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replicate.cpp
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Tue, Nov 5, 00:02

replicate.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 "stdlib.h"
#include "string.h"
#include "replicate.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "force.h"
#include "domain.h"
#include "comm.h"
#include "special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define MAXATOMS 0x7FFFFFFF
#define EPSILON 1.0e-6
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
Replicate::Replicate(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Replicate::command(int narg, char **arg)
{
int i,j,m,n;
if (domain->box_exist == 0)
error->all("Replicate command before simulation box is defined");
if (narg != 3) error->all("Illegal replicate command");
int me = comm->me;
int nprocs = comm->nprocs;
if (me == 0 && screen) fprintf(screen,"Replicating atoms ...\n");
// nrep = total # of replications
int nx = atoi(arg[0]);
int ny = atoi(arg[1]);
int nz = atoi(arg[2]);
int nrep = nx*ny*nz;
// error and warning checks
if (nx <= 0 || ny <= 0 || nz <= 0) error->all("Illegal replicate command");
if (domain->dimension == 2 && nz != 1)
error->all("Cannot replicate 2d simulation in z dimension");
if ((nx > 1 && domain->xperiodic == 0) ||
(ny > 1 && domain->yperiodic == 0) ||
(nz > 1 && domain->zperiodic == 0))
error->warning("Replicating in a non-periodic dimension");
if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
error->all("Cannot replicate with fixes that store atom quantities");
// maxtag = largest atom tag across all existing atoms
int maxtag = 0;
for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
maxtag = maxtag_all;
// maxmol = largest molecule tag across all existing atoms
int maxmol = 0;
if (atom->molecular) {
for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
int maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
maxmol = maxmol_all;
}
// 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 =
(double *) memory->smalloc(max_size*sizeof(double),"replicate:buf");
// old = original atom class
// atom = new replicated atom class
// if old atom style was hybrid, pass sub-style names to create_avec
Atom *old = atom;
atom = new Atom(lmp);
atom->settings(old);
int nstyles = 0;
char **keywords = NULL;
if (strcmp(old->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) old->avec;
nstyles = avec_hybrid->nstyles;
keywords = avec_hybrid->keywords;
}
atom->create_avec(old->atom_style,nstyles,keywords);
// check that new problem size will not be too large
// if N > 2^31, turn off tags
// if molecular, N/Nbonds/etc cannot be > 2^31 else tags/counts invalid
double rep = nrep;
if (rep*old->natoms > MAXATOMS) atom->tag_enable = 0;
if (atom->molecular) {
if (rep*old->natoms > MAXATOMS || rep*old->nbonds > MAXATOMS ||
rep*old->nangles > MAXATOMS || rep*old->ndihedrals > MAXATOMS ||
rep*old->nimpropers > MAXATOMS)
error->all("Too big a problem to replicate with molecular atom style");
}
// 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->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;
// 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_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();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_procs();
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];
}
}
if (atom->dipole) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->dipole_setflag[itype] = old->dipole_setflag[itype];
if (atom->dipole_setflag[itype])
atom->dipole[itype] = old->dipole[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 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 (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// 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,image,atom_offset,mol_offset;
double x[3],lamda[3];
double *coord;
int tag_enable = atom->tag_enable;
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 = (512 << 20) | (512 << 10) | 512;
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) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
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]);
}
}
}
}
} // end of proc loop
// free communication buffer and old atom class
memory->sfree(buf);
delete old;
// check that all atoms were assigned to procs
double natoms;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," %.15g atoms\n",natoms);
if (logfile) fprintf(logfile," %.15g atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all("Replicate did not assign all atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," %d bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," %d bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," %d angles\n",atom->nangles);
if (logfile) fprintf(logfile," %d angles\n",atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," %d dihedrals\n",atom->ndihedrals);
if (logfile) fprintf(logfile," %d dihedrals\n",atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," %d impropers\n",atom->nimpropers);
if (logfile) fprintf(logfile," %d impropers\n",atom->nimpropers);
}
}
// create global mapping and bond topology now that system is defined
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
Special special(lmp);
special.build();
}
}

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