141 lines
4.0 KiB
C++
141 lines
4.0 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://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 "string.h"
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#include "compute_property_molecule.h"
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#include "atom.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputePropertyMolecule::
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ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute property/molecule command");
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if (atom->molecular == 0)
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error->all("Compute property/molecule requires molecular atom style");
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nvalues = narg - 3;
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if (nvalues == 1) size_array_cols = 0;
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pack_choice = new FnPtrPack[nvalues];
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int i;
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for (int iarg = 3; iarg < narg; iarg++) {
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i = iarg-3;
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if (strcmp(arg[iarg],"mol") == 0)
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pack_choice[i] = &ComputePropertyMolecule::pack_mol;
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else error->all("Invalid keyword in compute property/molecule command");
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}
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// setup molecule-based data
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nmolecules = molecules_in_group(idlo,idhi);
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vector = NULL;
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array = NULL;
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if (nvalues == 1) {
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vector = (double *) memory->smalloc(nmolecules*sizeof(double),
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"property/molecule:vector");
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vector_flag = 1;
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size_vector = nmolecules;
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extvector = 0;
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} else {
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array = memory->create_2d_double_array(nmolecules,nvalues,
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"property/molecule:array");
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array_flag = 1;
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size_array_rows = nmolecules;
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size_array_cols = nvalues;
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extarray = 0;
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}
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// fill vector or array with molecule values
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if (nvalues == 1) {
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buf = vector;
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(this->*pack_choice[0])(0);
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} else {
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if (array) buf = &array[0][0];
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for (int n = 0; n < nvalues; n++)
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(this->*pack_choice[n])(n);
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}
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}
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/* ---------------------------------------------------------------------- */
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ComputePropertyMolecule::~ComputePropertyMolecule()
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{
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delete [] pack_choice;
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memory->sfree(vector);
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memory->destroy_2d_double_array(array);
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyMolecule::init()
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{
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int ntmp = molecules_in_group(idlo,idhi);
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if (ntmp != nmolecules)
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error->all("Molecule count changed in compute property/molecule");
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyMolecule::compute_vector()
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{
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invoked_vector = update->ntimestep;
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyMolecule::compute_array()
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{
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invoked_array = update->ntimestep;
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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 ComputePropertyMolecule::memory_usage()
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{
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double bytes = nmolecules*nvalues * sizeof(double);
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if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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one method for every keyword compute property/molecule can output
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the atom property is packed into buf starting at n with stride nvalues
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customize a new keyword by adding a method
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void ComputePropertyMolecule::pack_mol(int n)
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{
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for (int i = idlo; i <= idhi; i++)
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if (molmap[i-idlo] >= 0) {
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buf[n] = i;
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n += nvalues;
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}
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}
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