lammps/src/compute_property_chunk.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   LAMMPS development team: developers@lammps.org

   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_property_chunk.h"

#include "atom.h"
#include "compute_chunk_atom.h"
#include "error.h"
#include "memory.h"

#include <cstring>

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
    ComputeChunk(lmp, narg, arg), count_one(nullptr), count_all(nullptr)
{
  if (narg < 5) utils::missing_cmd_args(FLERR, "compute property/chunk", error);

  ComputePropertyChunk::init();

  // parse values

  nvalues = narg - 4;
  pack_choice = new FnPtrPack[nvalues];
  countflag = 0;

  int i;
  for (int iarg = 4; iarg < narg; iarg++) {
    i = iarg - 4;

    if (strcmp(arg[iarg], "count") == 0) {
      pack_choice[i] = &ComputePropertyChunk::pack_count;
      countflag = 1;
    } else if (strcmp(arg[iarg], "id") == 0) {
      if (!cchunk->compress)
        error->all(FLERR, "Compute chunk/atom stores no IDs for compute property/chunk");
      pack_choice[i] = &ComputePropertyChunk::pack_id;
    } else if (strcmp(arg[iarg], "coord1") == 0) {
      if (cchunk->ncoord < 1)
        error->all(FLERR, "Compute chunk/atom stores no coord1 for compute property/chunk");
      pack_choice[i] = &ComputePropertyChunk::pack_coord1;
    } else if (strcmp(arg[iarg], "coord2") == 0) {
      if (cchunk->ncoord < 2)
        error->all(FLERR, "Compute chunk/atom stores no coord2 for compute property/chunk");
      pack_choice[i] = &ComputePropertyChunk::pack_coord2;
    } else if (strcmp(arg[iarg], "coord3") == 0) {
      if (cchunk->ncoord < 3)
        error->all(FLERR, "Compute chunk/atom stores no coord3 for compute property/chunk");
      pack_choice[i] = &ComputePropertyChunk::pack_coord3;
    } else
      error->all(FLERR, "Unkown keyword {} in compute property/chunk command", arg[iarg]);
  }

  ComputePropertyChunk::allocate();

  if (nvalues == 1) {
    vector_flag = 1;
    size_vector = 0;
    size_vector_variable = 1;
    extvector = 0;
  } else {
    array_flag = 1;
    size_array_cols = nvalues;
    size_array_rows = 0;
    size_array_rows_variable = 1;
    extarray = 0;
  }
}

/* ---------------------------------------------------------------------- */

ComputePropertyChunk::~ComputePropertyChunk()
{
  delete[] pack_choice;
  memory->destroy(vector);
  memory->destroy(array);
  memory->destroy(count_one);
  memory->destroy(count_all);
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::compute_vector()
{
  ComputeChunk::compute_vector();

  if (countflag) ichunk = cchunk->ichunk;

  // fill vector

  buf = vector;
  (this->*pack_choice[0])(0);
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::compute_array()
{
  ComputeChunk::compute_array();

  if (countflag) ichunk = cchunk->ichunk;

  // fill array

  if (array) buf = &array[0][0];
  for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n);
}
/* ----------------------------------------------------------------------
   free and reallocate per-chunk arrays
------------------------------------------------------------------------- */

void ComputePropertyChunk::allocate()
{
  ComputeChunk::allocate();
  memory->destroy(vector);
  memory->destroy(array);
  memory->destroy(count_one);
  memory->destroy(count_all);
  maxchunk = nchunk;
  if (nvalues == 1)
    memory->create(vector, maxchunk, "property/chunk:vector");
  else
    memory->create(array, maxchunk, nvalues, "property/chunk:array");
  if (countflag) {
    memory->create(count_one, maxchunk, "property/chunk:count_one");
    memory->create(count_all, maxchunk, "property/chunk:count_all");
  }
}

/* ----------------------------------------------------------------------
   memory usage of local data
------------------------------------------------------------------------- */

double ComputePropertyChunk::memory_usage()
{
  double bytes = ComputeChunk::memory_usage();
  bytes += (bigint) nchunk * nvalues * sizeof(double);
  if (countflag) bytes += (double) nchunk * 2 * sizeof(int);
  return bytes;
}

/* ----------------------------------------------------------------------
   one method for every keyword compute property/chunk can output
   the property is packed into buf starting at n with stride nvalues
   customize a new keyword by adding a method
------------------------------------------------------------------------- */

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::pack_count(int n)
{
  int index;

  for (int m = 0; m < nchunk; m++) count_one[m] = 0;

  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  for (int i = 0; i < nlocal; i++) {
    if (mask[i] & groupbit) {
      index = ichunk[i] - 1;
      if (index < 0) continue;
      count_one[index]++;
    }
  }

  MPI_Allreduce(count_one, count_all, nchunk, MPI_INT, MPI_SUM, world);

  for (int m = 0; m < nchunk; m++) {
    buf[n] = count_all[m];
    n += nvalues;
  }
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::pack_id(int n)
{
  int *origID = cchunk->chunkID;
  for (int m = 0; m < nchunk; m++) {
    buf[n] = origID[m];
    n += nvalues;
  }
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::pack_coord1(int n)
{
  double **coord = cchunk->coord;
  for (int m = 0; m < nchunk; m++) {
    buf[n] = coord[m][0];
    n += nvalues;
  }
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::pack_coord2(int n)
{
  double **coord = cchunk->coord;
  for (int m = 0; m < nchunk; m++) {
    buf[n] = coord[m][1];
    n += nvalues;
  }
}

/* ---------------------------------------------------------------------- */

void ComputePropertyChunk::pack_coord3(int n)
{
  double **coord = cchunk->coord;
  for (int m = 0; m < nchunk; m++) {
    buf[n] = coord[m][2];
    n += nvalues;
  }
}