This class stores the (physical) properties of molecule types, and, in the case of multi-site molecules, the location of the sites relative to the the center-of-mass. More...

#include <ParticlePropertiesLibrary.h>

Inheritance diagram for ParticlePropertiesLibrary< floatType, intType >:

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Public Member Functions
	ParticlePropertiesLibrary (const double cutoff)
	Constructor.

	ParticlePropertiesLibrary (const ParticlePropertiesLibrary &particlePropertiesLibrary)=default
	Copy Constructor.

ParticlePropertiesLibrary &	operator= (const ParticlePropertiesLibrary &particlePropertiesLibrary)=default
	Copy assignment operator.

void	addSiteType (const intType siteId, const floatType mass)
	Registers a new single site type to the library with a given mass.

void	addLJParametersToSite (const intType siteId, const floatType epsilon, const floatType sigma)
	Adds the LJ properties of a single site type to the library.

void	addATMParametersToSite (const intType siteId, const floatType nu)
	Adds the ATM properties of a single site type to the library.

void	addMolType (const intType molId, const std::vector< intType > siteIds, const std::vector< std::array< floatType, 3 > > relPos, const std::array< floatType, 3 > momentOfInertia)
	Adds the properties of a molecule type to the library including: position and type of all sites, as well as the diagonalized moment of inertia.

void	calculateMixingCoefficients ()
	Calculates the actual mixing coefficients.

int	getNumberRegisteredSiteTypes () const
	Returns the number of registered site / single-site molecule types.

int	getNumberRegisteredMolTypes () const
	Returns the number of registered multi-site molecule types.

floatType	getEpsilon (intType i) const
	Getter for the site's epsilon.

floatType	getSigma (intType i) const
	Getter for the site's sigma.

floatType	getNu (intType i) const
	Getter for the site's nu.

floatType	getSiteMass (intType i) const
	Getter for the site's mass.

floatType	getMolMass (intType i) const
	Getter for a molecules' mass.

std::array< floatType, 3 >	getMomentOfInertia (intType i) const
	Getter for the multi-site molecule's diagonalized Moment of Inertia.

std::vector< std::array< floatType, 3 > >	getSitePositions (intType i) const
	Get relative site positions to a multi-site molecule's center-of-mass.

std::vector< intType >	getSiteTypes (intType i) const
	Get site types of a multi-site molecule.

intType	getNumSites (intType i) const
	Get number of sites of a multi-site molecule.

floatType	getMoleculesLargestSigma (intType i) const
	Get the largest sigma of any site of a multi-site molecule.

floatType	getMixing24Epsilon (intType i, intType j) const
	Returns the precomputed mixed epsilon * 24.

auto	getLJMixingData (intType i, intType j) const
	Get complete mixing data for one pair of LJ site types.

const double *	getLJMixingDataPtr (intType i, intType j)
	Get a pointer to Mixing Data for one pair of LJ site types.

floatType	getMixingSigmaSquared (intType i, intType j) const
	Returns precomputed mixed squared sigma for one pair of site types.

floatType	getMixingShift6 (intType i, intType j) const
	Returns precomputed mixed shift * 6 for one pair of site types.

floatType	getMixingNu (intType i, intType j, intType k) const
	Returns the precomputed mixed epsilon * 24.

auto	getATMMixingData (intType i, intType j, intType k) const
	Get complete mixing data for one triplet of ATM site types.

Static Public Member Functions
static double	calcShift6 (double epsilon24, double sigmaSquared, double cutoffSquared)
	Calculate the shift multiplied 6 of the lennard jones potential from given cutoff, epsilon, sigma.

Detailed Description

template<typename floatType = double, typename intType = unsigned long>
class ParticlePropertiesLibrary< floatType, intType >

This class stores the (physical) properties of molecule types, and, in the case of multi-site molecules, the location of the sites relative to the the center-of-mass.

It also provides mixed values for (force) calculations between known types.

ToDo: Add a function that computes the diagonalized Moment of Inertia and adjusts the rotation of the positions of the sites such that they correctly match the new axes.

Constructor & Destructor Documentation

◆ ParticlePropertiesLibrary() [1/2]

template<typename floatType = double, typename intType = unsigned long>

ParticlePropertiesLibrary< floatType, intType >::ParticlePropertiesLibrary ( const double cutoff )

inlineexplicit

Constructor.

Parameters

cutoff Cutoff for the Potential

◆ ParticlePropertiesLibrary() [2/2]

template<typename floatType = double, typename intType = unsigned long>

ParticlePropertiesLibrary< floatType, intType >::ParticlePropertiesLibrary ( const ParticlePropertiesLibrary< floatType, intType > & particlePropertiesLibrary )

default

Copy Constructor.

Parameters

particlePropertiesLibrary

Member Function Documentation

◆ addATMParametersToSite()

template<typename floatType , typename intType >

void ParticlePropertiesLibrary< floatType, intType >::addATMParametersToSite	(	const intType	siteId,
		const floatType	nu
	)

Adds the ATM properties of a single site type to the library.

Checks if a site with given siteId was already registered. Old values will be overwritten.

Parameters

siteId
nu

◆ addLJParametersToSite()

template<typename floatType , typename intType >

void ParticlePropertiesLibrary< floatType, intType >::addLJParametersToSite	(	const intType	siteId,
		const floatType	epsilon,
		const floatType	sigma
	)

Adds the LJ properties of a single site type to the library.

Checks if a site with given siteId was already registered. Old values will be overwritten.

Parameters

siteId
epsilon
sigma

◆ addMolType()

template<typename floatType , typename intType >

void ParticlePropertiesLibrary< floatType, intType >::addMolType	(	const intType	molId,
		const std::vector< intType >	siteIds,
		const std::vector< std::array< floatType, 3 > >	relPos,
		const std::array< floatType, 3 >	momentOfInertia
	)

Adds the properties of a molecule type to the library including: position and type of all sites, as well as the diagonalized moment of inertia.

If md-flexible has been compiled for single-site molecules, calls to this function result in an error. If the type id already exists the values will be overwritten.

Parameters

molId
siteIds	vector of IDs of sites
relPos	vector of relative positions
momentOfInertia	diagonalized moment of inertia as a array of 3 floats

◆ addSiteType()

template<typename floatType , typename intType >

void ParticlePropertiesLibrary< floatType, intType >::addSiteType	(	const intType	siteId,
		const floatType	mass
	)

Registers a new single site type to the library with a given mass.

Note: New sites must be registered with consecutive siteIds.; This only registers the site. Potential specific parameters must be added afterwards by calling e.g. addLJParametersToSite() for a Lennard-Jones Site.

Parameters

siteId
mass

◆ calcShift6()

template<typename floatType , typename intType >

double ParticlePropertiesLibrary< floatType, intType >::calcShift6	(	double	epsilon24,
		double	sigmaSquared,
		double	cutoffSquared
	)

static

Calculate the shift multiplied 6 of the lennard jones potential from given cutoff, epsilon, sigma.

The shift * 6 is then added to the total potential energy for every pairwise interaction within the cutoff.

Parameters

epsilon24	epsilon * 24
sigmaSquared	sigma squared
cutoffSquared	squared cutoff of the lennard-jones potential

Returns: shift multiplied by 6

◆ getATMMixingData()

template<typename floatType = double, typename intType = unsigned long>

auto ParticlePropertiesLibrary< floatType, intType >::getATMMixingData	(	intType	i,
		intType	j,
		intType	k
	)		const

inline

Get complete mixing data for one triplet of ATM site types.

Parameters

i	Id of site one.
j	Id of site two.
k	Id of site three.

Returns

◆ getEpsilon()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getEpsilon ( intType i ) const

Getter for the site's epsilon.

Parameters

i	Type Id of the site or single-site molecule.

Returns: epsilon_i

◆ getLJMixingData()

template<typename floatType = double, typename intType = unsigned long>

auto ParticlePropertiesLibrary< floatType, intType >::getLJMixingData	(	intType	i,
		intType	j
	)		const

inline

Get complete mixing data for one pair of LJ site types.

Parameters

i	Id of site one.
j	Id of site two.

Returns

◆ getLJMixingDataPtr()

template<typename floatType = double, typename intType = unsigned long>

const double * ParticlePropertiesLibrary< floatType, intType >::getLJMixingDataPtr	(	intType	i,
		intType	j
	)

inline

Get a pointer to Mixing Data for one pair of LJ site types.

Parameters

i	Id of site one.
j	Id of site two.

Returns

◆ getMixing24Epsilon()

template<typename floatType = double, typename intType = unsigned long>

floatType ParticlePropertiesLibrary< floatType, intType >::getMixing24Epsilon	(	intType	i,
		intType	j
	)		const

inline

Returns the precomputed mixed epsilon * 24.

Parameters

i	Id of site one.
j	Id of site two.

Returns: 24*epsilon_ij

◆ getMixingNu()

template<typename floatType = double, typename intType = unsigned long>

floatType ParticlePropertiesLibrary< floatType, intType >::getMixingNu	(	intType	i,
		intType	j,
		intType	k
	)		const

inline

Returns the precomputed mixed epsilon * 24.

Parameters

i	Id of site one.
j	Id of site two.
k	Id of site three.

Returns: nu_ijk

◆ getMixingShift6()

template<typename floatType = double, typename intType = unsigned long>

floatType ParticlePropertiesLibrary< floatType, intType >::getMixingShift6	(	intType	i,
		intType	j
	)		const

inline

Returns precomputed mixed shift * 6 for one pair of site types.

Parameters

i	siteId of site one.
j	siteId of site two.

Returns: shift * 6

◆ getMixingSigmaSquared()

template<typename floatType = double, typename intType = unsigned long>

floatType ParticlePropertiesLibrary< floatType, intType >::getMixingSigmaSquared	(	intType	i,
		intType	j
	)		const

inline

Returns precomputed mixed squared sigma for one pair of site types.

Parameters

i	Id of site one.
j	Id of site two.

Returns: sigma_ij²

◆ getMoleculesLargestSigma()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getMoleculesLargestSigma ( intType i ) const

Get the largest sigma of any site of a multi-site molecule.

Throws an error if support for multi-site molecules has not been compiled.

Parameters

i	Type Id of a multi-site molecule.

Returns: largest sigma of that molecule's sites

◆ getMolMass()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getMolMass ( intType i ) const

Getter for a molecules' mass.

For single site molecules, this automatically gets the mass of the site with the given ID. For multi site molecules, this gets the total mass of the molecule.

Parameters

i	Type Id of a multi-site molecule.

Returns: mass_i

◆ getMomentOfInertia()

template<typename floatType , typename intType >

std::array< floatType, 3 > ParticlePropertiesLibrary< floatType, intType >::getMomentOfInertia ( intType i ) const

Getter for the multi-site molecule's diagonalized Moment of Inertia.

Throws an error if support for multi-site molecules has not been compiled.

Parameters

i	Type Id of a multi-site molecule.

Returns: diagonalized moment of inertia, with each element of the returned array corresponding to a diagonal element of the MoI matrix/tensor.

◆ getNu()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getNu ( intType i ) const

Getter for the site's nu.

Parameters

i	Type Id of the site or single-site molecule.

Returns: nu_i

◆ getNumberRegisteredMolTypes()

template<typename floatType = double, typename intType = unsigned long>

int ParticlePropertiesLibrary< floatType, intType >::getNumberRegisteredMolTypes ( ) const

inline

Returns the number of registered multi-site molecule types.

Throws an error if support for multi-site molecules has not been compiled.

Returns: Number of registered multi-site molecule types.

◆ getNumberRegisteredSiteTypes()

template<typename floatType = double, typename intType = unsigned long>

int ParticlePropertiesLibrary< floatType, intType >::getNumberRegisteredSiteTypes ( ) const

inline

Returns the number of registered site / single-site molecule types.

Returns: Number of registered site types.

◆ getNumSites()

template<typename floatType , typename intType >

intType ParticlePropertiesLibrary< floatType, intType >::getNumSites ( intType i ) const

Get number of sites of a multi-site molecule.

Throws an error if support for multi-site molecules has not been compiled.

Parameters

i	Type Id of a multi-site molecule.

Returns: number of sites in molecule's of type Id

◆ getSigma()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getSigma ( intType i ) const

Getter for the site's sigma.

Parameters

i	Type Id of the site or single-site molecule.

Returns: sigma_i

◆ getSiteMass()

template<typename floatType , typename intType >

floatType ParticlePropertiesLibrary< floatType, intType >::getSiteMass ( intType i ) const

Getter for the site's mass.

Parameters

i	Type Id of the site or single-site molecule.

Returns: mass_i

◆ getSitePositions()

template<typename floatType , typename intType >

std::vector< std::array< floatType, 3 > > ParticlePropertiesLibrary< floatType, intType >::getSitePositions ( intType i ) const

Get relative site positions to a multi-site molecule's center-of-mass.

These site positions must be appropriately translated and rotated to be used.

Throws an error if support for multi-site molecules has not been compiled.

Parameters

i	Type Id of a multi-site molecule.

Returns: untranslated, non-rotated site positions

◆ getSiteTypes()

template<typename floatType , typename intType >

std::vector< intType > ParticlePropertiesLibrary< floatType, intType >::getSiteTypes ( intType i ) const

Get site types of a multi-site molecule.

Throws an error if support for multi-site molecules has not been compiled.

Parameters

i	Type Id of a multi-site molecule.

Returns: site type Ids.

◆ operator=()

template<typename floatType = double, typename intType = unsigned long>

ParticlePropertiesLibrary & ParticlePropertiesLibrary< floatType, intType >::operator= ( const ParticlePropertiesLibrary< floatType, intType > & particlePropertiesLibrary )

default

Copy assignment operator.

Parameters

particlePropertiesLibrary

Returns

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

/github/workspace/applicationLibrary/molecularDynamics/molecularDynamicsLibrary/ParticlePropertiesLibrary.h

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ParticlePropertiesLibrary() [1/2]

◆ ParticlePropertiesLibrary() [2/2]

Member Function Documentation

◆ addATMParametersToSite()

◆ addLJParametersToSite()

◆ addMolType()

◆ addSiteType()

◆ calcShift6()

◆ getATMMixingData()

◆ getEpsilon()

◆ getLJMixingData()

◆ getLJMixingDataPtr()

◆ getMixing24Epsilon()

◆ getMixingNu()

◆ getMixingShift6()

◆ getMixingSigmaSquared()

◆ getMoleculesLargestSigma()

◆ getMolMass()

◆ getMomentOfInertia()

◆ getNu()

◆ getNumberRegisteredMolTypes()

◆ getNumberRegisteredSiteTypes()

◆ getNumSites()

◆ getSigma()

◆ getSiteMass()

◆ getSitePositions()

◆ getSiteTypes()

◆ operator=()