git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10977 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_vacf.cpp

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+/* ----------------------------------------------------------------------
+   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 ret
+   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 "string.h"
+#include "compute_vacf.h"
+#include "atom.h"
+#include "update.h"
+#include "group.h"
+#include "modify.h"
+#include "fix_store.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg < 3) error->all(FLERR,"Illegal compute vacf command");
+
+  vector_flag = 1;
+  size_vector = 4;
+  extvector = 0;
+
+  // create a new fix STORE style
+  // id = compute-ID + COMPUTE_STORE, fix group = compute group
+
+  int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
+  id_fix = new char[n];
+  strcpy(id_fix,id);
+  strcat(id_fix,"_COMPUTE_STORE");
+
+  char **newarg = new char*[5];
+  newarg[0] = id_fix;
+  newarg[1] = group->names[igroup];
+  newarg[2] = (char *) "STORE";
+  newarg[3] = (char *) "1";
+  newarg[4] = (char *) "3";
+  modify->add_fix(5,newarg);
+  fix = (FixStore *) modify->fix[modify->nfix-1];
+  delete [] newarg;
+
+  // store current velocities in fix store array
+  // skip if reset from restart file
+
+  if (fix->restart_reset) fix->restart_reset = 0;
+  else {
+    double **voriginal = fix->astore;
+
+    double **v = atom->v;
+    int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	voriginal[i][0] = v[i][0];
+	voriginal[i][1] = v[i][1];
+	voriginal[i][2] = v[i][2];
+      } else voriginal[i][0] = voriginal[i][1] = voriginal[i][2] = 0.0;
+  }
+
+  // displacement vector
+
+  vector = new double[4];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVACF::~ComputeVACF()
+{
+  // check nfix in case all fixes have already been deleted
+
+  if (modify->nfix) modify->delete_fix(id_fix);
+
+  delete [] id_fix;
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVACF::init()
+{
+  // set fix which stores original atom velocities
+
+  int ifix = modify->find_fix(id_fix);
+  if (ifix < 0) error->all(FLERR,"Could not find compute vacf fix ID");
+  fix = (FixStore *) modify->fix[ifix];
+
+  // nvacf = # of atoms in group
+
+  nvacf = group->count(igroup);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVACF::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  double **voriginal = fix->astore;
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double vxsq,vysq,vzsq;
+  double vacf[4];
+  vacf[0] = vacf[1] = vacf[2] = vacf[3] = 0.0;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      vxsq = v[i][0] * voriginal[i][0];
+      vysq = v[i][1] * voriginal[i][1];
+      vzsq = v[i][2] * voriginal[i][2];
+      vacf[0] += vxsq;
+      vacf[1] += vysq;
+      vacf[2] += vzsq;
+      vacf[3] += vxsq + vysq + vzsq;
+    }
+
+  MPI_Allreduce(vacf,vector,4,MPI_DOUBLE,MPI_SUM,world);
+  if (nvacf) {
+    vector[0] /= nvacf;
+    vector[1] /= nvacf;
+    vector[2] /= nvacf;
+    vector[3] /= nvacf;
+  }
+}

src/compute_vacf.h

@@ -0,0 +1,57 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(vacf,ComputeVACF)
+
+#else
+
+#ifndef LMP_COMPUTE_VACF_H
+#define LMP_COMPUTE_VACF_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeVACF : public Compute {
+ public:
+  ComputeVACF(class LAMMPS *, int, char **);
+  ~ComputeVACF();
+  void init();
+  virtual void compute_vector();
+
+ protected:
+  bigint nvacf;
+  char *id_fix;
+  class FixStore *fix;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Could not find compute msd fix ID
+
+Self-explanatory.
+
+*/