git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/dump.cpp
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286
src/dump.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 "mpi.h"
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#include "stdlib.h"
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#include "string.h"
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#include "stdio.h"
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#include "dump.h"
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#include "atom.h"
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#include "update.h"
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#include "group.h"
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#include "output.h"
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#include "memory.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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Dump::Dump(int narg, char **arg)
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{
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MPI_Comm_rank(world,&me);
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MPI_Comm_size(world,&nprocs);
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int n = strlen(arg[0]) + 1;
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id = new char[n];
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strcpy(id,arg[0]);
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igroup = group->find(arg[1]);
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groupbit = group->bitmask[igroup];
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n = strlen(arg[2]) + 1;
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style = new char[n];
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strcpy(style,arg[2]);
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n = strlen(arg[4]) + 1;
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filename = new char[n];
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strcpy(filename,arg[4]);
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flush_flag = 1;
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format = NULL;
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format_user = NULL;
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maxbuf = 0;
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buf = NULL;
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// parse filename for special syntax
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// if contains '%', write one file per proc and replace % with proc-ID
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// if contains '*', write one file per timestep and replace * with timestep
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// check file suffixes
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// if ends in .bin = binary file
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// else if ends in .gz = gzipped text file
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// else ASCII text file
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compressed = 0;
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binary = 0;
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multifile = 0;
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multiproc = 0;
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char *ptr;
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if (ptr = strchr(filename,'%')) {
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multiproc = 1;
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char *extend = new char[strlen(filename) + 16];
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*ptr = '\0';
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sprintf(extend,"%s%d%s",filename,me,ptr+1);
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delete [] filename;
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n = strlen(extend) + 1;
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filename = new char[n];
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strcpy(filename,extend);
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delete [] extend;
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}
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if (strchr(filename,'*')) multifile = 1;
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char *suffix = filename + strlen(filename) - strlen(".bin");
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if (suffix > filename && strcmp(suffix,".bin") == 0) binary = 1;
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suffix = filename + strlen(filename) - strlen(".gz");
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if (suffix > filename && strcmp(suffix,".gz") == 0) compressed = 1;
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}
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/* ---------------------------------------------------------------------- */
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Dump::~Dump()
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{
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delete [] id;
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delete [] style;
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delete [] filename;
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delete [] format;
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delete [] format_default;
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delete [] format_user;
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memory->sfree(buf);
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// XTC style sets fp to NULL since it closes file in its destructor
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if (multifile == 0 && fp != NULL) {
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if (multiproc) fclose(fp);
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else if (me == 0) fclose(fp);
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}
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}
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/* ---------------------------------------------------------------------- */
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void Dump::write()
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{
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// if file per timestep, open new file
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if (multifile) openfile();
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// nme = # of dump lines this proc will contribute to dump
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// ntotal = total # of dump lines
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// nmax = max # of dump lines on any proc
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int nme = count();
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int ntotal,nmax;
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if (multiproc) nmax = nme;
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else {
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MPI_Allreduce(&nme,&ntotal,1,MPI_INT,MPI_SUM,world);
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MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
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}
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// write timestep header
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if (multiproc) write_header(nme);
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else if (me == 0) write_header(ntotal);
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// grow communication buffer if necessary
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if (nmax*size_one > maxbuf) {
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maxbuf = nmax*size_one;
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memory->sfree(buf);
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buf = (double *) memory->smalloc(maxbuf*sizeof(double),"dump:buf");
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}
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// pack my data into buf
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// send_size = # of quantities in buf
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int me_size = pack();
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// multiproc = 1 = each proc writes own data to own file
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// multiproc = 0 = all procs write to one file thru proc 0
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// proc 0 pings each proc, receives it's data, writes to file
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// all other procs wait for ping, send their data to proc 0
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if (multiproc) write_data(me_size/size_one,buf);
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else {
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int tmp,nlines;
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MPI_Status status;
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MPI_Request request;
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if (me == 0) {
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for (int iproc = 0; iproc < nprocs; iproc++) {
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if (iproc) {
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MPI_Irecv(buf,maxbuf,MPI_DOUBLE,iproc,0,world,&request);
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MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_DOUBLE,&nlines);
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nlines /= size_one;
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} else nlines = me_size/size_one;
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write_data(nlines,buf);
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}
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if (flush_flag) fflush(fp);
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} else {
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MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
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MPI_Rsend(buf,me_size,MPI_DOUBLE,0,0,world);
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}
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}
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// if file per timestep, close file
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if (multifile) {
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if (multiproc) fclose(fp);
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else if (me == 0) fclose(fp);
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}
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}
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/* ----------------------------------------------------------------------
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process params common to all dumps here
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if unknown param, call modify_param specific to the dump
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------------------------------------------------------------------------- */
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void Dump::modify_params(int narg, char **arg)
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{
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if (narg == 0) error->all("Illegal dump_modify command");
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int iarg = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"format") == 0) {
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if (iarg+2 > narg) error->all("Illegal dump_modify command");
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delete [] format_user;
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format_user = NULL;
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if (strcmp(arg[iarg+1],"none")) {
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int n = strlen(arg[iarg+1]) + 1;
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format_user = new char[n];
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strcpy(format_user,arg[iarg+1]);
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"flush") == 0) {
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if (iarg+2 > narg) error->all("Illegal dump_modify command");
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if (strcmp(arg[iarg+1],"yes") == 0) flush_flag = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) flush_flag = 0;
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else error->all("Illegal dump_modify command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"every") == 0) {
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if (iarg+2 > narg) error->all("Illegal dump_modify command");
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int n = atoi(arg[iarg+1]);
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if (n <= 0) error->all("Illegal dump_modify command");
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int idump;
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for (idump = 0; idump < output->ndump; idump++)
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if (strcmp(id,output->dump[idump]->id) == 0) break;
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output->dump_every[idump] = n;
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iarg += 2;
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} else {
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int n = modify_param(narg-iarg,&arg[iarg]);
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if (n == 0) error->all("Illegal dump_modify command");
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iarg += n;
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}
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}
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}
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/* ----------------------------------------------------------------------
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return # of bytes of allocated memory in buf
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------------------------------------------------------------------------- */
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int Dump::memory_usage()
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{
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int bytes = maxbuf * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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generic opening of a dump file
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ASCII or binary or gzipped
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some derived classes override this function
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------------------------------------------------------------------------- */
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void Dump::openfile()
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{
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// if one file per timestep, replace '*' with current timestep
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char *filecurrent;
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if (multifile == 0) filecurrent = filename;
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else {
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filecurrent = new char[strlen(filename) + 16];
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char *ptr = strchr(filename,'*');
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*ptr = '\0';
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sprintf(filecurrent,"%s%d%s",filename,update->ntimestep,ptr+1);
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*ptr = '*';
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}
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// open one file on proc 0 or file on every proc
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if (me == 0 || multiproc) {
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if (compressed) {
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#ifdef GZIP
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char gzip[128];
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sprintf(gzip,"gzip -6 > %s",filecurrent);
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fp = popen(gzip,"w");
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#else
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error->one("Cannot open gzipped file");
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#endif
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} else if (binary) {
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fp = fopen(filecurrent,"wb");
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} else {
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fp = fopen(filecurrent,"w");
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}
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if (fp == NULL) error->one("Cannot open dump file");
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}
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// delete string with timestep replaced
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if (multifile) delete [] filecurrent;
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}
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