git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4646 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2010-09-01 18:51:00 +00:00
parent b6ce16eee4
commit 333c561d22
35 changed files with 4471 additions and 4 deletions
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@ -0,0 +1,152 @@
+/* ----------------------------------------------------------------------
+   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: Andres Jaramillo-Botero (Caltech)
+------------------------------------------------------------------------- */
+
+#include "mpi.h"
+#include "string.h"
+#include "compute_temp_eff.h"
+#include "atom.h"
+#include "update.h"
+#include "force.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "group.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeTempEff::ComputeTempEff(LAMMPS *lmp, int narg, char **arg) : 
+  ComputeTemp(lmp, narg, arg)
+{
+  // error check
+
+  if (!atom->spin_flag || !atom->ervel_flag) 
+    error->all("Compute temp/eff requires atom attributes spin, ervel");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempEff::dof_compute()
+{
+  double natoms = group->count(igroup);
+  dof = domain->dimension * natoms;
+  dof -= extra_dof + fix_dof;	
+
+  int *spin = atom->spin;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  int one = 0;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (spin[i]) one++;
+    }
+  int nelectrons;
+  MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
+
+  // average over nuclear dof only
+
+  dof -= domain->dimension * nelectrons;
+
+  if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
+  else tfactor = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempEff::compute_scalar()
+{
+  invoked_scalar = update->ntimestep;
+
+  double **v = atom->v;
+  double *ervel = atom->ervel;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int *spin = atom->spin;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double massone;
+
+  double t = 0.0;
+   
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2])*rmass[i];
+        if (spin[i]) t += 0.75*rmass[i]*ervel[i]*ervel[i];
+      }
+    }
+  } else {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * 
+	  mass[type[i]];
+        if (spin[i]) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
+      }
+    }
+  }
+
+  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  if (dynamic) dof_compute();
+  scalar *= tfactor;
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempEff::compute_vector()
+{
+  int i;
+
+  invoked_vector = update->ntimestep;
+
+  double **v = atom->v;
+  double *ervel = atom->ervel;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int *spin = atom->spin;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double massone,ervel_adj,t[6];
+  for (i = 0; i < 6; i++) t[i] = 0.0;
+
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      t[0] += massone * v[i][0]*v[i][0];
+      t[1] += massone * v[i][1]*v[i][1];
+      t[2] += massone * v[i][2]*v[i][2];
+      t[3] += massone * v[i][0]*v[i][1];
+      t[4] += massone * v[i][0]*v[i][2];
+      t[5] += massone * v[i][1]*v[i][2];
+      if (spin[i]) {
+        t[0] += 0.75*massone*ervel[i]*ervel[i];
+        t[1] += 0.75*massone*ervel[i]*ervel[i];
+        t[2] += 0.75*massone*ervel[i]*ervel[i];
+      }
+    }
+
+  MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
+  for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
+}