git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3590 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_gyration_molecule.cpp

@@ -0,0 +1,186 @@
+/* ----------------------------------------------------------------------
+   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 "math.h"
+#include "compute_gyration_molecule.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp, 
+						 int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all("Illegal compute gyration/molecule command");
+
+  if (atom->molecular == 0)
+    error->all("Compute gyration/molecule requires molecular atom style");
+
+  vector_flag = 1;
+  extvector = 0;
+
+  // setup molecule-based data
+
+  nmolecules = molecules_in_group(idlo,idhi);
+  size_vector = nmolecules;
+
+  massproc = (double *) memory->smalloc(nmolecules*sizeof(double),
+					"gyration/molecule:massproc");
+  masstotal = (double *) memory->smalloc(nmolecules*sizeof(double),
+					 "gyration/molecule:masstotal");
+  com = memory->create_2d_double_array(nmolecules,3,"gyration/molecule:com");
+  comall = memory->create_2d_double_array(nmolecules,3,
+					  "gyration/molecule:comall");
+  rg = (double *) memory->smalloc(nmolecules*sizeof(double),
+				  "gyration/molecule:rg");
+  rgall = (double *) memory->smalloc(nmolecules*sizeof(double),
+				     "gyration/molecule:rgall");
+  vector = rgall;
+
+  // 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);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationMolecule::~ComputeGyrationMolecule()
+{
+  memory->sfree(massproc);
+  memory->sfree(masstotal);
+  memory->destroy_2d_double_array(com);
+  memory->destroy_2d_double_array(comall);
+  memory->sfree(rg);
+  memory->sfree(rgall);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationMolecule::init()
+{
+  int ntmp = molecules_in_group(idlo,idhi);
+  if (ntmp != nmolecules)
+    error->all("Molecule count changed in compute gyration/molecule");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationMolecule::compute_vector()
+{
+  int i,imol;
+  double xbox,ybox,zbox,dx,dy,dz;
+  double massone;
+
+  invoked_array = update->ntimestep;
+
+  for (i = 0; i < nmolecules; i++)
+    com[i][0] = com[i][1] = com[i][2] = 0.0;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *molecule = atom->molecule;
+  int *type = atom->type;
+  int *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+
+  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 (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      com[imol][0] += (x[i][0] + xbox*xprd) * massone;
+      com[imol][1] += (x[i][1] + ybox*yprd) * massone;
+      com[imol][2] += (x[i][2] + zbox*zprd) * 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];
+  }
+
+  for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
+
+  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;
+      imol = molecule[i];
+      if (molmap) imol = molmap[imol-idlo];
+      else imol--;
+      dx = (x[i][0] + xbox*xprd) - comall[imol][0];
+      dy = (x[i][1] + ybox*yprd) - comall[imol][1];
+      dz = (x[i][2] + zbox*zprd) - comall[imol][2];
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
+    }
+
+  MPI_Allreduce(rg,rgall,nmolecules,MPI_DOUBLE,MPI_SUM,world);
+
+  for (i = 0; i < nmolecules; i++) rgall[i] = sqrt(rgall[i]/masstotal[i]);
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeGyrationMolecule::memory_usage()
+{
+  double bytes = 4*nmolecules * sizeof(double);
+  if (molmap) bytes += nmolecules * sizeof(int);
+  bytes += 2*nmolecules*3 * sizeof(double);
+  return bytes;
+}