git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1572 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2008-03-05 18:16:59 +00:00
parent b0b1da1371
commit 6c6d45d796
3 changed files with 199 additions and 0 deletions
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@ -0,0 +1,159 @@
+/* ----------------------------------------------------------------------
+   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 "string.h"
+#include "compute_temp_com.h"
+#include "atom.h"
+#include "force.h"
+#include "group.h"
+#include "modify.h"
+#include "fix.h"
+#include "domain.h"
+#include "lattice.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(A,B) ((A) < (B)) ? (A) : (B)
+#define MAX(A,B) ((A) > (B)) ? (A) : (B)
+
+#define INVOKED_SCALAR 1
+#define INVOKED_VECTOR 2
+
+/* ---------------------------------------------------------------------- */
+
+ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all("Illegal compute temp command");
+
+  scalar_flag = vector_flag = 1;
+  size_vector = 6;
+  extscalar = 0;
+  extvector = 1;
+  tempflag = 1;
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeTempCOM::~ComputeTempCOM()
+{
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempCOM::init()
+{
+  fix_dof = 0;
+  for (int i = 0; i < modify->nfix; i++)
+    fix_dof += modify->fix[i]->dof(igroup);
+  recount();
+  masstotal = group->mass(igroup);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempCOM::recount()
+{
+  double natoms = group->count(igroup);
+  dof = domain->dimension * natoms;
+  dof -= extra_dof + fix_dof;
+  if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
+  else tfactor = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempCOM::compute_scalar()
+{
+  double vcm[3],vthermal[3];
+
+  invoked |= INVOKED_SCALAR;
+
+  if (dynamic) masstotal = group->mass(igroup);
+  group->vcm(igroup,masstotal,vcm);
+
+  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;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      vthermal[0] = v[i][0] - vcm[0];
+      vthermal[1] = v[i][1] - vcm[1];
+      vthermal[2] = v[i][2] - vcm[2];
+      if (mass)
+	t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + 
+	      vthermal[2]*vthermal[2]) * mass[type[i]];
+      else
+	t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + 
+	      vthermal[2]*vthermal[2]) * rmass[i];
+    }
+
+  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  if (dynamic) recount();
+  scalar *= tfactor;
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempCOM::compute_vector()
+{
+  int i;
+  double vcm[3],vthermal[3];
+
+  invoked |= INVOKED_VECTOR;
+
+  if (dynamic) masstotal = group->mass(igroup);
+  group->vcm(igroup,masstotal,vcm);
+
+  double **x = atom->x;
+  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) {
+      vthermal[0] = v[i][0] - vcm[0];
+      vthermal[1] = v[i][1] - vcm[1];
+      vthermal[2] = v[i][2] - vcm[2];
+
+      if (mass) massone = mass[type[i]];
+      else massone = rmass[i];
+      t[0] += massone * vthermal[0]*vthermal[0];
+      t[1] += massone * vthermal[1]*vthermal[1];
+      t[2] += massone * vthermal[2]*vthermal[2];
+      t[3] += massone * vthermal[0]*vthermal[1];
+      t[4] += massone * vthermal[0]*vthermal[2];
+      t[5] += massone * vthermal[1]*vthermal[2];
+    }
+
+  MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
+  for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
+}