git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9754 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2013-04-06 23:08:09 +00:00
parent 022e3c1c57
commit afac9a0f14
12 changed files with 371 additions and 55 deletions
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@ -0,0 +1,189 @@
+/* ----------------------------------------------------------------------
+   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 "stdlib.h"
+#include "string.h"
+#include "fix_store.h"
+#include "atom.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+{
+  if (narg != 5) error->all(FLERR,"Illegal fix store command");
+
+  // syntax: id group style 0/1 nvalue
+
+  restart_peratom = atoi(arg[3]);
+  nvalues = atoi(arg[4]);
+
+  vecflag = 0;
+  if (nvalues == 1) vecflag = 1;
+
+  // perform initial allocation of atom-based array
+  // register with Atom class
+
+  vstore = NULL;
+  astore = NULL;
+  grow_arrays(atom->nmax);
+  atom->add_callback(0);
+  if (restart_peratom) atom->add_callback(1);
+
+  // zero the storage
+  // since may be exchanged before filled by caller, e.g. fix store/force
+
+  int nlocal = atom->nlocal;
+  if (vecflag)
+    for (int i = 0; i < nlocal; i++)
+      vstore[i] = 0.0;
+  else 
+    for (int i = 0; i < nlocal; i++)
+      for (int j = 0; j < nvalues; j++)
+	astore[i][j] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixStore::~FixStore()
+{
+  // unregister callbacks to this fix from Atom class
+
+  atom->delete_callback(id,0);
+  if (restart_peratom) atom->delete_callback(id,1);
+
+  memory->destroy(vstore);
+  memory->destroy(astore);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixStore::setmask()
+{
+  int mask = 0;
+  return mask;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double FixStore::memory_usage()
+{
+  double bytes = atom->nmax*nvalues * sizeof(double);
+  return bytes;
+}
+
+/* ----------------------------------------------------------------------
+   allocate atom-based array
+------------------------------------------------------------------------- */
+
+void FixStore::grow_arrays(int nmax)
+{
+  if (vecflag) memory->grow(vstore,nmax,"store:vstore");
+  else memory->grow(astore,nmax,nvalues,"store:astore");
+}
+
+/* ----------------------------------------------------------------------
+   copy values within local atom-based array
+------------------------------------------------------------------------- */
+
+void FixStore::copy_arrays(int i, int j, int delflag)
+{
+  if (vecflag) vstore[j] = vstore[i];
+  else
+    for (int m = 0; m < nvalues; m++)
+      astore[j][m] = astore[i][m];
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based array for exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixStore::pack_exchange(int i, double *buf)
+{
+  if (vecflag) buf[0] = vstore[i];
+  else
+    for (int m = 0; m < nvalues; m++)
+      buf[m] = astore[i][m];
+  return nvalues;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values in local atom-based array from exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixStore::unpack_exchange(int nlocal, double *buf)
+{
+  if (vecflag) vstore[nlocal] = buf[0];
+  else 
+    for (int m = 0; m < nvalues; m++)
+      astore[nlocal][m] = buf[m];
+  return nvalues;
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based arrays for restart file
+------------------------------------------------------------------------- */
+
+int FixStore::pack_restart(int i, double *buf)
+{
+  buf[0] = nvalues+1;
+  if (vecflag) buf[1] = vstore[i];
+  else
+    for (int m = 0; m < nvalues; m++)
+      buf[m+1] = astore[i][m];
+  return nvalues+1;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values from atom->extra array to restart the fix
+------------------------------------------------------------------------- */
+
+void FixStore::unpack_restart(int nlocal, int nth)
+{
+  double **extra = atom->extra;
+
+  // skip to Nth set of extra values
+
+  int m = 0;
+  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
+  m++;
+
+  if (vecflag) vstore[nlocal] = extra[nlocal][m];
+  else
+    for (int i = 0; i < nvalues; i++) 
+      astore[nlocal][i] = extra[nlocal][m++];
+}
+
+/* ----------------------------------------------------------------------
+   maxsize of any atom's restart data
+------------------------------------------------------------------------- */
+
+int FixStore::maxsize_restart()
+{
+  return nvalues+1;
+}
+
+/* ----------------------------------------------------------------------
+   size of atom nlocal's restart data
+------------------------------------------------------------------------- */
+
+int FixStore::size_restart(int nlocal)
+{
+  return nvalues+1;
+}