diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp
index b34310bc9..92194557d 100644
--- a/src/compute_com_chunk.cpp
+++ b/src/compute_com_chunk.cpp
@@ -1,242 +1,243 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_com_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ONCE,NFREQ,EVERY};
/* ---------------------------------------------------------------------- */
ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute com/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
allocate();
firstflag = massneed = 1;
}
/* ---------------------------------------------------------------------- */
ComputeCOMChunk::~ComputeCOMChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
}
/* ---------------------------------------------------------------------- */
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 = (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
// done in setup, so that ComputeChunkAtom::setup() is already called
if (firstflag && cchunk->idsflag == ONCE) {
firstflag = massneed = 0;
compute_array();
}
}
/* ---------------------------------------------------------------------- */
void ComputeCOMChunk::compute_array()
{
int index;
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();
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;
if (massneed)
for (int i = 0; i < nchunk; i++) massproc[i] = 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 (int 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);
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);
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;
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure 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 = (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
------------------------------------------------------------------------- */
void ComputeCOMChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
- size_array_rows = maxchunk = nchunk;
+ 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");
array = comall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeCOMChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
return bytes;
}
diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp
index 91bcdf97c..a0148cd6d 100644
--- a/src/compute_gyration_chunk.cpp
+++ b/src/compute_gyration_chunk.cpp
@@ -1,357 +1,359 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "math.h"
#include "string.h"
#include "compute_gyration_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command");
// ID of compute chunk/atom
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
init();
// optional args
tensor = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"tensor") == 0) {
tensor = 1;
iarg++;
} else error->all(FLERR,"Illegal compute gyration/chunk command");
}
if (tensor) {
array_flag = 1;
size_array_cols = 6;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
} else {
vector_flag = 1;
size_vector = 0;
size_vector_variable = 1;
extvector = 0;
}
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
rg = rgall = NULL;
rgt = rgtall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk::~ComputeGyrationChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(rg);
memory->destroy(rgall);
memory->destroy(rgt);
memory->destroy(rgtall);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute gyration/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute gyration/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::compute_vector()
{
int i,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
com_chunk();
int *ichunk = cchunk->ichunk;
for (i = 0; i < nchunk; i++) rg[i] = 0.0;
// compute Rg 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;
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]];
rg[index] += (dx*dx + dy*dy + dz*dz) * massone;
}
MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++)
rgall[i] = sqrt(rgall[i]/masstotal[i]);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::compute_array()
{
int i,j,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
com_chunk();
int *ichunk = cchunk->ichunk;
for (i = 0; i < nchunk; i++)
for (j = 0; j < 6; j++) rgt[i][j] = 0.0;
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;
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]];
rgt[index][0] += dx*dx * massone;
rgt[index][1] += dy*dy * massone;
rgt[index][2] += dz*dz * massone;
rgt[index][3] += dx*dy * massone;
rgt[index][4] += dx*dz * massone;
rgt[index][5] += dy*dz * massone;
}
if (nchunk)
MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nchunk; i++)
for (j = 0; j < 6; j++)
rgtall[i][j] = rgtall[i][j]/masstotal[i];
}
/* ----------------------------------------------------------------------
calculate per-chunk COM, used by both scalar and tensor
------------------------------------------------------------------------- */
void ComputeGyrationChunk::com_chunk()
{
int index;
double massone;
double unwrap[3];
// 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();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
+ if (tensor) size_array_rows = nchunk;
+ else size_vector = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[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 (int 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 (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeGyrationChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeGyrationChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeGyrationChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeGyrationChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeGyrationChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeGyrationChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(rg);
memory->destroy(rgall);
memory->destroy(rgt);
memory->destroy(rgtall);
- size_array_rows = maxchunk = nchunk;
+ maxchunk = nchunk;
memory->create(massproc,maxchunk,"gyration/chunk:massproc");
memory->create(masstotal,maxchunk,"gyration/chunk:masstotal");
memory->create(com,maxchunk,3,"gyration/chunk:com");
memory->create(comall,maxchunk,3,"gyration/chunk:comall");
if (tensor) {
memory->create(rgt,maxchunk,6,"gyration/chunk:rgt");
memory->create(rgtall,maxchunk,6,"gyration/chunk:rgtall");
array = rgtall;
} else {
memory->create(rg,maxchunk,"gyration/chunk:rg");
memory->create(rgall,maxchunk,"gyration/chunk:rgall");
vector = rgall;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeGyrationChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
if (tensor) bytes += (bigint) maxchunk * 2*6 * sizeof(double);
else bytes += (bigint) maxchunk * 2 * sizeof(double);
return bytes;
}
diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp
index f04b29147..93229f413 100644
--- a/src/compute_inertia_chunk.cpp
+++ b/src/compute_inertia_chunk.cpp
@@ -1,256 +1,257 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_inertia_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command");
array_flag = 1;
size_array_cols = 6;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
inertia = inertiaall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeInertiaChunk::~ComputeInertiaChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(inertia);
memory->destroy(inertiaall);
}
/* ---------------------------------------------------------------------- */
void ComputeInertiaChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute inertia/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute inertia/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeInertiaChunk::compute_array()
{
int i,j,index;
double dx,dy,dz,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();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
+ size_array_rows = nchunk;
// zero local per-chunk values
for (int 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;
}
// 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 (int 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 (int i = 0; i < nchunk; i++) {
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);
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeInertiaChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeInertiaChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeInertiaChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeInertiaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeInertiaChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeInertiaChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(inertia);
memory->destroy(inertiaall);
- size_array_rows = maxchunk = nchunk;
+ maxchunk = nchunk;
memory->create(massproc,maxchunk,"inertia/chunk:massproc");
memory->create(masstotal,maxchunk,"inertia/chunk:masstotal");
memory->create(com,maxchunk,3,"inertia/chunk:com");
memory->create(comall,maxchunk,3,"inertia/chunk:comall");
memory->create(inertia,maxchunk,6,"inertia/chunk:inertia");
memory->create(inertiaall,maxchunk,6,"inertia/chunk:inertiaall");
array = inertiaall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeInertiaChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*6 * sizeof(double);
return bytes;
}
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index 180b420b3..5f060b1ff 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -1,261 +1,262 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_msd_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command");
array_flag = 1;
size_array_cols = 4;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
init();
massproc = masstotal = NULL;
com = comall = cominit = NULL;
msd = NULL;
firstflag = 1;
}
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::~ComputeMSDChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(cominit);
memory->destroy(msd);
}
/* ---------------------------------------------------------------------- */
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 = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
}
/* ----------------------------------------------------------------------
compute initial COM for each chunk
only once on timestep compute is defined, when firstflag = 1
------------------------------------------------------------------------- */
void ComputeMSDChunk::setup()
{
if (!firstflag) return;
firstflag = 0;
compute_array();
for (int i = 0; i < nchunk; i++) {
cominit[i][0] = comall[i][0];
cominit[i][1] = comall[i][1];
cominit[i][2] = comall[i][2];
}
}
/* ---------------------------------------------------------------------- */
void ComputeMSDChunk::compute_array()
{
int index;
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 *ichunk = cchunk->ichunk;
// first time call, allocate per-chunk arrays
// thereafter, require nchunk remain the same
- if (firstflag) allocate(n);
- else if (n != nchunk)
+ if (firstflag) {
+ nchunk = n;
+ allocate();
+ } else if (n != nchunk)
error->all(FLERR,"Compute msd/chunk nchunk is not static");
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
}
// compute current 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 (int 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 (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// MSD is difference between current and initial COM
// cominit does not yet exist when called from constructor
if (firstflag) return;
double dx,dy,dz;
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;
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure 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 = (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(int n)
+void ComputeMSDChunk::allocate()
{
- size_array_rows = nchunk = n;
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(cominit,nchunk,3,"msd/chunk:cominit");
memory->create(msd,nchunk,4,"msd/chunk:msd");
array = msd;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeMSDChunk::memory_usage()
{
double bytes = (bigint) nchunk * 2 * sizeof(double);
bytes += (bigint) nchunk * 3*3 * sizeof(double);
bytes += (bigint) nchunk * 4 * sizeof(double);
return bytes;
}
diff --git a/src/compute_msd_chunk.h b/src/compute_msd_chunk.h
index 8562aa976..269fb153b 100644
--- a/src/compute_msd_chunk.h
+++ b/src/compute_msd_chunk.h
@@ -1,78 +1,78 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(msd/chunk,ComputeMSDChunk)
#else
#ifndef LMP_COMPUTE_MSD_CHUNK_H
#define LMP_COMPUTE_MSD_CHUNK_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeMSDChunk : public Compute {
public:
ComputeMSDChunk(class LAMMPS *, int, char **);
~ComputeMSDChunk();
void init();
void setup();
void compute_array();
void lock_enable();
void lock_disable();
int lock_length();
void lock(class Fix *, bigint, bigint);
void unlock(class Fix *);
double memory_usage();
private:
int nchunk;
char *idchunk;
class ComputeChunkAtom *cchunk;
double *massproc,*masstotal;
double **com,**comall,**cominit;
double **msd;
int firstflag;
- void allocate(int);
+ void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Compute com/molecule requires molecular atom style
Self-explanatory.
E: Molecule count changed in compute com/molecule
Number of molecules must remain constant over time.
*/
diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp
index 28dffb926..0fc67118f 100644
--- a/src/compute_property_chunk.cpp
+++ b/src/compute_property_chunk.cpp
@@ -1,337 +1,338 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_property_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal compute property/chunk command");
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
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,
"Invalid keyword in compute property/chunk command");
}
// initialization
nchunk = 1;
maxchunk = 0;
vector = NULL;
array = NULL;
count_one = count_all = NULL;
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 [] idchunk;
delete [] pack_choice;
memory->destroy(vector);
memory->destroy(array);
memory->destroy(count_one);
memory->destroy(count_all);
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute property/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute property/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::compute_vector()
{
invoked_vector = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
if (nchunk > maxchunk) allocate();
+ if (nvalues == 1) size_vector = nchunk;
+ else size_array_rows = nchunk;
if (countflag) {
cchunk->compute_ichunk();
ichunk = cchunk->ichunk;
}
// fill vector
buf = vector;
(this->*pack_choice[0])(0);
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::compute_array()
{
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
if (nchunk > maxchunk) allocate();
+ if (nvalues == 1) size_vector = nchunk;
+ else size_array_rows = nchunk;
if (countflag) {
cchunk->compute_ichunk();
ichunk = cchunk->ichunk;
}
// fill array
if (array) buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputePropertyChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputePropertyChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputePropertyChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputePropertyChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputePropertyChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputePropertyChunk::allocate()
{
memory->destroy(vector);
memory->destroy(array);
memory->destroy(count_one);
memory->destroy(count_all);
-
- if (nvalues == 1) size_vector = maxchunk = nchunk;
- else size_array_rows = maxchunk = nchunk;
+ 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 = (bigint) nchunk * nvalues * sizeof(double);
if (countflag) bytes += (bigint) 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;
}
}
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 66b16ad2e..7767582ea 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -1,407 +1,408 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_temp_chunk.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command");
vector_flag = 1;
- size_vector = 1;
+ size_vector = 0;
size_vector_variable = 1;
extvector = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
biasflag = 0;
init();
// optional args
comflag = 0;
biasflag = 0;
id_bias = NULL;
adof = domain->dimension;
cdof = 0.0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
else error->all(FLERR,"Illegal compute temp/chunk command");
iarg += 2;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
biasflag = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
adof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"cdof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
cdof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/chunk command");
}
if (comflag && biasflag)
error->all(FLERR,"Cannot use both com and bias with compute temp/chunk");
// error check on bias compute
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
}
// chunk-based data
nchunk = 1;
maxchunk = 0;
ke = keall = NULL;
count = countall = NULL;
massproc = masstotal = NULL;
vcm = vcmall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeTempChunk::~ComputeTempChunk()
{
delete [] idchunk;
delete [] id_bias;
memory->destroy(ke);
memory->destroy(keall);
memory->destroy(count);
memory->destroy(countall);
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
}
/* ---------------------------------------------------------------------- */
void ComputeTempChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute temp/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute temp/chunk does not use chunk/atom compute");
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
void ComputeTempChunk::compute_vector()
{
int index;
invoked_vector = 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();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
+ size_vector = nchunk;
// calculate COM velocity for each chunk
if (comflag) vcm_compute();
// remove velocity bias
if (biasflag) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
count[i] = 0;
ke[i] = 0.0;
}
// compute temperature for each chunk
// option for removing COM velocity
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
if (!comflag) {
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
count[index]++;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
count[index]++;
}
}
} else {
double vx,vy,vz;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
ke[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
count[index]++;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
ke[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
count[index]++;
}
}
}
MPI_Allreduce(ke,keall,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(count,countall,nchunk,MPI_INT,MPI_SUM,world);
// restore velocity bias
if (biasflag) tbias->restore_bias_all();
// normalize temperatures by per-chunk DOF
double dof,tfactor;
double mvv2e = force->mvv2e;
double boltz = force->boltz;
for (int i = 0; i < nchunk; i++) {
dof = cdof + adof*countall[i];
if (dof > 0.0) tfactor = mvv2e / (dof * boltz);
else tfactor = 0.0;
keall[i] *= tfactor;
}
}
/* ----------------------------------------------------------------------
calculate velocity of COM for each chunk
------------------------------------------------------------------------- */
void ComputeTempChunk::vcm_compute()
{
int index;
double massone;
int *ichunk = cchunk->ichunk;
for (int i = 0; i < nchunk; i++) {
vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
massproc[i] = 0.0;
}
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int 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]];
vcm[index][0] += v[i][0] * massone;
vcm[index][1] += v[i][1] * massone;
vcm[index][2] += v[i][2] * massone;
massproc[index] += massone;
}
MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
vcmall[i][0] /= masstotal[i];
vcmall[i][1] /= masstotal[i];
vcmall[i][2] /= masstotal[i];
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeTempChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeTempChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeTempChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeTempChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeTempChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeTempChunk::allocate()
{
memory->destroy(ke);
memory->destroy(keall);
memory->destroy(count);
memory->destroy(countall);
- size_vector = maxchunk = nchunk;
+ maxchunk = nchunk;
memory->create(ke,maxchunk,"temp/chunk:ke");
memory->create(keall,maxchunk,"temp/chunk:keall");
memory->create(count,maxchunk,"temp/chunk:count");
memory->create(countall,maxchunk,"temp/chunk:countall");
vector = keall;
if (comflag) {
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
memory->create(massproc,maxchunk,"vcm/chunk:massproc");
memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTempChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes = (bigint) maxchunk * 2 * sizeof(int);
if (comflag) {
bytes += (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
}
return bytes;
}
diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp
index 8b29cc690..0568e2364 100644
--- a/src/compute_torque_chunk.cpp
+++ b/src/compute_torque_chunk.cpp
@@ -1,252 +1,253 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_torque_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
com = comall = NULL;
torque = torqueall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeTorqueChunk::~ComputeTorqueChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(torque);
memory->destroy(torqueall);
}
/* ---------------------------------------------------------------------- */
void ComputeTorqueChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute torque/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute torque/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeTorqueChunk::compute_array()
{
int i,j,index;
double dx,dy,dz,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();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
+ size_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
torque[i][0] = torque[i][1] = torque[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 (int 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 (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// compute torque on each chunk
double **f = atom->f;
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];
torque[i][0] += dy*f[i][2] - dz*f[i][1];
torque[i][1] += dz*f[i][0] - dx*f[i][2];
torque[i][2] += dx*f[i][1] - dy*f[i][0];
}
MPI_Allreduce(&torque[0][0],&torqueall[0][0],3*nchunk,
MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeTorqueChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeTorqueChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeTorqueChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeTorqueChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeTorqueChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeTorqueChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(torque);
memory->destroy(torqueall);
- size_array_rows = maxchunk = nchunk;
+ maxchunk = nchunk;
memory->create(massproc,maxchunk,"torque/chunk:massproc");
memory->create(masstotal,maxchunk,"torque/chunk:masstotal");
memory->create(com,maxchunk,3,"torque/chunk:com");
memory->create(comall,maxchunk,3,"torque/chunk:comall");
memory->create(torque,maxchunk,6,"torque/chunk:torque");
memory->create(torqueall,maxchunk,6,"torque/chunk:torqueall");
array = torqueall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTorqueChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
return bytes;
}
diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp
index 68e08c7ab..d7d7b8342 100644
--- a/src/compute_vcm_chunk.cpp
+++ b/src/compute_vcm_chunk.cpp
@@ -1,237 +1,238 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "string.h"
#include "compute_vcm_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ONCE,NFREQ,EVERY};
/* ---------------------------------------------------------------------- */
ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute vcm/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
massproc = masstotal = NULL;
vcm = vcmall = NULL;
allocate();
firstflag = massneed = 1;
}
/* ---------------------------------------------------------------------- */
ComputeVCMChunk::~ComputeVCMChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
}
/* ---------------------------------------------------------------------- */
void ComputeVCMChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for compute vcm/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute vcm/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeVCMChunk::setup()
{
// one-time calculation of per-chunk mass
// done in setup, so that ComputeChunkAtom::setup() is already called
if (firstflag && cchunk->idsflag == ONCE) {
firstflag = massneed = 0;
compute_array();
}
}
/* ---------------------------------------------------------------------- */
void ComputeVCMChunk::compute_array()
{
int index;
double massone;
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();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
+ size_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++)
vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
if (massneed)
for (int i = 0; i < nchunk; i++) massproc[i] = 0.0;
// compute VCM for each chunk
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int 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]];
vcm[index][0] += v[i][0] * massone;
vcm[index][1] += v[i][1] * massone;
vcm[index][2] += v[i][2] * massone;
if (massneed) massproc[index] += massone;
}
MPI_Allreduce(&vcm[0][0],&vcmall[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++) {
vcmall[i][0] /= masstotal[i];
vcmall[i][1] /= masstotal[i];
vcmall[i][2] /= masstotal[i];
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeVCMChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeVCMChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeVCMChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeVCMChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeVCMChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeVCMChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
- size_array_rows = maxchunk = nchunk;
+ maxchunk = nchunk;
memory->create(massproc,maxchunk,"vcm/chunk:massproc");
memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
array = vcmall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeVCMChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
return bytes;
}