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modified doc page, added examples

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This commit is contained in:
Steve Plimpton
2024-05-06 16:44:45 -06:00
parent 25a9bf1ff6
commit a4449fb6ff
24 changed files with 2015 additions and 163 deletions
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625
src/replicate.cpp
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@ -12,6 +12,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Chris Knight (ANL) for bbox option
Jake Gissinger (Stevens Institute of Technology) for bond/periodic option
------------------------------------------------------------------------- */
#include "replicate.h"
#include "accelerator_kokkos.h"
@ -70,13 +76,24 @@ void Replicate::command(int narg, char **arg)
utils::logmesg(lmp, "Replication is creating a {}x{}x{} = {} times larger system...\n",
nx, ny, nz, nrep);
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;
// optional keywords
bbox_flag = 0;
bond_flag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"bbox") == 0) {
bbox_flag = 1;
iarg++;
} else if (strcmp(arg[iarg],"bond/periodic") == 0) {
bond_flag = 1;
iarg++;
} else error->all(FLERR,"Illegal replicate command");
}
if (bond_flag) bbox_flag = 1;
// error and warning checks
if (nx <= 0 || ny <= 0 || nz <= 0)
@ -91,7 +108,7 @@ void Replicate::command(int narg, char **arg)
}
if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
error->all(FLERR,"Cannot replicate with fixes that store atom quantities");
error->all(FLERR,"Cannot replicate with fixes that store per-atom quantities");
// record wall time for atom replication
@ -110,24 +127,24 @@ void Replicate::command(int narg, char **arg)
// maxmol = largest molecule tag across all existing atoms
tagint maxmol = 0;
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;
}
// reset image flags for bondlist option
if (bondlist_flag)
// reset image flags to zero for bond/periodic option
if (bond_flag)
for (i=0; i<atom->nlocal; ++i)
atom->image[i] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// check image flags maximum extent
// _imagelo/hi = maximum extent of image flags in each dimension
// only efficient small image flags compared to new system
int _imagelo[3], _imagehi[3];
_imagelo[0] = 0;
_imagelo[1] = 0;
_imagelo[2] = 0;
@ -135,7 +152,7 @@ void Replicate::command(int narg, char **arg)
_imagehi[1] = 0;
_imagehi[2] = 0;
if (bbox_flag || bondlist_flag) {
if (bbox_flag || bond_flag) {
for (i=0; i<atom->nlocal; ++i) {
imageint image = atom->image[i];
@ -157,14 +174,14 @@ void Replicate::command(int narg, char **arg)
}
// unmap existing atoms via image flags
// no-op for bond/periodic option
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
// must do before new Atom class created, since size_restart() uses atom->nlocal
int max_size;
int send_size = atom->avec->size_restart();
@ -177,7 +194,7 @@ void Replicate::command(int narg, char **arg)
// atom = new replicated atom class
// also set atomKK for Kokkos version of Atom class
Atom *old = atom;
old = atom;
atomKK = nullptr;
if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp);
else atom = new Atom(lmp);
@ -216,7 +233,7 @@ void Replicate::command(int narg, char **arg)
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
// assign atom and topology counts in new Atom class from old Atom class
atom->natoms = old->natoms * nrep;
atom->nbonds = old->nbonds * nrep;
@ -258,18 +275,18 @@ void Replicate::command(int narg, char **arg)
// store old simulation box
int triclinic = domain->triclinic;
double old_xprd = domain->xprd;
double old_yprd = domain->yprd;
double old_zprd = domain->zprd;
old_xprd = domain->xprd;
old_yprd = domain->yprd;
old_zprd = domain->zprd;
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;
old_xy = domain->xy;
old_xz = domain->xz;
old_yz = domain->yz;
// setup new simulation box
// define new simulation box
domain->boxhi[0] = domain->boxlo[0] + nx*old_xprd;
domain->boxhi[1] = domain->boxlo[1] + ny*old_yprd;
@ -280,15 +297,14 @@ void Replicate::command(int narg, char **arg)
domain->yz *= nz;
}
// new problem setup using new box boundaries
// setup of new system using new atom counts and new box boundaries
// allocate atom arrays to size N, rounded up by AtomVec->DELTA
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);
@ -362,15 +378,23 @@ void Replicate::command(int narg, char **arg)
}
}
// 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
// use
if (!bbox_flag) {
replicate_by_proc(nx,ny,nz,sublo,subhi,buf);
} else {
replicate_by_bbox(nx,ny,nz,sublo,subhi,buf);
}
/*
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
@ -381,7 +405,7 @@ void Replicate::command(int narg, char **arg)
double *coord;
int tag_enable = atom->tag_enable;
if (bbox_flag || bondlist_flag) {
if (bbox_flag || bond_flag) {
// allgather size of buf on each proc
@ -456,7 +480,7 @@ void Replicate::command(int narg, char **arg)
// store x and tag for the whole system (before replication)
if (bondlist_flag) {
if (bond_flag) {
memory->create(old_x,old->natoms,3,"replicate:old_x");
memory->create(old_tag,old->natoms,"replicate:old_tag");
@ -668,13 +692,13 @@ void Replicate::command(int narg, char **arg)
if (atom->molecular == Atom::MOLECULAR) {
if (atom->avec->bonds_allow)
for (j = 0; j < atom->num_bond[i]; j++) {
if (bondlist_flag)
if (bond_flag)
newtag(atom0tag,atom->bond_atom[i][j]);
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) {
if (bond_flag) {
newtag(atom0tag,atom->angle_atom1[i][j]);
newtag(atom0tag,atom->angle_atom2[i][j]);
newtag(atom0tag,atom->angle_atom3[i][j]);
@ -686,7 +710,7 @@ void Replicate::command(int narg, char **arg)
}
if (atom->avec->dihedrals_allow)
for (j = 0; j < atom->num_dihedral[i]; j++) {
if (bondlist_flag) {
if (bond_flag) {
newtag(atom0tag,atom->dihedral_atom1[i][j]);
newtag(atom0tag,atom->dihedral_atom2[i][j]);
newtag(atom0tag,atom->dihedral_atom3[i][j]);
@ -700,7 +724,7 @@ void Replicate::command(int narg, char **arg)
}
if (atom->avec->impropers_allow)
for (j = 0; j < atom->num_improper[i]; j++) {
if (bondlist_flag) {
if (bond_flag) {
newtag(atom0tag,atom->improper_atom1[i][j]);
newtag(atom0tag,atom->improper_atom2[i][j]);
newtag(atom0tag,atom->improper_atom3[i][j]);
@ -725,7 +749,7 @@ void Replicate::command(int narg, char **arg)
memory->destroy(size_buf_rnk);
memory->destroy(disp_buf_rnk);
memory->destroy(buf_all);
if (bondlist_flag) {
if (bond_flag) {
memory->destroy(old_x);
memory->destroy(old_tag);
}
@ -825,8 +849,14 @@ void Replicate::command(int narg, char **arg)
}
}
}
} // if (bbox_flag || bondlist_flag)
} // if (bbox_flag || bond_flag)
*/
// free communication buffer and old atom class
memory->destroy(buf);
@ -889,8 +919,511 @@ void Replicate::command(int narg, char **arg)
}
/* ----------------------------------------------------------------------
find new tag for the atom 'atom2bond' bonded to atom 'atom0'
for bondlist option, useful for periodic loops or inconsistent image flags
simple replication algorithm, suitable for small proc count
------------------------------------------------------------------------- */
void Replicate::replicate_by_proc(int nx, int ny, int nz,
double *sublo, double *subhi, double *buf)
{
int i,j,m,n;
int ix,iy,iz;
int me = comm->me;
int nprocs = comm->nprocs;
int triclinic = domain->triclinic;
int tag_enable = atom->tag_enable;
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
tagint atom_offset,mol_offset;
imageint image;
double x[3],lamda[3];
double *coord;
// loop over all procs
// if this iteration of loop is me:
// pack my unmapped atom data into buf
// bcast it to all other procs
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
// x = new replicated position, remapped into new simulation box
// if atom is within my new subdomain, unpack it into new atom class
// adjust tag, mol #, coord, topology info as needed
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]);
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]);
}
}
}
}
}
}
/* ----------------------------------------------------------------------
more complex replication algorithm
uses bounding box of each proc's subdomain to avoid checking individual atoms
faster for large processor counts
required for bond/periodic option
------------------------------------------------------------------------- */
void Replicate::replicate_by_bbox(int nx, int ny, int nz,
double *sublo, double *subhi, double *buf)
{
int i,j,m,n;
int ix,iy,iz;
int me = comm->me;
int nprocs = comm->nprocs;
int triclinic = domain->triclinic;
int tag_enable = atom->tag_enable;
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
tagint atom_offset,mol_offset,atom0tag;
imageint image;
double x[3],lamda[3];
double *coord;
// 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;
// if bond/periodic option
// store old_x and old_tag for the entire original system
if (bond_flag) {
memory->create(old_x,old->natoms,3,"replicate:old_x");
memory->create(old_tag,old->natoms,"replicate:old_tag");
i = m = 0;
while (m < size_buf_all) {
old_x[i][0] = buf_all[m+1];
old_x[i][1] = buf_all[m+2];
old_x[i][2] = buf_all[m+3];
old_tag[i] = (tagint) ubuf(buf_all[m+4]).i;
old_map.insert({old_tag[i],i});
m += static_cast<int> (buf_all[m]);
i++;
}
}
// replication loop
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 can skip testing of any individual 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) {
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]);
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 (bond_flag)
newtag(atom0tag,atom->bond_atom[i][j]);
else atom->bond_atom[i][j] += atom_offset;
}
if (atom->avec->angles_allow)
for (j = 0; j < atom->num_angle[i]; j++) {
if (bond_flag) {
newtag(atom0tag,atom->angle_atom1[i][j]);
newtag(atom0tag,atom->angle_atom2[i][j]);
newtag(atom0tag,atom->angle_atom3[i][j]);
} 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 (bond_flag) {
newtag(atom0tag,atom->dihedral_atom1[i][j]);
newtag(atom0tag,atom->dihedral_atom2[i][j]);
newtag(atom0tag,atom->dihedral_atom3[i][j]);
newtag(atom0tag,atom->dihedral_atom4[i][j]);
} 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 (bond_flag) {
newtag(atom0tag,atom->improper_atom1[i][j]);
newtag(atom0tag,atom->improper_atom2[i][j]);
newtag(atom0tag,atom->improper_atom3[i][j]);
newtag(atom0tag,atom->improper_atom4[i][j]);
} 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]);
}
}
}
}
}
memory->destroy(size_buf_rnk);
memory->destroy(disp_buf_rnk);
memory->destroy(buf_all);
if (bond_flag) {
memory->destroy(old_x);
memory->destroy(old_tag);
}
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);
}
/* ----------------------------------------------------------------------
find new tag for atom 'atom2bond' bonded to atom 'atom0'
for bond/periodic option
useful for periodic loops or inconsistent image flags
reassign bond if > old boxlength / 2
------------------------------------------------------------------------- */