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lammps/src/read_dump_orig.cpp
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read_dump_orig.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.
Contributed by Timothy Sirk
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "read_dump.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "error.h"
#include "memory.h"
#include "irregular.h"
using namespace LAMMPS_NS;
#define MAXATOM 2000 //max atoms for one comm
#define MAXLINE 1024 //max char in a line
#define XYZ 1
#define XYZV 2
#define XYZI 4
/* ---------------------------------------------------------------------- */
ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
{
line = new char[MAXLINE];
keyword = new char[MAXLINE];
narg = maxarg = 0;
arg = NULL;
boxsize= new double[9]; // orth or tri
}
/* ---------------------------------------------------------------------- */
ReadDump::~ReadDump()
{
delete [] line;
delete [] keyword;
delete [] boxsize;
if(me==0) memory->destroy(buf);
}
/* ---------------------------------------------------------------------- */
void ReadDump::command(int narg, char **arg)
{
int ttime, assigned=0;
if (narg != 2) error->all(FLERR,"Illegal read_dump command");
// set some basic output info
// important for use with rerun
setup(false);
// clear old per-atom properties
if(clear) clearAtom();
// read a frame for given time
// pack whole frame into buffer
// optionally close file
if (me == 0)
{
open(arg[0]);
// set target step
ttime=atoi(arg[1]);
// read until requested step
findFrame(ttime);
// check header and load the frame
getHeader();
packFrame(true);
}
// communication to size buffer, etc
commBuffInfo();
// broadcast dump in chunks
// ratoms = remaining atoms to send
// nchunk = atoms to send this time
while(ratoms>0)
{
nchunk=MIN(ratoms,MAXATOM);
// nchunk to all procs
MPI_Bcast(&nchunk,1,MPI_INT,0,world);
// let procs find owned atoms
// pass in how many atoms already sent
sendCoord(ndatoms-ratoms);
// copy in new data to owned atoms
// keep track of how many atoms assigned
assigned += updateCoord();
ratoms=ratoms-MAXATOM;
}
// move atoms back inside simulation box and to new processors
migrateAtoms();
// summarize
int ntotal=0;
char str[128];
MPI_Allreduce(&assigned,&ntotal,1,MPI_INT,MPI_SUM,world);
sprintf(str,"Assigned %d of %d atoms from dump", ntotal,ndatoms);
if(me==0) error->message(FLERR,str);
// update the image flags
// don't bother to chunk
if ((exist & XYZI) == XYZI){
updateImages();
memory->destroy(imagebuf);
}
}
/* ----------------------------------------------------------------------
settings for read_dump
------------------------------------------------------------------------- */
void ReadDump::setup(bool rerun)
{
MPI_Comm_rank(world,&me);
// binary existance flags, add more as needed
// unset later if not present
exist = XYZ | XYZV | XYZI;
//set flags for default and rerun
if(rerun)
{
quiet=true; // not verbose
fileclose=false; // leave dump file open
clear=true; // clear per-atom properties before update
}
else
{
quiet=false;
fileclose=true;
clear=false;
}
}
/* ----------------------------------------------------------------------
clear arrays
------------------------------------------------------------------------- */
void ReadDump::clearAtom()
{
// per atom info to clear
double **v = atom->v;
for (int i = 0; i < atom->nlocal+atom->nghost; i++)
{
v[i][0] = 0.0;
v[i][1] = 0.0;
v[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
proc 0 opens dump file
test if gzipped
------------------------------------------------------------------------- */
void ReadDump::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else
{
error->one(FLERR,"Cannot open gzipped file");
}
if (fp == NULL)
{
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
/* ----------------------------------------------------------------------
find right frame
------------------------------------------------------------------------- */
void ReadDump::findFrame(int ttime)
{
// loop until section found with matching keyword
const char *keyword= (const char *)"TIMESTEP";
long int offset=0;
while (1)
{
if (fgets(line,MAXLINE,fp) == NULL) error->one(FLERR,"Unexpected end of file");
if (!strstr(line,keyword)) error->one(FLERR,"Bad dump format");
// found TIMESTEP
time=atoi(fgets(line,MAXLINE,fp));
line=fgets(line,MAXLINE,fp);
// position for NUMBER OF ATOMS
offset=ftell(fp);
line=fgets(line,MAXLINE,fp);
ndatoms=atoi(line);
if(time==ttime) break;
// no match, drop remaining header and atoms
skip_lines(5);
skip_lines(ndatoms);
}
// found frame
// reset file position to top of frame
fseek(fp, offset, SEEK_SET);
}
/* ----------------------------------------------------------------------
proc 0 reads N lines from file
------------------------------------------------------------------------- */
void ReadDump::skip_lines(int n)
{
char *eof=NULL;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
}
/* ----------------------------------------------------------------------
read header
------------------------------------------------------------------------- */
void ReadDump::getHeader()
{
bstride=1; // buffer stride must be at least 1
int count=0,xs=1;
// get num dump atoms
line=fgets(line,MAXLINE,fp);
ndatoms=atoi(line);
if (ndatoms != atom->natoms && !quiet)
error->warning(FLERR,"Different Natoms in dump snapshot");
fgets(line,MAXLINE,fp);
if (!strstr(line,"ITEM: BOX BOUNDS")) error->one(FLERR,"No box bounds"); // format check
//box sizes
if (domain->triclinic == 0)
{
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf",&boxsize[0],&boxsize[1]); // xlo xhi
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf",&boxsize[3],&boxsize[4]);
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf",&boxsize[6],&boxsize[7]);
}
else
{
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf %lf",&boxsize[0],&boxsize[1],&boxsize[2]); // xlo xhi xy
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf %lf",&boxsize[3],&boxsize[4],&boxsize[5]);
fgets(line,MAXLINE,fp);
sscanf (line,"%lf %lf %lf",&boxsize[6],&boxsize[7],&boxsize[8]);
}
// tokenize custom headers, can be any order
// record position of x,v,etc in dump header
fgets(line,MAXLINE,fp);
if (!strstr(line,"ATOMS")) error->one(FLERR,"Misplaced or Missing ATOMS section");
// position header, offset by two for zero index
int nheader=-2;
for (int i=0; i<10; i++) header[i]=-1;
char *pch = strtok(line," \n");
while (pch != NULL)
{
// fields to read
if(!strcmp(pch,"id")) header[0]=nheader;
if(!strcmp(pch,"x")) header[1]=nheader;
if(!strcmp(pch,"y")) header[2]=nheader;
if(!strcmp(pch,"z")) header[3]=nheader;
if(!strcmp(pch,"xu")) header[1]=nheader;
if(!strcmp(pch,"yu")) header[2]=nheader;
if(!strcmp(pch,"zu")) header[3]=nheader;
if(!strcmp(pch,"vx")) header[4]=nheader;
if(!strcmp(pch,"vy")) header[5]=nheader;
if(!strcmp(pch,"vz")) header[6]=nheader;
if(!strcmp(pch,"ix")) header[7]=nheader;
if(!strcmp(pch,"iy")) header[8]=nheader;
if(!strcmp(pch,"iz")) header[9]=nheader;
// scaled coordinates
if(!strcmp(pch,"xs") || !strcmp(pch,"xsu"))
{
header[1]=nheader;
xs=xs<<1;
}
if(!strcmp(pch,"ys") || !strcmp(pch,"ysu"))
{
header[2]=nheader;
xs=xs<<1;
}
if(!strcmp(pch,"zs") || !strcmp(pch,"zsu"))
{
header[3]=nheader;
xs=xs<<1;
}
pch = strtok(NULL, " \n");
nheader++;
}
// error if no id, warn for others
// check for id (required)
if(header[0]<0)
{
error->one(FLERR,"Missing ID in dump header");
}
// check for coordinates (optional)
for(int i=1; i<4; i++)
if(header[i]<0)
{
if(!quiet) error->warning(FLERR,"Missing coordinates in dump header");
exist=exist^XYZ;
break;
}
// check for velocities (optional)
for(int i=4; i<7; i++)
if(header[i]<0)
{
if(!quiet) error->warning(FLERR,"No velocities in dump header");
exist=exist^XYZV;
break;
}
// check for image flags (optional)
for(int i=7; i<10; i++)
if(header[i]<0)
{
if(!quiet) error->warning(FLERR,"No image flags in dump header");
exist=exist^XYZI;
break;
}
// map headers position to buffer position
// must have at least the ID
hndx[0]=count++;
if ((exist & XYZ) == XYZ)
{
if(!quiet) error->message(FLERR,"Reading coordinates");
bstride=bstride+3;
hndx[1]=count++;
hndx[2]=count++;
hndx[3]=count++;
// check scale coordinates
// all xs,ys,zs must be present
if (xs==8)
{
scale[0]=boxsize[1]-boxsize[0];
scale[1]=boxsize[4]-boxsize[3];
scale[2]=boxsize[7]-boxsize[6];
if(!quiet) error->message(FLERR,"Found scaled coordinates");
}
else scale[0]=scale[1]=scale[2]=1;
}
if ((exist & XYZV) == XYZV)
{
if(!quiet) error->message(FLERR,"Reading velocities");
bstride=bstride+3;
hndx[4]=count++;
hndx[5]=count++;
hndx[6]=count++;
}
if ((exist & XYZI) == XYZI)
{
if(!quiet) error->message(FLERR,"Reading image flags");
hndx[7]=count++;
hndx[8]=count++;
hndx[9]=count++;
}
}
/* ----------------------------------------------------------------------
read header
------------------------------------------------------------------------- */
void ReadDump::packFrame(bool fileclose)
{
char *pch;
double tmp;
int nheader;
//allocate
memory->create(buf,ndatoms,bstride,"command:buf");
// pack entire frame into a buffer
if((exist & XYZI) == XYZI)
{
memory->create(imagebuf,4*ndatoms,"command:imagebuf");
}
for(int i=0; i<ndatoms; i++)
{
fgets(line,MAXLINE,fp);
pch = strtok(line, " ");
nheader=0;
while (pch != NULL)
{
tmp=atof(pch);
if(nheader==header[0])
{
buf[i][hndx[0]]=tmp; // id
if((exist & XYZI) == XYZI) imagebuf[i*4]=(int)tmp; // id for images (optional)
}
if((exist & XYZ) == XYZ)
{
if(nheader==header[1]) buf[i][hndx[1]]=tmp*scale[0];
if(nheader==header[2]) buf[i][hndx[2]]=tmp*scale[1];
if(nheader==header[3]) buf[i][hndx[3]]=tmp*scale[2];
}
if((exist & XYZV) == XYZV)
{
if(nheader==header[4]) buf[i][hndx[4]]=tmp;
if(nheader==header[5]) buf[i][hndx[5]]=tmp;
if(nheader==header[6]) buf[i][hndx[6]]=tmp;
}
if((exist & XYZI) == XYZI)
{
// save image flags into seperate array
// can't compress to binary yet b/c ix iy iz can be in any order
if(nheader==header[7]) imagebuf[i*4+1]=(int)tmp;
if(nheader==header[8]) imagebuf[i*4+2]=(int)tmp;
if(nheader==header[9]) imagebuf[i*4+3]=(int)tmp;
}
nheader++;
pch = strtok (NULL, " ");
}
}
if(fileclose) fclose(fp);
}
/* ----------------------------------------------------------------------
Communicate some info about this frame
------------------------------------------------------------------------- */
void ReadDump::commBuffInfo()
{
// total number of atoms
MPI_Bcast(&ndatoms,1,MPI_INT,0,world);
// remaining atoms to comm
// begin with all atoms
ratoms=ndatoms;
// width of buffer
MPI_Bcast(&bstride,1,MPI_INT,0,world);
// update time
MPI_Bcast(&time,1,MPI_INT,0,world);
update->ntimestep=(bigint)time;
// existance bitflags
MPI_Bcast(&exist,1,MPI_INT,0,world);
// box size
MPI_Bcast(boxsize,9,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
broadcast all the dump atom info from a buffer. Could improve by
sending just sending one message to each proc that contains owned atoms
or just have each proc read the file?
------------------------------------------------------------------------- */
void ReadDump::sendCoord(int last)
{
if (domain->triclinic == 0)
{
domain->boxlo[0]=boxsize[0];
domain->boxhi[0]=boxsize[1];
domain->boxlo[1]=boxsize[3];
domain->boxhi[1]=boxsize[4];
domain->boxlo[2]=boxsize[6];
domain->boxhi[2]=boxsize[7];
}
else
{
domain->boxlo[0]=boxsize[0];
domain->boxhi[0]=boxsize[1];
domain->xy=boxsize[2];
domain->boxlo[1]=boxsize[3];
domain->boxhi[1]=boxsize[4];
domain->xy=boxsize[5];
domain->boxlo[2]=boxsize[6];
domain->boxhi[2]=boxsize[7];
domain->xy=boxsize[8];
}
int bsize=nchunk*bstride;
xbuffer = new double[bsize];
//fill buffer on proc 0
if(me==0)
{
int z=0;
for(int y=0; y<nchunk; y++)
{
for(int j=0; j<bstride; j++)
xbuffer[z+j]=buf[y+last][j];
z=z+bstride;
}
}
MPI_Bcast(xbuffer,bsize,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
update atoms using dump info
------------------------------------------------------------------------- */
int ReadDump::updateCoord()
{
double** x=atom->x;
double** v=atom->v;
int nlocal=atom->nlocal;
int assigned=0;
int j=0;
int id=0,gid=0;
// customize with more per-atom data
// nchunk atoms per comm
// need a global->local map
// make an array if no mapping exists
if(atom->map_style==0)
{
atom->map_style=1;
atom->map_init();
atom->map_set();
}
for(int n=0; n<nchunk; n++)
{
j=n*bstride;
gid=(int)xbuffer[j++];
id=atom->map( gid );
if(id >= 0 && id < nlocal)
{
// add more fields as needed
if((exist & XYZ) == XYZ)
{
x[id][0]=xbuffer[j++];
x[id][1]=xbuffer[j++];
x[id][2]=xbuffer[j++];
}
if((exist & XYZV) == XYZV)
{
v[id][0]=xbuffer[j++];
v[id][1]=xbuffer[j++];
v[id][2]=xbuffer[j++];
}
assigned++;
}
}
delete [] xbuffer;
// return the number of atoms updated
return assigned;
}
/* ----------------------------------------------------------------------
move atoms back inside simulation box and to new processors
use remap() instead of pbc() in case atoms moved a long distance
use irregular() in case atoms moved a long distance
------------------------------------------------------------------------- */
void ReadDump::migrateAtoms()
{
double **x = atom->x;
int nlocal = atom->nlocal;
// convert coord if tric box
if (domain->triclinic) domain->x2lamda(atom->nlocal);
// reset box and remap before communicating
// remap will modify image flags
domain->reset_box();
for (int i = 0; i < nlocal; i++) domain->remap(x[i],atom->image[i]);
// irregular comm
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
// convert coord if tric box
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
update the atoms image flags. must be done after remap.
------------------------------------------------------------------------- */
void ReadDump::updateImages()
{
int gid, lid; // global and local id
// allocate for images, except on proc 0
if(me != 0) memory->create(imagebuf,4*ndatoms,"command:imagebuf");
MPI_Bcast(imagebuf,ndatoms*4,MPI_INT,0,world);
for(int i=0; i<ndatoms; i++)
{
gid=(int)imagebuf[i*4];
lid=atom->map(gid);
if(lid >= 0 && lid < atom->nlocal)
{
atom->image[lid] = ((imagebuf[i*4+3] + 512 & 1023) << 20) | ((imagebuf[i*4+2] + 512 & 1023) << 10) | (imagebuf[i*4+1]+ 512 & 1023);
}
}
}
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