git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
345
src/replicate.cpp
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345
src/replicate.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "replicate.h"
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#include "atom.h"
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#include "atom_atomic.h"
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#include "force.h"
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#include "domain.h"
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#include "comm.h"
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#include "special.h"
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#include "memory.h"
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#include "error.h"
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#define AtomInclude
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#include "style.h"
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#undef AtomInclude
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#define LB_FACTOR 1.1
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#define MAXATOMS 0x7FFFFFFF
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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void Replicate::command(int narg, char **arg)
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{
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int i,j,m,n;
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if (domain->box_exist == 0)
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error->all("Replicate command before simulation box is defined");
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if (narg != 3) error->all("Illegal replicate command");
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int me = comm->me;
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int nprocs = comm->nprocs;
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if (me == 0 && screen) fprintf(screen,"Replicating atoms ...\n");
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// nrep = total # of replications
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int nx = atoi(arg[0]);
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int ny = atoi(arg[1]);
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int nz = atoi(arg[2]);
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int nrep = nx*ny*nz;
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// error and warning checks
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if (nx <= 0 || ny <= 0 || nz <= 0) error->all("Illegal replicate command");
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if (force->dimension == 2 && nz != 1)
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error->all("Cannot replicate 2d simulation in z dimension");
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if ((nx > 1 && domain->xperiodic == 0) ||
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(ny > 1 && domain->yperiodic == 0) ||
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(nz > 1 && domain->zperiodic == 0))
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error->warning("Replicating in a non-periodic dimension");
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if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
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error->all("Cannot replicate with fixes that store atom quantities");
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// maxtag = largest atom tag across all existing atoms
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int maxtag = 0;
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for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
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int maxtag_all;
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MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
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maxtag = maxtag_all;
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// maxmol = largest molecule tag across all existing atoms
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int maxmol = 0;
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if (atom->molecular) {
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for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
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int maxmol_all;
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MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
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maxmol = maxmol_all;
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}
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// unmap existing atoms via image flags
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for (i = 0; i < atom->nlocal; i++)
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domain->unmap(atom->x[i][0],atom->x[i][1],atom->x[i][2],atom->image[i]);
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// nwords, words = list of atom style keywords
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// old = original atom class
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// atom = new replicated atom class
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char **words;
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int nwords = atom->style2arg(words);
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Atom *old = atom;
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if (0) return; // dummy line to enable else-if macro expansion
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#define AtomClass
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#define AtomStyle(key,Class) \
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else if (strcmp(old->style,#key) == 0) atom = new Class(nwords,words);
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#include "style.h"
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#undef AtomClass
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atom->settings(old);
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for (i = 0; i < nwords; i++) delete [] words[i];
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delete [] words;
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// check that new problem size will not be too large
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// if N > 2^31, turn off tags
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// if molecular, N,Nbonds,etc cannot be > 2^31 else tags/counts invalid
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double rep = nrep;
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if (rep*old->natoms > MAXATOMS) atom->tag_enable = 0;
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if (atom->molecular) {
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if (rep*old->natoms > MAXATOMS || rep*old->nbonds > MAXATOMS ||
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rep*old->nangles > MAXATOMS || rep*old->ndihedrals > MAXATOMS ||
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rep*old->nimpropers > MAXATOMS)
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error->all("Too big a problem to replicate with molecular atom style");
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}
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// assign atom and topology counts in new class from old one
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atom->natoms = old->natoms * nrep;
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atom->nbonds = old->nbonds * nrep;
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atom->nangles = old->nangles * nrep;
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atom->ndihedrals = old->ndihedrals * nrep;
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atom->nimpropers = old->nimpropers * nrep;
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atom->ntypes = old->ntypes;
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atom->nbondtypes = old->nbondtypes;
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atom->nangletypes = old->nangletypes;
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atom->ndihedraltypes = old->ndihedraltypes;
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atom->nimpropertypes = old->nimpropertypes;
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atom->bond_per_atom = old->bond_per_atom;
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atom->angle_per_atom = old->angle_per_atom;
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atom->dihedral_per_atom = old->dihedral_per_atom;
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atom->improper_per_atom = old->improper_per_atom;
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// store old simulation box
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double oldxprd = domain->xprd;
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double oldyprd = domain->yprd;
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double oldzprd = domain->zprd;
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// setup new simulation box
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domain->boxxhi = domain->boxxlo + nx*oldxprd;
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domain->boxyhi = domain->boxylo + ny*oldyprd;
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domain->boxzhi = domain->boxzlo + nz*oldzprd;
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// new problem setup using new box boundaries
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if (nprocs == 1) n = static_cast<int> (atom->natoms);
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else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
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atom->allocate_type_arrays();
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atom->grow(n);
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domain->set_initial_box();
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domain->set_global_box();
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comm->set_procs();
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domain->set_local_box();
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// sub xyz lo/hi = new processor sub-domain
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double subxlo = domain->subxlo;
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double subxhi = domain->subxhi;
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double subylo = domain->subylo;
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double subyhi = domain->subyhi;
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double subzlo = domain->subzlo;
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double subzhi = domain->subzhi;
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// copy type arrays to new atom class
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if (atom->mass_require) {
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for (int itype = 1; itype <= atom->ntypes; itype++) {
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atom->mass_setflag[itype] = old->mass_setflag[itype];
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if (atom->mass_setflag[itype]) atom->mass[itype] = old->mass[itype];
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}
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}
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if (atom->dipole_require) {
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for (int itype = 1; itype <= atom->ntypes; itype++) {
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atom->dipole_setflag[itype] = old->dipole_setflag[itype];
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if (atom->dipole_setflag[itype])
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atom->dipole[itype] = old->dipole[itype];
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}
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}
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// communication buffer for all my atom's info
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// max_size = largest buffer needed by any proc
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int max_size;
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int send_size = old->size_restart();
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MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
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double *buf;
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buf = (double *) memory->smalloc(max_size*sizeof(double),"replicate:buf");
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// loop over all procs
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// if this iteration of loop is me:
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// pack my unmapped atom data into buf
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// bcast it to all other procs
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// for each atom in buf, each proc performs 3d replicate loop:
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// xnew,ynew,znew = new replicated position
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// unpack atom into new atom class from buf if I own it
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// adjust tag, mol #, coord, topology info as needed
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int ix,iy,iz,image,atom_offset,mol_offset;
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double xnew,ynew,znew;
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int tag_enable = atom->tag_enable;
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for (int iproc = 0; iproc < nprocs; iproc++) {
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if (me == iproc) {
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n = 0;
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for (i = 0; i < old->nlocal; i++) n += old->pack_restart(i,&buf[n]);
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}
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MPI_Bcast(&n,1,MPI_INT,iproc,world);
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MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world);
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for (ix = 0; ix < nx; ix++) {
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for (iy = 0; iy < ny; iy++) {
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for (iz = 0; iz < nz; iz++) {
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m = 0;
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while (m < n) {
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xnew = buf[m+1] + ix*oldxprd;
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ynew = buf[m+2] + iy*oldyprd;
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znew = buf[m+3] + iz*oldzprd;
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image = (512 << 20) | (512 << 10) | 512;
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domain->remap(xnew,ynew,znew,image);
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if (xnew >= subxlo && xnew < subxhi &&
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ynew >= subylo && ynew < subyhi &&
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znew >= subzlo && znew < subzhi) {
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m += atom->unpack_restart(&buf[m]);
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i = atom->nlocal - 1;
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if (tag_enable)
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atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
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else atom_offset = 0;
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mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
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atom->x[i][0] = xnew;
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atom->x[i][1] = ynew;
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atom->x[i][2] = znew;
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atom->tag[i] += atom_offset;
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atom->image[i] = image;
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if (atom->molecular) {
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if (atom->molecule[i] > 0)
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atom->molecule[i] += mol_offset;
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if (atom->bonds_allow)
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for (j = 0; j < atom->num_bond[i]; j++)
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atom->bond_atom[i][j] += atom_offset;
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if (atom->angles_allow)
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for (j = 0; j < atom->num_angle[i]; j++) {
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atom->angle_atom1[i][j] += atom_offset;
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atom->angle_atom2[i][j] += atom_offset;
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atom->angle_atom3[i][j] += atom_offset;
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}
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if (atom->dihedrals_allow)
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for (j = 0; j < atom->num_dihedral[i]; j++) {
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atom->dihedral_atom1[i][j] += atom_offset;
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atom->dihedral_atom2[i][j] += atom_offset;
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atom->dihedral_atom3[i][j] += atom_offset;
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atom->dihedral_atom4[i][j] += atom_offset;
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}
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if (atom->impropers_allow)
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for (j = 0; j < atom->num_improper[i]; j++) {
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atom->improper_atom1[i][j] += atom_offset;
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atom->improper_atom2[i][j] += atom_offset;
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atom->improper_atom3[i][j] += atom_offset;
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atom->improper_atom4[i][j] += atom_offset;
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}
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}
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} else m += static_cast<int> (buf[m]);
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} // end of while loop over one proc's atom list
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}
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}
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}
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} // end of proc loop
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// free communication buffer and old atom class
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memory->sfree(buf);
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delete old;
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// check that all atoms were assigned to procs
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double natoms;
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double rlocal = atom->nlocal;
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MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
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if (me == 0) {
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if (screen) fprintf(screen," %.15g atoms\n",natoms);
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if (logfile) fprintf(logfile," %.15g atoms\n",natoms);
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}
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if (natoms != atom->natoms)
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error->all("Replicate did not assign all atoms correctly");
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if (me == 0) {
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if (atom->nbonds) {
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if (screen) fprintf(screen," %d bonds\n",atom->nbonds);
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if (logfile) fprintf(logfile," %d bonds\n",atom->nbonds);
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}
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if (atom->nangles) {
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if (screen) fprintf(screen," %d angles\n",atom->nangles);
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if (logfile) fprintf(logfile," %d angles\n",atom->nangles);
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}
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if (atom->ndihedrals) {
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if (screen) fprintf(screen," %d dihedrals\n",atom->ndihedrals);
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if (logfile) fprintf(logfile," %d dihedrals\n",atom->ndihedrals);
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}
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if (atom->nimpropers) {
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if (screen) fprintf(screen," %d impropers\n",atom->nimpropers);
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if (logfile) fprintf(logfile," %d impropers\n",atom->nimpropers);
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}
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}
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// create global mapping and bond topology now that system is defined
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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}
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if (atom->molecular) {
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Special special;
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special.build();
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}
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}
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