remove old versions of read_dump and rerun w/o parallel reading support

/* -*- c++ -*- ----------------------------------------------------------

   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

------------------------------------------------------------------------- */

#ifdef COMMAND_CLASS

CommandStyle(read_dump2,ReadDump2)

#else

#ifndef LMP_READ_DUMP2_H

#define LMP_READ_DUMP2_H

#include <cstdio>

#include "pointers.h"

namespace LAMMPS_NS {

class ReadDump2 : protected Pointers {

 public:

  ReadDump2(class LAMMPS *);

  ~ReadDump2();

  void command(int, char **);

  void store_files(int, char **);

  void setup_reader(int, char **);

  bigint seek(bigint, int);

  void header(int);

  bigint next(bigint, bigint, int, int);

  void atoms();

  int fields_and_keywords(int, char **);

private:

  int me,nprocs;

  FILE *fp;

  int dimension;

  int triclinic;

  int nfile;               // # of dump files to process

  char **files;            // list of file names

  int currentfile;         // currently open file

  int boxflag;             // overwrite simulation with dump file box params

  int replaceflag,addflag; // flags for processing dump snapshot atoms

  int trimflag,purgeflag;

  int scaleflag;           // user 0/1 if dump file coords are unscaled/scaled

  int wrapflag;            // user 0/1 if dump file coords are unwrapped/wrapped

  char *readerstyle;       // style of dump files to read

  int nfield;              // # of fields to extract from dump file

  int *fieldtype;          // type of each field = X,VY,IZ,etc

  char **fieldlabel;       // user specified label for field

  double **fields;         // per-atom field values

  int scaled;              // 0/1 if dump file coords are unscaled/scaled

  int wrapped;             // 0/1 if dump file coords are unwrapped/wrapped

  double box[3][3];         // dump file box parameters

  double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;  // dump snapshot box params

  double xprd,yprd,zprd;

  bigint nsnapatoms;        // # of atoms in dump file shapshot

  int npurge,nreplace,ntrim,nadd;     // stats on processed atoms

  int addproc;                        // proc that should add next atom

  int yindex,zindex;                  // field index for Y,Z coords

  int *uflag;               // set to 1 if snapshot atom matches owned atom

  int *ucflag,*ucflag_all;  // set to 1 if snapshot chunk atom was processed

  class Reader *reader;           // class that reads dump file

  int whichtype(char *);

  void process_atoms(int);

  void delete_atoms();

  double xfield(int, int);

  double yfield(int, int);

  double zfield(int, int);

};

}

#endif

#endif

/* ERROR/WARNING messages:

E: Read_dump command before simulation box is defined

The read_dump command cannot be used before a read_data, read_restart,

or create_box command.

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the

documentation for the command.  You can use -echo screen as a

command-line option when running LAMMPS to see the offending line.

E: Dump file does not contain requested snapshot

Self-explanatory.

E: Unknown dump reader style

The choice of dump reader style via the format keyword is unknown.

E: No box information in dump, must use 'box no'

UNDOCUMENTED

E: Read_dump triclinic status does not match simulation

Both the dump snapshot and the current LAMMPS simulation must

be using either an orthogonal or triclinic box.

E: Read_dump field not found in dump file

Self-explanatory.

E: Read_dump xyz fields do not have consistent scaling/wrapping

Self-explanatory.

E: All read_dump x,y,z fields must be specified for scaled, triclinic coords

For triclinic boxes and scaled coordinates you must specify all 3 of

the x,y,z fields, else LAMMPS cannot reconstruct the unscaled

coordinates.

E: Too many total atoms

See the setting for bigint in the src/lmptype.h file.

E: Read dump of atom property that isn't allocated

Self-explanatory.

E: Duplicate fields in read_dump command

Self-explanatory.

E: If read_dump purges it cannot replace or trim

These operations are not compatible.  See the read_dump doc

page for details.

E: Read_dump cannot use 'add keep' without atom IDs

UNDOCUMENTED

E: Cannot add atoms if dump file does not store atom type

UNDOCUMENTED

U: No box information in dump. You have to use 'box no'

Self-explanatory.

*/

/* ----------------------------------------------------------------------

   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 <cstdlib>

#include <cstring>

#include "rerun2.h"

#include "read_dump2.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"

#include "force.h"

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

Rerun2::Rerun2(LAMMPS *lmp) : Pointers(lmp) {}

/* ---------------------------------------------------------------------- */

void Rerun2::command(int narg, char **arg)

{

  if (domain->box_exist == 0)

    error->all(FLERR,"Rerun command before simulation box is defined");

  if (narg < 2) error->all(FLERR,"Illegal rerun command");

  // 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"

  // use MAXBIGINT -1 so Output can add 1 to it and still be a big int

  bigint first = 0;

  bigint last = MAXBIGINT - 1;

  int nevery = 0;

  int nskip = 1;

  int startflag = 0;

  int stopflag = 0;

  bigint start = -1;

  bigint stop = -1;

  while (iarg < narg) {

    if (strcmp(arg[iarg],"first") == 0) {

      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");

      first = force->bnumeric(FLERR,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 = force->bnumeric(FLERR,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 = force->inumeric(FLERR,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 = force->inumeric(FLERR,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 = force->bnumeric(FLERR,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 = force->bnumeric(FLERR,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");

  }

  int nremain = narg - iarg - 1;

  if (nremain <= 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 and post-"format" args

  ReadDump2 *rd = new ReadDump2(lmp);

  rd->store_files(nfile,arg);

  if (nremain)

    nremain = rd->fields_and_keywords(nremain,&arg[narg-nremain]);

  else nremain = rd->fields_and_keywords(0,NULL);

  if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);

  else rd->setup_reader(0,NULL);

  // perform the pseudo run

  // invoke lmp->init() only once

  // read all relevant snapshots

  // use setup_minimal() since atoms are already owned by correct procs

  // addstep_compute_all() insures energy/virial computed on every snapshot

  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();

  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->init();

    update->integrate->setup_minimal(1);

    modify->end_of_step();

    if (firstflag) output->setup();

    else if (output->next) output->write(ntimestep);

    firstflag = 0;

    ntimestep = rd->next(ntimestep,last,nevery,nskip);

    if (stopflag && ntimestep > stop)

      error->all(FLERR,"Read rerun dump file timestep > specified stop");

    if (ntimestep < 0) break;

  }

  // insure thermo output on last dump timestep

  output->next_thermo = update->ntimestep;

  output->write(update->ntimestep);

  timer->barrier_stop();

  update->integrate->cleanup();

  // set update->nsteps to ndump for Finish stats to print

  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;

}

/* -*- c++ -*- ----------------------------------------------------------

   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(rerun2,Rerun2)

#else

#ifndef LMP_RERUN2_H

#define LMP_RERUN2_H

#include "pointers.h"

namespace LAMMPS_NS {

class Rerun2 : protected Pointers {

 public:

  Rerun2(class LAMMPS *);

  void command(int, char **);

};

}

#endif

#endif

/* ERROR/WARNING messages:

E: Rerun command before simulation box is defined

The rerun command cannot be used before a read_data, read_restart, or

create_box command.

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the

documentation for the command.  You can use -echo screen as a

command-line option when running LAMMPS to see the offending line.

E: Rerun dump file does not contain requested snapshot

Self-explanatory.

E: Read rerun dump file timestep > specified stop

Self-explanatory.

*/