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

src/fix_heat.cpp

@@ -0,0 +1,91 @@
+/* ----------------------------------------------------------------------
+   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

@@ -0,0 +1,35 @@
+/* ----------------------------------------------------------------------
+   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

@@ -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

@@ -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

@@ -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)