git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3496 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_displace_atom.cpp

@@ -71,7 +71,6 @@ ComputeDisplaceAtom::~ComputeDisplaceAtom()
 void ComputeDisplaceAtom::init()
 {
   // set fix which stores original atom coords
-  // check if is correct style
 
   int ifix = modify->find_fix(id_fix);
   if (ifix < 0) error->all("Could not find compute displace/atom fix ID");
@@ -109,6 +108,7 @@ void ComputeDisplaceAtom::compute_peratom()
   double xprd = domain->xprd;
   double yprd = domain->yprd;
   double zprd = domain->zprd;
+
   int xbox,ybox,zbox;
   double dx,dy,dz;
 

src/compute_msd.cpp

@@ -0,0 +1,196 @@
+/* ----------------------------------------------------------------------
+   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.h"
+#include "atom.h"
+#include "update.h"
+#include "group.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg < 3) error->all("Illegal compute msd command");
+
+  vector_flag = 1;
+  size_vector = 4;
+  extvector = 0;
+
+  // optional args
+
+  comflag = 0;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"com") == 0) {
+      if (iarg+2 > narg) error->all("Illegal compute msd command");
+      if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
+      else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
+      else error->all("Illegal compute msd command");
+      iarg += 2;
+    } else error->all("Illegal compute msd command");
+  }
+
+  // create a new fix coord/original style with or without com keyword
+  // id = compute-ID + coord_original, fix group = compute group
+
+  int n = strlen(id) + strlen("_coord_original") + 1;
+  id_fix = new char[n];
+  strcpy(id_fix,id);
+  strcat(id_fix,"_coord_original");
+
+  char **newarg = new char*[5];
+  newarg[0] = id_fix;
+  newarg[1] = group->names[igroup];
+  newarg[2] = (char *) "coord/original";
+  newarg[3] = (char *) "com";
+  newarg[4] = (char *) "yes";
+  if (comflag) modify->add_fix(5,newarg);
+  else modify->add_fix(3,newarg);
+  delete [] newarg;
+
+  vector = new double[4];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMSD::~ComputeMSD()
+{
+  // check nfix in case all fixes have already been deleted
+
+  if (modify->nfix) modify->delete_fix(id_fix);
+
+  delete [] id_fix;
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMSD::init()
+{
+  // set fix which stores original atom coords
+
+  int ifix = modify->find_fix(id_fix);
+  if (ifix < 0) error->all("Could not find compute msd fix ID");
+  fix = modify->fix[ifix];
+
+  // nmsd = # of atoms in group
+
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  nmsd = 0;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) nmsd++;
+
+  int nmsd_all;
+  MPI_Allreduce(&nmsd,&nmsd_all,1,MPI_INT,MPI_SUM,world);
+  nmsd = nmsd_all;
+
+  masstotal = group->mass(igroup);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMSD::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  // cm = current center of mass
+
+  double cm[3];
+  if (comflag) group->xcm(igroup,masstotal,cm);
+
+  // 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->vector_atom;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *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[4];
+  msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
+
+  if (domain->triclinic == 0) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	xbox = (image[i] & 1023) - 512;
+	ybox = (image[i] >> 10 & 1023) - 512;
+	zbox = (image[i] >> 20) - 512;
+	if (comflag) {
+	  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];
+	} else {
+	  dx = x[i][0] + xbox*xprd - xoriginal[i][0];
+	  dy = x[i][1] + ybox*yprd - xoriginal[i][1];
+	  dz = x[i][2] + zbox*zprd - xoriginal[i][2];
+	}
+	msd[0] += dx*dx;
+	msd[1] += dy*dy;
+	msd[2] += dz*dz;
+	msd[3] += dx*dx + dy*dy + dz*dz;
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	xbox = (image[i] & 1023) - 512;
+	ybox = (image[i] >> 10 & 1023) - 512;
+	zbox = (image[i] >> 20) - 512;
+	if (comflag) {
+	  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];
+	} else {
+	  dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
+	  dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
+	  dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
+	}
+	msd[0] += dx*dx;
+	msd[1] += dy*dy;
+	msd[2] += dz*dz;
+	msd[3] += dx*dx + dy*dy + dz*dz;
+      }
+  }
+
+  MPI_Allreduce(msd,vector,4,MPI_DOUBLE,MPI_SUM,world);
+  if (nmsd) {
+    vector[0] /= nmsd;
+    vector[1] /= nmsd;
+    vector[2] /= nmsd;
+    vector[3] /= nmsd;
+  }
+}

src/compute_msd.h

@@ -0,0 +1,37 @@
+/* ----------------------------------------------------------------------
+   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 COMPUTE_MSD_H
+#define COMPUTE_MSD_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeMSD : public Compute {
+ public:
+  ComputeMSD(class LAMMPS *, int, char **);
+  ~ComputeMSD();
+  void init();
+  void compute_vector();
+
+ private:
+  int comflag,nmsd;
+  double masstotal;
+  char *id_fix;
+  class Fix *fix;
+};
+
+}
+
+#endif

src/fix_coord_original.cpp

@@ -27,13 +27,28 @@ using namespace LAMMPS_NS;
 FixCoordOriginal::FixCoordOriginal(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
-  if (narg != 3) error->all("Illegal fix coord/original command");
+  if (narg < 3) error->all("Illegal fix coord/original command");
 
   restart_peratom = 1;
   peratom_flag = 1;
   size_peratom = 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 coord/original 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 coord/original command");
+      iarg += 2;
+    } else error->all("Illegal fix coord/original command");
+  }
+
   // perform initial allocation of atom-based array
   // register with Atom class
 
@@ -42,16 +57,31 @@ FixCoordOriginal::FixCoordOriginal(LAMMPS *lmp, int narg, char **arg) :
   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]);
-    else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
+    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;
   }
 }
 

src/style.h

@@ -84,6 +84,7 @@ CommandStyle(write_restart,WriteRestart)
 #include "compute_heat_flux.h"
 #include "compute_ke.h"
 #include "compute_ke_atom.h"
+#include "compute_msd.h"
 #include "compute_pe.h"
 #include "compute_pe_atom.h"
 #include "compute_pressure.h"
@@ -110,6 +111,7 @@ ComputeStyle(group/group,ComputeGroupGroup)
 ComputeStyle(heat/flux,ComputeHeatFlux)
 ComputeStyle(ke,ComputeKE)
 ComputeStyle(ke/atom,ComputeKEAtom)
+ComputeStyle(msd,ComputeMSD)
 ComputeStyle(pe,ComputePE)
 ComputeStyle(pe/atom,ComputePEAtom)
 ComputeStyle(pressure,ComputePressure)