git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3616 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_property_molecule.cpp

@@ -0,0 +1,140 @@
+/* ----------------------------------------------------------------------
+   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_property_molecule.h"
+#include "atom.h"
+#include "update.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputePropertyMolecule::
+ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg < 4) error->all("Illegal compute property/molecule command");
+
+  if (atom->molecular == 0)
+    error->all("Compute property/molecule requires molecular atom style");
+
+  nvalues = narg - 3;
+  if (nvalues == 1) size_array_cols = 0;
+
+  pack_choice = new FnPtrPack[nvalues];
+
+  int i;
+  for (int iarg = 3; iarg < narg; iarg++) {
+    i = iarg-3;
+
+    if (strcmp(arg[iarg],"mol") == 0)
+      pack_choice[i] = &ComputePropertyMolecule::pack_mol;
+    else error->all("Invalid keyword in compute property/molecule command");
+  }
+
+  // setup molecule-based data
+
+  nmolecules = molecules_in_group(idlo,idhi);
+
+  vector = NULL;
+  array = NULL;
+
+  if (nvalues == 1) {
+    vector = (double *) memory->smalloc(nmolecules*sizeof(double),
+					"property/molecule:vector");
+    vector_flag = 1;
+    size_vector = nmolecules;
+    extvector = 0;
+  } else {
+    array = memory->create_2d_double_array(nmolecules,nvalues,
+					   "property/molecule:array");
+    array_flag = 1;
+    size_array_rows = nmolecules;
+    size_array_cols = nvalues;
+    extarray = 0;
+  }
+  
+  // fill vector or array with molecule values
+
+  if (nvalues == 1) {
+    buf = vector;
+    (this->*pack_choice[0])(0);
+  } else {
+    if (array) buf = &array[0][0];
+    for (int n = 0; n < nvalues; n++)
+      (this->*pack_choice[n])(n);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePropertyMolecule::~ComputePropertyMolecule()
+{
+  delete [] pack_choice;
+  memory->sfree(vector);
+  memory->destroy_2d_double_array(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePropertyMolecule::init()
+{
+  int ntmp = molecules_in_group(idlo,idhi);
+  if (ntmp != nmolecules)
+    error->all("Molecule count changed in compute property/molecule");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePropertyMolecule::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePropertyMolecule::compute_array()
+{
+  invoked_array = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputePropertyMolecule::memory_usage()
+{
+  double bytes = nmolecules*nvalues * sizeof(double);
+  if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
+  return bytes;
+}
+
+/* ----------------------------------------------------------------------
+   one method for every keyword compute property/molecule can output
+   the atom property is packed into buf starting at n with stride nvalues
+   customize a new keyword by adding a method
+------------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePropertyMolecule::pack_mol(int n)
+{
+  for (int i = idlo; i <= idhi; i++)
+    if (molmap[i-idlo] >= 0) {
+      buf[n] = i;
+      n += nvalues;
+    }
+}

src/compute_property_molecule.h

@@ -0,0 +1,44 @@
+/* ----------------------------------------------------------------------
+   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_PROPERTY_MOLECULE_H
+#define COMPUTE_PROPERTY_MOLECULE_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePropertyMolecule : public Compute {
+ public:
+  ComputePropertyMolecule(class LAMMPS *, int, char **);
+  ~ComputePropertyMolecule();
+  void init();
+  void compute_vector();
+  void compute_array();
+  double memory_usage();
+
+ private:
+  int nvalues,nmolecules;
+  int idlo,idhi;
+
+  double *buf;
+
+  typedef void (ComputePropertyMolecule::*FnPtrPack)(int);
+  FnPtrPack *pack_choice;              // ptrs to pack functions
+
+  void pack_mol(int);
+};
+
+}
+
+#endif