Represents the force field used in simulations. More...

Collaboration diagram for ForceField:

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Classes
struct	InsensitiveCompare
	Comparator for case-insensitive string comparison. More...

Public Types
enum class	ChargeMethod : int { Ewald = 0 , Coulomb = 1 , Wolf = 2 , ModifiedWolf = 3 }
	Enumeration of methods used for electrostatic interactions. More...

enum class	MixingRule : int { Lorentz_Berthelot = 0 , Jorgensen = 1 }
	Enumeration of mixing rules for cross interactions. More...

enum class	PotentialEnergySurfaceType : std::size_t { None = 0 , SecondOrderPolynomialTestFunction = 1 , ThirdOrderPolynomialTestFunction = 2 , FourthOrderPolynomialTestFunction = 3 , FifthOrderPolynomialTestFunction = 4 , SixthOrderPolynomialTestFunction = 5 , ExponentialNonPolynomialTestFunction = 6 , MullerBrown = 7 , Eckhardt = 8 , GonzalezSchlegel = 9 }

enum class	InterpolationGridType : std::size_t { LennardJones = 0 , LennardJonesRepulsion = 1 , LennardJonesAttraction = 2 , EwaldReal = 3 }

enum class	InterpolationScheme : std::size_t { Polynomial = 1 , Tricubic = 8 , Triquintic = 27 }

Public Member Functions
	ForceField () noexcept=default
	Default constructor for the ForceField struct.

	ForceField (std::vector< PseudoAtom > pseudoAtoms, std::vector< VDWParameters > parameters, MixingRule mixingRule, double cutOffFrameworkVDW, double cutOffMoleculeVDW, double cutOffCoulomb, bool shifted, bool tailCorrections, bool useCharge=true) noexcept(false)
	Constructs a ForceField with specified parameters.

	ForceField (std::string filePath) noexcept(false)
	Constructs a ForceField by reading parameters from a file.

VDWParameters &	operator() (std::size_t row, std::size_t col)

const VDWParameters &	operator[] (std::size_t row) const

const VDWParameters &	operator() (std::size_t row, std::size_t col) const

bool	operator== (const ForceField &other) const

void	applyMixingRule ()
	Applies the mixing rule to compute cross-interaction parameters.

double	cutOffVDW (std::size_t i, std::size_t j) const
	Returns the cut-off distance for van der Waals interactions between two pseudo-atoms.

void	preComputePotentialShift ()
	Pre-computes the potential shift for interactions.

void	preComputeTailCorrection ()
	Pre-computes the tail corrections for interactions.

std::string	printPseudoAtomStatus () const
	Returns a string representation of the pseudo-atom status.

std::string	printCutOffAutoStatus () const

std::string	printForceFieldStatus () const
	Returns a string representation of the force field status.

std::vector< nlohmann::json >	jsonPseudoAtomStatus () const
	Returns a JSON representation of the pseudo-atom status.

nlohmann::json	jsonForceFieldStatus () const
	Returns a JSON representation of the force field status.

std::optional< std::size_t >	findPseudoAtom (const std::string &name) const
	Finds the index of a pseudo-atom by name.

void	initializeEwaldParameters (const SimulationBox &simulationBox)
	Initializes the Ewald parameters based on the simulation box.

void	initializeAutomaticCutOff (const SimulationBox &simulationBox)

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

void	validateInput (const nlohmann::basic_json< nlohmann::raspa_map > &parsed_data)

Static Public Member Functions
static std::optional< ForceField >	readForceField (std::optional< std::string > directoryName, std::string forceFieldFileName) noexcept(false)
	Reads a ForceField from a file.

static std::optional< std::size_t >	findPseudoAtom (const std::vector< PseudoAtom > pseudoAtoms, const std::string &name)
	Finds the index of a pseudo-atom by name in a given list.

Public Attributes
std::uint64_t	versionNumber {1}
	Version number of the force field format.

std::vector< VDWParameters >	data {}
	Interaction parameters between pseudo-atoms; size is numberOfPseudoAtoms squared.

std::vector< bool >	shiftPotentials {}
	Indicates if potential shift is applied between pairs of atoms.

std::vector< bool >	tailCorrections {}
	Indicates if tail corrections are applied between pairs of atoms.

MixingRule	mixingRule {MixingRule::Lorentz_Berthelot}
	Mixing rule used for cross interactions.

bool	cutOffFrameworkVDWAutomatic {false}

double	cutOffFrameworkVDW {12.0}
	Cut-off distance for VDW interactions between framework and molecules.

bool	cutOffMoleculeVDWAutomatic {false}

double	cutOffMoleculeVDW {12.0}
	Cut-off distance for VDW interactions between molecules.

bool	cutOffCoulombAutomatic {true}

double	cutOffCoulomb {12.0}
	Cut-off distance for Coulomb interactions.

double	dualCutOff {6.0}
	Inner cut-off distance when using dual cut-off scheme.

std::size_t	numberOfPseudoAtoms {0}
	Number of pseudo-atoms defined in the force field.

std::vector< PseudoAtom >	pseudoAtoms {}
	List of pseudo-atoms in the force field.

ChargeMethod	chargeMethod {ChargeMethod::Ewald}
	Method used for calculating electrostatic interactions.

double	EwaldPrecision {1e-6}
	Desired precision for Ewald summation.

double	EwaldAlpha {0.265058}
	Ewald convergence parameter alpha.

int3	numberOfWaveVectors {8, 8, 8}
	Number of wave vectors in each direction for Ewald summation.

std::size_t	reciprocalIntegerCutOffSquared
	Squared integer cut-off in reciprocal space.

double	reciprocalCutOffSquared
	Squared cut-off distance in reciprocal space.

bool	automaticEwald {true}
	Indicates if Ewald parameters are computed automatically.

bool	useCharge {true}
	Indicates if charges are used in calculations.

bool	omitEwaldFourier {false}
	If true, omits the Fourier component in Ewald summation.

double	energyOverlapCriteria {1e6}
	Energy criteria for considering overlaps.

std::size_t	numberOfTrialDirections { 10 }

std::size_t	numberOfTorsionTrialDirections { 100 }

std::size_t	numberOfFirstBeadPositions { 10 }

double	minimumRosenbluthFactor {1e-150}
	Minimum allowed Rosenbluth factor.

bool	useDualCutOff {false}
	Indicates if dual cut-off scheme is used.

bool	omitInterInteractions {false}
	If true, omits interactions between molecules.

bool	computePolarization {false}
	Indicates if polarization effects are computed.

bool	omitInterPolarization {true}
	If true, omits polarization between molecules.

bool	hasExternalField {false}

PotentialEnergySurfaceType	potentialEnergySurfaceType {PotentialEnergySurfaceType::SecondOrderPolynomialTestFunction}

double3	potentialEnergySurfaceOrigin {0.0, 0.0, 0.0}

std::vector< std::size_t >	gridPseudoAtomIndices

double	spacingVDWGrid {0.15}

double	spacingCoulombGrid {0.15}

std::optional< int3 >	numberOfVDWGridPoints {}

std::optional< int3 >	numberOfCoulombGridPoints {}

std::size_t	numberOfGridTestPoints {100000}

bool	interpolationSchemeAuto {true}

InterpolationScheme	interpolationScheme {InterpolationScheme::Polynomial}

Static Public Attributes
static const std::set< std::string, InsensitiveCompare >	options
	Set of general option keys accepted in the input data.

Friends
Archive< std::ofstream > &	operator<< (Archive< std::ofstream > &archive, const ForceField &f)

Archive< std::ifstream > &	operator>> (Archive< std::ifstream > &archive, ForceField &f)

Detailed Description

Represents the force field used in simulations.

The ForceField struct contains all parameters and methods related to force field calculations, including van der Waals interactions, electrostatics, Ewald summation parameters, mixing rules, and methods to initialize and compute these parameters.

Member Enumeration Documentation

◆ ChargeMethod

enum class ForceField::ChargeMethod : int

strong

Enumeration of methods used for electrostatic interactions.

Enumerator
Ewald	Ewald summation method.
Coulomb	Direct Coulomb interactions.
Wolf	Wolf summation method.
ModifiedWolf	Modified Wolf method.

◆ MixingRule

enum class ForceField::MixingRule : int

strong

Enumeration of mixing rules for cross interactions.

Enumerator
Lorentz_Berthelot	Lorentz-Berthelot mixing rule.

Constructor & Destructor Documentation

◆ ForceField() [1/2]

ForceField::ForceField	(	std::vector< PseudoAtom >	pseudoAtoms,
		std::vector< VDWParameters >	parameters,
		MixingRule	mixingRule,
		double	cutOffFrameworkVDW,
		double	cutOffMoleculeVDW,
		double	cutOffCoulomb,
		bool	shifted,
		bool	tailCorrections,
		bool	useCharge = `true`
	)

Constructs a ForceField with specified parameters.

Initializes the force field using the provided pseudo-atoms, van der Waals parameters, mixing rule, cut-off distances, and flags for shifting potentials and tail corrections.

Parameters

pseudoAtoms	Vector of pseudo-atoms.
parameters	Vector of van der Waals self-interaction parameters.
mixingRule	The mixing rule to use for cross interactions.
cutOffFrameworkVDW	Cut-off distance for VDW interactions between framework and molecules.
cutOffMoleculeVDW	Cut-off distance for VDW interactions between molecules.
cutOffCoulomb	Cut-off distance for Coulomb interactions.
shifted	If true, applies potential shift to interactions.
tailCorrections	If true, applies tail corrections to interactions.
useCharge	If true, includes electrostatic interactions.

◆ ForceField() [2/2]

ForceField::ForceField ( std::string filePath )

Constructs a ForceField by reading parameters from a file.

Initializes the force field by parsing a force field file specified by the file path.

Parameters

filePath Path to the force field file.

Member Function Documentation

◆ applyMixingRule()

void ForceField::applyMixingRule ( )

Applies the mixing rule to compute cross-interaction parameters.

Calculates the interaction parameters between different pseudo-atoms using the specified mixing rule.

◆ cutOffVDW()

double ForceField::cutOffVDW	(	std::size_t	i,
		std::size_t	j
	)		const

Returns the cut-off distance for van der Waals interactions between two pseudo-atoms.

Parameters

i	Index of the first pseudo-atom.
j	Index of the second pseudo-atom.

Returns: The cut-off distance for VDW interactions.

◆ findPseudoAtom() [1/2]

std::optional< std::size_t > ForceField::findPseudoAtom ( const std::string & name ) const

Finds the index of a pseudo-atom by name.

Searches for a pseudo-atom with the given name and returns its index if found.

Parameters

name	Name of the pseudo-atom.

Returns: Optional index of the pseudo-atom.

◆ findPseudoAtom() [2/2]

static std::optional< std::size_t > ForceField::findPseudoAtom	(	const std::vector< PseudoAtom >	pseudoAtoms,
		const std::string &	name
	)

static

Finds the index of a pseudo-atom by name in a given list.

Searches for a pseudo-atom with the given name in the provided vector and returns its index if found.

Parameters

pseudoAtoms	Vector of pseudo-atoms to search.
name	Name of the pseudo-atom.

Returns: Optional index of the pseudo-atom.

◆ initializeEwaldParameters()

void ForceField::initializeEwaldParameters ( const SimulationBox & simulationBox )

Initializes the Ewald parameters based on the simulation box.

Calculates the Ewald alpha parameter and the number of wave vectors required for the desired precision.

Parameters

simulationBox The simulation box to use for initialization.

◆ jsonForceFieldStatus()

nlohmann::json ForceField::jsonForceFieldStatus ( ) const

Returns a JSON representation of the force field status.

Generates a JSON object containing information about the force field parameters.

Returns: A JSON object representing the force field status.

◆ jsonPseudoAtomStatus()

std::vector< nlohmann::json > ForceField::jsonPseudoAtomStatus ( ) const

Returns a JSON representation of the pseudo-atom status.

Generates a JSON array containing information about the pseudo-atoms.

Returns: A vector of JSON objects representing the pseudo-atoms.

◆ preComputePotentialShift()

void ForceField::preComputePotentialShift ( )

Pre-computes the potential shift for interactions.

Calculates the potential shift for each pair of pseudo-atoms if shifting is enabled.

◆ preComputeTailCorrection()

void ForceField::preComputeTailCorrection ( )

Pre-computes the tail corrections for interactions.

Calculates the tail correction energy for each pair of pseudo-atoms if tail corrections are enabled.

◆ printForceFieldStatus()

std::string ForceField::printForceFieldStatus ( ) const

Returns a string representation of the force field status.

Generates a detailed string containing information about the force field parameters.

Returns: A string representing the force field status.

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◆ printPseudoAtomStatus()

std::string ForceField::printPseudoAtomStatus ( ) const

Returns a string representation of the pseudo-atom status.

Generates a detailed string containing information about the pseudo-atoms.

Returns: A string representing the pseudo-atom status.

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◆ readForceField()

static std::optional< ForceField > ForceField::readForceField	(	std::optional< std::string >	directoryName,
		std::string	forceFieldFileName
	)

static

Reads a ForceField from a file.

Attempts to read the force field parameters from the specified file.

Parameters

directoryName	Optional directory name where the file is located.
forceFieldFileName	Name of the force field file.

Returns: An optional ForceField object if successful.

◆ repr()

std::string ForceField::repr ( ) const

inline

Returns a string representation of the ForceField.

Combines the pseudo-atom status and force field status into a single string.

Returns: A string representing the ForceField.

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Member Data Documentation

◆ options

const std::set<std::string, InsensitiveCompare> ForceField::options

static

Set of general option keys accepted in the input data.

This set contains all the general configuration keys that are recognized at the top level of the input JSON. It is used to validate the presence of only known keys.

◆ reciprocalCutOffSquared

double ForceField::reciprocalCutOffSquared

Initial value:

{

std::numeric_limits<double>::max()}

Squared cut-off distance in reciprocal space.

◆ reciprocalIntegerCutOffSquared

std::size_t ForceField::reciprocalIntegerCutOffSquared

Initial value:

{

std::numeric_limits<std::size_t>::max()}

Squared integer cut-off in reciprocal space.

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

src/raspakit/forcefield/forcefield.ixx

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ ChargeMethod

◆ MixingRule

Constructor & Destructor Documentation

◆ ForceField() [1/2]

◆ ForceField() [2/2]

Member Function Documentation

◆ applyMixingRule()

◆ cutOffVDW()

◆ findPseudoAtom() [1/2]

◆ findPseudoAtom() [2/2]

◆ initializeEwaldParameters()

◆ jsonForceFieldStatus()

◆ jsonPseudoAtomStatus()

◆ preComputePotentialShift()

◆ preComputeTailCorrection()

◆ printForceFieldStatus()

◆ printPseudoAtomStatus()

◆ readForceField()

◆ repr()

Member Data Documentation

◆ options

◆ reciprocalCutOffSquared

◆ reciprocalIntegerCutOffSquared