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Introduce ComputeChunk class with shared functionality of all /chunk computes

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This commit is contained in:
Axel Kohlmeyer
2023-03-18 05:55:03 -04:00
parent fce1f8e0af
commit 1ccb0f8d8d
29 changed files with 958 additions and 2050 deletions
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141
src/compute_com_chunk.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,22 +18,18 @@
#include "domain.h"
#include "error.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
enum{ONCE,NFREQ,EVERY};
enum { ONCE, NFREQ, EVERY };
/* ---------------------------------------------------------------------- */
ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idchunk(nullptr), masstotal(nullptr), massproc(nullptr), com(nullptr), comall(nullptr)
ComputeChunk(lmp, narg, arg), masstotal(nullptr), massproc(nullptr), com(nullptr),
comall(nullptr)
{
if (narg != 4) error->all(FLERR,"Illegal compute com/chunk command");
if (narg != 4) error->all(FLERR, "Illegal compute com/chunk command");
array_flag = 1;
size_array_cols = 3;
@ -42,26 +37,14 @@ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
idchunk = utils::strdup(arg[3]);
ComputeCOMChunk::init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
allocate();
firstflag = massneed = 1;
ComputeCOMChunk::allocate();
}
/* ---------------------------------------------------------------------- */
ComputeCOMChunk::~ComputeCOMChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
@ -70,18 +53,6 @@ ComputeCOMChunk::~ComputeCOMChunk()
/* ---------------------------------------------------------------------- */
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 = dynamic_cast<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
@ -101,23 +72,12 @@ void ComputeCOMChunk::compute_array()
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();
ComputeChunk::compute_array();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
size_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
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;
@ -133,86 +93,32 @@ void ComputeCOMChunk::compute_array()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
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);
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);
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;
} else
comall[i][0] = comall[i][1] = comall[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods ensure 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 = dynamic_cast<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
------------------------------------------------------------------------- */
@ -224,10 +130,10 @@ void ComputeCOMChunk::allocate()
memory->destroy(com);
memory->destroy(comall);
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");
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;
}
@ -237,7 +143,8 @@ void ComputeCOMChunk::allocate()
double ComputeCOMChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (double) maxchunk * 2*3 * sizeof(double);
double bytes = ComputeChunk::memory_usage();
bytes += (bigint) maxchunk * 2 * sizeof(double);
bytes += (double) maxchunk * 2 * 3 * sizeof(double);
return bytes;
}