Commit 0a8ca112 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4774 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 3b4a8b53

src/GRANULAR/pair_gran_hooke_history.cpp

+13 −0
Original line number Diff line number Diff line
@@ -466,6 +466,11 @@ double PairGranHookeHistory::init_one(int i, int j) 
void PairGranHookeHistory::write_restart(FILE *fp)

{

  write_restart_settings(fp);



  int i,j;

  for (i = 1; i <= atom->ntypes; i++)

    for (j = i; j <= atom->ntypes; j++)

      fwrite(&setflag[i][j],sizeof(int),1,fp);

}



/* ----------------------------------------------------------------------
@@ -476,6 +481,14 @@ void PairGranHookeHistory::read_restart(FILE *fp) 
{

  read_restart_settings(fp);

  allocate();



  int i,j;

  int me = comm->me;

  for (i = 1; i <= atom->ntypes; i++)

    for (j = i; j <= atom->ntypes; j++) {

      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);

      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);

    }

}



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

src/fix_read_restart.cpp

0 → 100644
+126 −0
Original line number Diff line number Diff line 
/* ----------------------------------------------------------------------

   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 "stdlib.h"

#include "fix_read_restart.h"

#include "atom.h"

#include "memory.h"



using namespace LAMMPS_NS;



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



FixReadRestart::FixReadRestart(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg)

{

  nextra = atoi(arg[3]);

  int nfix = atoi(arg[4]);



  // perform initial allocation of atom-based array

  // register with Atom class



  count = NULL;

  extra = NULL;

  grow_arrays(atom->nmax);

  atom->add_callback(0);



  // extra = copy of atom->extra



  double **atom_extra = atom->extra;

  int nlocal = atom->nlocal;

  int i,j,m;



  for (i = 0; i < nlocal; i++) {

    m = 0;

    for (j = 0; j < nfix; j++) m += static_cast<int> (atom_extra[i][m]);

    count[i] = m;

    for (j = 0; j < m; j++) extra[i][j] = atom_extra[i][j];

  }

}



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



FixReadRestart::~FixReadRestart()

{

  // unregister callback to this fix from Atom class

 

  atom->delete_callback(id,0);



  // delete locally stored arrays



  memory->sfree(count);

  memory->destroy_2d_double_array(extra);

}



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



int FixReadRestart::setmask()

{

  int mask = 0;

  return mask;

}



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

   memory usage of local atom-based array

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



double FixReadRestart::memory_usage()

{

  double bytes = atom->nmax*nextra * sizeof(double);

  bytes += atom->nmax * sizeof(int);

  return bytes;

}



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

   allocate atom-based array

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



void FixReadRestart::grow_arrays(int nmax)

{

  count =

    (int *) memory->srealloc(count,nmax*sizeof(int),"read_restart:count");

  extra =

    memory->grow_2d_double_array(extra,nmax,nextra,"read_restart:extra");

}



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

   copy values within local atom-based array

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



void FixReadRestart::copy_arrays(int i, int j)

{

  count[j] = count[i];

  for (int m = 0; m < count[i]; m++) extra[j][m] = extra[i][m];

}



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

   pack values in local atom-based array for exchange with another proc

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



int FixReadRestart::pack_exchange(int i, double *buf)

{

  buf[0] = count[i];

  for (int m = 0; m < count[i]; m++) buf[m+1] = extra[i][m];

  return count[i]+1;

}



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

   unpack values in local atom-based array from exchange with another proc

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



int FixReadRestart::unpack_exchange(int nlocal, double *buf)

{

  count[nlocal] = static_cast<int> (buf[0]);

  for (int m = 0; m < count[nlocal]; m++) extra[nlocal][m] = buf[m+1];

  return count[nlocal]+1;

}

src/fix_read_restart.h

0 → 100644
+49 −0
Original line number Diff line number Diff line 
/* ----------------------------------------------------------------------

   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 FIX_CLASS



FixStyle(READ_RESTART,FixReadRestart)



#else



#ifndef LMP_FIX_READ_RESTART_H

#define LMP_FIX_READ_RESTART_H



#include "fix.h"



namespace LAMMPS_NS {



class FixReadRestart : public Fix {

 public:

  int *count;

  double **extra;



  FixReadRestart(class LAMMPS *, int, char **);

  ~FixReadRestart();

  int setmask();



  double memory_usage();

  void grow_arrays(int);

  void copy_arrays(int, int);

  int pack_exchange(int, double *);

  int unpack_exchange(int, double *);



 private:

  int nextra;          // max number of extra values for any atom

};



}



#endif

#endif

src/modify.cpp

+3 −1
Original line number Diff line number Diff line
@@ -91,6 +91,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp) 
  nfix_restart_peratom = 0;

  id_restart_peratom = style_restart_peratom = NULL;

  index_restart_peratom = NULL;

  nfix_restart_save = 0;



  ncompute = maxcompute = 0;

  compute = NULL;
@@ -146,8 +147,9 @@ void Modify::init() 
  int i,j;



  // delete storage of restart info since it is not valid after 1st run

  // read_restart sets nfix_restart_save so will persist to actual 1st run



  restart_deallocate();

  if (!nfix_restart_save) restart_deallocate();



  // create lists of fixes to call at each stage of run

src/modify.h

+2 −1
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ class Modify : protected Pointers { 
  int restart_pbc_any;       // 1 if any fix sets restart_pbc

  int nfix_restart_global;   // stored fix global info from restart file

  int nfix_restart_peratom;  // stored fix peratom info from restart file

  int nfix_restart_save;     // 1 if init() should not whack restart info



  class Fix **fix;           // list of fixes

  int *fmask;                // bit mask for when each fix is applied

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