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lammps/src/replicate.cpp
jrgissing 2a4dbe5bbc bondlist_flag correction
2022-02-13 13:51:20 -05:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "replicate.h"
#include "accelerator_kokkos.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "memory.h"
#include "special.h"
#include <cstring>
using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
Replicate::Replicate(LAMMPS *lmp) : Command(lmp) {}
/* ---------------------------------------------------------------------- */
void Replicate::command(int narg, char **arg)
{
int i,j,m,n;
if (domain->box_exist == 0)
error->all(FLERR,"Replicate command before simulation box is defined");
if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
int me = comm->me;
int nprocs = comm->nprocs;
if (me == 0) utils::logmesg(lmp,"Replicating atoms ...\n");
// nrep = total # of replications
int nx = utils::inumeric(FLERR,arg[0],false,lmp);
int ny = utils::inumeric(FLERR,arg[1],false,lmp);
int nz = utils::inumeric(FLERR,arg[2],false,lmp);
int nrep = nx*ny*nz;
allnrep[0] = nx;
allnrep[1] = ny;
allnrep[2] = nz;
int bbox_flag = 0;
int bondlist_flag = 0;
if (narg == 4) {
if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1;
if (strcmp(arg[3],"bondlist") == 0) bondlist_flag = 1;
}
// error and warning checks
if (nx <= 0 || ny <= 0 || nz <= 0)
error->all(FLERR,"Illegal replicate command");
if (domain->dimension == 2 && nz != 1)
error->all(FLERR,"Cannot replicate 2d simulation in z dimension");
if ((nx > 1 && domain->xperiodic == 0) ||
(ny > 1 && domain->yperiodic == 0) ||
(nz > 1 && domain->zperiodic == 0)) {
if (comm->me == 0)
error->warning(FLERR,"Replicating in a non-periodic dimension");
}
if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
error->all(FLERR,"Cannot replicate with fixes that store atom quantities");
// record wall time for atom replication
MPI_Barrier(world);
double time1 = platform::walltime();
// maxtag = original largest atom tag across all existing atoms
maxtag = 0;
if (atom->tag_enable) {
for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxtag = maxtag_all;
}
// maxmol = largest molecule tag across all existing atoms
tagint maxmol = 0;
if (atom->molecule_flag) {
for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol = maxmol_all;
}
// check image flags maximum extent
// only efficient small image flags compared to new system
int _imagelo[3], _imagehi[3];
_imagelo[0] = 0;
_imagelo[1] = 0;
_imagelo[2] = 0;
_imagehi[0] = 0;
_imagehi[1] = 0;
_imagehi[2] = 0;
if (bbox_flag || bondlist_flag) {
for (i=0; i<atom->nlocal; ++i) {
imageint image = atom->image[i];
int xbox = (image & IMGMASK) - IMGMAX;
int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
int zbox = (image >> IMG2BITS) - IMGMAX;
if (xbox < _imagelo[0]) _imagelo[0] = xbox;
if (ybox < _imagelo[1]) _imagelo[1] = ybox;
if (zbox < _imagelo[2]) _imagelo[2] = zbox;
if (xbox > _imagehi[0]) _imagehi[0] = xbox;
if (ybox > _imagehi[1]) _imagehi[1] = ybox;
if (zbox > _imagehi[2]) _imagehi[2] = zbox;
}
MPI_Allreduce(MPI_IN_PLACE, &(_imagelo[0]), 3, MPI_INT, MPI_MIN, world);
MPI_Allreduce(MPI_IN_PLACE, &(_imagehi[0]), 3, MPI_INT, MPI_MAX, world);
}
// unmap existing atoms via image flags
for (i = 0; i < atom->nlocal; i++)
domain->unmap(atom->x[i],atom->image[i]);
// communication buffer for all my atom's info
// max_size = largest buffer needed by any proc
// must do before new Atom class created,
// since size_restart() uses atom->nlocal
int max_size;
int send_size = atom->avec->size_restart();
MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf;
memory->create(buf,max_size,"replicate:buf");
// old = original atom class
// atom = new replicated atom class
// also set atomKK for Kokkos version of Atom class
old = atom;
atomKK = nullptr;
if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp);
else atom = new Atom(lmp);
atom->settings(old);
// transfer molecule templates. needs to be done early for atom style template
if (old->nmolecule) {
atom->molecules = (Molecule **) memory->smalloc((old->nmolecule)*sizeof(Molecule *),
"atom::molecules");
atom->nmolecule = old->nmolecule;
for (i = 0; i < old->nmolecule; ++i)
atom->molecules[i] = old->molecules[i];
memory->sfree(old->molecules);
old->molecules = nullptr;
old->nmolecule = 0;
}
atom->create_avec(old->atom_style,old->avec->nargcopy,old->avec->argcopy,0);
// check that new system will not be too large
// new tags cannot exceed MAXTAGINT
// new system sizes cannot exceed MAXBIGINT
if (atom->tag_enable) {
bigint maxnewtag = maxtag + (nrep-1)*old->natoms;
if (maxnewtag < 0 || maxnewtag >= MAXTAGINT)
error->all(FLERR,"Replicated system atom IDs are too big");
}
if (nrep*old->natoms < 0 || nrep*old->natoms >= MAXBIGINT ||
nrep*old->nbonds < 0 || nrep*old->nbonds >= MAXBIGINT ||
nrep*old->nangles < 0 || nrep*old->nangles >= MAXBIGINT ||
nrep*old->ndihedrals < 0 || nrep*old->ndihedrals >= MAXBIGINT ||
nrep*old->nimpropers < 0 || nrep*old->nimpropers >= MAXBIGINT)
error->all(FLERR,"Replicated system is too big");
// assign atom and topology counts in new class from old one
atom->natoms = old->natoms * nrep;
atom->nbonds = old->nbonds * nrep;
atom->nangles = old->nangles * nrep;
atom->ndihedrals = old->ndihedrals * nrep;
atom->nimpropers = old->nimpropers * nrep;
atom->nellipsoids = old->nellipsoids * nrep;
atom->nlines = old->nlines * nrep;
atom->ntris = old->ntris * nrep;
atom->nbodies = old->nbodies * nrep;
atom->ntypes = old->ntypes;
atom->nbondtypes = old->nbondtypes;
atom->nangletypes = old->nangletypes;
atom->ndihedraltypes = old->ndihedraltypes;
atom->nimpropertypes = old->nimpropertypes;
atom->bond_per_atom = old->bond_per_atom;
atom->angle_per_atom = old->angle_per_atom;
atom->dihedral_per_atom = old->dihedral_per_atom;
atom->improper_per_atom = old->improper_per_atom;
atom->extra_bond_per_atom = old->extra_bond_per_atom;
atom->extra_angle_per_atom = old->extra_angle_per_atom;
atom->extra_dihedral_per_atom = old->extra_dihedral_per_atom;
atom->extra_improper_per_atom = old->extra_improper_per_atom;
atom->maxspecial = old->maxspecial;
// store old simulation box
int triclinic = domain->triclinic;
double old_xprd = domain->xprd;
double old_yprd = domain->yprd;
double old_zprd = domain->zprd;
double old_center[3];
for (i = 0; i < 3; i++) {
old_prd_half[i] = domain->prd_half[i];
old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]);
}
double old_xy = domain->xy;
double old_xz = domain->xz;
double old_yz = domain->yz;
// setup new simulation box
domain->boxhi[0] = domain->boxlo[0] + nx*old_xprd;
domain->boxhi[1] = domain->boxlo[1] + ny*old_yprd;
domain->boxhi[2] = domain->boxlo[2] + nz*old_zprd;
if (triclinic) {
domain->xy *= ny;
domain->xz *= nz;
domain->yz *= nz;
}
// new problem setup using new box boundaries
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
// allocate atom arrays to size N, rounded up by AtomVec->DELTA
bigint nbig = n;
nbig = atom->avec->roundup(nbig);
n = static_cast<int> (nbig);
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
// copy type arrays to new atom class
if (atom->mass) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->mass_setflag[itype] = old->mass_setflag[itype];
if (atom->mass_setflag[itype]) atom->mass[itype] = old->mass[itype];
}
}
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all replicated atoms will be owned even with round-off
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
double sublo[3],subhi[3];
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2];
}
} else {
if (domain->xperiodic) {
if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0];
if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0];
}
if (domain->yperiodic) {
if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1];
if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1];
}
if (domain->zperiodic) {
if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2];
if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2];
}
}
// loop over all procs
// if this iteration of loop is me:
// pack my unmapped atom data into buf
// bcast it to all other procs
// performs 3d replicate loop with while loop over atoms in buf
// x = new replicated position, remapped into simulation box
// unpack atom into new atom class from buf if I own it
// adjust tag, mol #, coord, topology info as needed
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
int ix,iy,iz;
tagint atom_offset,mol_offset,atom0tag;
imageint image;
double x[3],lamda[3],shiftsign[3];
double *coord;
int tag_enable = atom->tag_enable;
if (bbox_flag || bondlist_flag) {
// allgather size of buf on each proc
n = 0;
for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
int * size_buf_rnk;
memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk");
MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world);
// size of buf_all
int size_buf_all = 0;
MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world);
if (me == 0) {
auto mesg = fmt::format(" bounding box image = ({} {} {}) "
"to ({} {} {})\n",
_imagelo[0],_imagelo[1],_imagelo[2],
_imagehi[0],_imagehi[1],_imagehi[2]);
mesg += fmt::format(" bounding box extra memory = {:.2f} MB\n",
(double)size_buf_all*sizeof(double)/1024/1024);
utils::logmesg(lmp,mesg);
}
// rnk offsets
int *disp_buf_rnk;
memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk");
disp_buf_rnk[0] = 0;
for (i = 1; i < nprocs; i++)
disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1];
// allgather buf_all
double * buf_all;
memory->create(buf_all, size_buf_all, "replicate:buf_all");
MPI_Allgatherv(buf,n,MPI_DOUBLE,buf_all,size_buf_rnk,disp_buf_rnk,
MPI_DOUBLE,world);
// bounding box of original unwrapped system
double _orig_lo[3], _orig_hi[3];
if (triclinic) {
_orig_lo[0] = domain->boxlo[0] +
_imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz;
_orig_lo[1] = domain->boxlo[1] +
_imagelo[1] * old_yprd + _imagelo[2] * old_yz;
_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;
_orig_hi[0] = domain->boxlo[0] +
(_imagehi[0]+1) * old_xprd +
(_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz;
_orig_hi[1] = domain->boxlo[1] +
(_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz;
_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
} else {
_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd;
_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd;
_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;
_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd;
_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd;
_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
}
double _lo[3], _hi[3];
int num_replicas_added = 0;
// let's repurpose the old atom class to allow atom->map for all atoms
// tag and x for the whole system (before replication) stored in 'old'
m = 0;
old->nlocal = 0;
while (m < size_buf_all) m += old_avec->unpack_restart(&buf_all[m],old);
old->map_init();
old->map_set();
for (ix = 0; ix < nx; ix++) {
for (iy = 0; iy < ny; iy++) {
for (iz = 0; iz < nz; iz++) {
thisrep[0] = ix;
thisrep[1] = iy;
thisrep[2] = iz;
// domain->remap() overwrites coordinates, so always recompute here
if (triclinic) {
_lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz;
_hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz;
_lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz;
_hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz;
_lo[2] = _orig_lo[2] + iz * old_zprd;
_hi[2] = _orig_hi[2] + iz * old_zprd;
} else {
_lo[0] = _orig_lo[0] + ix * old_xprd;
_hi[0] = _orig_hi[0] + ix * old_xprd;
_lo[1] = _orig_lo[1] + iy * old_yprd;
_hi[1] = _orig_hi[1] + iy * old_yprd;
_lo[2] = _orig_lo[2] + iz * old_zprd;
_hi[2] = _orig_hi[2] + iz * old_zprd;
}
// test if bounding box of shifted replica overlaps sub-domain of proc
// if not, then skip testing atoms
int xoverlap = 1;
int yoverlap = 1;
int zoverlap = 1;
if (triclinic) {
double _llo[3];
domain->x2lamda(_lo,_llo);
double _lhi[3];
domain->x2lamda(_hi,_lhi);
if (_llo[0] > (subhi[0] - EPSILON)
|| _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
if (_llo[1] > (subhi[1] - EPSILON)
|| _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
if (_llo[2] > (subhi[2] - EPSILON)
|| _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
} else {
if (_lo[0] > (subhi[0] - EPSILON)
|| _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
if (_lo[1] > (subhi[1] - EPSILON)
|| _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
if (_lo[2] > (subhi[2] - EPSILON)
|| _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
}
int overlap = 0;
if (xoverlap && yoverlap && zoverlap) overlap = 1;
// if no overlap, test if bounding box wrapped back into new system
if (!overlap) {
// wrap back into cell
imageint imagelo = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
domain->remap(&(_lo[0]), imagelo);
int xboxlo = (imagelo & IMGMASK) - IMGMAX;
int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX;
int zboxlo = (imagelo >> IMG2BITS) - IMGMAX;
imageint imagehi = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
domain->remap(&(_hi[0]), imagehi);
int xboxhi = (imagehi & IMGMASK) - IMGMAX;
int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX;
int zboxhi = (imagehi >> IMG2BITS) - IMGMAX;
if (triclinic) {
double _llo[3];
_llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2];
domain->x2lamda(_llo,_lo);
double _lhi[3];
_lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2];
domain->x2lamda(_lhi,_hi);
}
// test all fragments for any overlap; ok to include false positives
int _xoverlap1 = 0;
int _xoverlap2 = 0;
if (!xoverlap) {
if (xboxlo < 0) {
_xoverlap1 = 1;
if (_lo[0] > (subhi[0] - EPSILON)) _xoverlap1 = 0;
}
if (xboxhi > 0) {
_xoverlap2 = 1;
if (_hi[0] < (sublo[0] + EPSILON)) _xoverlap2 = 0;
}
if (_xoverlap1 || _xoverlap2) xoverlap = 1;
}
int _yoverlap1 = 0;
int _yoverlap2 = 0;
if (!yoverlap) {
if (yboxlo < 0) {
_yoverlap1 = 1;
if (_lo[1] > (subhi[1] - EPSILON)) _yoverlap1 = 0;
}
if (yboxhi > 0) {
_yoverlap2 = 1;
if (_hi[1] < (sublo[1] + EPSILON)) _yoverlap2 = 0;
}
if (_yoverlap1 || _yoverlap2) yoverlap = 1;
}
int _zoverlap1 = 0;
int _zoverlap2 = 0;
if (!zoverlap) {
if (zboxlo < 0) {
_zoverlap1 = 1;
if (_lo[2] > (subhi[2] - EPSILON)) _zoverlap1 = 0;
}
if (zboxhi > 0) {
_zoverlap2 = 1;
if (_hi[2] < (sublo[2] + EPSILON)) _zoverlap2 = 0;
}
if (_zoverlap1 || _zoverlap2) zoverlap = 1;
}
// does either fragment overlap w/ sub-domain
if (xoverlap && yoverlap && zoverlap) overlap = 1;
}
// while loop over one proc's atom list
if (overlap) {
num_replicas_added++;
m = 0;
while (m < size_buf_all) {
for (j = 0; j < 3; j++) {
if (buf_all[m+j+1] > old_center[j]) shiftsign[j] = 1;
else shiftsign[j] = -1;
}
image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
if (triclinic == 0) {
x[0] = buf_all[m+1] + ix*old_xprd;
x[1] = buf_all[m+2] + iy*old_yprd;
x[2] = buf_all[m+3] + iz*old_zprd;
} else {
x[0] = buf_all[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
x[1] = buf_all[m+2] + iy*old_yprd + iz*old_yz;
x[2] = buf_all[m+3] + iz*old_zprd;
}
domain->remap(x,image);
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf_all[m],atom);
i = atom->nlocal - 1;
if (tag_enable)
atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
else atom_offset = 0;
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
atom->x[i][0] = x[0];
atom->x[i][1] = x[1];
atom->x[i][2] = x[2];
atom0tag = atom->tag[i];
atom->tag[i] += atom_offset;
atom->image[i] = image;
if (atom->molecular != Atom::ATOMIC) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
if (atom->molecular == Atom::MOLECULAR) {
if (atom->avec->bonds_allow)
for (j = 0; j < atom->num_bond[i]; j++) {
if (bondlist_flag)
newtag(atom0tag,atom->bond_atom[i][j],shiftsign);
else atom->bond_atom[i][j] += atom_offset;
}
if (atom->avec->angles_allow)
for (j = 0; j < atom->num_angle[i]; j++) {
if (bondlist_flag) {
newtag(atom0tag,atom->angle_atom1[i][j],shiftsign);
newtag(atom0tag,atom->angle_atom2[i][j],shiftsign);
newtag(atom0tag,atom->angle_atom3[i][j],shiftsign);
} else {
atom->angle_atom1[i][j] += atom_offset;
atom->angle_atom2[i][j] += atom_offset;
atom->angle_atom3[i][j] += atom_offset;
}
}
if (atom->avec->dihedrals_allow)
for (j = 0; j < atom->num_dihedral[i]; j++) {
if (bondlist_flag) {
newtag(atom0tag,atom->dihedral_atom1[i][j],shiftsign);
newtag(atom0tag,atom->dihedral_atom2[i][j],shiftsign);
newtag(atom0tag,atom->dihedral_atom3[i][j],shiftsign);
newtag(atom0tag,atom->dihedral_atom4[i][j],shiftsign);
} else {
atom->dihedral_atom1[i][j] += atom_offset;
atom->dihedral_atom2[i][j] += atom_offset;
atom->dihedral_atom3[i][j] += atom_offset;
atom->dihedral_atom4[i][j] += atom_offset;
}
}
if (atom->avec->impropers_allow)
for (j = 0; j < atom->num_improper[i]; j++) {
if (bondlist_flag) {
newtag(atom0tag,atom->improper_atom1[i][j],shiftsign);
newtag(atom0tag,atom->improper_atom2[i][j],shiftsign);
newtag(atom0tag,atom->improper_atom3[i][j],shiftsign);
newtag(atom0tag,atom->improper_atom4[i][j],shiftsign);
} else {
atom->improper_atom1[i][j] += atom_offset;
atom->improper_atom2[i][j] += atom_offset;
atom->improper_atom3[i][j] += atom_offset;
atom->improper_atom4[i][j] += atom_offset;
}
}
}
}
} else m += static_cast<int> (buf_all[m]);
}
} // if (overlap)
}
}
}
memory->destroy(size_buf_rnk);
memory->destroy(disp_buf_rnk);
memory->destroy(buf_all);
int sum = 0;
MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world);
double avg = (double) sum / nprocs;
if (me == 0)
utils::logmesg(lmp," average # of replicas added to proc = {:.2f} out "
"of {} ({:.2f}%)\n",avg,nx*ny*nz,avg/(nx*ny*nz)*100.0);
} else {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (me == iproc) {
n = 0;
for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
}
MPI_Bcast(&n,1,MPI_INT,iproc,world);
MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world);
for (ix = 0; ix < nx; ix++) {
for (iy = 0; iy < ny; iy++) {
for (iz = 0; iz < nz; iz++) {
// while loop over one proc's atom list
m = 0;
while (m < n) {
image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
if (triclinic == 0) {
x[0] = buf[m+1] + ix*old_xprd;
x[1] = buf[m+2] + iy*old_yprd;
x[2] = buf[m+3] + iz*old_zprd;
} else {
x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
x[2] = buf[m+3] + iz*old_zprd;
}
domain->remap(x,image);
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m],atom);
i = atom->nlocal - 1;
if (tag_enable)
atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
else atom_offset = 0;
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
atom->x[i][0] = x[0];
atom->x[i][1] = x[1];
atom->x[i][2] = x[2];
atom->tag[i] += atom_offset;
atom->image[i] = image;
if (atom->molecular != Atom::ATOMIC) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
if (atom->molecular == Atom::MOLECULAR) {
if (atom->avec->bonds_allow)
for (j = 0; j < atom->num_bond[i]; j++)
atom->bond_atom[i][j] += atom_offset;
if (atom->avec->angles_allow)
for (j = 0; j < atom->num_angle[i]; j++) {
atom->angle_atom1[i][j] += atom_offset;
atom->angle_atom2[i][j] += atom_offset;
atom->angle_atom3[i][j] += atom_offset;
}
if (atom->avec->dihedrals_allow)
for (j = 0; j < atom->num_dihedral[i]; j++) {
atom->dihedral_atom1[i][j] += atom_offset;
atom->dihedral_atom2[i][j] += atom_offset;
atom->dihedral_atom3[i][j] += atom_offset;
atom->dihedral_atom4[i][j] += atom_offset;
}
if (atom->avec->impropers_allow)
for (j = 0; j < atom->num_improper[i]; j++) {
atom->improper_atom1[i][j] += atom_offset;
atom->improper_atom2[i][j] += atom_offset;
atom->improper_atom3[i][j] += atom_offset;
atom->improper_atom4[i][j] += atom_offset;
}
}
}
} else m += static_cast<int> (buf[m]);
}
}
}
}
}
} // if (bbox_flag || bondlist_flag)
// free communication buffer and old atom class
memory->destroy(buf);
delete old;
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
utils::logmesg(lmp," {} atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all(FLERR,"Replicate did not assign all atoms correctly");
if (me == 0) {
const char *molstyle = "";
if (atom->molecular == Atom::TEMPLATE) molstyle = "template ";
if (atom->nbonds) {
utils::logmesg(lmp," {} {}bonds\n",atom->nbonds,molstyle);
}
if (atom->nangles) {
utils::logmesg(lmp," {} {}angles\n",atom->nangles,molstyle);
}
if (atom->ndihedrals) {
utils::logmesg(lmp," {} {}dihedrals\n",atom->ndihedrals,molstyle);
}
if (atom->nimpropers) {
utils::logmesg(lmp," {} {}impropers\n",atom->nimpropers,molstyle);
}
}
// check that atom IDs are valid
atom->tag_check();
// create global mapping of atoms
if (atom->map_style != Atom::MAP_NONE) {
atom->map_init();
atom->map_set();
}
// create special bond lists for molecular systems
if (atom->molecular == Atom::MOLECULAR) {
Special special(lmp);
special.build();
}
// total time
MPI_Barrier(world);
if (me == 0)
utils::logmesg(lmp," replicate CPU = {:.3f} seconds\n",platform::walltime()-time1);
}
/* ----------------------------------------------------------------------
find new tag for the atom 'atom2bond' bonded to atom 'atom0'
for bondlist option, useful for periodic loops or inconsistent image flags
reassign bond if > old boxlength / 2
------------------------------------------------------------------------- */
void Replicate::newtag(tagint atom0tag, tagint &tag2bond, double shiftsign[]) {
double del[3];
int rep2bond[3], repshift[3] = {0, 0, 0};
int atom0 = old->map(atom0tag);
int atom2bond = old->map(tag2bond);
for (int i = 0; i < 3; i++) {
del[i] = fabs(old->x[atom0][i] - old->x[atom2bond][i]);
if (del[i] > old_prd_half[i]) repshift[i] = shiftsign[i];
rep2bond[i] = thisrep[i] + repshift[i];
if (rep2bond[i] >= allnrep[i]) rep2bond[i] = 0;
if (rep2bond[i] < 0) rep2bond[i] = allnrep[i]-1;
}
tag2bond = (tag2bond + rep2bond[2]*allnrep[1]*allnrep[0]*maxtag
+ rep2bond[1]*allnrep[0]*maxtag + rep2bond[0]*maxtag);
}
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