forked from lijiext/lammps
293 lines
9.3 KiB
C++
293 lines
9.3 KiB
C++
// ATC_Method headers
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#include "MoleculeSet.h"
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#include "ATC_Method.h"
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#include "LammpsInterface.h"
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#include "ATC_Error.h"
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#include <queue>
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#include <utility>
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#include <sstream>
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using std::multimap;
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using std::map;
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using std::pair;
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using std::set;
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using std::stringstream;
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namespace ATC {
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Class MoleculeSet
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//--------------------------------------------------------
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Constructor
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//--------------------------------------------------------
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MoleculeSet::MoleculeSet(ATC_Method * atc, int groupBit) :
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atc_(atc),
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groupBit_(groupBit),
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lammps_(atc->lammps_interface())
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{
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// do nothing
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}
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//--------------------------------------------------------
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// Destructor
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//--------------------------------------------------------
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MoleculeSet::~MoleculeSet()
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{
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clear();
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}
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//--------------------------------------------------------
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// clear
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//--------------------------------------------------------
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void MoleculeSet::clear()
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{
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moleculeToAtoms_.clear();
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localMoleculeToAtoms_.clear();
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}
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//--------------------------------------------------------
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// initialize
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//--------------------------------------------------------
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void MoleculeSet::initialize(map<int,double> * globalAtomsPerMolecule)
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{
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// determine the total number of molecules in this group
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// essentially ripped Compute::molecules_in_group from lammps
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// find lo/hi molecule ID for any atom in group
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int i;
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int *molecule = lammps_->atom_to_molecule();
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const int *mask = lammps_->atom_mask();
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int nlocal = lammps_->nlocal();
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int lo = lammps_->natoms();
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int hi = -1;
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int flag = 0;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupBit_) {
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if (molecule[i] == 0) flag = 1;
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lo = MIN(lo,molecule[i]);
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hi = MAX(hi,molecule[i]);
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}
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}
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int flagall;
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lammps_->int_allsum(&flag,&flagall);
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if (flagall) throw ATC_Error("Atom with molecule ID = 0 included in atc molecule group");
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int globalLo, globalHi;
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lammps_->int_allmin(&lo,&globalLo);
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lammps_->int_allmax(&hi,&globalHi);
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if (globalLo == lammps_->natoms()) throw ATC_Error("MoleculeSet:initialize - no molecules correspond to the group");
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// molmap = vector of length nlen
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// set to 1 for IDs that appear in group across all procs, else 0
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int nlen = globalHi-globalLo+1;
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int * localCount = new int[nlen];
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for (i = 0; i < nlen; i++) localCount[i] = 0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupBit_)
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localCount[molecule[i]-globalLo]++;
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int * globalCount = new int[nlen];
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lammps_->int_allsum(localCount,globalCount,nlen);
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// nmolecules = # of non-zero IDs in molmap
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// molmap[i] = index of molecule, skipping molecules not in group with -1
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nMoleculesTotal_ = 0;
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for (i = 0; i < nlen; i++)
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if (globalCount[i]) nMoleculesTotal_++;
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if (globalAtomsPerMolecule) {
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for (i = 0; i < nlen; i++)
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if (globalCount[i]) globalAtomsPerMolecule->insert(pair<int,double>(i+globalLo,double(globalCount[i])));
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}
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// deallocate storage
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delete [] localCount;
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delete [] globalCount;
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}
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//--------------------------------------------------------
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// atoms_by_global_molecule
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//--------------------------------------------------------
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set<int> MoleculeSet::atoms_by_global_molecule(int id) const
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{
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if (need_reset()) reset();
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typedef multimap<int, set<int> >::const_iterator MMIT;
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typedef set<int>::const_iterator SIT;
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pair<MMIT,MMIT> mol = moleculeToAtoms_.equal_range(id);
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set<int> realAtoms;
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const set<int> * myAtoms;
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for (MMIT molIt = mol.first; molIt != mol.second; molIt++) {
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myAtoms = &(molIt->second);
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for (SIT atomIt = myAtoms->begin(); atomIt != myAtoms->end(); atomIt++)
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realAtoms.insert(*atomIt);
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}
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return realAtoms;
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}
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//--------------------------------------------------------
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// atoms_by_local_molecule
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//--------------------------------------------------------
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const set<int> & MoleculeSet::atoms_by_local_molecule(int id) const
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{
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if (need_reset()) reset();
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return localMoleculeToAtoms_[id]->second;
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}
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//--------------------------------------------------------
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// set_local_molecules_to_atoms
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//--------------------------------------------------------
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void MoleculeSet::set_local_molecules_to_atoms() const
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{
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localMoleculeToAtoms_.clear();
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localMoleculeToAtoms_.reserve(moleculeToAtoms_.size());
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multimap<int, set<int> >::const_iterator molecule;
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for (molecule = moleculeToAtoms_.begin(); molecule != moleculeToAtoms_.end(); molecule++)
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localMoleculeToAtoms_.push_back(molecule);
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}
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Class SmallMoleculeSet
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//--------------------------------------------------------
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Constructor
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//--------------------------------------------------------
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SmallMoleculeSet::SmallMoleculeSet(ATC_Method * atc, int groupBit,
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PerAtomQuantity<int> * bondList, PerAtomQuantity<int> * /* numBond */) :
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MoleculeSet(atc,groupBit),
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bondList_(bondList)
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{
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}
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//--------------------------------------------------------
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// Destructor
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//--------------------------------------------------------
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SmallMoleculeSet::~SmallMoleculeSet()
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{
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}
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//--------------------------------------------------------
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// clear
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//--------------------------------------------------------
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void SmallMoleculeSet::clear()
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{
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MoleculeSet::clear();
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}
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//--------------------------------------------------------
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// initialize
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//--------------------------------------------------------
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void SmallMoleculeSet::initialize(std::map<int, double> * globalAtomsPerMolecule)
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{
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// make sure newton_bond is off, otherwise use large molecule set
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if (lammps_->newton_bond())
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throw ATC_Error("Cannot use newton_bond with small molecules");
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MoleculeSet::initialize(globalAtomsPerMolecule);
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}
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//--------------------------------------------------------
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// reset
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//--------------------------------------------------------
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void SmallMoleculeSet::reset() const
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{
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stringstream message;
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using std::queue;
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moleculeToAtoms_.clear();
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lammps_->forward_comm_fix();
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int * numBond = lammps_->num_bond();
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int ** bondAtom = lammps_->bond_atom();
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// add in real atoms for molecules
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int *molecule = lammps_->atom_to_molecule();
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const int *mask = lammps_->atom_mask();
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int nlocal = lammps_->nlocal();
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_atomFound_.resize(atc_->nproc_ghost());
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_atomFound_ = false;
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int nmol = 0;
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for (int i = 0; i < nlocal; i++) {
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queue<int> myQueue;
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if ((mask[i] & groupBit_) && !_atomFound_(i)) {
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set<int> myAtoms;
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myAtoms.insert(i);
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_atomFound_(i) = true;
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for (int j = 0; j < numBond[i]; j++) {
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int localIdx = lammps_->local_to_global_map(bondAtom[i][j]);
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if (!_atomFound_(localIdx)) {
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myQueue.push(localIdx);
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_atomFound_(localIdx) = true;
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}
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}
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while (!myQueue.empty()) {
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int myIdx = myQueue.front();
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myQueue.pop();
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myAtoms.insert(myIdx);
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for (int j = 0; j < numBond[myIdx]; j++) {
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int localIdx = lammps_->local_to_global_map(bondAtom[myIdx][j]);
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if (!_atomFound_(localIdx)) {
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myQueue.push(localIdx);
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_atomFound_(localIdx) = true;
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}
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}
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}
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nmol++;
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moleculeToAtoms_.insert(pair<int,set<int> >(molecule[i],myAtoms));
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}
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}
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// set local molecule order
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MoleculeSet::set_local_molecules_to_atoms();
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needReset_ = false;
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}
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//--------------------------------------------------------
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// atoms_by_global_molecule
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//--------------------------------------------------------
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set<int> SmallMoleculeSet::atoms_by_global_molecule(int id) const
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{
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// take all atoms and prune out ghosts
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set<int> realAtoms = MoleculeSet::atoms_by_global_molecule(id);
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remove_proc_ghosts(realAtoms);
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return realAtoms;
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}
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//--------------------------------------------------------
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// local_fraction
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//--------------------------------------------------------
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double SmallMoleculeSet::local_fraction(int id) const
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{
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if (need_reset()) reset();
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set<int> realAtoms = (localMoleculeToAtoms_[id])->second;
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int totalAtoms = realAtoms.size();
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remove_proc_ghosts(realAtoms);
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return double(realAtoms.size())/double(totalAtoms);
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}
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//--------------------------------------------------------
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// remove_proc_ghosts
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//--------------------------------------------------------
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void SmallMoleculeSet::remove_proc_ghosts(set<int> & atomSet) const
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{
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int nlocalIdx = lammps_->nlocal() - 1;
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set<int>::const_iterator atomIt;
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for (atomIt = atomSet.begin(); atomIt != atomSet.end(); atomIt++) {
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if (*atomIt > nlocalIdx)
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atomSet.erase(atomIt);
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}
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}
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};
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