Commit 467e7efb authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@504 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 7e1e28af

src/fix_heat.cpp

0 → 100644
+91 −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.

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



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

   Contributing author: Paul Crozier (SNL)

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



#include "math.h"

#include "stdlib.h"

#include "string.h"

#include "fix_heat.h"

#include "atom.h"

#include "domain.h"

#include "group.h"

#include "force.h"

#include "update.h"

#include "error.h"



using namespace LAMMPS_NS;



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



FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)

{

  if (narg < 4) error->all("Illegal fix heat command");



  nevery = atoi(arg[3]);

  if (nevery <= 0) error->all("Illegal fix heat command");



  heat = atof(arg[4]);

  heat *= nevery*update->dt*force->ftm2v;



  // cannot have 0 atoms in group



  if (group->count(igroup) == 0.0) error->all("Fix heat group has no atoms");

}



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



int FixHeat::setmask()

{

  int mask = 0;

  mask |= END_OF_STEP;

  return mask;

}



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



void FixHeat::init()

{

  masstotal = group->mass(igroup);

}



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



void FixHeat::end_of_step()

{ 

  double **v = atom->v;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;



  double vsub[3],vcm[3];



  double ke = group->ke(igroup);

  group->vcm(igroup,masstotal,vcm);

  double vcmsq = vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2];

  double escale = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);

  if (escale < 0.0) error->all("Illegal fix heat attempt");

  double r = sqrt(escale);



  vsub[0] = (r-1.0) * vcm[0];

  vsub[1] = (r-1.0) * vcm[1];

  vsub[2] = (r-1.0) * vcm[2];

  

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

    if (mask[i] & groupbit) {

      v[i][0] = r*v[i][0] - vsub[0];

      v[i][1] = r*v[i][1] - vsub[1];

      v[i][2] = r*v[i][2] - vsub[2];

    }

}

src/fix_heat.h

0 → 100644
+35 −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.

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



#ifndef FIX_HEAT_H

#define FIX_HEAT_H



#include "fix.h"



namespace LAMMPS_NS {



class FixHeat : public Fix {

 public:

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

  int setmask();

  void init();

  void end_of_step();



 private:

  double heat;

  double masstotal;

};



}



#endif

src/group.cpp

+42 −6
Original line number Diff line number Diff line
@@ -20,6 +20,7 @@ 
#include "domain.h"

#include "atom.h"

#include "atom_vec_hybrid.h"

#include "force.h"

#include "region.h"

#include "memory.h"

#include "error.h"
@@ -467,19 +468,19 @@ double Group::mass(int igroup) 
  double *rmass = atom->rmass;

  int nlocal = atom->nlocal;



  double m = 0.0;

  double one = 0.0;



  if (mass) {

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

      if (mask[i] & groupbit) m += mass[type[i]];

      if (mask[i] & groupbit) one += mass[type[i]];

  } else {

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

      if (mask[i] & groupbit) m += rmass[i];

      if (mask[i] & groupbit) one += rmass[i];

  }



  double mall;

  MPI_Allreduce(&m,&mall,1,MPI_DOUBLE,MPI_SUM,world);

  return mall;

  double all;

  MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);

  return all;

}



/* ----------------------------------------------------------------------
@@ -671,6 +672,41 @@ void Group::fcm(int igroup, double *cm) 
  MPI_Allreduce(flocal,cm,3,MPI_DOUBLE,MPI_SUM,world);

}



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

   compute the total kinetic energy of group and return it

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



double Group::ke(int igroup)

{

  int groupbit = bitmask[igroup];



  double **v = atom->v;

  int *mask = atom->mask;

  int *type = atom->type;

  double *mass = atom->mass;

  double *rmass = atom->rmass;

  int nlocal = atom->nlocal;



  double one = 0.0;



  if (mass) {

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

      if (mask[i] & groupbit)

	one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *

	  mass[type[i]];

  } else {

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

      if (mask[i] & groupbit)

	one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *

	  rmass[i];

  }

  

  double all;

  MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);

  all *= 0.5 * force->mvv2e;

  return all;

}



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

   compute the radius-of-gyration of group around center-of-mass cm

   must unwrap atoms to compute Rg correctly

src/group.h

+1 −0
Original line number Diff line number Diff line
@@ -42,6 +42,7 @@ class Group : protected Pointers { 
  void xcm(int, double, double *);         // center-of-mass coords of group

  void vcm(int, double, double *);         // center-of-mass velocity of group

  void fcm(int, double *);                 // total force on group

  double ke(int);                          // kinetic energy of group

  double gyration(int, double, double *);  // radius-of-gyration of group

  void angmom(int, double *, double *);    // angular momentum of group

  void inertia(int, double *, double [3][3]);     // inertia tensor

src/style.h

+2 −0
Original line number Diff line number Diff line
@@ -137,6 +137,7 @@ DumpStyle(xyz,DumpXYZ) 
#include "fix_enforce2d.h"

#include "fix_gravity.h"

#include "fix_gyration.h"

#include "fix_heat.h"

#include "fix_indent.h"

#include "fix_langevin.h"

#include "fix_line_force.h"
@@ -184,6 +185,7 @@ FixStyle(efield,FixEfield) 
FixStyle(enforce2d,FixEnforce2D)

FixStyle(gravity,FixGravity)

FixStyle(gyration,FixGyration)

FixStyle(heat,FixHeat)

FixStyle(indent,FixIndent)

FixStyle(langevin,FixLangevin)

FixStyle(lineforce,FixLineForce)

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