lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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 "run.h"
#include <cstring>
#include "domain.h"
#include "update.h"
#include "force.h"
#include "integrate.h"
#include "modify.h"
#include "output.h"
#include "finish.h"
#include "input.h"
#include "timer.h"
#include "error.h"

using namespace LAMMPS_NS;

#define MAXLINE 2048

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

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

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

void Run::command(int narg, char **arg)
{
  if (narg < 1) error->all(FLERR,"Illegal run command");

  if (domain->box_exist == 0)
    error->all(FLERR,"Run command before simulation box is defined");

  // ignore run command, if walltime limit was already reached

  if (timer->is_timeout()) return;

  bigint nsteps_input = force->bnumeric(FLERR,arg[0]);

  // parse optional args

  int uptoflag = 0;
  int startflag = 0;
  int stopflag = 0;
  bigint start,stop;
  int preflag = 1;
  int postflag = 1;
  int nevery = 0;
  int ncommands = 0;
  int first,last;

  int iarg = 1;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"upto") == 0) {
      if (iarg+1 > narg) error->all(FLERR,"Illegal run command");
      uptoflag = 1;
      iarg += 1;
    } else if (strcmp(arg[iarg],"start") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
      startflag = 1;
      start = force->bnumeric(FLERR,arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"stop") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
      stopflag = 1;
      stop = force->bnumeric(FLERR,arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"pre") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
      if (strcmp(arg[iarg+1],"no") == 0) preflag = 0;
      else if (strcmp(arg[iarg+1],"yes") == 0) preflag = 1;
      else error->all(FLERR,"Illegal run command");
      iarg += 2;
    } else if (strcmp(arg[iarg],"post") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
      if (strcmp(arg[iarg+1],"no") == 0) postflag = 0;
      else if (strcmp(arg[iarg+1],"yes") == 0) postflag = 1;
      else error->all(FLERR,"Illegal run command");
      iarg += 2;

      // all remaining args are commands
      // first,last = arg index of first/last commands
      // set ncommands = 0 if single command and it is NULL

    } else if (strcmp(arg[iarg],"every") == 0) {
      if (iarg+3 > narg) error->all(FLERR,"Illegal run command");
      nevery = force->inumeric(FLERR,arg[iarg+1]);
      if (nevery <= 0) error->all(FLERR,"Illegal run command");
      first = iarg+2;
      last = narg-1;
      ncommands = last-first + 1;
      if (ncommands == 1 && strcmp(arg[first],"NULL") == 0) ncommands = 0;
      iarg = narg;
    } else error->all(FLERR,"Illegal run command");
  }

  // set nsteps as integer, using upto value if specified

  int nsteps;
  if (!uptoflag) {
    if (nsteps_input < 0 || nsteps_input > MAXSMALLINT)
      error->all(FLERR,"Invalid run command N value");
    nsteps = static_cast<int> (nsteps_input);
  } else {
    bigint delta = nsteps_input - update->ntimestep;
    if (delta < 0 || delta > MAXSMALLINT)
      error->all(FLERR,"Invalid run command upto value");
    nsteps = static_cast<int> (delta);
  }

  // error check

  if (startflag) {
    if (start < 0)
      error->all(FLERR,"Invalid run command start/stop value");
    if (start > update->ntimestep)
      error->all(FLERR,"Run command start value is after start of run");
  }
  if (stopflag) {
    if (stop < 0)
      error->all(FLERR,"Invalid run command start/stop value");
    if (stop < update->ntimestep + nsteps)
      error->all(FLERR,"Run command stop value is before end of run");
  }

  if (!preflag && strstr(update->integrate_style,"respa"))
    error->all(FLERR,"Run flag 'pre no' not compatible with r-RESPA");

  // if nevery, make copies of arg strings that are commands
  // required because re-parsing commands via input->one() will wipe out args

  char **commands = NULL;
  if (nevery && ncommands > 0) {
    commands = new char*[ncommands];
    ncommands = 0;
    for (int i = first; i <= last; i++) {
      int n = strlen(arg[i]) + 1;
      commands[ncommands] = new char[n];
      strcpy(commands[ncommands],arg[i]);
      ncommands++;
    }
  }

  // perform a single run
  // use start/stop to set begin/end step
  // if pre or 1st run, do System init/setup,
  //   else just init timer and setup output
  // if post, do full Finish, else just print time

  update->whichflag = 1;
  timer->init_timeout();

  if (nevery == 0) {
    update->nsteps = nsteps;
    update->firststep = update->ntimestep;
    update->laststep = update->ntimestep + nsteps;
    if (update->laststep < 0 || update->laststep < update->firststep)
      error->all(FLERR,"Too many timesteps");

    if (startflag) update->beginstep = start;
    else update->beginstep = update->firststep;
    if (stopflag) update->endstep = stop;
    else update->endstep = update->laststep;

    if (preflag || update->first_update == 0) {
      lmp->init();
      update->integrate->setup(1);
    } else output->setup(0);

    timer->init();
    timer->barrier_start();
    update->integrate->run(nsteps);
    timer->barrier_stop();

    update->integrate->cleanup();

    Finish finish(lmp);
    finish.end(postflag);

  // perform multiple runs optionally interleaved with invocation command(s)
  // use start/stop to set begin/end step
  // if pre or 1st iteration of multiple runs, do System init/setup,
  //   else just init timer and setup output
  // if post or last iteration, do full Finish, else just print time

  } else {
    int iter = 0;
    int nleft = nsteps;
    while (nleft > 0 || iter == 0) {
      if (timer->is_timeout()) break;
      timer->init_timeout();

      nsteps = MIN(nleft,nevery);

      update->nsteps = nsteps;
      update->firststep = update->ntimestep;
      update->laststep = update->ntimestep + nsteps;
      if (update->laststep < 0 || update->laststep < update->firststep)
        error->all(FLERR,"Too many timesteps");

      if (startflag) update->beginstep = start;
      else update->beginstep = update->firststep;
      if (stopflag) update->endstep = stop;
      else update->endstep = update->laststep;

      if (preflag || iter == 0) {
        lmp->init();
        update->integrate->setup(1);
      } else output->setup(0);

      timer->init();
      timer->barrier_start();
      update->integrate->run(nsteps);
      timer->barrier_stop();

      update->integrate->cleanup();

      Finish finish(lmp);
      if (postflag || nleft <= nsteps) finish.end(1);
      else finish.end(0);

      // wrap command invocation with clearstep/addstep
      // since a command may invoke computes via variables

      if (ncommands) {
        modify->clearstep_compute();
        for (int i = 0; i < ncommands; i++) input->one(commands[i]);
        modify->addstep_compute(update->ntimestep + nevery);
      }

      nleft -= nsteps;
      iter++;
    }
  }

  update->whichflag = 0;
  update->firststep = update->laststep = 0;
  update->beginstep = update->endstep = 0;

  if (commands) {
    for (int i = 0; i < ncommands; i++) delete [] commands[i];
    delete [] commands;
  }
}