git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3611 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix_store_coord.cpp

@@ -0,0 +1,212 @@
+/* ----------------------------------------------------------------------
+   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_coord.h"
+#include "atom.h"
+#include "domain.h"
+#include "group.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreCoord::FixStoreCoord(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg < 3) error->all("Illegal fix store/coord command");
+
+  restart_peratom = 1;
+  peratom_flag = 1;
+  size_peratom_cols = 3;
+  peratom_freq = 1;
+
+  // optional args
+
+  int comflag = 0;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"com") == 0) {
+      if (iarg+2 > narg) error->all("Illegal fix store/coord command");
+      if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
+      else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
+      else error->all("Illegal fix store/coord command");
+      iarg += 2;
+    } else error->all("Illegal fix store/coord command");
+  }
+
+  // perform initial allocation of atom-based array
+  // register with Atom class
+
+  xoriginal = NULL;
+  grow_arrays(atom->nmax);
+  atom->add_callback(0);
+  atom->add_callback(1);
+
+  // cm = original center of mass
+
+  double cm[3];
+  if (comflag) {
+    double masstotal = group->mass(igroup);
+    group->xcm(igroup,masstotal,cm);
+  }
+
+  // xoriginal = initial unwrapped positions of atoms
+  // relative to center of mass if comflag is set
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *image = atom->image;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      domain->unmap(x[i],image[i],xoriginal[i]);
+      if (comflag) {
+	xoriginal[i][0] -= cm[0];
+	xoriginal[i][1] -= cm[1];
+	xoriginal[i][2] -= cm[2];
+      }
+    } else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreCoord::~FixStoreCoord()
+{
+  // unregister callbacks to this fix from Atom class
+ 
+  atom->delete_callback(id,0);
+  atom->delete_callback(id,1);
+
+  memory->destroy_2d_double_array(xoriginal);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixStoreCoord::setmask()
+{
+  int mask = 0;
+  return mask;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double FixStoreCoord::memory_usage()
+{
+  double bytes = atom->nmax*3 * sizeof(double);
+  return bytes;
+}
+
+/* ----------------------------------------------------------------------
+   allocate atom-based array
+------------------------------------------------------------------------- */
+
+void FixStoreCoord::grow_arrays(int nmax)
+{
+  xoriginal =
+    memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
+  array_atom = xoriginal;
+}
+
+/* ----------------------------------------------------------------------
+   copy values within local atom-based array
+------------------------------------------------------------------------- */
+
+void FixStoreCoord::copy_arrays(int i, int j)
+{
+  xoriginal[j][0] = xoriginal[i][0];
+  xoriginal[j][1] = xoriginal[i][1];
+  xoriginal[j][2] = xoriginal[i][2];
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based array for exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixStoreCoord::pack_exchange(int i, double *buf)
+{
+  buf[0] = xoriginal[i][0];
+  buf[1] = xoriginal[i][1];
+  buf[2] = xoriginal[i][2];
+  return 3;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values in local atom-based array from exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixStoreCoord::unpack_exchange(int nlocal, double *buf)
+{
+  xoriginal[nlocal][0] = buf[0];
+  xoriginal[nlocal][1] = buf[1];
+  xoriginal[nlocal][2] = buf[2];
+  return 3;
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based arrays for restart file
+------------------------------------------------------------------------- */
+
+int FixStoreCoord::pack_restart(int i, double *buf)
+{
+  buf[0] = 4;
+  buf[1] = xoriginal[i][0];
+  buf[2] = xoriginal[i][1];
+  buf[3] = xoriginal[i][2];
+  return 4;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values from atom->extra array to restart the fix
+------------------------------------------------------------------------- */
+
+void FixStoreCoord::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++;
+
+  xoriginal[nlocal][0] = extra[nlocal][m++];
+  xoriginal[nlocal][1] = extra[nlocal][m++];
+  xoriginal[nlocal][2] = extra[nlocal][m++];
+}
+
+/* ----------------------------------------------------------------------
+   maxsize of any atom's restart data
+------------------------------------------------------------------------- */
+
+int FixStoreCoord::maxsize_restart()
+{
+  return 4;
+}
+
+/* ----------------------------------------------------------------------
+   size of atom nlocal's restart data
+------------------------------------------------------------------------- */
+
+int FixStoreCoord::size_restart(int nlocal)
+{
+  return 4;
+}

src/fix_store_coord.h

@@ -0,0 +1,43 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef FIX_STORE_COORD_H
+#define FIX_STORE_COORD_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixStoreCoord : public Fix {
+ public:
+  FixStoreCoord(class LAMMPS *, int, char **);
+  ~FixStoreCoord();
+  int setmask();
+
+  double memory_usage();
+  void grow_arrays(int);
+  void copy_arrays(int, int);
+  int pack_exchange(int, double *);
+  int unpack_exchange(int, double *);
+  int pack_restart(int, double *);
+  void unpack_restart(int, int);
+  int size_restart(int);
+  int maxsize_restart();
+
+ private:
+  double **xoriginal;         // original coords of atoms
+};
+
+}
+
+#endif

src/fix_store_force.cpp

@@ -0,0 +1,139 @@
+/* ----------------------------------------------------------------------
+   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 "string.h"
+#include "fix_store_force.h"
+#include "atom.h"
+#include "update.h"
+#include "group.h"
+#include "respa.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreForce::FixStoreForce(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg < 3) error->all("Illegal fix store/coord command");
+
+  peratom_flag = 1;
+  size_peratom_cols = 3;
+  peratom_freq = 1;
+
+  nmax = atom->nmax;
+  foriginal = memory->create_2d_double_array(nmax,3,"store/force:foriginal");
+  array_atom = foriginal;
+
+  // zero the array since dump may access it on timestep 0
+  // zero the array since a variable may access it before first run
+
+  int nlocal = atom->nlocal;
+  for (int i = 0; i < nlocal; i++)
+    foriginal[i][0] = foriginal[i][1] = foriginal[i][2] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreForce::~FixStoreForce()
+{
+  memory->destroy_2d_double_array(foriginal);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixStoreForce::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  mask |= POST_FORCE_RESPA;
+  mask |= MIN_POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::init()
+{
+  if (strcmp(update->integrate_style,"respa") == 0)
+    nlevels_respa = ((Respa *) update->integrate)->nlevels;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::setup(int vflag)
+{
+  if (strcmp(update->integrate_style,"verlet") == 0)
+    post_force(vflag);
+  else {
+    ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+    post_force_respa(vflag,nlevels_respa-1,0);
+    ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::min_setup(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::post_force(int vflag)
+{
+  if (atom->nlocal > nmax) {
+    nmax = atom->nmax;
+    memory->destroy_2d_double_array(foriginal);
+    foriginal = memory->create_2d_double_array(nmax,3,"store/force:foriginal");
+    array_atom = foriginal;
+  }
+
+  double **f = atom->f;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      foriginal[i][0] = f[i][0];
+      foriginal[i][1] = f[i][1];
+      foriginal[i][2] = f[i][2];
+    } else foriginal[i][0] = foriginal[i][1] = foriginal[i][2] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::post_force_respa(int vflag, int ilevel, int iloop)
+{
+  if (ilevel == nlevels_respa-1) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreForce::min_post_force(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double FixStoreForce::memory_usage()
+{
+  double bytes = atom->nmax*3 * sizeof(double);
+  return bytes;
+}

src/fix_store_force.h

@@ -0,0 +1,42 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef FIX_STORE_FORCE_H
+#define FIX_STORE_FORCE_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixStoreForce : public Fix {
+ public:
+  FixStoreForce(class LAMMPS *, int, char **);
+  ~FixStoreForce();
+  int setmask();
+  void init();
+  void setup(int);
+  void min_setup(int);
+  void post_force(int);
+  void post_force_respa(int, int, int);
+  void min_post_force(int);
+  double memory_usage();
+
+ private:
+  int nlevels_respa;
+  int nmax;
+  double **foriginal;         // stored force on atoms
+};
+
+}
+
+#endif