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dump_molfile.cpp
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Sat, Jun 8, 11:44

dump_molfile.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 author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "dump_molfile.h"
#include "domain.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "output.h"
#include "group.h"
#include "memory.h"
#include "error.h"
#include "molfile_interface.h"
using namespace LAMMPS_NS;
typedef MolfileInterface MFI;
// syntax:
// dump <id> <groupid> molfile <every> <filename> <type> [<path>]
// path defaults to "." -> will look for .so files in CWD.
//
// XXX: potential change: add more options and make them optional
// path <path>
// template <file> <type> (import name and topology information from file)
// bonds <yes|no> (write out bond information)
// topology <yes|no> (write out all topology information)
/* ---------------------------------------------------------------------- */
DumpMolfile::DumpMolfile(LAMMPS *lmp, int narg, char **arg)
: Dump(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal dump molfile command");
if (binary || compressed || multiproc)
error->all(FLERR,"Invalid dump molfile filename");
// required settings
sort_flag = 1;
sortcol = 0;
// storage for collected information
size_one = 4;
if (atom->molecule_flag) ++size_one;
if (atom->q_flag) ++size_one;
if (atom->rmass_flag) ++size_one;
if (atom->radius_flag) ++size_one;
need_structure = 0;
unwrap_flag = 0;
velocity_flag = 0;
topology_flag = 0;
ntotal = 0;
me = comm->me;
coords = vels = masses = charges = radiuses = NULL;
types = molids = NULL;
ntypes = atom->ntypes;
typenames = NULL;
// allocate global array for atom coords
bigint n = group->count(igroup);
if (n > MAXSMALLINT/sizeof(float))
error->all(FLERR,"Too many atoms for dump molfile");
if (n < 1)
error->all(FLERR,"Not enough atoms for dump molfile");
natoms = static_cast<int>(n);
if (me == 0) {
memory->create(types,natoms,"dump:types");
memory->create(coords,3*natoms,"dump:coords");
if (atom->molecule_flag) memory->create(molids,natoms,"dump:molids");
if (atom->q_flag) memory->create(charges,natoms,"dump:charges");
if (atom->rmass_flag) memory->create(masses,natoms,"dump:masses");
if (atom->radius_flag) memory->create(radiuses,natoms,"dump:radiuses");
mf = new MolfileInterface(arg[5],MFI::M_WRITE);
const char *path = (const char *) ".";
if (narg > 6)
path=arg[6];
if (mf->find_plugin(path)!= MFI::E_MATCH)
error->one(FLERR,"No suitable molfile plugin found");
if (screen)
fprintf(screen,"Dump '%s' uses molfile plugin: %s\n",
id, mf->get_plugin_name());
if (logfile)
fprintf(logfile,"Dump '%s' uses molfile plugin: %s\n",
id,mf->get_plugin_name());
}
}
/* ---------------------------------------------------------------------- */
DumpMolfile::~DumpMolfile()
{
if (me == 0) {
mf->close();
memory->destroy(types);
memory->destroy(coords);
memory->destroy(vels);
memory->destroy(masses);
memory->destroy(charges);
memory->destroy(radiuses);
delete mf;
}
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
}
/* ---------------------------------------------------------------------- */
void DumpMolfile::init_style()
{
if (sort_flag == 0 || sortcol != 0)
error->all(FLERR,"Dump molfile requires sorting by atom ID");
if (me == 0) {
/* initialize typenames array to numeric types by default */
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
/* a 32-bit int can be maximally 10 digits plus sign */
typenames[itype] = new char[12];
sprintf(typenames[itype],"%d",itype);
}
}
// open single file, one time only
if (multifile == 0) openfile();
}
}
/* ---------------------------------------------------------------------- */
void DumpMolfile::write()
{
// simulation box dimensions
if (domain->triclinic == 1) {
double *h = domain->h;
double alen = h[0];
double blen = sqrt(h[5]*h[5] + h[1]*h[1]);
double clen = sqrt(h[4]*h[4] + h[3]*h[3] + h[2]*h[2]);
cell[0] = alen;
cell[1] = blen;
cell[2] = clen;
cell[3] = (90.0 - asin((h[5]*h[4] + h[1]*h[3]) / blen/clen)); // alpha
cell[4] = (90.0 - asin((h[0]*h[4]) / alen/clen)); // beta
cell[5] = (90.0 - asin((h[0]*h[5]) / alen/blen)); // gamma
} else {
cell[0] = domain->xprd;
cell[1] = domain->yprd;
cell[2] = domain->zprd;
cell[3] = cell[4] = cell[5] = 90.0f;
}
// nme = # of dump lines this proc will contribute to dump
nme = count();
bigint bnme = nme;
// ntotal = total # of dump lines
// nmax = max # of dump lines on any proc
int nmax;
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
// for single file output, the number of atoms must not change.
if (natoms != ntotal) {
if (multifile == 0) {
error->all(FLERR,"Single file molfile dump needs constant #atoms");
} else {
natoms = ntotal;
}
}
ntotal = 0;
// if file per timestep, open new file
if (multifile) openfile();
// insure proc 0 can receive everyone's info
// limit nmax*size_one to int since used as arg in MPI_Rsend() below
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
error->all(FLERR,"Too much per-proc info for dump");
maxbuf = nmax;
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
if (nmax > maxids) {
maxids = nmax;
memory->destroy(ids);
memory->create(ids,maxids,"dump:ids");
}
pack(ids);
sort();
int tmp,nlines;
MPI_Status status;
MPI_Request request;
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,0,0,world);
}
}
/* ---------------------------------------------------------------------- */
void DumpMolfile::openfile()
{
// single file, already opened, so just return
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
need_structure = 1;
if (me == 0) {
// close open file, if needed.
if (mf->is_open()) mf->close();
// if one file per timestep, replace '*' with current timestep
char *filecurrent = new char[strlen(filename) + 16];
if (multifile == 0) {
strcpy(filecurrent,filename);
} else {
char *ptr = strchr(filename,'*');
char *p1 = filename;
char *p2 = filecurrent;
while (p1 != ptr)
*p2++ = *p1++;
if (padflag == 0) {
sprintf(p2,BIGINT_FORMAT "%s",update->ntimestep,ptr+1);
} else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%0%d%s%%s",padflag,&bif[1]);
sprintf(p2,pad,update->ntimestep,ptr+1);
}
}
if (mf->open(filecurrent,&natoms))
error->one(FLERR,"Cannot open dump file");
delete[] filecurrent;
}
}
/* ---------------------------------------------------------------------- */
void DumpMolfile::pack(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
double **x = atom->x;
tagint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
m = n = 0;
if (unwrap_flag) {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
int ix = (image[i] & IMGMASK) - IMGMAX;
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int iz = (image[i] >> IMG2BITS) - IMGMAX;
buf[m++] = type[i];
if (domain->triclinic) {
buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
buf[m++] = x[i][1] + iy * yprd + iz * yz;
buf[m++] = x[i][2] + iz * zprd;
} else {
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
}
if (atom->molecule_flag) buf[m++] = atom->molecule[i];
if (atom->q_flag) buf[m++] = atom->q[i];
if (atom->rmass_flag) buf[m++] = atom->mass[i];
if (atom->radius_flag) buf[m++] = atom->radius[i];
ids[n++] = tag[i];
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
if (atom->molecule_flag) buf[m++] = atom->molecule[i];
if (atom->q_flag) buf[m++] = atom->q[i];
if (atom->rmass_flag) buf[m++] = atom->mass[i];
if (atom->radius_flag) buf[m++] = atom->radius[i];
ids[n++] = tag[i];
}
}
}
/* ---------------------------------------------------------------------- */
void DumpMolfile::write_data(int n, double *mybuf)
{
if (me == 0) {
// copy buf atom coords into global arrays
int m = 0;
for (int i = 0; i < n; i++) {
types[ntotal] = static_cast<int>(mybuf[m++]);
coords[3*ntotal + 0] = mybuf[m++];
coords[3*ntotal + 1] = mybuf[m++];
coords[3*ntotal + 2] = mybuf[m++];
if (atom->molecule_flag) molids[ntotal] = static_cast<int>(mybuf[m++]);
if (atom->q_flag) charges[ntotal] = mybuf[m++];
if (atom->rmass_flag) masses[ntotal] = mybuf[m++];
if (atom->radius_flag) radiuses[ntotal] = mybuf[m++];
++ntotal;
}
// if last chunk of atoms in this snapshot, write global arrays to file
if (ntotal == natoms) {
ntotal = 0;
if (need_structure) {
mf->property(MFI::P_NAME,types,typenames);
if (atom->molecule_flag)
mf->property(MFI::P_RESI,molids);
if (atom->rmass_flag) {
mf->property(MFI::P_MASS,masses);
} else {
mf->property(MFI::P_MASS,types,atom->mass);
}
if (atom->q_flag)
mf->property(MFI::P_CHRG,charges);
if (atom->radius_flag)
mf->property(MFI::P_RADS,radiuses);
// update/write structure information in plugin
mf->structure();
need_structure = 0;
}
double simtime = update->ntimestep * update->dt;
mf->timestep(coords,NULL,cell,&simtime);
}
}
}
/* ---------------------------------------------------------------------- */
int DumpMolfile::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"unwrap") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR, "Dump modify element names do not match atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
int n = strlen(arg[itype]) + 1;
typenames[itype] = new char[n];
strcpy(typenames[itype],arg[itype]);
}
return ntypes+1;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
bigint DumpMolfile::memory_usage()
{
bigint bytes = Dump::memory_usage();
bytes += memory->usage(coords,natoms*3);
bytes += sizeof(MFI);
return bytes;
}

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