git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13098 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_com_chunk.cpp

@@ -0,0 +1,242 @@
+/* ----------------------------------------------------------------------
+   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_com_chunk.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "compute_chunk_atom.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{ONCE,NFREQ,EVERY};
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 4) error->all(FLERR,"Illegal compute com/chunk command");
+
+  array_flag = 1;
+  size_array_cols = 3;
+  size_array_rows = 0;
+  size_array_rows_variable = 1;
+  extarray = 0;
+
+  // ID of compute chunk/atom
+
+  int n = strlen(arg[3]) + 1;
+  idchunk = new char[n];
+  strcpy(idchunk,arg[3]);
+
+  init();
+
+  // chunk-based data
+
+  nchunk = 1;
+  maxchunk = 0;
+  massproc = masstotal = NULL;
+  com = comall = NULL;
+  allocate();
+
+  firstflag = massneed = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCOMChunk::~ComputeCOMChunk()
+{
+  delete [] idchunk;
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(com);
+  memory->destroy(comall);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCOMChunk::init()
+{
+  int icompute = modify->find_compute(idchunk);
+  if (icompute < 0)
+    error->all(FLERR,"Chunk/atom compute does not exist for compute com/chunk");
+  cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+  if (strcmp(cchunk->style,"chunk/atom") != 0)
+    error->all(FLERR,"Compute com/chunk does not use chunk/atom compute");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCOMChunk::setup()
+{
+  // one-time calculation of per-chunk mass
+  // done in setup, so that ComputeChunkAtom::setup() is already called
+
+  if (firstflag && cchunk->idsflag == ONCE) {
+    firstflag = massneed = 0;
+    compute_array();
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCOMChunk::compute_array()
+{
+  int index;
+  double massone;
+  double unwrap[3];
+
+  invoked_array = update->ntimestep;
+
+  // compute chunk/atom assigns atoms to chunk IDs
+  // extract ichunk index vector from compute
+  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+  nchunk = cchunk->setup_chunks();
+  cchunk->compute_ichunk();
+  int *ichunk = cchunk->ichunk;
+
+  if (nchunk > maxchunk) allocate();
+
+  // zero local per-chunk values
+
+  for (int i = 0; i < nchunk; i++)
+    com[i][0] = com[i][1] = com[i][2] = 0.0;
+  if (massneed)
+    for (int i = 0; i < nchunk; i++) massproc[i] = 0.0;
+
+  // compute COM for each chunk
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  imageint *image = atom->image;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      index = ichunk[i]-1;
+      if (index < 0) continue;
+      if (rmass) massone = rmass[i];
+      else massone = mass[type[i]];
+      domain->unmap(x[i],image[i],unwrap);
+      com[index][0] += unwrap[0] * massone;
+      com[index][1] += unwrap[1] * massone;
+      com[index][2] += unwrap[2] * massone;
+      if (massneed) massproc[index] += massone;
+    }
+
+  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  if (massneed)
+    MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+
+  for (int i = 0; i < nchunk; i++) {
+    if (masstotal[i] > 0.0) {
+      comall[i][0] /= masstotal[i];
+      comall[i][1] /= masstotal[i];
+      comall[i][2] /= masstotal[i];
+    } else comall[i][0] = comall[i][1] = comall[i][2] = 0.0;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   lock methods: called by fix ave/time
+   these methods insure vector/array size is locked for Nfreq epoch
+     by passing lock info along to compute chunk/atom
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   increment lock counter
+------------------------------------------------------------------------- */
+
+void ComputeCOMChunk::lock_enable()
+{
+  cchunk->lockcount++;
+}
+
+/* ----------------------------------------------------------------------
+   decrement lock counter in compute chunk/atom, it if still exists
+------------------------------------------------------------------------- */
+
+void ComputeCOMChunk::lock_disable()
+{
+  int icompute = modify->find_compute(idchunk);
+  if (icompute >= 0) {
+    cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+    cchunk->lockcount--;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   calculate and return # of chunks = length of vector/array
+------------------------------------------------------------------------- */
+
+int ComputeCOMChunk::lock_length()
+{
+  nchunk = cchunk->setup_chunks();
+  return nchunk;
+}
+
+/* ----------------------------------------------------------------------
+   set the lock from startstep to stopstep
+------------------------------------------------------------------------- */
+
+void ComputeCOMChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
+{
+  cchunk->lock(fixptr,startstep,stopstep);
+}
+
+/* ----------------------------------------------------------------------
+   unset the lock
+------------------------------------------------------------------------- */
+
+void ComputeCOMChunk::unlock(Fix *fixptr)
+{
+  cchunk->unlock(fixptr);
+}
+
+/* ----------------------------------------------------------------------
+   free and reallocate per-chunk arrays
+------------------------------------------------------------------------- */
+
+void ComputeCOMChunk::allocate()
+{
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(com);
+  memory->destroy(comall);
+  size_array_rows = maxchunk = nchunk;
+  memory->create(massproc,maxchunk,"com/chunk:massproc");
+  memory->create(masstotal,maxchunk,"com/chunk:masstotal");
+  memory->create(com,maxchunk,3,"com/chunk:com");
+  memory->create(comall,maxchunk,3,"com/chunk:comall");
+  array = comall;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeCOMChunk::memory_usage()
+{
+  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  bytes += (bigint) maxchunk * 2*3 * sizeof(double);
+  return bytes;
+}