Introduce ComputeChunk class with shared functionality of all /chunk computes
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -22,19 +21,16 @@
|
||||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg), idchunk(nullptr), id_fix(nullptr), massproc(nullptr),
|
||||
masstotal(nullptr), com(nullptr), comall(nullptr), msd(nullptr)
|
||||
ComputeChunk(lmp, narg, arg), id_fix(nullptr), massproc(nullptr), masstotal(nullptr),
|
||||
com(nullptr), comall(nullptr), msd(nullptr)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command");
|
||||
if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
|
||||
|
||||
array_flag = 1;
|
||||
size_array_cols = 4;
|
||||
@ -42,11 +38,6 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
|
||||
size_array_rows_variable = 1;
|
||||
extarray = 0;
|
||||
|
||||
// ID of compute chunk/atom
|
||||
|
||||
idchunk = utils::strdup(arg[3]);
|
||||
|
||||
firstflag = 1;
|
||||
ComputeMSDChunk::init();
|
||||
|
||||
// create a new fix STORE style for reference positions
|
||||
@ -58,7 +49,7 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
|
||||
fix = dynamic_cast<FixStoreGlobal *>(
|
||||
modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1", id_fix,group->names[igroup])));
|
||||
modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1", id_fix, group->names[igroup])));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -70,7 +61,6 @@ ComputeMSDChunk::~ComputeMSDChunk()
|
||||
if (modify->nfix) modify->delete_fix(id_fix);
|
||||
|
||||
delete[] id_fix;
|
||||
delete[] idchunk;
|
||||
memory->destroy(massproc);
|
||||
memory->destroy(masstotal);
|
||||
memory->destroy(com);
|
||||
@ -82,19 +72,14 @@ ComputeMSDChunk::~ComputeMSDChunk()
|
||||
|
||||
void ComputeMSDChunk::init()
|
||||
{
|
||||
int icompute = modify->find_compute(idchunk);
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Chunk/atom compute does not exist for compute msd/chunk");
|
||||
cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
|
||||
if (strcmp(cchunk->style,"chunk/atom") != 0)
|
||||
error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
|
||||
ComputeChunk::init();
|
||||
|
||||
// set fix which stores reference atom coords
|
||||
// if firstflag, will be created in setup()
|
||||
|
||||
if (!firstflag) {
|
||||
fix = dynamic_cast<FixStoreGlobal *>(modify->get_fix_by_id(id_fix));
|
||||
if (!fix) error->all(FLERR,"Could not find compute msd/chunk fix with ID {}", id_fix);
|
||||
if (!fix) error->all(FLERR, "Could not find compute msd/chunk fix with ID {}", id_fix);
|
||||
}
|
||||
}
|
||||
|
||||
@ -113,7 +98,7 @@ void ComputeMSDChunk::setup()
|
||||
// otherwise reset its size now and initialize to current COM
|
||||
|
||||
if (fix->nrow == nchunk && fix->ncol == 3) return;
|
||||
fix->reset_global(nchunk,3);
|
||||
fix->reset_global(nchunk, 3);
|
||||
|
||||
double **cominit = fix->astore;
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
@ -132,25 +117,15 @@ void ComputeMSDChunk::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
|
||||
|
||||
int n = cchunk->setup_chunks();
|
||||
cchunk->compute_ichunk();
|
||||
int oldnchunk = nchunk;
|
||||
ComputeChunk::compute_array();
|
||||
int *ichunk = cchunk->ichunk;
|
||||
|
||||
// first time call, allocate per-chunk arrays
|
||||
// thereafter, require nchunk remain the same
|
||||
|
||||
if (firstflag) {
|
||||
nchunk = n;
|
||||
allocate();
|
||||
size_array_rows = nchunk;
|
||||
} else if (n != nchunk)
|
||||
error->all(FLERR,"Compute msd/chunk nchunk is not static");
|
||||
if (!firstflag && (oldnchunk != nchunk))
|
||||
error->all(FLERR, "Compute msd/chunk nchunk is not static");
|
||||
|
||||
// zero local per-chunk values
|
||||
|
||||
@ -171,19 +146,21 @@ void ComputeMSDChunk::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);
|
||||
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);
|
||||
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 (int i = 0; i < nchunk; i++) {
|
||||
if (masstotal[i] > 0.0) {
|
||||
@ -198,87 +175,32 @@ void ComputeMSDChunk::compute_array()
|
||||
|
||||
if (firstflag) return;
|
||||
|
||||
double dx,dy,dz;
|
||||
double dx, dy, dz;
|
||||
double **cominit = fix->astore;
|
||||
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
dx = comall[i][0] - cominit[i][0];
|
||||
dy = comall[i][1] - cominit[i][1];
|
||||
dz = comall[i][2] - cominit[i][2];
|
||||
msd[i][0] = dx*dx;
|
||||
msd[i][1] = dy*dy;
|
||||
msd[i][2] = dz*dz;
|
||||
msd[i][3] = dx*dx + dy*dy + dz*dz;
|
||||
msd[i][0] = dx * dx;
|
||||
msd[i][1] = dy * dy;
|
||||
msd[i][2] = dz * dz;
|
||||
msd[i][3] = dx * dx + dy * dy + dz * dz;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
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 ComputeMSDChunk::lock_enable()
|
||||
{
|
||||
cchunk->lockcount++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
decrement lock counter in compute chunk/atom, it if still exists
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMSDChunk::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 ComputeMSDChunk::lock_length()
|
||||
{
|
||||
nchunk = cchunk->setup_chunks();
|
||||
return nchunk;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set the lock from startstep to stopstep
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMSDChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
|
||||
{
|
||||
cchunk->lock(fixptr,startstep,stopstep);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unset the lock
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMSDChunk::unlock(Fix *fixptr)
|
||||
{
|
||||
cchunk->unlock(fixptr);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
one-time allocate of per-chunk arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMSDChunk::allocate()
|
||||
{
|
||||
memory->create(massproc,nchunk,"msd/chunk:massproc");
|
||||
memory->create(masstotal,nchunk,"msd/chunk:masstotal");
|
||||
memory->create(com,nchunk,3,"msd/chunk:com");
|
||||
memory->create(comall,nchunk,3,"msd/chunk:comall");
|
||||
memory->create(msd,nchunk,4,"msd/chunk:msd");
|
||||
ComputeChunk::allocate();
|
||||
memory->create(massproc, nchunk, "msd/chunk:massproc");
|
||||
memory->create(masstotal, nchunk, "msd/chunk:masstotal");
|
||||
memory->create(com, nchunk, 3, "msd/chunk:com");
|
||||
memory->create(comall, nchunk, 3, "msd/chunk:comall");
|
||||
memory->create(msd, nchunk, 4, "msd/chunk:msd");
|
||||
array = msd;
|
||||
}
|
||||
|
||||
@ -288,8 +210,9 @@ void ComputeMSDChunk::allocate()
|
||||
|
||||
double ComputeMSDChunk::memory_usage()
|
||||
{
|
||||
double bytes = (bigint) nchunk * 2 * sizeof(double);
|
||||
bytes += (double) nchunk * 2*3 * sizeof(double);
|
||||
double bytes = ComputeChunk::memory_usage();
|
||||
bytes += (bigint) nchunk * 2 * sizeof(double);
|
||||
bytes += (double) nchunk * 2 * 3 * sizeof(double);
|
||||
bytes += (double) nchunk * 4 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user