Represents a framework in the simulation system. More...

Collaboration diagram for Framework:

[legend]

Public Member Functions
	Framework ()
	Default constructor for the Framework struct.

	Framework (std::size_t componentId, const ForceField &forceField, std::string componentName, SimulationBox simulationBox, std::size_t spaceGroupHallNumber, const std::vector< Atom > &definedAtoms, const std::vector< Atom > &fractionalAtoms, int3 numberOfUnitCells) noexcept(false)
	Constructs a Framework programmatically with specified parameters.

void	determineUniqueAtomTypes ()

void	makeSuperCell ()
	Constructs the supercell by replicating the unit cell atoms.

std::vector< Atom >	makeSuperCell (int3 numberOfCells) const

std::vector< double3 >	fractionalAtomPositionsUnitCell () const

std::vector< double3 >	cartesianAtomPositionsUnitCell () const

std::vector< double2 >	atomUnitCellLennardJonesPotentialParameters (const ForceField &forceField) const

std::optional< double >	computeLargestNonOverlappingFreeRadius (const ForceField &forceField, double3 probe_position, double well_depth_factor) const

bool	computeVanDerWaalsRadiusOverlap (const ForceField &forceField, double3 probe_position) const

bool	computeOverlap (const ForceField &forceField, double3 probe_position, double well_depth_factor, std::size_t probe_type, std::make_signed_t< std::size_t > skip) const

std::string	printStatus (const ForceField &forceField) const
	Generates a string representation of the framework status.

std::string	printBreakthroughStatus () const
	Generates a string representation of the breakthrough status.

nlohmann::json	jsonStatus () const
	Generates a JSON representation of the framework status.

std::string	repr () const
	Returns a string representation of the Framework.

Static Public Member Functions
static Framework	makeFAU (const ForceField &forceField, int3 replicate={1, 1, 1})

static Framework	makeITQ29 (const ForceField &forceField, int3 replicate={1, 1, 1})

static Framework	makeMFI (const ForceField &forceField, int3 replicate={1, 1, 1})

static Framework	makeCHA (const ForceField &forceField, int3 replicate={1, 1, 1})

Public Attributes
std::uint64_t	versionNumber {1}
	Version number for serialization purposes.

SimulationBox	simulationBox
	Simulation box defining the unit cell dimensions.

std::size_t	spaceGroupHallNumber {1}
	Space group number according to the Hall notation.

int3	numberOfUnitCells {1, 1, 1}
	Number of unit cells in each dimension for the supercell.

std::size_t	frameworkId {0}
	Identifier for the framework.

std::string	name {}
	Name of the framework component.

std::string	filename {}
	File name of the framework.

std::size_t	numberOfComponents {1}

bool	rigid {true}
	Flag indicating if the framework is rigid.

double	mass {0.0}
	Total mass of the framework.

double	unitCellMass {0.0}
	Mass of the unit cell.

double	netCharge {0.0}
	Net charge of the framework.

double	smallestCharge {0.0}
	Smallest atomic charge in the framework.

double	largestCharge {0.0}
	Largest atomic charge in the framework.

std::vector< Atom >	definedAtoms {}
	Fractional Atoms defining the unit cell before symmetry operations.

std::vector< Atom >	fractionalUnitCellAtoms
	Fractional atoms in the unit cell after applying symmetry operations.

std::vector< Atom >	unitCellAtoms
	Cartesian atoms in the unit cell after applying symmetry operations.

std::vector< Atom >	atoms {}
	All Cartesian atoms in the framework after constructing the supercell.

std::unordered_set< std::size_t >	uniqueAtomTypes {}

std::vector< std::size_t >	chiralCenters {}
	Indices of chiral centers in the framework.

std::vector< BondPotential >	bonds {}
	Bonds within the framework.

std::vector< std::pair< std::size_t, std::size_t > >	bondDipoles {}
	Pairs of atoms forming bond dipoles.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t > >	bends {}
	Triplets of atoms forming angle bends.

std::vector< std::pair< std::size_t, std::size_t > >	UreyBradley {}
	Pairs of atoms for Urey-Bradley interactions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	inversionBends {}
	Quartets of atoms for inversion bends.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	Torsion {}
	Quartets of atoms forming torsions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	ImproperTorsions {}
	Quartets of atoms forming improper torsions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t > >	bondBonds {}
	Triplets of atoms for bond-bond interactions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t > >	stretchBends {}
	Triplets of atoms for stretch-bend interactions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	bendBends {}
	Quartets of atoms for bend-bend interactions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	stretchTorsions {}
	Quartets of atoms for stretch-torsion interactions.

std::vector< std::tuple< std::size_t, std::size_t, std::size_t, std::size_t > >	bendTorsions {}
	Quartets of atoms for bend-torsion interactions.

std::vector< std::pair< std::size_t, std::size_t > >	intraVDW {}
	Pairs of atoms for intramolecular van der Waals interactions.

std::vector< std::pair< std::size_t, std::size_t > >	intraCoulomb {}
	Pairs of atoms for intramolecular Coulomb interactions.

std::vector< std::pair< std::size_t, std::size_t > >	excludedIntraCoulomb {}
	Pairs of atoms excluded from intramolecular Coulomb interactions.

Friends
Archive< std::ofstream > &	operator<< (Archive< std::ofstream > &archive, const Framework &c)

Archive< std::ifstream > &	operator>> (Archive< std::ifstream > &archive, Framework &c)

Detailed Description

Represents a framework in the simulation system.

The Framework struct encapsulates the properties and behaviors of a framework (e.g., a solid lattice or crystalline structure) within the simulation. It includes information about the simulation box, atoms within the framework, and various structural and force field parameters. The struct provides constructors for initializing frameworks from files or programmatically, and methods to process and output framework data.

Constructor & Destructor Documentation

◆ Framework() [1/2]

Framework::Framework ( )

Default constructor for the Framework struct.

Initializes an empty Framework object with default values.

◆ Framework() [2/2]

Framework::Framework	(	std::size_t	componentId,
		const ForceField &	forceField,
		std::string	componentName,
		SimulationBox	simulationBox,
		std::size_t	spaceGroupHallNumber,
		const std::vector< Atom > &	definedAtoms,
		const std::vector< Atom > &	fractionalAtoms,
		int3	numberOfUnitCells
	)

Constructs a Framework programmatically with specified parameters.

Initializes a Framework using provided simulation box, space group number, defined atoms, and unit cell information, allowing for programmatic creation of frameworks without file input.

Parameters

componentId	Identifier for the framework component.
forceField	Reference to the force field containing pseudo-atom definitions.
componentName	Name of the framework component.
simulationBox	Simulation box defining the unit cell dimensions.
spaceGroupHallNumber	Space group number according to the Hall notation.
definedAtoms	Vector of atoms defining the positions and types within the unit cell.
numberOfUnitCells	Number of unit cells in each dimension to construct the supercell.

Member Function Documentation

◆ jsonStatus()

nlohmann::json Framework::jsonStatus ( ) const

Generates a JSON representation of the framework status.

Creates a JSON object containing detailed information about the framework, suitable for serialization or logging.

Returns: A JSON object representing the framework status.

◆ makeSuperCell()

void Framework::makeSuperCell ( )

Constructs the supercell by replicating the unit cell atoms.

Generates the full framework structure by replicating the unit cell atoms according to the specified number of unit cells in each dimension.

◆ printBreakthroughStatus()

std::string Framework::printBreakthroughStatus ( ) const

Generates a string representation of the breakthrough status.

Returns: A string representing the breakthrough status.

◆ printStatus()

std::string Framework::printStatus ( const ForceField & forceField ) const

Generates a string representation of the framework status.

Creates a formatted string containing detailed information about the framework, including atom types, positions, charges, and bond information.

Parameters

forceField Reference to the force field containing pseudo-atom definitions.

Returns: A string representing the framework status.

◆ repr()

std::string Framework::repr ( ) const

Returns a string representation of the Framework.

Generates a string that includes the framework's ID, name, number of atoms, net charge, mass, and other relevant information.

Returns: A string representing the Framework.

The documentation for this struct was generated from the following file:

src/raspakit/framework.ixx

Public Member Functions

Static Public Member Functions

Public Attributes

Friends