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lammps/src/create_bonds.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: Mike Salerno (NRL) added single methods
------------------------------------------------------------------------- */
#include <cstdlib>
#include <cstring>
#include "create_bonds.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "comm.h"
#include "group.h"
#include "special.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{MANY,SBOND,SANGLE,SDIHEDRAL};
/* ---------------------------------------------------------------------- */
CreateBonds::CreateBonds(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void CreateBonds::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use create_bonds unless atoms have IDs");
if (atom->molecular != 1)
error->all(FLERR,"Cannot use create_bonds with non-molecular system");
if (narg < 4) error->all(FLERR,"Illegal create_bonds command");
// parse args
int style;
int iarg = 0;
if (strcmp(arg[0],"many") == 0) {
style = MANY;
if (narg != 6) error->all(FLERR,"Illegal create_bonds command");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Cannot find create_bonds group ID");
group1bit = group->bitmask[igroup];
igroup = group->find(arg[2]);
if (igroup == -1) error->all(FLERR,"Cannot find create_bonds group ID");
group2bit = group->bitmask[igroup];
btype = force->inumeric(FLERR,arg[3]);
rmin = force->numeric(FLERR,arg[4]);
rmax = force->numeric(FLERR,arg[5]);
if (rmin > rmax) error->all(FLERR,"Illegal create_bonds command");
iarg = 6;
} else if (strcmp(arg[0],"single/bond") == 0) {
style = SBOND;
if (narg < 4) error->all(FLERR,"Illegal create_bonds command");
btype = force->inumeric(FLERR,arg[1]);
batom1 = force->tnumeric(FLERR,arg[2]);
batom2 = force->tnumeric(FLERR,arg[3]);
if (batom1 == batom2)
error->all(FLERR,"Illegal create_bonds command");
iarg = 4;
} else if (strcmp(arg[0],"single/angle") == 0) {
style = SANGLE;
if (narg < 5) error->all(FLERR,"Illegal create_bonds command");
atype = force->inumeric(FLERR,arg[1]);
aatom1 = force->tnumeric(FLERR,arg[2]);
aatom2 = force->tnumeric(FLERR,arg[3]);
aatom3 = force->tnumeric(FLERR,arg[4]);
if ((aatom1 == aatom2) || (aatom1 == aatom3) || (aatom2 == aatom3))
error->all(FLERR,"Illegal create_bonds command");
iarg = 5;
} else if (strcmp(arg[0],"single/dihedral") == 0) {
style = SDIHEDRAL;
if (narg < 6) error->all(FLERR,"Illegal create_bonds command");
dtype = force->inumeric(FLERR,arg[1]);
datom1 = force->tnumeric(FLERR,arg[2]);
datom2 = force->tnumeric(FLERR,arg[3]);
datom3 = force->tnumeric(FLERR,arg[4]);
datom4 = force->tnumeric(FLERR,arg[5]);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR,"Illegal create_bonds command");
iarg = 6;
} else error->all(FLERR,"Illegal create_bonds command");
// optional args
int specialflag = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"special") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_bonds command");
if (strcmp(arg[iarg+1],"yes") == 0) specialflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) specialflag = 0;
else error->all(FLERR,"Illegal create_bonds command");
iarg += 2;
} else error->all(FLERR,"Illegal create_bonds command");
}
// error checks
if (style == MANY) {
if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in create_bonds command");
if (specialflag == 0)
error->all(FLERR,"Cannot use special no with create_bonds many");
} else if (style == SBOND) {
if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in create_bonds command");
} else if (style == SANGLE) {
if (atype <= 0 || atype > atom->nangletypes)
error->all(FLERR,"Invalid angle type in create_bonds command");
} else if (style == SDIHEDRAL) {
if (dtype <= 0 || dtype > atom->ndihedraltypes)
error->all(FLERR,"Invalid dihedral type in create_bonds command");
}
// invoke creation method
if (style == MANY) many();
else if (style == SBOND) single_bond();
else if (style == SANGLE) single_angle();
else if (style == SDIHEDRAL) single_dihedral();
// trigger special list build
if (specialflag) {
Special special(lmp);
special.build();
}
}
/* ---------------------------------------------------------------------- */
void CreateBonds::many()
{
double rminsq = rmin*rmin;
double rmaxsq = rmax*rmax;
// store state before bond creation
bigint nbonds_previous = atom->nbonds;
// request a full neighbor list for use by this command
int irequest = neighbor->request(this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->command = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->requests[irequest]->command_style = "create_bonds";
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
// error check on cutoff
// if no pair style, neighbor list will be empty
if (force->pair == NULL)
error->all(FLERR,"Create_bonds requires a pair style be defined");
if (rmax > neighbor->cutneighmax)
error->all(FLERR,"Create_bonds max distance > neighbor cutoff");
if (rmax > neighbor->cutneighmin && comm->me == 0)
error->warning(FLERR,"Create_bonds max distance > minimum neighbor cutoff");
// require special_bonds 1-2 weights = 0.0 and KSpace = NULL
// so that already bonded atom pairs do not appear in neighbor list
// otherwise with newton_bond = 1,
// would be hard to check if I-J bond already existed
// note that with KSpace, pair with weight = 0 could still be in neigh list
if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0)
error->all(FLERR,"Create_bonds command requires "
"special_bonds 1-2 weights be 0.0");
if (force->kspace)
error->all(FLERR,"Create_bonds command requires "
"no kspace_style be defined");
// setup domain, communication and neighboring
// acquire ghosts and build standard neighbor lists
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build(1);
// build neighbor list this command needs based on earlier request
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(list);
// loop over all neighs of each atom
// compute distance between two atoms consistently on both procs
// add bond if group and distance criteria are met
// check that bond list does not overflow
tagint *tag = atom->tag;
int *mask = atom->mask;
double **x = atom->x;
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
double newton_bond = force->newton_bond;
int nlocal = atom->nlocal;
int i,j,ii,jj,inum,jnum,flag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
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;
// only consider bond creation if I,J distance between 2 cutoffs
// compute rsq identically on both I,J loop iterations
// if I,J tags equal, do not bond atom to itself
if (tag[i] < tag[j]) {
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
} else if (tag[i] > tag[j]) {
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;
} else continue;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rminsq || rsq > rmaxsq) continue;
// only consider bond creation if igroup and jgroup match I,J atoms
flag = 0;
if ((mask[i] & group1bit) && (mask[j] & group2bit)) flag = 1;
if ((mask[i] & group2bit) && (mask[j] & group1bit)) flag = 1;
if (!flag) continue;
// create bond, check for overflow
// on I,J loop iterations, store with 1 or 2 atoms based on newton_bond
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 create_bonds");
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
}
}
}
// recount bonds
bigint nbonds = 0;
for (int i = 0; i < nlocal; i++) nbonds += num_bond[i];
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (!force->newton_bond) atom->nbonds /= 2;
// print new bond count
bigint nadd_bonds = atom->nbonds - nbonds_previous;
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Added " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
nadd_bonds,atom->nbonds);
}
if (logfile) {
fprintf(logfile,"Added " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
nadd_bonds,atom->nbonds);
}
}
}
/* ---------------------------------------------------------------------- */
void CreateBonds::single_bond()
{
int m;
// check that 2 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(batom1);
const int idx2 = atom->map(batom2);
int count = 0;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 2)
error->all(FLERR,"Create_bonds single/bond atoms do not exist");
// create bond once or 2x if newton_bond set
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
if ((m = idx1) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
bond_atom[m][num_bond[m]] = batom2;
num_bond[m]++;
}
atom->nbonds++;
if (force->newton_bond) return;
if ((m = idx2) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
bond_atom[m][num_bond[m]] = batom1;
num_bond[m]++;
}
}
/* ---------------------------------------------------------------------- */
void CreateBonds::single_angle()
{
int m;
// check that 3 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(aatom1);
const int idx2 = atom->map(aatom2);
const int idx3 = atom->map(aatom3);
int count = 0;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
if ((idx3 >= 0) && (idx3 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 3)
error->all(FLERR,"Create_bonds single/angle atoms do not exist");
// create angle once or 3x if newton_bond set
int *num_angle = atom->num_angle;
int **angle_type = atom->angle_type;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
if ((m = idx2) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
angle_atom3[m][num_angle[m]] = aatom3;
num_angle[m]++;
}
atom->nangles++;
if (force->newton_bond) return;
if ((m = idx1) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
angle_atom3[m][num_angle[m]] = aatom3;
num_angle[m]++;
}
if ((m = idx3) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
angle_atom3[m][num_angle[m]] = aatom3;
num_angle[m]++;
}
}
/* ---------------------------------------------------------------------- */
void CreateBonds::single_dihedral()
{
int m;
// check that 4 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(datom1);
const int idx2 = atom->map(datom2);
const int idx3 = atom->map(datom3);
const int idx4 = atom->map(datom4);
int count = 0;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
if ((idx3 >= 0) && (idx3 < nlocal)) count++;
if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 4)
error->all(FLERR,"Create_bonds single/dihedral atoms do not exist");
// create bond once or 4x if newton_bond set
int *num_dihedral = atom->num_dihedral;
int **dihedral_type = atom->dihedral_type;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
dihedral_atom3[m][num_dihedral[m]] = datom3;
dihedral_atom4[m][num_dihedral[m]] = datom4;
num_dihedral[m]++;
}
atom->ndihedrals++;
if (force->newton_bond) return;
if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
dihedral_atom3[m][num_dihedral[m]] = datom3;
dihedral_atom4[m][num_dihedral[m]] = datom4;
num_dihedral[m]++;
}
if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
dihedral_atom3[m][num_dihedral[m]] = datom3;
dihedral_atom4[m][num_dihedral[m]] = datom4;
num_dihedral[m]++;
}
if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
dihedral_atom3[m][num_dihedral[m]] = datom3;
dihedral_atom4[m][num_dihedral[m]] = datom4;
num_dihedral[m]++;
}
}
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