forked from lijiext/lammps
298 lines
8.9 KiB
C++
298 lines
8.9 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_dipole_chunk.h"
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#include "atom.h"
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#include "compute_chunk_atom.h"
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#include "domain.h"
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#include "error.h"
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#include "math_special.h"
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#include "memory.h"
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#include "modify.h"
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#include "update.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace MathSpecial;
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enum { MASSCENTER, GEOMCENTER };
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/* ---------------------------------------------------------------------- */
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ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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idchunk(nullptr), massproc(nullptr), masstotal(nullptr), chrgproc(nullptr),
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chrgtotal(nullptr), com(nullptr),
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comall(nullptr), dipole(nullptr), dipoleall(nullptr)
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{
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if ((narg != 4) && (narg != 5))
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error->all(FLERR,"Illegal compute dipole/chunk command");
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array_flag = 1;
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size_array_cols = 4;
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size_array_rows = 0;
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size_array_rows_variable = 1;
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extarray = 0;
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// ID of compute chunk/atom
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idchunk = utils::strdup(arg[3]);
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usecenter = MASSCENTER;
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if (narg == 5) {
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if (strncmp(arg[4],"geom",4) == 0) usecenter = GEOMCENTER;
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else if (strcmp(arg[4],"mass") == 0) usecenter = MASSCENTER;
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else error->all(FLERR,"Illegal compute dipole/chunk command");
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}
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init();
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// chunk-based data
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nchunk = 1;
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maxchunk = 0;
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allocate();
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}
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/* ---------------------------------------------------------------------- */
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ComputeDipoleChunk::~ComputeDipoleChunk()
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{
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delete [] idchunk;
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(chrgproc);
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memory->destroy(chrgtotal);
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memory->destroy(com);
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memory->destroy(comall);
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memory->destroy(dipole);
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memory->destroy(dipoleall);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDipoleChunk::init()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for "
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"compute dipole/chunk");
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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if (strcmp(cchunk->style,"chunk/atom") != 0)
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error->all(FLERR,"Compute dipole/chunk does not use chunk/atom compute");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDipoleChunk::compute_array()
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{
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int i,index;
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double massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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int *ichunk = cchunk->ichunk;
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if (nchunk > maxchunk) allocate();
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size_array_rows = nchunk;
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// zero local per-chunk values
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for (i = 0; i < nchunk; i++) {
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massproc[i] = chrgproc[i] = 0.0;
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com[i][0] = com[i][1] = com[i][2] = 0.0;
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dipole[i][0] = dipole[i][1] = dipole[i][2] = dipole[i][3] = 0.0;
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}
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// compute COM for each chunk
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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imageint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double *q = atom->q;
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double **mu = atom->mu;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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index = ichunk[i]-1;
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if (index < 0) continue;
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if (usecenter == MASSCENTER) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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} else massone = 1.0; // usecenter == GEOMCENTER
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domain->unmap(x[i],image[i],unwrap);
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massproc[index] += massone;
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if (atom->q_flag) chrgproc[index] += atom->q[i];
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com[index][0] += unwrap[0] * massone;
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com[index][1] += unwrap[1] * massone;
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com[index][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(chrgproc,chrgtotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nchunk; i++) {
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if (masstotal[i] > 0.0) {
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comall[i][0] /= masstotal[i];
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comall[i][1] /= masstotal[i];
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comall[i][2] /= masstotal[i];
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}
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}
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// compute dipole for each chunk
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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index = ichunk[i]-1;
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if (index < 0) continue;
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domain->unmap(x[i],image[i],unwrap);
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if (atom->q_flag) {
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dipole[index][0] += q[i]*unwrap[0];
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dipole[index][1] += q[i]*unwrap[1];
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dipole[index][2] += q[i]*unwrap[2];
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}
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if (atom->mu_flag) {
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dipole[index][0] += mu[i][0];
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dipole[index][1] += mu[i][1];
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dipole[index][2] += mu[i][2];
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}
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}
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}
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MPI_Allreduce(&dipole[0][0],&dipoleall[0][0],4*nchunk,
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MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nchunk; i++) {
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// correct for position dependence with charged chunks
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dipoleall[i][0] -= chrgtotal[i]*comall[i][0];
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dipoleall[i][1] -= chrgtotal[i]*comall[i][1];
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dipoleall[i][2] -= chrgtotal[i]*comall[i][2];
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// compute total dipole moment
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dipoleall[i][3] = sqrt(square(dipoleall[i][0])
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+ square(dipoleall[i][1])
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+ square(dipoleall[i][2]));
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}
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}
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/* ----------------------------------------------------------------------
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lock methods: called by fix ave/time
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these methods insure vector/array size is locked for Nfreq epoch
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by passing lock info along to compute chunk/atom
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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increment lock counter
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------------------------------------------------------------------------- */
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void ComputeDipoleChunk::lock_enable()
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{
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cchunk->lockcount++;
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}
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/* ----------------------------------------------------------------------
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decrement lock counter in compute chunk/atom, it if still exists
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------------------------------------------------------------------------- */
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void ComputeDipoleChunk::lock_disable()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute >= 0) {
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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cchunk->lockcount--;
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}
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}
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/* ----------------------------------------------------------------------
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calculate and return # of chunks = length of vector/array
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------------------------------------------------------------------------- */
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int ComputeDipoleChunk::lock_length()
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{
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nchunk = cchunk->setup_chunks();
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return nchunk;
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}
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/* ----------------------------------------------------------------------
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set the lock from startstep to stopstep
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------------------------------------------------------------------------- */
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void ComputeDipoleChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
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{
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cchunk->lock(fixptr,startstep,stopstep);
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}
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/* ----------------------------------------------------------------------
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unset the lock
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------------------------------------------------------------------------- */
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void ComputeDipoleChunk::unlock(Fix *fixptr)
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{
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cchunk->unlock(fixptr);
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}
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/* ----------------------------------------------------------------------
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free and reallocate per-chunk arrays
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------------------------------------------------------------------------- */
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void ComputeDipoleChunk::allocate()
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{
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(chrgproc);
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memory->destroy(chrgtotal);
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memory->destroy(com);
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memory->destroy(comall);
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memory->destroy(dipole);
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memory->destroy(dipoleall);
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maxchunk = nchunk;
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memory->create(massproc,maxchunk,"dipole/chunk:massproc");
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memory->create(masstotal,maxchunk,"dipole/chunk:masstotal");
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memory->create(chrgproc,maxchunk,"dipole/chunk:chrgproc");
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memory->create(chrgtotal,maxchunk,"dipole/chunk:chrgtotal");
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memory->create(com,maxchunk,3,"dipole/chunk:com");
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memory->create(comall,maxchunk,3,"dipole/chunk:comall");
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memory->create(dipole,maxchunk,4,"dipole/chunk:dipole");
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memory->create(dipoleall,maxchunk,4,"dipole/chunk:dipoleall");
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array = dipoleall;
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeDipoleChunk::memory_usage()
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{
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double bytes = (bigint) maxchunk * 2 * sizeof(double);
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bytes += (double)maxchunk * 2*3 * sizeof(double);
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bytes += (double)maxchunk * 2*4 * sizeof(double);
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return bytes;
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}
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