lammps/src/compute_omega_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_omega_chunk.h"

#include "atom.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "error.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "memory.h"

using namespace LAMMPS_NS;

#define EPSILON 1.0e-6

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

ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
    comall(nullptr), inertia(nullptr), inertiaall(nullptr), angmom(nullptr), angmomall(nullptr),
    omega(nullptr)
{
  if (narg != 4) error->all(FLERR, "Illegal compute omega/chunk command");

  array_flag = 1;
  size_array_cols = 3;
  size_array_rows = 0;
  size_array_rows_variable = 1;
  extarray = 0;

  ComputeOmegaChunk::init();
  ComputeOmegaChunk::allocate();
}

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

ComputeOmegaChunk::~ComputeOmegaChunk()
{
  memory->destroy(massproc);
  memory->destroy(masstotal);
  memory->destroy(com);
  memory->destroy(comall);
  memory->destroy(angmom);
  memory->destroy(angmomall);
  memory->destroy(inertia);
  memory->destroy(inertiaall);
  memory->destroy(omega);
}

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

void ComputeOmegaChunk::compute_array()
{
  int i, j, m, index;
  double dx, dy, dz, massone;
  double unwrap[3];

  ComputeChunk::compute_array();
  int *ichunk = cchunk->ichunk;

  if (nchunk > maxchunk) allocate();
  size_array_rows = nchunk;

  // zero local per-chunk values

  for (i = 0; i < nchunk; i++) {
    massproc[i] = 0.0;
    com[i][0] = com[i][1] = com[i][2] = 0.0;
    for (j = 0; j < 6; j++) inertia[i][j] = 0.0;
    angmom[i][0] = angmom[i][1] = angmom[i][2] = 0.0;
    omega[i][0] = omega[i][1] = omega[i][2] = 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 (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);
      massproc[index] += massone;
      com[index][0] += unwrap[0] * massone;
      com[index][1] += unwrap[1] * massone;
      com[index][2] += unwrap[2] * massone;
    }

  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);

  for (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];
    }
  }

  // compute inertia tensor for each chunk

  for (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);
      dx = unwrap[0] - comall[index][0];
      dy = unwrap[1] - comall[index][1];
      dz = unwrap[2] - comall[index][2];
      inertia[index][0] += massone * (dy * dy + dz * dz);
      inertia[index][1] += massone * (dx * dx + dz * dz);
      inertia[index][2] += massone * (dx * dx + dy * dy);
      inertia[index][3] -= massone * dx * dy;
      inertia[index][4] -= massone * dy * dz;
      inertia[index][5] -= massone * dx * dz;
    }

  MPI_Allreduce(&inertia[0][0], &inertiaall[0][0], 6 * nchunk, MPI_DOUBLE, MPI_SUM, world);

  // compute angmom for each chunk

  double **v = atom->v;

  for (i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      index = ichunk[i] - 1;
      if (index < 0) continue;
      domain->unmap(x[i], image[i], unwrap);
      dx = unwrap[0] - comall[index][0];
      dy = unwrap[1] - comall[index][1];
      dz = unwrap[2] - comall[index][2];
      if (rmass)
        massone = rmass[i];
      else
        massone = mass[type[i]];
      angmom[index][0] += massone * (dy * v[i][2] - dz * v[i][1]);
      angmom[index][1] += massone * (dz * v[i][0] - dx * v[i][2]);
      angmom[index][2] += massone * (dx * v[i][1] - dy * v[i][0]);
    }

  MPI_Allreduce(&angmom[0][0], &angmomall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);

  // compute omega for each chunk

  double determinant, invdeterminant;
  double idiag[3], ex[3], ey[3], ez[3], cross[3];
  double ione[3][3], inverse[3][3], evectors[3][3];
  double *iall, *mall;

  for (m = 0; m < nchunk; m++) {

    // determinant = triple product of rows of inertia matrix

    iall = &inertiaall[m][0];
    determinant = iall[0] * (iall[1] * iall[2] - iall[4] * iall[4]) +
        iall[3] * (iall[4] * iall[5] - iall[3] * iall[2]) +
        iall[5] * (iall[3] * iall[4] - iall[1] * iall[5]);

    ione[0][0] = iall[0];
    ione[1][1] = iall[1];
    ione[2][2] = iall[2];
    ione[0][1] = ione[1][0] = iall[3];
    ione[1][2] = ione[2][1] = iall[4];
    ione[0][2] = ione[2][0] = iall[5];

    // non-singular I matrix
    // use L = Iw, inverting I to solve for w

    if (determinant > EPSILON) {
      inverse[0][0] = ione[1][1] * ione[2][2] - ione[1][2] * ione[2][1];
      inverse[0][1] = -(ione[0][1] * ione[2][2] - ione[0][2] * ione[2][1]);
      inverse[0][2] = ione[0][1] * ione[1][2] - ione[0][2] * ione[1][1];

      inverse[1][0] = -(ione[1][0] * ione[2][2] - ione[1][2] * ione[2][0]);
      inverse[1][1] = ione[0][0] * ione[2][2] - ione[0][2] * ione[2][0];
      inverse[1][2] = -(ione[0][0] * ione[1][2] - ione[0][2] * ione[1][0]);

      inverse[2][0] = ione[1][0] * ione[2][1] - ione[1][1] * ione[2][0];
      inverse[2][1] = -(ione[0][0] * ione[2][1] - ione[0][1] * ione[2][0]);
      inverse[2][2] = ione[0][0] * ione[1][1] - ione[0][1] * ione[1][0];

      invdeterminant = 1.0 / determinant;
      for (i = 0; i < 3; i++)
        for (j = 0; j < 3; j++) inverse[i][j] *= invdeterminant;

      mall = &angmomall[m][0];
      omega[m][0] = inverse[0][0] * mall[0] + inverse[0][1] * mall[1] + inverse[0][2] * mall[2];
      omega[m][1] = inverse[1][0] * mall[0] + inverse[1][1] * mall[1] + inverse[1][2] * mall[2];
      omega[m][2] = inverse[2][0] * mall[0] + inverse[2][1] * mall[1] + inverse[2][2] * mall[2];

      // handle each (nearly) singular I matrix
      // due to 2-atom chunk or linear molecule
      // use jacobi3() and angmom_to_omega() to calculate valid omega

    } else {
      int ierror = MathEigen::jacobi3(ione, idiag, evectors);
      if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for omega/chunk");

      ex[0] = evectors[0][0];
      ex[1] = evectors[1][0];
      ex[2] = evectors[2][0];
      ey[0] = evectors[0][1];
      ey[1] = evectors[1][1];
      ey[2] = evectors[2][1];
      ez[0] = evectors[0][2];
      ez[1] = evectors[1][2];
      ez[2] = evectors[2][2];

      // enforce 3 evectors as a right-handed coordinate system
      // flip 3rd vector if needed

      MathExtra::cross3(ex, ey, cross);
      if (MathExtra::dot3(cross, ez) < 0.0) MathExtra::negate3(ez);

      // if any principal moment < scaled EPSILON, set to 0.0

      double max;
      max = MAX(idiag[0], idiag[1]);
      max = MAX(max, idiag[2]);

      if (idiag[0] < EPSILON * max) idiag[0] = 0.0;
      if (idiag[1] < EPSILON * max) idiag[1] = 0.0;
      if (idiag[2] < EPSILON * max) idiag[2] = 0.0;

      // calculate omega using diagonalized inertia matrix

      MathExtra::angmom_to_omega(&angmomall[m][0], ex, ey, ez, idiag, &omega[m][0]);
    }
  }
}
/* ----------------------------------------------------------------------
   free and reallocate per-chunk arrays
------------------------------------------------------------------------- */

void ComputeOmegaChunk::allocate()
{
  ComputeChunk::allocate();
  memory->destroy(massproc);
  memory->destroy(masstotal);
  memory->destroy(com);
  memory->destroy(comall);
  memory->destroy(inertia);
  memory->destroy(inertiaall);
  memory->destroy(angmom);
  memory->destroy(angmomall);
  memory->destroy(omega);
  maxchunk = nchunk;
  memory->create(massproc, maxchunk, "omega/chunk:massproc");
  memory->create(masstotal, maxchunk, "omega/chunk:masstotal");
  memory->create(com, maxchunk, 3, "omega/chunk:com");
  memory->create(comall, maxchunk, 3, "omega/chunk:comall");
  memory->create(inertia, maxchunk, 6, "omega/chunk:inertia");
  memory->create(inertiaall, maxchunk, 6, "omega/chunk:inertiaall");
  memory->create(angmom, maxchunk, 3, "omega/chunk:angmom");
  memory->create(angmomall, maxchunk, 3, "omega/chunk:angmomall");
  memory->create(omega, maxchunk, 3, "omega/chunk:omega");
  array = omega;
}

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

double ComputeOmegaChunk::memory_usage()
{
  double bytes = ComputeChunk::memory_usage();
  bytes += (bigint) maxchunk * 2 * sizeof(double);
  bytes += (double) maxchunk * 2 * 3 * sizeof(double);
  bytes += (double) maxchunk * 2 * 6 * sizeof(double);
  bytes += (double) maxchunk * 2 * 3 * sizeof(double);
  bytes += (double) maxchunk * 3 * sizeof(double);
  return bytes;
}