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MoleculeSet.h
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Thu, Sep 12, 14:44

MoleculeSet.h
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// A class for managing the data associated with sets of molecules
#ifndef PER_MOLECULE_SET_H
#define PER_MOLECULE_SET_H
// ATC_Method headers
#include "LammpsInterface.h"
#include "DependencyManager.h"
#include <map>
#include <set>
#include <vector>
namespace ATC {
// forward declarations
class ATC_Method;
template <typename T> class PerAtomQuantity;
/**
* @class MoleculeSet
* @brief A class for handling all the data associated with sets of molecules
*/
class MoleculeSet : public DependencyManager {
public:
MoleculeSet(ATC_Method * atc, int groupBit);
virtual ~MoleculeSet();
/** reset all data */
virtual void clear();
/** initialize global data */
virtual void initialize(std::map<int, double> * globalAtomsPerMolecule = NULL);
/** reset the number of atoms/molecules on this processor */
void reset_nlocal() {this->set_reset();};
/** recompute data when atoms cross processors */
void post_exchange() {this->set_reset();};
/** access the number of total molecules */
int global_molecule_count() const {return nMoleculesTotal_;};
/** access the number of local molecules */
int local_molecule_count() const {if (need_reset()) reset(); return moleculeToAtoms_.size();};
/** access molecule atoms by lammps id */
std::set<int> atoms_by_global_molecule(int id) const;
/** access molecules by local indexing */
const std::set<int> & atoms_by_local_molecule(int id) const;
/** access fraction of a locally indexed molecule on this processor */
virtual double local_fraction(int id) const = 0;
/** use global index to get local index */
//int global_to_local(int id) const;
/** use local index to get global index */
int local_to_global(int id) const {return (*localMoleculeToAtoms_[id]).first;};
protected:
/** pointer for access to atc data */
ATC_Method * atc_;
/** lammps group bit corresponding to desired molecules */
int groupBit_;
/** pointer to lammps interface */
const LammpsInterface * lammps_;
/** total number of molecules in this group */
// see Compute::molecules_in_group
int nMoleculesTotal_;
/** multimap from lammps molecule id to ids of consituent atoms, all atoms are real */
// multiple map to account for periodic images
mutable std::multimap<int, std::set<int> > moleculeToAtoms_;
/** vector in processor-local molecule order to constituent atom sets, atoms include ghosts */
mutable std::vector< std::map<int, std::set<int> >::const_iterator > localMoleculeToAtoms_;
/** resets the quantity based on the latest data */
virtual void reset() const = 0;
/** creates the ordered list of local molecules */
void set_local_molecules_to_atoms() const;
private:
// do not define this
MoleculeSet();
};
/**
* @class SmallMoleculeSet
* @brief A class for handling data for small molecules, i.e., molecules with maximum distance between atoms less than the lammps cutoff radius. Atom ids are in [0,nlocalTotal-1].
*/
class SmallMoleculeSet : public MoleculeSet {
public:
SmallMoleculeSet(ATC_Method * atc, int groupBit,
PerAtomQuantity<int> * bondList = NULL,
PerAtomQuantity<int> * numBond = NULL);
virtual ~SmallMoleculeSet();
/** reset all data */
virtual void clear();
/** initialize global data */
virtual void initialize(std::map<int, double> * globalAtomsPerMolecule = NULL);
/** access molecule atoms by lammps id */
std::set<int> atoms_by_global_molecule(int id) const;
/** access fraction of a locally indexed molecule on this processor */
virtual double local_fraction(int id) const;
protected:
/** store the number of atoms in a molecule on this processor */
//std::map<int, int> localAtomsPerMolecule_;
/** resets the quantity based on the latest data */
virtual void reset() const;
/** data structure containing bond list information, forces parallel communication of bond lists */
PerAtomQuantity<int> * bondList_;
/** data structure containing bond list information, forces parallel communication of bond lists */
PerAtomQuantity<int> * numBond_;
/** removes processor ghosts from a set of atom ids */
void remove_proc_ghosts(std::set<int> & atomSet) const;
// workspace variable for determining if we've hit an internal atom already
mutable Array<bool> _atomFound_;
private:
// do not define this
SmallMoleculeSet();
};
};
#endif

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