Introduce ComputeChunk class with shared functionality of all /chunk computes
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -14,25 +13,21 @@
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#include "compute_inertia_chunk.h"
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#include <cstring>
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "compute_chunk_atom.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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#include "memory.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr), comall(nullptr),
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inertia(nullptr), inertiaall(nullptr)
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ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
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comall(nullptr), inertia(nullptr), inertiaall(nullptr)
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{
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if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command");
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if (narg != 4) error->all(FLERR, "Illegal compute inertia/chunk command");
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array_flag = 1;
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size_array_cols = 6;
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@ -40,24 +35,14 @@ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
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size_array_rows_variable = 1;
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extarray = 0;
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// ID of compute chunk/atom
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idchunk = utils::strdup(arg[3]);
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ComputeInertiaChunk::init();
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// chunk-based data
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nchunk = 1;
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maxchunk = 0;
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allocate();
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ComputeInertiaChunk::allocate();
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}
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/* ---------------------------------------------------------------------- */
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ComputeInertiaChunk::~ComputeInertiaChunk()
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{
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delete [] idchunk;
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(com);
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@ -68,38 +53,15 @@ ComputeInertiaChunk::~ComputeInertiaChunk()
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/* ---------------------------------------------------------------------- */
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void ComputeInertiaChunk::init()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for "
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"compute inertia/chunk");
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cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
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if (strcmp(cchunk->style,"chunk/atom") != 0)
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error->all(FLERR,"Compute inertia/chunk does not use chunk/atom compute");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeInertiaChunk::compute_array()
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{
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int i,j,index;
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double dx,dy,dz,massone;
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int i, j, index;
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double dx, dy, dz, massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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ComputeChunk::compute_array();
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int *ichunk = cchunk->ichunk;
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if (nchunk > maxchunk) allocate();
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size_array_rows = nchunk;
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// zero local per-chunk values
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for (i = 0; i < nchunk; i++) {
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@ -120,19 +82,21 @@ void ComputeInertiaChunk::compute_array()
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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index = ichunk[i]-1;
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index = ichunk[i] - 1;
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if (index < 0) continue;
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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domain->unmap(x[i],image[i],unwrap);
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if (rmass)
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massone = rmass[i];
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else
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massone = mass[type[i]];
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domain->unmap(x[i], image[i], unwrap);
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massproc[index] += massone;
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com[index][0] += unwrap[0] * massone;
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com[index][1] += unwrap[1] * massone;
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com[index][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
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MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
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for (i = 0; i < nchunk; i++) {
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if (masstotal[i] > 0.0) {
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@ -146,83 +110,26 @@ void ComputeInertiaChunk::compute_array()
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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index = ichunk[i]-1;
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index = ichunk[i] - 1;
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if (index < 0) continue;
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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domain->unmap(x[i],image[i],unwrap);
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if (rmass)
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massone = rmass[i];
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else
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massone = mass[type[i]];
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domain->unmap(x[i], image[i], unwrap);
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dx = unwrap[0] - comall[index][0];
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dy = unwrap[1] - comall[index][1];
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dz = unwrap[2] - comall[index][2];
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inertia[index][0] += massone * (dy*dy + dz*dz);
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inertia[index][1] += massone * (dx*dx + dz*dz);
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inertia[index][2] += massone * (dx*dx + dy*dy);
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inertia[index][3] -= massone * dx*dy;
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inertia[index][4] -= massone * dy*dz;
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inertia[index][5] -= massone * dx*dz;
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inertia[index][0] += massone * (dy * dy + dz * dz);
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inertia[index][1] += massone * (dx * dx + dz * dz);
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inertia[index][2] += massone * (dx * dx + dy * dy);
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inertia[index][3] -= massone * dx * dy;
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inertia[index][4] -= massone * dy * dz;
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inertia[index][5] -= massone * dx * dz;
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}
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MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nchunk,
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MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&inertia[0][0], &inertiaall[0][0], 6 * nchunk, MPI_DOUBLE, MPI_SUM, world);
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}
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/* ----------------------------------------------------------------------
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lock methods: called by fix ave/time
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these methods ensure vector/array size is locked for Nfreq epoch
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by passing lock info along to compute chunk/atom
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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increment lock counter
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------------------------------------------------------------------------- */
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void ComputeInertiaChunk::lock_enable()
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{
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cchunk->lockcount++;
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}
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/* ----------------------------------------------------------------------
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decrement lock counter in compute chunk/atom, it if still exists
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------------------------------------------------------------------------- */
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void ComputeInertiaChunk::lock_disable()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute >= 0) {
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cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
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cchunk->lockcount--;
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}
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}
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/* ----------------------------------------------------------------------
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calculate and return # of chunks = length of vector/array
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------------------------------------------------------------------------- */
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int ComputeInertiaChunk::lock_length()
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{
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nchunk = cchunk->setup_chunks();
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return nchunk;
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}
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/* ----------------------------------------------------------------------
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set the lock from startstep to stopstep
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------------------------------------------------------------------------- */
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void ComputeInertiaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
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{
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cchunk->lock(fixptr,startstep,stopstep);
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}
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/* ----------------------------------------------------------------------
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unset the lock
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------------------------------------------------------------------------- */
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void ComputeInertiaChunk::unlock(Fix *fixptr)
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{
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cchunk->unlock(fixptr);
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}
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/* ----------------------------------------------------------------------
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free and reallocate per-chunk arrays
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------------------------------------------------------------------------- */
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@ -236,12 +143,12 @@ void ComputeInertiaChunk::allocate()
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memory->destroy(inertia);
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memory->destroy(inertiaall);
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maxchunk = nchunk;
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memory->create(massproc,maxchunk,"inertia/chunk:massproc");
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memory->create(masstotal,maxchunk,"inertia/chunk:masstotal");
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memory->create(com,maxchunk,3,"inertia/chunk:com");
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memory->create(comall,maxchunk,3,"inertia/chunk:comall");
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memory->create(inertia,maxchunk,6,"inertia/chunk:inertia");
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memory->create(inertiaall,maxchunk,6,"inertia/chunk:inertiaall");
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memory->create(massproc, maxchunk, "inertia/chunk:massproc");
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memory->create(masstotal, maxchunk, "inertia/chunk:masstotal");
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memory->create(com, maxchunk, 3, "inertia/chunk:com");
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memory->create(comall, maxchunk, 3, "inertia/chunk:comall");
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memory->create(inertia, maxchunk, 6, "inertia/chunk:inertia");
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memory->create(inertiaall, maxchunk, 6, "inertia/chunk:inertiaall");
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array = inertiaall;
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}
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@ -251,8 +158,9 @@ void ComputeInertiaChunk::allocate()
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double ComputeInertiaChunk::memory_usage()
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{
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double bytes = (bigint) maxchunk * 2 * sizeof(double);
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bytes += (double) maxchunk * 2*3 * sizeof(double);
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bytes += (double) maxchunk * 2*6 * sizeof(double);
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double bytes = ComputeChunk::memory_usage();
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bytes += (bigint) maxchunk * 2 * sizeof(double);
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bytes += (double) maxchunk * 2 * 3 * sizeof(double);
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bytes += (double) maxchunk * 2 * 6 * sizeof(double);
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return bytes;
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}
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