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

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;
+}