Represents a component within the simulation system. More...

Collaboration diagram for Component:

[legend]

Public Types
enum class	Type : std::size_t { Adsorbate = 0 , Cation = 1 }
	Enumeration of component types. More...

enum class	GrowType : std::size_t { Rigid = 0 , Flexible = 1 }
	Enumeration of growth types for the component. More...

enum class	Shape : std::size_t { NonLinear = 0 , Linear = 1 , Point = 2 }
	Enumeration of molecular shapes. More...

enum class	Chirality : std::size_t { NoCharility = 0 , S_Chiral = 1 , R_Chiral = 2 }

enum class	PressureScale { Log = 0 , Normal = 1 }
	Enumeration of pressure scaling types. More...

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

	Component (Component::Type type, std::size_t currentComponent, const ForceField &forceField, const std::string &componentName, std::optional< const std::string > fileName, std::size_t numberOfBlocks, std::size_t numberOfLambdaBins, const MCMoveProbabilities &systemProbabilities=MCMoveProbabilities(), std::optional< double > fugacityCoefficient=std::nullopt, bool thermodynamicIntegration=false) noexcept(false)
	Constructs a Component from a file.

	Component (std::size_t componentId, const ForceField &forceField, std::string componentName, double T_c, double P_c, double w, std::vector< Atom > definedAtoms, const ConnectivityTable &connectivityTable, const Potentials::IntraMolecularPotentials &intraMolecularPotentials, std::size_t numberOfBlocks, std::size_t numberOfLambdaBins, const MCMoveProbabilities &systemProbabilities=MCMoveProbabilities(), std::optional< double > fugacityCoefficient=std::nullopt, bool thermodynamicIntegration=false) noexcept(false)
	Constructs a Component programmatically.

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

std::string	printStatus (const ForceField &forceField, double inputPressure) const
	Generates a string representing the component's current status.

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

nlohmann::json	jsonStatus () const
	Serializes the component's status to JSON.

void	computeRigidProperties ()
	Computes rigid body properties of the component.

double3	computeCenterOfMass (std::vector< Atom > atom_list) const
	Computes the center of mass for a given list of atoms.

std::vector< Atom >	rotatePositions (const simd_quatd &q) const
	Rotates the positions of all atoms using a given quaternion.

std::vector< Atom >	copiedAtoms (std::span< Atom > molecule) const
	Creates a copy of the component's atoms based on a molecule span.

std::pair< Molecule, std::vector< Atom > >	equilibratedMoleculeRandomInBox (RandomNumber &random, const SimulationBox &simulationBox) const
	Generates an equilibrated molecule randomly placed within a simulation box.

std::pair< Molecule, std::vector< Atom > >	translate (const Molecule &molecule, std::span< Atom > molecule_atoms, double3 displacement) const
	Translates a molecule by a specified displacement.

std::pair< Molecule, std::vector< Atom > >	rotate (const Molecule &molecule, std::span< Atom > molecule_atoms, simd_quatd rotation) const
	Rotates a molecule using a specified rotation quaternion.

ConnectivityTable	readConnectivityTable (std::size_t size, const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

std::vector< BondPotential >	readBondPotentials (const ForceField &forceField, const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

std::vector< BendPotential >	readBendPotentials (const ForceField &forceField, const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

std::vector< TorsionPotential >	readTorsionPotentials (const ForceField &forceField, const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

std::vector< VanDerWaalsPotential >	readVanDerWaalsPotentials (const ForceField &forceField, const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

std::vector< std::vector< std::size_t > >	readPartialReinsertionFixedAtoms (const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

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

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

Type	type {0}
	Type of the component (Adsorbate or Cation).

GrowType	growType {0}
	Growth type of the component.

std::size_t	componentId {0}
	Unique identifier for the component.

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

std::optional< std::string >	filenameData {}
	Optional filename containing component data.

std::string	filename {}
	Filename associated with the component.

std::vector< double4 >	blockingPockets {}
	List of blocking pockets defined by position and radius.

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

std::size_t	translationalDegreesOfFreedom {}
	Number of translational degrees of freedom.

std::size_t	rotationalDegreesOfFreedom {}
	Number of rotational degrees of freedom.

double	criticalTemperature {0.0}
	Critical temperature of the component [K].

double	criticalPressure {0.0}
	Critical pressure of the component [Pa].

double	acentricFactor {0.0}
	Acentric factor of the component [-].

double	molFraction {1.0}
	Mole fraction of the component [-].

bool	swappable {false}
	Flag indicating if the component is swappable.

double	partialPressure {0.0}
	Partial pressure of the component [Pa].

double	totalMass {0.0}
	Total mass of the component [kg].

std::optional< double >	fugacityCoefficient {}
	Optional fugacity coefficient [-].

double	amountOfExcessMolecules {0.0}
	Amount of excess molecules [-].

double	bulkFluidDensity {0.0}
	Bulk fluid density [kg/m³].

double	compressibility {0.0}
	Compressibility of the component [-].

std::optional< double >	idealGasRosenbluthWeight {}
	Optional ideal gas Rosenbluth weight [-].

std::optional< double >	idealGasEnergy {}
	Optional ideal gas energy [J].

double	netCharge {0.0}
	Net charge of the component [e].

std::size_t	startingBead {0}
	Starting bead index for simulations.

std::vector< std::pair< Atom, double > >	definedAtoms {}
	List of defined atoms and their masses.

double3	inertiaVector {}
	Inertia vector of the component.

double3	inverseInertiaVector {}
	Inverse of the inertia vector.

Shape	shapeType
	Shape type of the molecule.

std::vector< Atom >	atoms {}
	List of atoms in the component.

ConnectivityTable	connectivityTable {}
	Connectivity table for the component.

Potentials::IntraMolecularPotentials	intraMolecularPotentials {}
	List of internal potentials.

std::vector< Atom >	grownAtoms {}

std::vector< std::vector< std::size_t > >	partialReinsertionFixedAtoms {}

std::size_t	initialNumberOfMolecules {0}
	Initial number of molecules in the component.

PropertyLambdaProbabilityHistogram	lambdaGC
	Lambda probability histogram for Gibbs-Chebyshev integration.

PropertyLambdaProbabilityHistogram	lambdaGibbs
	Lambda probability histogram for Gibbs integration.

bool	hasFractionalMolecule {false}
	Flag indicating if the component has fractional molecules.

MCMoveProbabilities	mc_moves_probabilities
	Move probabilities for Monte Carlo simulations.

MCMoveStatistics	mc_moves_statistics

MCMoveCpuTime	mc_moves_cputime
	CPU time statistics for Monte Carlo moves.

std::vector< CBMCMoveStatistics >	cbmc_moves_statistics

PropertyWidom	averageRosenbluthWeights
	Average Rosenbluth weights for Widom insertion.

double	lnPartitionFunction {0}
	Natural logarithm of the partition function [-].

MultiSiteIsotherm	isotherm {}
	Isotherm information for the component.

double	massTransferCoefficient {0.0}
	Mass transfer coefficient [1/s].

double	axialDispersionCoefficient {0.0}
	Axial dispersion coefficient [m²/s].

bool	isCarrierGas {false}
	Flag indicating if the component is a carrier gas.

std::size_t	columnPressure {0}
	Column index for pressure data.

std::size_t	columnLoading {1}
	Column index for loading data.

std::size_t	columnError {2}
	Column index for error data.

PressureScale	pressureScale {PressureScale::Log}
	Pressure scaling type.

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

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

Detailed Description

Represents a component within the simulation system.

The Component struct encapsulates all properties and behaviors associated with a simulation component, such as adsorbates or cations. It includes various physical properties, molecular structures, and simulation parameters necessary for conducting simulations. The struct provides constructors for initializing components from files or programmatically and includes methods for computing physical properties and manipulating molecular positions.

Member Enumeration Documentation

◆ GrowType

enum class Component::GrowType : std::size_t

strong

Enumeration of growth types for the component.

Enumerator
Rigid	Rigid growth type.
Flexible	Flexible growth type.

◆ PressureScale

enum class Component::PressureScale

strong

Enumeration of pressure scaling types.

Enumerator
Log	Logarithmic pressure scaling.
Normal	Normal pressure scaling.

◆ Shape

enum class Component::Shape : std::size_t

strong

Enumeration of molecular shapes.

Enumerator
NonLinear	Non-linear molecular shape.
Linear	Linear molecular shape.
Point	Point-particle molecular shape.

◆ Type

enum class Component::Type : std::size_t

strong

Enumeration of component types.

Enumerator
Adsorbate	Represents an adsorbate component.
Cation	Represents a cation component.

Constructor & Destructor Documentation

◆ Component() [1/3]

Component::Component ( )

Default constructor for the Component struct.

Initializes a Component object with default values.

◆ Component() [2/3]

Component::Component	(	Component::Type	type,
		std::size_t	currentComponent,
		const ForceField &	forceField,
		const std::string &	componentName,
		std::optional< const std::string >	fileName,
		std::size_t	numberOfBlocks,
		std::size_t	numberOfLambdaBins,
		const MCMoveProbabilities &	systemProbabilities = `MCMoveProbabilities()`,
		std::optional< double >	fugacityCoefficient = `std::nullopt`,
		bool	thermodynamicIntegration = `false`
	)

Constructs a Component from a file.

Initializes a Component by reading data from a specified file, using the provided force field and simulation parameters.

Parameters

type	The type of the component (Adsorbate or Cation).
currentComponent	The current component ID.
forceField	The force field used for parsing atom types and interactions.
componentName	The name of the component.
fileName	Optional filename containing component data.
numberOfBlocks	The number of simulation blocks.
numberOfLambdaBins	The number of lambda bins for scaling.
systemProbabilities	Move probabilities for the Monte Carlo simulation.
fugacityCoefficient	Optional fugacity coefficient.
thermodynamicIntegration	Flag indicating if thermodynamic integration is used.

Exceptions

std::runtime_error If the component file cannot be read or parsed.

◆ Component() [3/3]

Component::Component	(	std::size_t	componentId,
		const ForceField &	forceField,
		std::string	componentName,
		double	T_c,
		double	P_c,
		double	w,
		std::vector< Atom >	definedAtoms,
		const ConnectivityTable &	connectivityTable,
		const Potentials::IntraMolecularPotentials &	intraMolecularPotentials,
		std::size_t	numberOfBlocks,
		std::size_t	numberOfLambdaBins,
		const MCMoveProbabilities &	systemProbabilities = `MCMoveProbabilities()`,
		std::optional< double >	fugacityCoefficient = `std::nullopt`,
		bool	thermodynamicIntegration = `false`
	)

Constructs a Component programmatically.

Initializes a Component with specified physical properties and molecular structure.

Parameters

componentId	The unique identifier for the component.
forceField	The force field used for defining atom properties.
componentName	The name of the component.
T_c	The critical temperature of the component.
P_c	The critical pressure of the component.
w	The acentric factor of the component.
atomList	A list of atoms defining the component's molecular structure.
numberOfBlocks	The number of simulation blocks.
numberOfLambdaBins	The number of lambda bins for scaling.
systemProbabilities	Move probabilities for the Monte Carlo simulation.
fugacityCoefficient	Optional fugacity coefficient.
thermodynamicIntegration	Flag indicating if thermodynamic integration is used.

Exceptions

std::runtime_error If pseudo-atoms are not recognized or data is invalid.

Member Function Documentation

◆ computeCenterOfMass()

double3 Component::computeCenterOfMass ( std::vector< Atom > atom_list ) const

Computes the center of mass for a given list of atoms.

Calculates the center of mass position based on the provided atom list.

Parameters

atom_list The list of atoms to compute the center of mass for.

Returns: The center of mass position as a double3 vector.

◆ computeRigidProperties()

void Component::computeRigidProperties ( )

Computes rigid body properties of the component.

Calculates properties such as the center of mass, inertia tensor, and degrees of freedom based on the defined atoms.

◆ copiedAtoms()

std::vector< Atom > Component::copiedAtoms ( std::span< Atom > molecule ) const

Creates a copy of the component's atoms based on a molecule span.

Copies and adjusts the positions of atoms relative to a given molecule.

Parameters

molecule A span representing the molecule to copy atoms from.

Returns: A vector of copied atoms with adjusted positions.

◆ equilibratedMoleculeRandomInBox()

std::pair< Molecule, std::vector< Atom > > Component::equilibratedMoleculeRandomInBox	(	RandomNumber &	random,
		const SimulationBox &	simulationBox
	)		const

Generates an equilibrated molecule randomly placed within a simulation box.

Rotates and translates the molecule randomly to ensure equilibration within the simulation box.

Parameters

random	A random number generator instance.
simulationBox	The simulation box within which to place the molecule.

Returns: A pair containing the equilibrated molecule and its corresponding atoms.

◆ jsonStatus()

nlohmann::json Component::jsonStatus ( ) const

Serializes the component's status to JSON.

Converts the component's current status and properties into a JSON object.

Returns: A JSON object representing the component's status.

◆ printBreakthroughStatus()

std::string Component::printBreakthroughStatus ( ) const

Generates a string representing the breakthrough status of the component.

Compiles breakthrough-related properties and parameters of the component into a formatted string.

Returns: A string detailing the breakthrough status of the component.

◆ printStatus()

std::string Component::printStatus	(	const ForceField &	forceField,
		double	inputPressure
	)		const

Generates a string representing the component's current status.

Compiles various properties and parameters of the component into a formatted string.

Parameters

forceField The force field used for interpreting atom types.

Returns: A string detailing the component's status.

◆ readComponent()

void Component::readComponent	(	const ForceField &	forceField,
		const std::string &	fileName
	)

Reads component data from a file.

Parses component information from the specified file using the provided force field.

Parameters

forceField	The force field used for parsing atom types and interactions.
fileName	The name of the file containing component data.

Exceptions

std::runtime_error If the file cannot be found, opened, or parsed correctly.

◆ repr()

std::string Component::repr ( ) const

Returns a string representation of the Component.

Generates a simple string indicating a test representation of the Component.

Returns: A string representing the Component.

◆ rotate()

std::pair< Molecule, std::vector< Atom > > Component::rotate	(	const Molecule &	molecule,
		std::span< Atom >	molecule_atoms,
		simd_quatd	rotation
	)		const

Rotates a molecule using a specified rotation quaternion.

Applies a rotation to the entire molecule based on the provided quaternion.

Parameters

molecule	The molecule to rotate.
molecule_atoms	A span representing the atoms of the molecule.
rotation	The quaternion representing the rotation to apply.

Returns: A pair containing the rotated molecule and its corresponding atoms.

◆ rotatePositions()

std::vector< Atom > Component::rotatePositions ( const simd_quatd & q ) const

Rotates the positions of all atoms using a given quaternion.

Applies a rotation to the atom positions based on the provided quaternion.

Parameters

q	The quaternion representing the rotation.

Returns: A vector of atoms with updated positions after rotation.

◆ translate()

std::pair< Molecule, std::vector< Atom > > Component::translate	(	const Molecule &	molecule,
		std::span< Atom >	molecule_atoms,
		double3	displacement
	)		const

Translates a molecule by a specified displacement.

Moves the entire molecule by the given displacement vector.

Parameters

molecule	The molecule to translate.
molecule_atoms	A span representing the atoms of the molecule.
displacement	The displacement vector to apply.

Returns: A pair containing the translated molecule and its corresponding atoms.

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

src/raspakit/component.ixx

Public Types

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ GrowType

◆ PressureScale

◆ Shape

◆ Type

Constructor & Destructor Documentation

◆ Component() [1/3]

◆ Component() [2/3]

◆ Component() [3/3]

Member Function Documentation

◆ computeCenterOfMass()

◆ computeRigidProperties()

◆ copiedAtoms()

◆ equilibratedMoleculeRandomInBox()

◆ jsonStatus()

◆ printBreakthroughStatus()

◆ printStatus()

◆ readComponent()

◆ repr()

◆ rotate()

◆ rotatePositions()

◆ translate()