From 4e7957e74422038f4328b2bc56aaed2df5f172ec Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 24 Dec 2009 14:48:17 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3616 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/compute_property_molecule.cpp | 140 ++++++++++++++++++++++++++++++ src/compute_property_molecule.h | 44 ++++++++++ 2 files changed, 184 insertions(+) create mode 100644 src/compute_property_molecule.cpp create mode 100644 src/compute_property_molecule.h diff --git a/src/compute_property_molecule.cpp b/src/compute_property_molecule.cpp new file mode 100644 index 0000000000..c7b37e266b --- /dev/null +++ b/src/compute_property_molecule.cpp @@ -0,0 +1,140 @@ +/* ---------------------------------------------------------------------- + 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_molecule.h" +#include "atom.h" +#include "update.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputePropertyMolecule:: +ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 4) error->all("Illegal compute property/molecule command"); + + if (atom->molecular == 0) + error->all("Compute property/molecule requires molecular atom style"); + + nvalues = narg - 3; + if (nvalues == 1) size_array_cols = 0; + + pack_choice = new FnPtrPack[nvalues]; + + int i; + for (int iarg = 3; iarg < narg; iarg++) { + i = iarg-3; + + if (strcmp(arg[iarg],"mol") == 0) + pack_choice[i] = &ComputePropertyMolecule::pack_mol; + else error->all("Invalid keyword in compute property/molecule command"); + } + + // setup molecule-based data + + nmolecules = molecules_in_group(idlo,idhi); + + vector = NULL; + array = NULL; + + if (nvalues == 1) { + vector = (double *) memory->smalloc(nmolecules*sizeof(double), + "property/molecule:vector"); + vector_flag = 1; + size_vector = nmolecules; + extvector = 0; + } else { + array = memory->create_2d_double_array(nmolecules,nvalues, + "property/molecule:array"); + array_flag = 1; + size_array_rows = nmolecules; + size_array_cols = nvalues; + extarray = 0; + } + + // fill vector or array with molecule values + + if (nvalues == 1) { + buf = vector; + (this->*pack_choice[0])(0); + } else { + if (array) buf = &array[0][0]; + for (int n = 0; n < nvalues; n++) + (this->*pack_choice[n])(n); + } +} + +/* ---------------------------------------------------------------------- */ + +ComputePropertyMolecule::~ComputePropertyMolecule() +{ + delete [] pack_choice; + memory->sfree(vector); + memory->destroy_2d_double_array(array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyMolecule::init() +{ + int ntmp = molecules_in_group(idlo,idhi); + if (ntmp != nmolecules) + error->all("Molecule count changed in compute property/molecule"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyMolecule::compute_vector() +{ + invoked_vector = update->ntimestep; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyMolecule::compute_array() +{ + invoked_array = update->ntimestep; +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double ComputePropertyMolecule::memory_usage() +{ + double bytes = nmolecules*nvalues * sizeof(double); + if (molmap) bytes += (idhi-idlo+1) * sizeof(int); + return bytes; +} + +/* ---------------------------------------------------------------------- + one method for every keyword compute property/molecule can output + the atom property is packed into buf starting at n with stride nvalues + customize a new keyword by adding a method +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyMolecule::pack_mol(int n) +{ + for (int i = idlo; i <= idhi; i++) + if (molmap[i-idlo] >= 0) { + buf[n] = i; + n += nvalues; + } +} diff --git a/src/compute_property_molecule.h b/src/compute_property_molecule.h new file mode 100644 index 0000000000..f564d61b30 --- /dev/null +++ b/src/compute_property_molecule.h @@ -0,0 +1,44 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifndef COMPUTE_PROPERTY_MOLECULE_H +#define COMPUTE_PROPERTY_MOLECULE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePropertyMolecule : public Compute { + public: + ComputePropertyMolecule(class LAMMPS *, int, char **); + ~ComputePropertyMolecule(); + void init(); + void compute_vector(); + void compute_array(); + double memory_usage(); + + private: + int nvalues,nmolecules; + int idlo,idhi; + + double *buf; + + typedef void (ComputePropertyMolecule::*FnPtrPack)(int); + FnPtrPack *pack_choice; // ptrs to pack functions + + void pack_mol(int); +}; + +} + +#endif