Commit 81dbacf3 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3610 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 2f2c5124

src/fix_coord_original.cpp

deleted100644 → 0
+0 −214
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 "string.h"

#include "fix_coord_original.h"

#include "atom.h"

#include "domain.h"

#include "group.h"

#include "memory.h"

#include "error.h"



using namespace LAMMPS_NS;



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



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

  Fix(lmp, narg, arg)

{

  if (narg < 3) error->all("Illegal fix coord/original command");



  restart_peratom = 1;

  peratom_flag = 1;

  size_peratom_cols = 3;

  peratom_freq = 1;



  // optional args



  int comflag = 0;



  int iarg = 3;

  while (iarg < narg) {

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

      if (iarg+2 > narg) error->all("Illegal fix coord/original command");

      if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;

      else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;

      else error->all("Illegal fix coord/original command");

      iarg += 2;

    } else error->all("Illegal fix coord/original command");

  }



  // perform initial allocation of atom-based array

  // register with Atom class



  xoriginal = NULL;

  grow_arrays(atom->nmax);

  atom->add_callback(0);

  atom->add_callback(1);



  // cm = original center of mass



  double cm[3];

  if (comflag) {

    double masstotal = group->mass(igroup);

    group->xcm(igroup,masstotal,cm);

  }



  // xoriginal = initial unwrapped positions of atoms

  // relative to center of mass if comflag is set



  double **x = atom->x;

  int *mask = atom->mask;

  int *image = atom->image;

  int nlocal = atom->nlocal;



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

    if (mask[i] & groupbit) {

      domain->unmap(x[i],image[i],xoriginal[i]);

      if (comflag) {

	xoriginal[i][0] -= cm[0];

	xoriginal[i][1] -= cm[1];

	xoriginal[i][2] -= cm[2];

      }

    } else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;

  }

}



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



FixCoordOriginal::~FixCoordOriginal()

{

  // unregister callbacks to this fix from Atom class

 

  atom->delete_callback(id,0);

  atom->delete_callback(id,1);



  // delete locally stored array



  memory->destroy_2d_double_array(xoriginal);

}



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



int FixCoordOriginal::setmask()

{

  int mask = 0;

  return mask;

}



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

   memory usage of local atom-based array

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



double FixCoordOriginal::memory_usage()

{

  double bytes = atom->nmax*3 * sizeof(double);

  return bytes;

}



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

   allocate atom-based array

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



void FixCoordOriginal::grow_arrays(int nmax)

{

  xoriginal =

    memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");

  array_atom = xoriginal;

}



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

   copy values within local atom-based array

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



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

{

  xoriginal[j][0] = xoriginal[i][0];

  xoriginal[j][1] = xoriginal[i][1];

  xoriginal[j][2] = xoriginal[i][2];

}



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

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

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



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

{

  buf[0] = xoriginal[i][0];

  buf[1] = xoriginal[i][1];

  buf[2] = xoriginal[i][2];

  return 3;

}



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

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

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



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

{

  xoriginal[nlocal][0] = buf[0];

  xoriginal[nlocal][1] = buf[1];

  xoriginal[nlocal][2] = buf[2];

  return 3;

}



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

   pack values in local atom-based arrays for restart file

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



int FixCoordOriginal::pack_restart(int i, double *buf)

{

  buf[0] = 4;

  buf[1] = xoriginal[i][0];

  buf[2] = xoriginal[i][1];

  buf[3] = xoriginal[i][2];

  return 4;

}



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

   unpack values from atom->extra array to restart the fix

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



void FixCoordOriginal::unpack_restart(int nlocal, int nth)

{

  double **extra = atom->extra;



  // skip to Nth set of extra values



  int m = 0;

  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

  m++;



  xoriginal[nlocal][0] = extra[nlocal][m++];

  xoriginal[nlocal][1] = extra[nlocal][m++];

  xoriginal[nlocal][2] = extra[nlocal][m++];

}



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

   maxsize of any atom's restart data

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



int FixCoordOriginal::maxsize_restart()

{

  return 4;

}



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

   size of atom nlocal's restart data

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



int FixCoordOriginal::size_restart(int nlocal)

{

  return 4;

}

src/fix_coord_original.h

deleted100644 → 0
+0 −43
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.

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



#ifndef FIX_COORD_ORIGINAL_H

#define FIX_COORD_ORIGINAL_H



#include "fix.h"



namespace LAMMPS_NS {



class FixCoordOriginal : public Fix {

 public:

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

  ~FixCoordOriginal();

  int setmask();



  double memory_usage();

  void grow_arrays(int);

  void copy_arrays(int, int);

  int pack_exchange(int, double *);

  int unpack_exchange(int, double *);

  int pack_restart(int, double *);

  void unpack_restart(int, int);

  int size_restart(int);

  int maxsize_restart();



 private:

  double **xoriginal;         // original coords of atoms

};



}



#endif

src/style.h

+4 −2
Original line number Diff line number Diff line
@@ -189,7 +189,6 @@ DumpStyle(xyz,DumpXYZ) 
#include "fix_ave_spatial.h"

#include "fix_ave_time.h"

#include "fix_box_relax.h"

#include "fix_coord_original.h"

#include "fix_deform.h"

#include "fix_deposit.h"

#include "fix_drag.h"
@@ -228,6 +227,8 @@ DumpStyle(xyz,DumpXYZ) 
#include "fix_spring.h"

#include "fix_spring_rg.h"

#include "fix_spring_self.h"

#include "fix_store_coord.h"

#include "fix_store_force.h"

#include "fix_temp_berendsen.h"

#include "fix_temp_rescale.h"

#include "fix_thermal_conductivity.h"
@@ -248,7 +249,6 @@ FixStyle(ave/histo,FixAveHisto) 
FixStyle(ave/spatial,FixAveSpatial)

FixStyle(ave/time,FixAveTime)

FixStyle(box/relax,FixBoxRelax)

FixStyle(coord/original,FixCoordOriginal)

FixStyle(deform,FixDeform)

FixStyle(deposit,FixDeposit)

FixStyle(drag,FixDrag)
@@ -287,6 +287,8 @@ FixStyle(SHEAR_HISTORY,FixShearHistory) 
FixStyle(spring,FixSpring)

FixStyle(spring/rg,FixSpringRG)

FixStyle(spring/self,FixSpringSelf)

FixStyle(store/coord,FixStoreCoord)

FixStyle(store/force,FixStoreForce)

FixStyle(temp/berendsen,FixTempBerendsen)

FixStyle(temp/rescale,FixTempRescale)

FixStyle(thermal/conductivity,FixThermalConductivity)

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