git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1507 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_group_group.cpp

@@ -0,0 +1,201 @@
+/* ----------------------------------------------------------------------
+   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 "mpi.h"
+#include "compute_group_group.h"
+#include "atom.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "group.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define INVOKED_SCALAR 1
+#define INVOKED_VECTOR 2
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg != 4) error->all("Illegal compute group/group command");
+
+  scalar_flag = vector_flag = 1;
+  size_vector = 3;
+  extscalar = 1;
+  extvector = 1;
+
+  jgroup = group->find(arg[3]);
+  if (jgroup == -1) error->all("Compute group/group group ID does not exist");
+  jgroupbit = group->bitmask[jgroup];
+
+  vector = new double[3];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGroupGroup::~ComputeGroupGroup()
+{
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGroupGroup::init()
+{
+  if (force->pair == NULL) error->all("Bad");
+  pair = force->pair;
+  cutsq = force->pair->cutsq;
+
+  // need an occasional half neighbor list
+
+  int irequest = neighbor->request((void *) this);
+  neighbor->requests[irequest]->pair = 0;
+  neighbor->requests[irequest]->compute = 1;
+  neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGroupGroup::init_list(int id, NeighList *ptr)
+{
+  list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeGroupGroup::compute_scalar()
+{
+  invoked |= INVOKED_SCALAR;
+  invoked |= INVOKED_VECTOR;
+
+  interact();
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGroupGroup::compute_vector()
+{
+  invoked |= INVOKED_SCALAR;
+  invoked |= INVOKED_VECTOR;
+
+  interact();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGroupGroup::interact()
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz;
+  double rsq,eng,fpair,factor_coul,factor_lj;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  double **x = atom->x;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int nall = nlocal + atom->nghost;
+  double *special_coul = force->special_coul;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+
+  // invoke half neighbor list (will copy or build if necessary)
+
+  neighbor->build_one(list->index);
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+  // skip if i,j are not in 2 groups
+
+  double one[4],all[4];
+  one[0] = one[1] = one[2] = one[3] = 0.0;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    if (mask[i] & groupbit) othergroupbit = jgroupbit;
+    else if (mask[i] & jgroupbit) othergroupbit = groupbit;
+    else continue;
+
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+
+      if (j < nall) factor_coul = factor_lj = 1.0;
+      else {
+	factor_coul = special_coul[j/nall];
+	factor_lj = special_lj[j/nall];
+	j %= nall;
+      }
+
+      if (!(mask[j] & othergroupbit)) continue;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+	eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+	// energy only computed once so tally full amount
+	// force tally is jgroup acting on igroup
+
+	if (newton_pair || j < nlocal) {
+	  one[0] += eng;
+	  if (othergroupbit == jgroupbit) {
+	    one[1] += delx*fpair;
+	    one[2] += dely*fpair;
+	    one[3] += delz*fpair;
+	  }
+	  if (othergroupbit == groupbit) {
+	    one[1] -= delx*fpair;
+	    one[2] -= dely*fpair;
+	    one[3] -= delz*fpair;
+	  }
+
+	// energy computed twice so tally half amount
+	// only tally force if I own igroup atom
+
+	} else {
+	  one[0] += 0.5*eng;
+	  if (othergroupbit == jgroupbit) {
+	    one[1] += delx*fpair;
+	    one[2] += dely*fpair;
+	    one[3] += delz*fpair;
+	  }
+	}
+      }
+    }
+  }
+
+  MPI_Allreduce(one,all,4,MPI_DOUBLE,MPI_SUM,world);
+  scalar = all[0];
+  vector[0] = all[1]; vector[1] = all[2]; vector[2] = all[3];
+}

src/compute_group_group.h

@@ -0,0 +1,41 @@
+/* ----------------------------------------------------------------------
+   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_GROUP_GROUP_H
+#define COMPUTE_GROUP_GROUP_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeGroupGroup : public Compute {
+ public:
+  ComputeGroupGroup(class LAMMPS *, int, char **);
+  ~ComputeGroupGroup();
+  void init();
+  void init_list(int, class NeighList *);
+  double compute_scalar();
+  void compute_vector();
+
+ private:
+  int jgroup,jgroupbit,othergroupbit;
+  double **cutsq;
+  class Pair *pair;
+  class NeighList *list;
+
+  void interact();
+};
+
+}
+
+#endif

src/style.h

@@ -79,6 +79,7 @@ CommandStyle(write_restart,WriteRestart)
 #include "compute_centro_atom.h"
 #include "compute_coord_atom.h"
 #include "compute_displace_atom.h"
+#include "compute_group_group.h"
 #include "compute_ke_atom.h"
 #include "compute_pe.h"
 #include "compute_pe_atom.h"
@@ -98,6 +99,7 @@ CommandStyle(write_restart,WriteRestart)
 ComputeStyle(centro/atom,ComputeCentroAtom)
 ComputeStyle(coord/atom,ComputeCoordAtom)
 ComputeStyle(displace/atom,ComputeDisplaceAtom)
+ComputeStyle(group/group,ComputeGroupGroup)
 ComputeStyle(ke/atom,ComputeKEAtom)
 ComputeStyle(pe,ComputePE)
 ComputeStyle(pe/atom,ComputePEAtom)