git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9998 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_msd.cpp

@@ -18,7 +18,6 @@
 #include "group.h"
 #include "domain.h"
 #include "modify.h"
-#include "fix.h"
 #include "fix_store.h"
 #include "error.h"
 

src/compute_msd.h

@@ -27,11 +27,11 @@ namespace LAMMPS_NS {
 class ComputeMSD : public Compute {
  public:
   ComputeMSD(class LAMMPS *, int, char **);
-  ~ComputeMSD();
+  virtual ~ComputeMSD();
   void init();
-  void compute_vector();
+  virtual void compute_vector();
 
- private:
+ protected:
   int comflag,nmsd;
   double masstotal;
   char *id_fix;

src/compute_msd_nongauss.cpp

@@ -0,0 +1,102 @@
+/* ----------------------------------------------------------------------
+   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 "compute_msd_nongauss.h"
+#include "atom.h"
+#include "update.h"
+#include "group.h"
+#include "domain.h"
+#include "fix_store.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMSDNonGauss::ComputeMSDNonGauss(LAMMPS *lmp, int narg, char **arg) :
+  ComputeMSD(lmp, narg, arg)
+{
+  size_vector = 3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMSDNonGauss::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  // cm = current center of mass
+
+  double cm[3];
+  if (comflag) group->xcm(igroup,masstotal,cm);
+  else cm[0] = cm[1] = cm[2] = 0.0;
+
+  // dx,dy,dz = displacement of atom from original position
+  // original unwrapped position is stored by fix
+  // relative to center of mass if comflag is set
+  // for triclinic, need to unwrap current atom coord via h matrix
+
+  double **xoriginal = fix->astore;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  tagint *image = atom->image;
+  int nlocal = atom->nlocal;
+
+  double *h = domain->h;
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+
+  double dx,dy,dz;
+  int xbox,ybox,zbox;
+
+  double msd[2];
+  msd[0] = msd[1] = 0.0;
+
+  if (domain->triclinic == 0) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        xbox = (image[i] & IMGMASK) - IMGMAX;
+        ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+        zbox = (image[i] >> IMG2BITS) - IMGMAX;
+        dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
+        dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
+        dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
+        msd[0] += dx*dx + dy*dy + dz*dz;
+        msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        xbox = (image[i] & IMGMASK) - IMGMAX;
+        ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+        zbox = (image[i] >> IMG2BITS) - IMGMAX;
+        dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
+          cm[0] - xoriginal[i][0];
+        dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
+        dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
+        msd[0] += dx*dx + dy*dy + dz*dz;
+        msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
+      }
+  }
+
+  MPI_Allreduce(msd,vector,2,MPI_DOUBLE,MPI_SUM,world);
+  if (nmsd) {
+    vector[0] /= nmsd;
+    vector[1] /= nmsd;
+    vector[2] = (3*vector[1])/(5*vector[0]*vector[0]) - 1;
+  }
+}

src/compute_msd_nongauss.h

@@ -0,0 +1,51 @@
+/* ----------------------------------------------------------------------
+   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(msd/nongauss,ComputeMSDNonGauss)
+
+#else
+
+#ifndef LMP_COMPUTE_MSD_NONGAUSS_H
+#define LMP_COMPUTE_MSD_NONGAUSS_H
+
+#include "compute_msd.h"
+
+namespace LAMMPS_NS {
+
+class ComputeMSDNonGauss : public ComputeMSD {
+ public:
+  ComputeMSDNonGauss(class LAMMPS *, int, char **);
+  ~ComputeMSDNonGauss() {}
+  void compute_vector();
+};
+
+}
+
+#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.
+
+*/