Detailed Description

Generates initial configurations for molecules of one species.

Definition at line 38 of file Generator.h.

#include <Generator.h>

Inheritance diagram for McMd::Generator:

Public Member Functions
	Generator (Species &species, System &system)
	Constructor. More...

virtual	~Generator ()
	Destructor. More...

void	setBondPotential (BondPotential &bondPotential)
	Create an association with a BondPotential. More...

virtual bool	generate (int nMolecule, Array< double > const &diameters, CellList &cellList)
	Generate nMolecule molecules of the associated Species. More...

Static Public Member Functions
static void	setupCellList (int atomCapacity, Boundary &boundary, const Array< double > &diameters, CellList &cellList)
	Allocate any required memory for the cell list. More...

Protected Member Functions
bool	attemptPlaceAtom (Atom &atom, const Array< double > &diameters, CellList &cellList)
	Attempt to place an atom. More...

virtual bool	attemptPlaceMolecule (Molecule &molecule, const Array< double > &diameters, CellList &cellList)=0
	Attempt to insert an entire molecule (pure virtual). More...

const Species &	species ()
	Get the associated Species by reference. More...

Simulation &	simulation ()
	Get the associated Simulation by reference. More...

System &	system ()
	Get the associated System by reference. More...

const Boundary &	boundary () const
	Get the associated Boundary by reference. More...

const BondPotential &	bondPotential ()
	Get the associated BondPotential by reference. More...

Constructor & Destructor Documentation

McMd::Generator::Generator	(	Species &	species,
		System &	system
	)

Constructor.

Parameters

species	associated Species object
system	parent System

Definition at line 25 of file Generator.cpp.

McMd::Generator::~Generator ( )

virtual

Destructor.

Definition at line 38 of file Generator.cpp.

Member Function Documentation

void McMd::Generator::setBondPotential ( BondPotential & bondPotential )

Create an association with a BondPotential.

Parameters

bondPotential BondPotential

Definition at line 45 of file Generator.cpp.

References bondPotential().

Referenced by McMd::generatorFactory().

bool McMd::Generator::generate	(	int	nMolecule,
		Array< double > const &	diameters,
		CellList &	cellList
	)

virtual

Generate nMolecule molecules of the associated Species.

Precondition: Size of diameters array == number of atom types

Parameters

nMolecule	desired number of molecules
diameters	array of excluded volume diameters for atomTypes
cellList	CellList object

Definition at line 87 of file Generator.cpp.

References McMd::System::addMolecule(), McMd::CellList::atomCapacity(), McMd::Simulation::atomCapacity(), attemptPlaceMolecule(), Util::Log::file(), McMd::Simulation::getMolecule(), Simp::Species::id(), Simp::Species::isMutable(), Simp::Species::mutator(), McMd::System::removeMolecule(), McMd::SpeciesMutator::setMoleculeState(), simulation(), McMd::System::simulation(), species(), McMd::Simulation::species(), system(), and UTIL_CHECK.

Referenced by McMd::McSystem::generateMolecules(), and McMd::MdSystem::generateMolecules().

void McMd::Generator::setupCellList	(	int	atomCapacity,
		Boundary &	boundary,
		const Array< double > &	diameters,
		CellList &	cellList
	)

static

Allocate any required memory for the cell list.

Parameters

atomCapacity	maximum allowed atom id + 1
boundary	Boundary object, periodic unit cell
diameters	array of excluded volume diameters
cellList	CellList to be allocated

Definition at line 131 of file Generator.cpp.

References Util::Array< Data >::capacity(), McMd::CellList::setAtomCapacity(), and McMd::CellList::setup().

Referenced by McMd::McSystem::generateMolecules(), and McMd::MdSystem::generateMolecules().

bool McMd::Generator::attemptPlaceAtom	(	Atom &	atom,
		const Array< double > &	diameters,
		CellList &	cellList
	)

protected

Attempt to place an atom.

The proposed position for the atom should be set upon entry. This function checks if the atom position is within the hard-core cutoff distance of any atoms that are already in the cell list. The cutoff distance for atoms of types i and j is the average of the excluded volume diameters for types i and j. If the atom position satisfies this geometrical constraint, the atom is added to the cell list and returns true. If it does not, the function returns false.

Parameters

atom	new Atom, with proposed position already set
diameters	array of excluded diameters for atom types
cellList	CellList object containing existing atoms

Returns: true on success, false on failure.

Definition at line 52 of file Generator.cpp.

References McMd::CellList::addAtom(), boundary(), Simp::OrthorhombicBoundary::distanceSq(), McMd::CellList::getNeighbors(), McMd::Atom::position(), Simp::OrthorhombicBoundary::shift(), Util::FSArray< Data, Capacity >::size(), and McMd::Atom::typeId().

Referenced by McMd::PointGenerator::attemptPlaceMolecule(), and McMd::LinearGenerator::attemptPlaceMolecule().

virtual bool McMd::Generator::attemptPlaceMolecule	(	Molecule &	molecule,
		const Array< double > &	diameters,
		CellList &	cellList
	)

protectedpure virtual

Attempt to insert an entire molecule (pure virtual).

Parameters

molecule	new molecule, with unknown atomic positions
diameters	array of excluded volume diameters for types
cellList	CellList object storing existing atoms

Returns: true on success, false on failure.

Referenced by generate().

const Species & McMd::Generator::species ( )

inlineprotected

Get the associated Species by reference.

Definition at line 184 of file Generator.h.

Referenced by McMd::LinearGenerator::attemptPlaceMolecule(), and generate().

Simulation & McMd::Generator::simulation ( )

inlineprotected

Get the associated Simulation by reference.

Definition at line 190 of file Generator.h.

Referenced by McMd::PointGenerator::attemptPlaceMolecule(), McMd::LinearGenerator::attemptPlaceMolecule(), and generate().

System & McMd::Generator::system ( )

inlineprotected

Get the associated System by reference.

Definition at line 196 of file Generator.h.

Referenced by generate().

const Boundary & McMd::Generator::boundary ( ) const

inlineprotected

Get the associated Boundary by reference.

Definition at line 202 of file Generator.h.

Referenced by attemptPlaceAtom(), McMd::PointGenerator::attemptPlaceMolecule(), and McMd::LinearGenerator::attemptPlaceMolecule().

const BondPotential & McMd::Generator::bondPotential ( )

inlineprotected

Get the associated BondPotential by reference.

Definition at line 209 of file Generator.h.

Referenced by McMd::LinearGenerator::attemptPlaceMolecule(), and setBondPotential().

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Static Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation