff = force->numeric(FLERR,arg[6]);
btype = force->inumeric(FLERR,arg[7]);
if (iatomtype < 1 || iatomtype > atom->ntypes ||
jatomtype < 1 || jatomtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/create command");
if (btype < 1 || btype > atom->nbondtypes)
error->all(FLERR,"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;
atype = dtype = itype = 0;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"iparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
imaxbond = force->inumeric(FLERR,arg[iarg+1]);
inewtype = force->inumeric(FLERR,arg[iarg+2]);
if (imaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (inewtype < 1 || inewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"jparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
jmaxbond = force->inumeric(FLERR,arg[iarg+1]);
jnewtype = force->inumeric(FLERR,arg[iarg+2]);
if (jmaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (jnewtype < 1 || jnewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create 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/create command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"atype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
atype = force->inumeric(FLERR,arg[iarg+1]);
if (atype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else if (strcmp(arg[iarg],"dtype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
dtype = force->inumeric(FLERR,arg[iarg+1]);
if (dtype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else if (strcmp(arg[iarg],"itype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
itype = force->inumeric(FLERR,arg[iarg+1]);
if (itype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else error->all(FLERR,"Illegal fix bond/create command");
}
// error check
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all(FLERR,
"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
// 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;
maxcreate = 0;
created = NULL;
// copy = special list for one atom
// size = ms^2 + ms is sufficient
// b/c in rebuild_special_one() neighs of all 1-2s are added,
// then a dedup(), then neighs of all 1-3s are added, then final dedup()
// this means intermediate size cannot exceed ms^2 + ms
int maxspecial = atom->maxspecial;
copy = new tagint[maxspecial*maxspecial + maxspecial];
// 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(finalpartner);
memory->destroy(distsq);
memory->destroy(created);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// check cutoff for iatomtype,jatomtype
if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
// enable angle/dihedral/improper creation if atype/dtype/itype
// option was used and a force field has been specified
if (atype && force->angle) {
angleflag = 1;
if (atype > atom->nangletypes)
error->all(FLERR,"Fix bond/create angle type is invalid");
} else angleflag = 0;
if (dtype && force->dihedral) {
dihedralflag = 1;
if (dtype > atom->ndihedraltypes)
error->all(FLERR,"Fix bond/create dihedral type is invalid");
} else dihedralflag = 0;
if (itype && force->improper) {
improperflag = 1;
if (itype > atom->nimpropertypes)
error->all(FLERR,"Fix bond/create improper type is invalid");
} else improperflag = 0;
if (force->improper) {
if (force->improper_match("class2") || force->improper_match("ring"))
error->all(FLERR,"Cannot yet use fix bond/create with this "
"improper style");
}
// need a half neighbor list, built every Nevery steps
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
lastcheck = -1;
}
/* ---------------------------------------------------------------------- */
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, 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;
tagint **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(FLERR,"Fix bond/create needs ghost atoms "
"from further away");
bondcount[m]++;
}
}
}
// if newton_bond is set, need to sum bondcount
commflag = 1;
if (newton_bond) comm->reverse_comm_fix(this,1);
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::post_integrate()
{
int i,j,k,m,n,ii,jj,inum,jnum,itype,jtype,n1,n2,n3,possible;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
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
// needs to be <= test b/c neighbor list could have been re-built in
// same timestep as last post_integrate() call, but afterwards
// NOTE: no longer think is needed, due to error tests on atom->map()
// NOTE: if delete, can also delete lastcheck and check_ghosts()
//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();
// forward comm of bondcount, so ghosts have it
commflag = 1;
comm->forward_comm_fix(this,1);
// 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/create:partner");
memory->create(finalpartner,nmax,"bond/create:finalpartner");
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;
finalpartner[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;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *mask = atom->mask;
int *type = atom->type;
neighbor->build_one(list,1);
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];
j &= NEIGHMASK;
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;
// do not allow a duplicate bond to be created
// check 1-2 neighbors of atom I
for (k = 0; k < nspecial[i][0]; k++)
if (special[i][k] == tag[j]) possible = 0;
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 = 2;
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 = 2;
comm->forward_comm_fix(this,2);
// create bonds for atoms I own
// only if both atoms list each other as winning bond partner
// and probability constraint is satisfied
// if other atom is owned by another proc, it should do same thing
int **bond_type = atom->bond_type;
int newton_bond = force->newton_bond;
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 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;
}
}
// if newton_bond is set, only store with I or J
// if not newton_bond, store bond with both I and J
// atom J will also do this consistently, whatever proc it is on
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,"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, whatever proc it is on
// need to first remove tag[j] from later in list if it appears
// prevents list from overflowing, will be rebuilt in rebuild_special_one()
slist = special[i];
n1 = nspecial[i][0];
n2 = nspecial[i][1];
n3 = nspecial[i][2];
for (m = n1; m < n3; m++)
if (slist[m] == tag[j]) break;
if (m < n3) {
for (n = m; n < n3-1; n++) slist[n] = slist[n+1];
n3--;
if (m < n2) n2--;
}
if (n3 == atom->maxspecial)
error->one(FLERR,
"New bond exceeded special list size in fix bond/create");
for (m = n3; m > n1; m--) slist[m] = slist[m-1];
slist[n1] = tag[j];
nspecial[i][0] = n1+1;
nspecial[i][1] = n2+1;
nspecial[i][2] = n3+1;
// increment bondcount, convert atom to new type if limit reached
// atom J will also do this, whatever proc it is on
bondcount[i]++;
if (type[i] == iatomtype) {
if (bondcount[i] == imaxbond) type[i] = inewtype;
} else {
if (bondcount[i] == jmaxbond) type[i] = jnewtype;
}
// store final created bond partners and count the created bond once
finalpartner[i] = tag[j];
finalpartner[j] = tag[i];
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
// this insures neigh lists will immediately reflect the topology changes
// done if any bonds created
if (createcount) next_reneighbor = update->ntimestep;
if (!createcount) return;
// communicate final partner and 1-2 special neighbors
// 1-2 neighs already reflect created bonds
commflag = 3;
comm->forward_comm_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. a bond partner outside of cutoff length
ncreate = 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 (ncreate == maxcreate) {
maxcreate += DELTA;
memory->grow(created,maxcreate,2,"bond/create:created");
}
created[ncreate][0] = tag[i];
created[ncreate][1] = finalpartner[i];
ncreate++;
}
}
// update special neigh lists of all atoms affected by any created bond
// also add angles/dihedrals/impropers induced by created 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 created
and special list of 1 to be properly updated
if I own atom 1, but not 2,3,4, and bond 3-4 is added
then 2,3 will be ghosts and 3 will store 4 as its finalpartner
------------------------------------------------------------------------- */
void FixBondCreate::check_ghosts()
{
int i,j,n;
tagint *slist;
int **nspecial = atom->nspecial;
tagint **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/create needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
/* ----------------------------------------------------------------------
double loop over my atoms and created bonds
influenced = 1 if atom's topology is affected by any created bond
yes if is one of 2 atoms in bond
yes if either atom ID appears in as 1-2 or 1-3 in atom's special list
else no
if influenced by any created bond:
rebuild the atom's special list of 1-2,1-3,1-4 neighs
check for angles/dihedrals/impropers to create due modified special list
------------------------------------------------------------------------- */
void FixBondCreate::update_topology()
{
int i,j,k,n,influence,influenced;
tagint id1,id2;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
nangles = 0;
ndihedrals = 0;
nimpropers = 0;
overflow = 0;
//printf("NCREATE %d: ",ncreate);
//for (i = 0; i < ncreate; i++)
// printf(" %d %d,",created[i][0],created[i][1]);
//printf("\n");
for (i = 0; i < nlocal; i++) {
influenced = 0;
slist = special[i];
for (j = 0; j < ncreate; j++) {
id1 = created[j][0];
id2 = created[j][1];
influence = 0;
if (tag[i] == id1 || tag[i] == id2) influence = 1;
else {
n = nspecial[i][1];
for (k = 0; k < n; k++)
if (slist[k] == id1 || slist[k] == id2) {
influence = 1;
break;
}
}
if (!influence) continue;
influenced = 1;
}
// rebuild_special_one() first, since used by create_angles, etc
if (influenced) {
rebuild_special_one(i);
if (angleflag) create_angles(i);
if (dihedralflag) create_dihedrals(i);
if (improperflag) create_impropers(i);
}
}
int overflowall;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_SUM,world);
if (overflowall) error->all(FLERR,"Fix bond/create induced too many "
"angles/dihedrals/impropers per atom");
int newton_bond = force->newton_bond;
int all;
if (angleflag) {
MPI_Allreduce(&nangles,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 3;
atom->nangles += all;
}
if (dihedralflag) {
MPI_Allreduce(&ndihedrals,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->ndihedrals += all;
}
if (improperflag) {
MPI_Allreduce(&nimpropers,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->nimpropers += all;
}
}
/* ----------------------------------------------------------------------
re-build special list of atom M
does not affect 1-2 neighs (already include effects of new bond)
affects 1-3 and 1-4 neighs due to other atom's augmented 1-2 neighs
------------------------------------------------------------------------- */
void FixBondCreate::rebuild_special_one(int m)
{
int i,j,n,n1,cn1,cn2,cn3;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
// existing 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]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
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);
if (cn2 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
// 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]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
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);
if (cn3 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
// 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));
}
/* ----------------------------------------------------------------------
create any angles owned by atom M induced by newly created bonds
walk special list to find all possible angles to create
only add an angle if a new bond is one of its 2 bonds (I-J,J-K)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 3 atoms in angle
------------------------------------------------------------------------- */
void FixBondCreate::create_angles(int m)
{
int i,j,n,i2local,n1,n2;
tagint i1,i2,i3;
tagint *s1list,*s2list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
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];
// atom M is central atom in angle
// double loop over 1-2 neighs
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// consider all angles, only add if:
// a new bond is in the angle and atom types match
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
// angle = i1-i2-i3
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3
if (num_angle < atom->angle_per_atom) {
angle_type[num_angle] = atype;
angle_atom1[num_angle] = i1;
angle_atom2[num_angle] = i2;
angle_atom3[num_angle] = i3;
num_angle++;
nangles++;
} else overflow = 1;
}
}
atom->num_angle[m] = num_angle;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 1 in angle
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
for (j = 0; j < n2; j++) {
i3 = s2list[j];
if (i3 == i1) continue;
// angle = i1-i2-i3
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3
if (num_angle < atom->angle_per_atom) {
angle_type[num_angle] = atype;
angle_atom1[num_angle] = i1;
angle_atom2[num_angle] = i2;
angle_atom3[num_angle] = i3;
num_angle++;
nangles++;
} else overflow = 1;
}
}
atom->num_angle[m] = num_angle;
}
/* ----------------------------------------------------------------------
create any dihedrals owned by atom M induced by newly created bonds
walk special list to find all possible dihedrals to create
only add a dihedral if a new bond is one of its 3 bonds (I-J,J-K,K-L)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 4 atoms in dihedral
------------------------------------------------------------------------- */
void FixBondCreate::create_dihedrals(int m)
{
int i,j,k,n,i1local,i2local,i3local,n1,n2,n3;
tagint i1,i2,i3,i4;
tagint *s1list,*s2list,*s3list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
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];
// atom M is 2nd atom in dihedral
// double loop over 1-2 neighs
// two triple loops: one over neighs at each end of triplet
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// avoid double counting due to another atom being 2nd atom in same dihedral
// by requiring ID of 2nd atom < ID of 3rd atom
// don't do this if newton bond off since want to double count
// consider all dihedrals, only add if:
// a new bond is in the dihedral and atom types match
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
if (force->newton_bond && i2 > i3) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i3 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i3) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i1;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i3;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
for (i = 0; i < n2; i++) {
i1 = s2list[i];
if (force->newton_bond && i2 > i1) continue;
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i1local];
n3 = nspecial[i1local][0];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i3-i2-i1-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i3;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i1;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
atom->num_dihedral[m] = num_dihedral;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 1 in dihedral
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
for (j = 0; j < n2; j++) {
i3 = s2list[j];
if (i3 == i1) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i3 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i3) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i1;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i3;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
}
/* ----------------------------------------------------------------------
create any impropers owned by atom M induced by newly created bonds
walk special list to find all possible impropers to create
only add an improper if a new bond is one of its 3 bonds (I-J,I-K,I-L)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 4 atoms in improper
------------------------------------------------------------------------- */
void FixBondCreate::create_impropers(int m)
{
int i,j,k,n,i1local,n1,n2;
tagint i1,i2,i3,i4;
tagint *s1list,*s2list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
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];
// atom M is central atom in improper
// triple loop over 1-2 neighs
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// consider all impropers, only add if:
// a new bond is in the improper and atom types match
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
for (j = i+1; j < n1; j++) {
i3 = s1list[j];
for (k = j+1; k < n1; k++) {
i4 = s1list[k];
// improper = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3,i4
if (num_improper < atom->improper_per_atom) {
improper_type[num_improper] = itype;
improper_atom1[num_improper] = i1;
improper_atom2[num_improper] = i2;
improper_atom3[num_improper] = i3;
improper_atom4[num_improper] = i4;
num_improper++;
nimpropers++;
} else overflow = 1;
}
}
}
atom->num_improper[m] = num_improper;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 2 in improper
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s1list = special[i1local];
n1 = nspecial[i1local][0];
for (j = 0; j < n1; j++) {
i3 = s1list[j];
if (i3 == i1 || i3 == i2) continue;
for (k = j+1; k < n1; k++) {
i4 = s1list[k];
if (i4 == i1 || i4 == i2) continue;
// improper = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_improper < atom->improper_per_atom) {
improper_type[num_improper] = itype;
improper_atom1[num_improper] = i1;
improper_atom2[num_improper] = i2;
improper_atom3[num_improper] = i3;
improper_atom4[num_improper] = i4;
num_improper++;
nimpropers++;
} else overflow = 1;
}
}
}
}
}
/* ----------------------------------------------------------------------
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 FixBondCreate::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 FixBondCreate::post_integrate_respa(int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m,ns;
m = 0;
if (commflag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(bondcount[j]).d;
}
return m;
}
if (commflag == 2) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(partner[j]).d;
buf[m++] = probability[j];
}
return m;
}
int **nspecial = atom->nspecial;
tagint **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 FixBondCreate::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
m = 0;
last = first + n;
if (commflag == 1) {
for (i = first; i < last; i++)
bondcount[i] = (int) ubuf(buf[m++]).i;
} else if (commflag == 2) {
for (i = first; i < last; i++) {
partner[i] = (tagint) ubuf(buf[m++]).i;
probability[i] = buf[m++];
}
} else {
int **nspecial = atom->nspecial;
tagint **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 FixBondCreate::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (commflag == 1) {
for (i = first; i < last; i++)
buf[m++] = ubuf(bondcount[i]).d;
return m;
}
for (i = first; i < last; i++) {
buf[m++] = ubuf(partner[i]).d;
buf[m++] = distsq[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
if (commflag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
bondcount[j] += (int) ubuf(buf[m++]).i;
}
} else {
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;
}
}
}
/* ----------------------------------------------------------------------
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, int delflag)
{
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 == 0) return (double) createcount;
return (double) createcounttotal;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondCreate::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes = 2*nmax * sizeof(tagint);
bytes += nmax * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::print_bb()
{
for (int i = 0; i < atom->nlocal; i++) {
printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
for (int j = 0; j < atom->num_bond[i]; j++) {
printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
for (int j = 0; j < atom->num_angle[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
atom->angle_atom1[i][j], atom->angle_atom2[i][j],
atom->angle_atom3[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
for (int j = 0; j < atom->num_dihedral[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
atom->dihedral_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
for (int j = 0; j < atom->num_improper[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",",atom->improper_atom1[i][j],
atom->improper_atom2[i][j],atom->improper_atom3[i][j],
atom->improper_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %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(" " TAGINT_FORMAT,atom->special[i][j]);
}
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s " TAGINT_FORMAT ": %d %d %d nspecial: ",str,m,n1,n2,n3);
for (int j = 0; j < n3; j++) printf(" %d",v[j]);
printf("\n");
}

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