git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9124 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_gyration_molecule.cpp

@@ -141,7 +141,6 @@ void ComputeGyrationMolecule::compute_vector()
   double *rmass = atom->rmass;
   int nlocal = atom->nlocal;
 
-
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       imol = molecule[i];

src/compute_inertia_molecule.cpp

@@ -0,0 +1,184 @@
+/* ----------------------------------------------------------------------
+   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 "compute_inertia_molecule.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeInertiaMolecule::
+ComputeInertiaMolecule(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR,"Illegal compute inertia/molecule command");
+
+  if (atom->molecular == 0)
+    error->all(FLERR,"Compute inertia/molecule requires molecular atom style");
+
+  array_flag = 1;
+  size_array_cols = 6;
+  extarray = 0;
+
+  // setup molecule-based data
+
+  nmolecules = molecules_in_group(idlo,idhi);
+  size_array_rows = nmolecules;
+
+  memory->create(massproc,nmolecules,"inertia/molecule:massproc");
+  memory->create(masstotal,nmolecules,"inertia/molecule:masstotal");
+  memory->create(com,nmolecules,3,"inertia/molecule:com");
+  memory->create(comall,nmolecules,3,"inertia/molecule:comall");
+  memory->create(inertia,nmolecules,6,"inertia/molecule:inertia");
+  memory->create(inertiaall,nmolecules,6,"inertia/molecule:inertiaall");
+  array = inertiaall;
+
+  // compute masstotal for each molecule
+
+  int *mask = atom->mask;
+  int *molecule = atom->molecule;
+  int *type = atom->type;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  int i,imol;
+  double massone;
+
+  for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
+
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      massproc[imol] += massone;
+    }
+
+  MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeInertiaMolecule::~ComputeInertiaMolecule()
+{
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(com);
+  memory->destroy(comall);
+  memory->destroy(inertia);
+  memory->destroy(inertiaall);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeInertiaMolecule::init()
+{
+  int ntmp = molecules_in_group(idlo,idhi);
+  if (ntmp != nmolecules)
+    error->all(FLERR,"Molecule count changed in compute inertia/molecule");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeInertiaMolecule::compute_array()
+{
+  int i,j,imol;
+  double dx,dy,dz,massone;
+  double unwrap[3];
+
+  invoked_array = update->ntimestep;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *molecule = atom->molecule;
+  int *type = atom->type;
+  tagint *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  // center-of-mass for each molecule
+
+  for (i = 0; i < nmolecules; i++)
+    com[i][0] = com[i][1] = com[i][2] = 0.0;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      domain->unmap(x[i],image[i],unwrap);
+      com[imol][0] += unwrap[0] * massone;
+      com[imol][1] += unwrap[1] * massone;
+      com[imol][2] += unwrap[2] * massone;
+    }
+
+  MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
+                MPI_DOUBLE,MPI_SUM,world);
+  for (i = 0; i < nmolecules; i++) {
+    comall[i][0] /= masstotal[i];
+    comall[i][1] /= masstotal[i];
+    comall[i][2] /= masstotal[i];
+  }
+
+  // inertia tensor for each molecule
+
+  for (i = 0; i < nmolecules; i++)
+    for (j = 0; j < 6; j++)
+      inertia[i][j] = 0.0;
+
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      domain->unmap(x[i],image[i],unwrap);
+      dx = unwrap[0] - com[imol][0];
+      dy = unwrap[1] - com[imol][1];
+      dz = unwrap[2] - com[imol][2];
+      inertia[imol][0] += massone * (dy*dy + dz*dz);
+      inertia[imol][1] += massone * (dx*dx + dz*dz);
+      inertia[imol][2] += massone * (dx*dx + dy*dy);
+      inertia[imol][3] -= massone * dx*dy;
+      inertia[imol][4] -= massone * dy*dz;
+      inertia[imol][5] -= massone * dx*dz;
+    }
+
+  MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nmolecules,
+                MPI_DOUBLE,MPI_SUM,world);
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeInertiaMolecule::memory_usage()
+{
+  double bytes = 2*nmolecules * sizeof(double);
+  if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
+  bytes += 2*nmolecules*3 * sizeof(double);
+  bytes += 2*nmolecules*6 * sizeof(double);
+  return bytes;
+}

src/compute_inertia_molecule.h

@@ -0,0 +1,65 @@
+/* ----------------------------------------------------------------------
+   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(inertia/molecule,ComputeInertiaMolecule)
+
+#else
+
+#ifndef LMP_COMPUTE_INERTIA_MOLECULE_H
+#define LMP_COMPUTE_INERTIA_MOLECULE_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeInertiaMolecule : public Compute {
+ public:
+  ComputeInertiaMolecule(class LAMMPS *, int, char **);
+  ~ComputeInertiaMolecule();
+  void init();
+  void compute_array();
+  double memory_usage();
+
+ private:
+  int nmolecules;
+  int idlo,idhi;
+
+  double *massproc,*masstotal;
+  double **com,**comall;
+  double **inertia,**inertiaall;
+};
+
+}
+
+#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: Compute com/molecule requires molecular atom style
+
+Self-explanatory.
+
+E: Molecule count changed in compute com/molecule
+
+Number of molecules must remain constant over time.
+
+*/