Commit 0808bd4c authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1292 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent b4fabf0d

src/compute_displace_atom.cpp

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

   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 "math.h"

#include "string.h"

#include "compute_displace_atom.h"

#include "atom.h"

#include "domain.h"

#include "modify.h"

#include "fix.h"

#include "memory.h"

#include "error.h"



using namespace LAMMPS_NS;



#define INVOKED_PERATOM 4



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



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

  Compute(lmp, narg, arg)

{

  if (narg != 4) error->all("Illegal compute displace/atom command");



  peratom_flag = 1;

  size_peratom = 4;



  // store fix ID which stores original atom coords



  int n = strlen(arg[3]) + 1;

  id_fix = new char[n];

  strcpy(id_fix,arg[3]);



  int ifix = modify->find_fix(id_fix);

  if (ifix < 0) error->all("Could not find compute displace/atom fix ID");



  nmax = 0;

  displace = NULL;

}



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



ComputeDisplaceAtom::~ComputeDisplaceAtom()

{

  delete [] id_fix;

  memory->destroy_2d_double_array(displace);

}



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



void ComputeDisplaceAtom::init()

{

  // set fix which stores original atom coords

  // check if is correct style



  int ifix = modify->find_fix(id_fix);

  if (ifix < 0) error->all("Could not find compute displace/atom fix ID");

  fix = modify->fix[ifix];



  if (strcmp(fix->style,"coord/original") != 0)

    error->all("Invalid fix style used in compute displace/atom command");

}



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



void ComputeDisplaceAtom::compute_peratom()

{

  invoked |= INVOKED_PERATOM;



  // grow local displacement array if necessary



  if (atom->nmax > nmax) {

    memory->destroy_2d_double_array(displace);

    nmax = atom->nmax;

    displace =

      memory->create_2d_double_array(nmax,4,"compute/displace/atom:displace");

    vector_atom = displace;

  }



  // dx,dy,dz = displacement of atom from original position

  // original unwrapped position is stored by fix

  // for triclinic, need to unwrap current atom coord via h matrix



  double **xoriginal = fix->vector_atom;



  double **x = atom->x;

  int *mask = atom->mask;

  int *image = atom->image;

  int nlocal = atom->nlocal;



  double *h = domain->h;

  double xprd = domain->xprd;

  double yprd = domain->yprd;

  double zprd = domain->zprd;

  int xbox,ybox,zbox;

  double dx,dy,dz;



  if (domain->triclinic == 0) {

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

      if (mask[i] & groupbit) {

	xbox = (image[i] & 1023) - 512;

	ybox = (image[i] >> 10 & 1023) - 512;

	zbox = (image[i] >> 20) - 512;

	dx = x[i][0] + xbox*xprd - xoriginal[i][0];

	dy = x[i][1] + ybox*yprd - xoriginal[i][1];

	dz = x[i][2] + zbox*zprd - xoriginal[i][2];

	displace[i][0] = dx;

	displace[i][1] = dy;

	displace[i][2] = dz;

	displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);

      } else displace[i][0] = displace[i][1] =

	       displace[i][2] = displace[i][3] = 0.0;



  } else {

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

      if (mask[i] & groupbit) {

	xbox = (image[i] & 1023) - 512;

	ybox = (image[i] >> 10 & 1023) - 512;

	zbox = (image[i] >> 20) - 512;

	dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];

	dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];

	dz = x[i][2] + h[2]*zbox - xoriginal[i][2];

	displace[i][0] = dx;

	displace[i][1] = dy;

	displace[i][2] = dz;

	displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);

      } else displace[i][0] = displace[i][1] =

	       displace[i][2] = displace[i][3] = 0.0;

  }

}



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

   memory usage of local atom-based array

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



double ComputeDisplaceAtom::memory_usage()

{

  double bytes = nmax*4 * sizeof(double);

  return bytes;

}

src/compute_displace_atom.h

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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 COMPUTE_DISPLACE_ATOM_H

#define COMPUTE_DISPLACE_ATOM_H



#include "compute.h"



namespace LAMMPS_NS {



class ComputeDisplaceAtom : public Compute {

 public:

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

  ~ComputeDisplaceAtom();

  void init();

  void compute_peratom();

  double memory_usage();



 private:

  int nmax;

  double **displace;

  char *id_fix;

  class Fix *fix;

};



}



#endif

src/fix_coord_original.cpp

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

   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 = 3;

  peratom_freq = 1;



  // 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);



  // xoriginal = initial unwrapped positions of atoms

  

  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]);

    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");

  vector_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

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

   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 −0
Original line number Diff line number Diff line
@@ -78,6 +78,7 @@ CommandStyle(write_restart,WriteRestart) 
#ifdef ComputeInclude

#include "compute_centro_atom.h"

#include "compute_coord_atom.h"

#include "compute_displace_atom.h"

#include "compute_ke_atom.h"

#include "compute_pe.h"

#include "compute_pe_atom.h"
@@ -96,6 +97,7 @@ CommandStyle(write_restart,WriteRestart) 
#ifdef ComputeClass

ComputeStyle(centro/atom,ComputeCentroAtom)

ComputeStyle(coord/atom,ComputeCoordAtom)

ComputeStyle(displace/atom,ComputeDisplaceAtom)

ComputeStyle(ke/atom,ComputeKEAtom)

ComputeStyle(pe,ComputePE)

ComputeStyle(pe/atom,ComputePEAtom)
@@ -138,6 +140,7 @@ DumpStyle(xyz,DumpXYZ) 
#include "fix_ave_spatial.h"

#include "fix_ave_time.h"

#include "fix_com.h"

#include "fix_coord_original.h"

#include "fix_deform.h"

#include "fix_deposit.h"

#include "fix_drag.h"
@@ -190,6 +193,7 @@ FixStyle(aveforce,FixAveForce) 
FixStyle(ave/spatial,FixAveSpatial)

FixStyle(ave/time,FixAveTime)

FixStyle(com,FixCOM)

FixStyle(coord/original,FixCoordOriginal)

FixStyle(deform,FixDeform)

FixStyle(deposit,FixDeposit)

FixStyle(drag,FixDrag)

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