git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8236 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/read_dump.cpp

@@ -49,7 +49,7 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
   dimension = domain->dimension;
   triclinic = domain->triclinic;
 
-  nfiles = 0;
+  nfile = 0;
   files = NULL;
 
   nfield = 0;
@@ -59,13 +59,14 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
   uflag = ucflag = ucflag_all = NULL;
 
   reader = NULL;
+  fp = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
 
 ReadDump::~ReadDump()
 {
-  for (int i = 0; i < nfiles; i++) delete [] files[i];
+  for (int i = 0; i < nfile; i++) delete [] files[i];
   delete [] files;
   for (int i = 0; i < nfield; i++) delete [] fieldlabel[i];
   delete [] fieldlabel;
@@ -113,7 +114,6 @@ void ReadDump::command(int narg, char **arg)
   bigint natoms_prev = atom->natoms;
   atoms();
 
-  // NOTE: this logic is not yet right
   if (me == 0) close();
 
   // print out stats
@@ -158,10 +158,10 @@ void ReadDump::command(int narg, char **arg)
 
 void ReadDump::store_files(int nstr, char **str)
 {
-  nfiles = nstr;
+  nfile = nstr;
-  files = new char*[nfiles];
+  files = new char*[nfile];
 
-  for (int i = 0; i < nfiles; i++) {
+  for (int i = 0; i < nfile; i++) {
     int n = strlen(str[i]) + 1;
     files[i] = new char[n];
     strcpy(files[i],str[i]);
@@ -184,7 +184,6 @@ void ReadDump::setup_reader()
 
 /* ----------------------------------------------------------------------
    seek Nrequest timestep in one or more dump files
-   Nrequest can be a timestamp or -1 to match first step with exact = 0
    if exact = 1, must find exactly Nrequest
    if exact = 0, find first step >= Nrequest
    return matching ntimestep or -1 if did not find a match
@@ -196,7 +195,11 @@ bigint ReadDump::seek(bigint nrequest, int exact)
   bigint ntimestep;
 
   if (me == 0) {
-    for (ifile = 0; ifile < nfiles; ifile++) {
+
+    // exit file loop when dump timestep >= nrequest
+    // or files exhausted
+
+    for (ifile = 0; ifile < nfile; ifile++) {
       ntimestep = -1;
       open(files[ifile]);
       reader->file(fp);
@@ -211,9 +214,9 @@ bigint ReadDump::seek(bigint nrequest, int exact)
     }
 
     currentfile = ifile;
-    if (ntimestep < nrequest) close();
     if (ntimestep < nrequest) ntimestep = -1;
     if (exact && ntimestep != nrequest) ntimestep = -1;
+    if (ntimestep < 0) close();
   }
 
   MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
@@ -223,34 +226,48 @@ bigint ReadDump::seek(bigint nrequest, int exact)
 /* ----------------------------------------------------------------------
    find next matching snapshot in one or more dump files
    Ncurrent = current timestep from last snapshot
-   Nstop = match no timestep bigger than Nstop
+   Nlast = match no timestep bigger than Nlast
    Nevery = only match timesteps that are a multiple of Nevery
    Nskip = skip every this many timesteps
    return matching ntimestep or -1 if did not find a match
 ------------------------------------------------------------------------- */
 
-bigint ReadDump::next(bigint ncurrent, bigint nstop, int nevery, int nskip)
+bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
 {
   int ifile,eofflag;
   bigint ntimestep;
 
-  // NOTE: this logic is not yet right
-
   if (me == 0) {
-    for (ifile = currentfile; ifile < nfiles; ifile++) {
+
+    // exit file loop when dump timestep matches all criteria
+    // or files exhausted
+
+    int iskip = 0;
+
+    for (ifile = currentfile; ifile < nfile; ifile++) {
       ntimestep = -1;
       if (ifile != currentfile) open(files[ifile]);
       reader->file(fp);
       while (1) {
         eofflag = reader->read_time(ntimestep);
-        if (eofflag) ntimestep = -1;
+        if (iskip == nskip) iskip = 0;
-        break;
+        iskip++;
+        if (eofflag) break;
+        if (ntimestep <= ncurrent) break;
+        if (ntimestep > nlast) break;
+        if (nevery && ntimestep % nevery) reader->skip();
+        else if (iskip < nskip) reader->skip();
+        else break;
       }
-      if (ntimestep > ncurrent) break;
+      if (eofflag) close();
-      close();
+      else break;
     }
 
     currentfile = ifile;
+    if (eofflag) ntimestep = -1;
+    if (ntimestep <= ncurrent) ntimestep = -1;
+    if (ntimestep > nlast) ntimestep = -1;
+    if (ntimestep < 0) close();
   }
 
   MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
@@ -860,6 +877,8 @@ void ReadDump::open(char *file)
 
 void ReadDump::close()
 {
+  if (fp == NULL) return;
   if (compressed) pclose(fp);
   else fclose(fp);
+  fp = NULL;
 }

src/read_dump.h

@@ -48,7 +48,7 @@ private:
   int dimension;
   int triclinic;
 
-  int nfiles;              // # of dump files to process
+  int nfile;               // # of dump files to process
   char **files;            // list of file names
   int currentfile;         // currently open file
 

src/rerun.cpp

@@ -0,0 +1,177 @@
+/* ----------------------------------------------------------------------
+   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 "lmptype.h"
+#include "stdlib.h"
+#include "string.h"
+#include "rerun.h"
+#include "read_dump.h"
+#include "domain.h"
+#include "update.h"
+#include "integrate.h"
+#include "modify.h"
+#include "output.h"
+#include "finish.h"
+#include "timer.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void Rerun::command(int narg, char **arg)
+{
+  if (narg < 2) error->all(FLERR,"Illegal rerun command");
+
+  if (domain->box_exist == 0)
+    error->all(FLERR,"Rerun command before simulation box is defined");
+
+  // list of dump files = args until a keyword
+
+  int iarg = 0;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"first") == 0) break;
+    if (strcmp(arg[iarg],"last") == 0) break;
+    if (strcmp(arg[iarg],"every") == 0) break;
+    if (strcmp(arg[iarg],"skip") == 0) break;
+    if (strcmp(arg[iarg],"start") == 0) break;
+    if (strcmp(arg[iarg],"stop") == 0) break;
+    if (strcmp(arg[iarg],"dump") == 0) break;
+    iarg++;
+  }
+  int nfile = iarg;
+  if (nfile == 0 || nfile == narg) error->all(FLERR,"Illegal rerun command");
+
+  // parse optional args up until "dump"
+
+  bigint first = 0;
+  bigint last = MAXBIGINT;
+  int nevery = 0;
+  int nskip = 1;
+  int startflag = 0;
+  int stopflag = 0;
+  bigint start,stop;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"first") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      first = ATOBIGINT(arg[iarg+1]);
+      if (first < 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"last") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      last = ATOBIGINT(arg[iarg+1]);
+      if (last < 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"every") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      nevery = atoi(arg[iarg+1]);
+      if (nevery < 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"skip") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      nskip = atoi(arg[iarg+1]);
+      if (nskip <= 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"start") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      startflag = 1;
+      start = ATOBIGINT(arg[iarg+1]);
+      if (start < 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"stop") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      stopflag = 1;
+      stop = ATOBIGINT(arg[iarg+1]);
+      if (stop < 0) error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"dump") == 0) {
+      break;
+    } else error->all(FLERR,"Illegal rerun command");
+  }
+
+  if (strcmp(arg[iarg],"dump") != 0) error->all(FLERR,"Illegal rerun command");
+  if (first > last) error->all(FLERR,"Illegal rerun command");
+  if (startflag && stopflag && start > stop) 
+    error->all(FLERR,"Illegal rerun command");
+
+  // pass list of filenames to ReadDump, along with post-"dump" args
+
+  ReadDump *rd = new ReadDump(lmp);
+
+  rd->store_files(nfile,arg);
+  rd->fields_and_keywords(narg-iarg-1,&arg[iarg+1]);
+  rd->setup_reader();
+
+  // perform the psuedo run
+  // invoke lmp->init() only once
+  // read all relevant snapshots
+  // uset setup_minimal() since atoms are already owned by correct procs
+  // addstep_compute_all() insures energy/virial computed on every snapshot
+  // set update->nsteps to ndump for Finish stats to print
+
+  update->whichflag = 1;
+
+  if (startflag) update->beginstep = update->firststep = start;
+  else update->beginstep = update->firststep = first;
+  if (stopflag) update->endstep = update->laststep = stop;
+  else update->endstep = update->laststep = last;
+
+  int firstflag = 1;
+  int ndump = 0;
+
+  lmp->init();
+
+  timer->init();
+  timer->barrier_start(TIME_LOOP);
+
+  bigint ntimestep = rd->seek(first,0);
+  if (ntimestep < 0)
+    error->all(FLERR,"Rerun dump file does not contain requested snapshot");
+
+  while (1) {
+    ndump++;
+    rd->header(firstflag);
+    update->reset_timestep(ntimestep);
+    rd->atoms();
+
+    modify->addstep_compute_all(ntimestep);
+    update->integrate->setup_minimal(1);
+    output->setup(firstflag,firstflag);
+    firstflag = 0;
+  
+    ntimestep = rd->next(ntimestep,last,nevery,nskip);
+    if (ntimestep < 0) break;
+  }
+
+  timer->barrier_stop(TIME_LOOP);
+
+  update->integrate->cleanup();
+
+  update->nsteps = ndump;
+
+  Finish finish(lmp);
+  finish.end(1);
+
+  update->whichflag = 0;
+  update->firststep = update->laststep = 0;
+  update->beginstep = update->endstep = 0;
+
+  // clean-up
+
+  delete rd;
+}

src/rerun.h

@@ -0,0 +1,36 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(rerun,Rerun)
+
+#else
+
+#ifndef LMP_RERUN_H
+#define LMP_RERUN_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Rerun : protected Pointers {
+ public:
+  Rerun(class LAMMPS *);
+  void command(int, char **);
+};
+
+}
+
+#endif
+#endif