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

Collaboration diagram for Framework:

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Public Types
enum class	UseChargesFrom : std::size_t { PseudoAtoms = 0 , CIF_File = 1 , ChargeEquilibration }
	Enumeration for specifying the source of atomic charges. More...

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

	Framework (std::size_t currentComponent, const ForceField &forceField, const std::string &componentName, std::optional< const std::string > fileName, std::optional< int3 > numberOfUnitCells, Framework::UseChargesFrom useChargesFrom) noexcept(false)
	Constructs a Framework from a file with specified parameters.

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

void	readFramework (const ForceField &forceField, const std::string &fileName)
	Reads framework data from a file.

void	expandDefinedAtomsToUnitCell ()
	Expands defined atoms to fill the unit cell using symmetry operations.

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< 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.

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::optional< std::string >	filenameData {}
	Optional file name containing framework data.

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.

UseChargesFrom	useChargesFrom {UseChargesFrom::PseudoAtoms}
	Source of atomic charges.

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 >	unitCellAtoms
	Fractional atoms in the unit cell after applying symmetry operations.

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

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.

Member Enumeration Documentation

◆ UseChargesFrom

enum class Framework::UseChargesFrom : std::size_t

strong

Enumeration for specifying the source of atomic charges.

UseChargesFrom defines the source from which atomic charges should be obtained. Options include using charges from pseudo-atoms, the CIF file, or by performing charge equilibration calculations.

Enumerator
PseudoAtoms	Use charges from pseudo-atoms defined in the force field.
CIF_File	Use charges specified in the CIF file.
ChargeEquilibration	Compute charges using charge equilibration methods.

Constructor & Destructor Documentation

◆ Framework() [1/3]

Framework::Framework ( )

Default constructor for the Framework struct.

Initializes an empty Framework object with default values.

◆ Framework() [2/3]

Framework::Framework	(	std::size_t	currentComponent,
		const ForceField &	forceField,
		const std::string &	componentName,
		std::optional< const std::string >	fileName,
		std::optional< int3 >	numberOfUnitCells,
		Framework::UseChargesFrom	useChargesFrom
	)

Constructs a Framework from a file with specified parameters.

Initializes a Framework using data from a specified file, setting up the simulation box, atoms, and other properties based on the provided force field and unit cell information.

Parameters

currentComponent	Identifier for the current framework component.
forceField	Reference to the force field containing pseudo-atom definitions.
componentName	Name of the framework component.
fileName	Optional file name containing framework data (e.g., a CIF file).
numberOfUnitCells	Number of unit cells in each dimension to construct the supercell.
useChargesFrom	Source of atomic charges (pseudo-atoms, CIF file, or charge equilibration).

◆ Framework() [3/3]

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

◆ expandDefinedAtomsToUnitCell()

void Framework::expandDefinedAtomsToUnitCell ( )

Expands defined atoms to fill the unit cell using symmetry operations.

Applies space group symmetry operations to the defined atoms to generate all atoms within the unit cell.

◆ 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.

◆ readFramework()

void Framework::readFramework	(	const ForceField &	forceField,
		const std::string &	fileName
	)

Reads framework data from a file.

Reads the framework structure, including atoms and simulation box, from the specified file, applying symmetry operations and setting up the framework for simulation.

Parameters

forceField	Reference to the force field containing pseudo-atom definitions.
fileName	File name containing the framework data (e.g., a CIF file).

◆ 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 Types

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ UseChargesFrom

Constructor & Destructor Documentation

◆ Framework() [1/3]

◆ Framework() [2/3]

◆ Framework() [3/3]

Member Function Documentation

◆ expandDefinedAtomsToUnitCell()

◆ jsonStatus()

◆ makeSuperCell()

◆ printBreakthroughStatus()

◆ printStatus()

◆ readFramework()

◆ repr()