Page MenuHomec4science
Files F66072056

compute_omega_chunk.cpp
No OneTemporary
Actions

File Metadata

Created
Sat, Jun 8, 02:15

compute_omega_chunk.cpp
View Options

/* ----------------------------------------------------------------------
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_omega_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idchunk(NULL),massproc(NULL),masstotal(NULL),com(NULL),comall(NULL),
inertia(NULL),inertiaall(NULL),angmom(NULL),angmomall(NULL),omega(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
array_flag = 1;
size_array_cols = 3;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// 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;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk::~ComputeOmegaChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(angmom);
memory->destroy(angmomall);
memory->destroy(inertia);
memory->destroy(inertiaall);
memory->destroy(omega);
}
/* ---------------------------------------------------------------------- */
void ComputeOmegaChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute omega/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute omega/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeOmegaChunk::compute_array()
{
int i,j,m,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;
angmom[i][0] = angmom[i][1] = angmom[i][2] = 0.0;
omega[i][0] = omega[i][1] = omega[i][2] = 0.0;
}
// compute COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (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++) {
if (masstotal[i] > 0.0) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
}
// compute inertia tensor for each chunk
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
inertia[index][0] += massone * (dy*dy + dz*dz);
inertia[index][1] += massone * (dx*dx + dz*dz);
inertia[index][2] += massone * (dx*dx + dy*dy);
inertia[index][3] -= massone * dx*dy;
inertia[index][4] -= massone * dy*dz;
inertia[index][5] -= massone * dx*dz;
}
MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nchunk,
MPI_DOUBLE,MPI_SUM,world);
// compute angmom for each chunk
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
angmom[index][0] += massone * (dy*v[i][2] - dz*v[i][1]);
angmom[index][1] += massone * (dz*v[i][0] - dx*v[i][2]);
angmom[index][2] += massone * (dx*v[i][1] - dy*v[i][0]);
}
MPI_Allreduce(&angmom[0][0],&angmomall[0][0],3*nchunk,
MPI_DOUBLE,MPI_SUM,world);
// compute omega for each chunk
double determinant,invdeterminant;
double idiag[3],ex[3],ey[3],ez[3],cross[3];
double ione[3][3],inverse[3][3],evectors[3][3];
double *iall,*mall;
for (m = 0; m < nchunk; m++) {
// determinant = triple product of rows of inertia matrix
iall = &inertiaall[m][0];
determinant = iall[0] * (iall[1]*iall[2] - iall[4]*iall[4]) +
iall[3] * (iall[4]*iall[5] - iall[3]*iall[2]) +
iall[5] * (iall[3]*iall[4] - iall[1]*iall[5]);
ione[0][0] = iall[0];
ione[1][1] = iall[1];
ione[2][2] = iall[2];
ione[0][1] = ione[1][0] = iall[3];
ione[1][2] = ione[2][1] = iall[4];
ione[0][2] = ione[2][0] = iall[5];
// non-singular I matrix
// use L = Iw, inverting I to solve for w
if (determinant > EPSILON) {
inverse[0][0] = ione[1][1]*ione[2][2] - ione[1][2]*ione[2][1];
inverse[0][1] = -(ione[0][1]*ione[2][2] - ione[0][2]*ione[2][1]);
inverse[0][2] = ione[0][1]*ione[1][2] - ione[0][2]*ione[1][1];
inverse[1][0] = -(ione[1][0]*ione[2][2] - ione[1][2]*ione[2][0]);
inverse[1][1] = ione[0][0]*ione[2][2] - ione[0][2]*ione[2][0];
inverse[1][2] = -(ione[0][0]*ione[1][2] - ione[0][2]*ione[1][0]);
inverse[2][0] = ione[1][0]*ione[2][1] - ione[1][1]*ione[2][0];
inverse[2][1] = -(ione[0][0]*ione[2][1] - ione[0][1]*ione[2][0]);
inverse[2][2] = ione[0][0]*ione[1][1] - ione[0][1]*ione[1][0];
invdeterminant = 1.0/determinant;
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
inverse[i][j] *= invdeterminant;
mall = &angmomall[m][0];
omega[m][0] = inverse[0][0]*mall[0] + inverse[0][1]*mall[1] +
inverse[0][2]*mall[2];
omega[m][1] = inverse[1][0]*mall[0] + inverse[1][1]*mall[1] +
inverse[1][2]*mall[2];
omega[m][2] = inverse[2][0]*mall[0] + inverse[2][1]*mall[1] +
inverse[2][2]*mall[2];
// handle each (nearly) singular I matrix
// due to 2-atom chunk or linear molecule
// use jacobi() and angmom_to_omega() to calculate valid omega
} else {
int ierror = MathExtra::jacobi(ione,idiag,evectors);
if (ierror) error->all(FLERR,
"Insufficient Jacobi rotations for omega/chunk");
ex[0] = evectors[0][0];
ex[1] = evectors[1][0];
ex[2] = evectors[2][0];
ey[0] = evectors[0][1];
ey[1] = evectors[1][1];
ey[2] = evectors[2][1];
ez[0] = evectors[0][2];
ez[1] = evectors[1][2];
ez[2] = evectors[2][2];
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
// if any principal moment < scaled EPSILON, set to 0.0
double max;
max = MAX(idiag[0],idiag[1]);
max = MAX(max,idiag[2]);
if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
// calculate omega using diagonalized inertia matrix
MathExtra::angmom_to_omega(&angmomall[m][0],ex,ey,ez,idiag,&omega[m][0]);
}
}
}
/* ----------------------------------------------------------------------
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 ComputeOmegaChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeOmegaChunk::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 ComputeOmegaChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeOmegaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeOmegaChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeOmegaChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(inertia);
memory->destroy(inertiaall);
memory->destroy(angmom);
memory->destroy(angmomall);
memory->destroy(omega);
maxchunk = nchunk;
memory->create(massproc,maxchunk,"omega/chunk:massproc");
memory->create(masstotal,maxchunk,"omega/chunk:masstotal");
memory->create(com,maxchunk,3,"omega/chunk:com");
memory->create(comall,maxchunk,3,"omega/chunk:comall");
memory->create(inertia,maxchunk,6,"omega/chunk:inertia");
memory->create(inertiaall,maxchunk,6,"omega/chunk:inertiaall");
memory->create(angmom,maxchunk,3,"omega/chunk:angmom");
memory->create(angmomall,maxchunk,3,"omega/chunk:angmomall");
memory->create(omega,maxchunk,3,"omega/chunk:omega");
array = omega;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeOmegaChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*6 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 3 * sizeof(double);
return bytes;
}

Event Timeline

c4science · Help