git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2007-01-30 00:31:11 +00:00
parent 209f169cbc
commit 284c1f2d04
70 changed files with 16898 additions and 0 deletions
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@ -0,0 +1,134 @@
+/* ----------------------------------------------------------------------
+   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 "mpi.h"
+#include "stdlib.h"
+#include "compute_temp_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "modify.h"
+#include "fix.h"
+#include "group.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg != 6) error->all("Illegal compute temp/partial command");
+
+  xflag = atoi(arg[3]);
+  yflag = atoi(arg[4]);
+  zflag = atoi(arg[5]);
+
+  scalar_flag = vector_flag = 1;
+  size_vector = 6;
+  extensive = 0;
+  tempflag = 1;
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeTempPartial::~ComputeTempPartial()
+{
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempPartial::init()
+{
+  fix_dof = 0;
+  for (int i = 0; i < modify->nfix; i++)
+    fix_dof += modify->fix[i]->dof(igroup);
+  recount();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempPartial::recount()
+{
+  double natoms = group->count(igroup);
+  dof = (xflag+yflag+zflag) * natoms;
+  dof -= extra_dof + fix_dof;
+  if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
+  else tfactor = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempPartial::compute_scalar()
+{
+  double **v = atom->v;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double t = 0.0;
+
+  if (mass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit)
+	t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + 
+	      zflag*v[i][2]*v[i][2]) * mass[type[i]];
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit)
+	t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + 
+	      zflag*v[i][2]*v[i][2]) * rmass[i];
+  }
+    
+  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  if (dynamic) recount();
+  scalar *= tfactor;
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempPartial::compute_vector()
+{
+  int i;
+
+  double **v = atom->v;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double massone,t[6];
+  for (i = 0; i < 6; i++) t[i] = 0.0;
+
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (mass) massone = mass[type[i]];
+      else massone = rmass[i];
+      t[0] += massone * xflag*v[i][0]*v[i][0];
+      t[1] += massone * yflag*v[i][1]*v[i][1];
+      t[2] += massone * zflag*v[i][2]*v[i][2];
+      t[3] += massone * xflag*yflag*v[i][0]*v[i][1];
+      t[4] += massone * xflag*zflag*v[i][0]*v[i][2];
+      t[5] += massone * yflag*zflag*v[i][1]*v[i][2];
+    }
+
+  MPI_Allreduce(&t,&vector,6,MPI_DOUBLE,MPI_SUM,world);
+  for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
+}