Accumulates energy components during simulation. More...

Public Member Functions
	RunningEnergy ()
	Default constructor initializing all energy components to zero.

std::string	printMC () const
	Generates a formatted string of Monte Carlo energy components.

std::string	printMD () const
	Generates a formatted string of molecular dynamics energy components.

std::string	printMCDiff (RunningEnergy &other) const
	Generates a formatted string comparing energy components between two Monte Carlo states.

std::string	printMDDiff (RunningEnergy &other) const
	Generates a formatted string comparing energy components between two molecular dynamics states.

std::string	printMC (const std::string &label) const
	Generates a labeled formatted string of Monte Carlo energy components.

std::string	printMD (const std::string &label, double referenceEnergy) const
	Generates a labeled formatted string of molecular dynamics energy components, including conserved energy and drift.

nlohmann::json	jsonMC () const
	Generates a JSON object of Monte Carlo energy components.

nlohmann::json	jsonMD () const
	Generates a JSON object of molecular dynamics energy components.

double	potentialEnergy () const
	Computes the total potential energy.

double	CoulombEnergy () const
	Computes the total Coulombic energy.

double	kineticEnergy () const
	Computes the total kinetic energy.

double	ewaldFourier () const
	Computes the total Ewald Fourier energy.

double	conservedEnergy () const
	Computes the conserved energy in molecular dynamics simulations.

double	dudlambda (double lambda) const
	Computes the derivative of the potential energy with respect to lambda.

void	zero ()
	Resets all energy components to zero.

RunningEnergy &	operator+= (const RunningEnergy &b)

RunningEnergy &	operator-= (const RunningEnergy &b)

RunningEnergy	operator- () const

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

double	externalFieldVDW
	Energy from van der Waals interactions with external field.

double	frameworkMoleculeVDW
	Energy from van der Waals interactions between framework and molecules.

double	moleculeMoleculeVDW
	Energy from van der Waals interactions between molecules.

double	externalFieldCharge
	Energy from Coulomb interactions with external field.

double	frameworkMoleculeCharge
	Energy from Coulomb interactions between framework and molecules.

double	moleculeMoleculeCharge
	Energy from Coulomb interactions between molecules.

double	ewald_fourier
	Fourier component of Ewald sum for Coulomb interactions.

double	ewald_self
	Self-interaction correction in Ewald sum.

double	ewald_exclusion
	Exclusion term in Ewald sum for Coulomb interactions.

double	bond

double	ureyBradley

double	bend

double	inversionBend

double	outOfPlaneBend

double	torsion

double	improperTorsion

double	bondBond

double	bondBend

double	bondTorsion

double	bendBend

double	bendTorsion

double	intraVDW
	Intramolecular van der Waals energy.

double	intraCoul
	Intramolecular Coulomb energy.

double	tail
	Tail correction energy for van der Waals interactions.

double	polarization
	Energy contribution from polarization effects.

double	dudlambdaVDW
	Derivative of van der Waals energy with respect to lambda.

double	dudlambdaCharge
	Derivative of Coulomb energy with respect to lambda (real space).

double	dudlambdaEwald
	Derivative of Coulomb energy with respect to lambda (Ewald sum).

double	translationalKineticEnergy
	Translational kinetic energy.

double	rotationalKineticEnergy
	Rotational kinetic energy.

double	NoseHooverEnergy
	Energy associated with Nose-Hoover thermostat/barostat.

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

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

Detailed Description

Accumulates energy components during simulation.

The RunningEnergy struct stores various components of energy calculated during a simulation run, including potential and kinetic energies, as well as contributions from various interactions such as van der Waals and Coulomb forces. It provides methods to calculate total energies, perform arithmetic operations, and output energy information.

Constructor & Destructor Documentation

◆ RunningEnergy()

RunningEnergy::RunningEnergy ( )

inline

Default constructor initializing all energy components to zero.

Initializes all the energy components and related terms to zero, preparing the RunningEnergy object for accumulation during simulation.

Member Function Documentation

◆ conservedEnergy()

double RunningEnergy::conservedEnergy ( ) const

inline

Computes the conserved energy in molecular dynamics simulations.

Sums up the total potential energy, kinetic energy, and energy associated with the Nose-Hoover thermostat/barostat to compute the conserved energy in molecular dynamics simulations.

Returns: The conserved energy.

◆ CoulombEnergy()

double RunningEnergy::CoulombEnergy ( ) const

inline

Computes the total Coulombic energy.

Sums up the Coulombic energy components, including framework-molecule Coulomb interactions, molecule-molecule Coulomb interactions, and Ewald sums.

Returns: The total Coulombic energy.

◆ dudlambda()

double RunningEnergy::dudlambda ( double lambda ) const

inline

Computes the derivative of the potential energy with respect to lambda.

Calculates the derivative of the potential energy with respect to the scaling parameter lambda, considering both van der Waals and Coulombic interactions.

Parameters

lambda The scaling parameter.

Returns: The derivative of the potential energy with respect to lambda.

◆ ewaldFourier()

double RunningEnergy::ewaldFourier ( ) const

inline

Computes the total Ewald Fourier energy.

Sums up the Fourier components of the Ewald sum, including the Fourier term, self-interaction correction, and exclusion term.

Returns: The total Ewald Fourier energy.

◆ jsonMC()

nlohmann::json RunningEnergy::jsonMC ( ) const

Generates a JSON object of Monte Carlo energy components.

Returns a JSON object containing the total potential energy and individual energy components relevant for Monte Carlo simulations.

Returns: A JSON object representing the energy components in Monte Carlo simulations.

◆ jsonMD()

nlohmann::json RunningEnergy::jsonMD ( ) const

Generates a JSON object of molecular dynamics energy components.

Returns a JSON object containing the total potential and kinetic energies, as well as individual energy components relevant for molecular dynamics simulations.

Returns: A JSON object representing the energy components in molecular dynamics simulations.

◆ kineticEnergy()

double RunningEnergy::kineticEnergy ( ) const

inline

Computes the total kinetic energy.

Sums up the translational and rotational kinetic energies.

Returns: The total kinetic energy.

◆ potentialEnergy()

double RunningEnergy::potentialEnergy ( ) const

inline

Computes the total potential energy.

Sums up all the potential energy components, including interactions with external fields, framework-molecule interactions, molecule-molecule interactions, Ewald sums, intramolecular energies, tail corrections, and polarization.

Returns: The total potential energy.

◆ printMC() [1/2]

std::string RunningEnergy::printMC ( ) const

Generates a formatted string of Monte Carlo energy components.

Returns a string containing the total potential energy and individual energy components relevant for Monte Carlo simulations, formatted for display.

Returns: A string representing the energy components in Monte Carlo simulations.

◆ printMC() [2/2]

std::string RunningEnergy::printMC ( const std::string & label ) const

Generates a labeled formatted string of Monte Carlo energy components.

Returns a string containing the total potential energy and individual energy components relevant for Monte Carlo simulations, with an additional label for identification.

Parameters

label A string label to include in the output.

Returns: A labeled string representing the energy components in Monte Carlo simulations.

◆ printMCDiff()

std::string RunningEnergy::printMCDiff ( RunningEnergy & other ) const

Generates a formatted string comparing energy components between two Monte Carlo states.

Computes the difference between the current RunningEnergy and another instance, and returns a string that shows the comparison of energy components, highlighting any drifts or discrepancies.

Parameters

other Another RunningEnergy instance to compare with.

Returns: A string representing the differences in energy components between two Monte Carlo states.

◆ printMD() [1/2]

std::string RunningEnergy::printMD ( ) const

Generates a formatted string of molecular dynamics energy components.

Returns a string containing the total potential and kinetic energies, as well as individual energy components relevant for molecular dynamics simulations, formatted for display.

Returns: A string representing the energy components in molecular dynamics simulations.

◆ printMD() [2/2]

std::string RunningEnergy::printMD	(	const std::string &	label,
		double	referenceEnergy
	)		const

Generates a labeled formatted string of molecular dynamics energy components, including conserved energy and drift.

Returns a string containing the total potential and kinetic energies, conserved energy, drift from a reference energy, and individual energy components relevant for molecular dynamics simulations, with an additional label for identification.

Parameters

label	A string label to include in the output.
referenceEnergy	The reference energy to compute the drift.

Returns: A labeled string representing the energy components in molecular dynamics simulations.

◆ printMDDiff()

std::string RunningEnergy::printMDDiff ( RunningEnergy & other ) const

Generates a formatted string comparing energy components between two molecular dynamics states.

Computes the difference between the current RunningEnergy and another instance, and returns a string that shows the comparison of energy components, highlighting any drifts or discrepancies in molecular dynamics simulations.

Parameters

other Another RunningEnergy instance to compare with.

Returns: A string representing the differences in energy components between two molecular dynamics states.

◆ zero()

void RunningEnergy::zero ( )

inline

Resets all energy components to zero.

Sets all the energy components and related terms to zero, effectively clearing the accumulated energies.

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

src/raspakit/running_energy.ixx

Public Member Functions

Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ RunningEnergy()

Member Function Documentation

◆ conservedEnergy()

◆ CoulombEnergy()

◆ dudlambda()

◆ ewaldFourier()

◆ jsonMC()

◆ jsonMD()

◆ kineticEnergy()

◆ potentialEnergy()

◆ printMC() [1/2]

◆ printMC() [2/2]

◆ printMCDiff()

◆ printMD() [1/2]

◆ printMD() [2/2]

◆ printMDDiff()

◆ zero()