Atom Struct Reference

Represents an atom in the simulation system. More...

Public Member Functions
	Atom () noexcept=default
	Default constructor for the Atom struct.
	Atom (double3 position, double charge, double scalingVDW, double scalingCoulomb, std::uint32_t moleculeId, std::uint16_t type, std::uint8_t componentId, std::uint8_t groupId, std::uint8_t isFractional)
	Constructs an Atom with specified parameters.
	Atom (double3 position, double charge, double lambda, std::uint32_t moleculeId, std::uint16_t type, std::uint8_t componentId, std::uint8_t groupId, std::uint8_t isFractional)
	Constructs an Atom with lambda-dependent scaling.
void	setScaling (double lambda)
	Sets the scaling factors based on lambda.
void	setScalingFullyOn ()
	Fully activates scaling factors.
void	setScalingFullyOff ()
	Fully deactivates scaling factors.
void	setScalingToInteger ()
	Sets scaling factors to integer values.
std::string	repr () const
	Returns a string representation of the Atom.

Public Attributes
double3	position
	The position of the atom in 3D space.
double3	velocity {}
	The velocity of the atom.
double3	gradient {}
	The gradient acting on the atom.
double	charge
	The electric charge of the atom.
double	scalingVDW {1.0}
	Scaling factor for van der Waals interactions.
double	scalingCoulomb {1.0}
	Scaling factor for Coulomb interactions.
std::uint32_t	moleculeId {0}
	Identifier for the molecule this atom belongs to.
std::uint16_t	type {0}
	Type identifier of the atom.
std::uint8_t	componentId {0}
	Component identifier within the system.
std::uint8_t	groupId: 4
	Group identifier, defaults to false.
std::uint8_t	isFractional: 4
	Fractional or not, defaults to false.

Friends
Archive< std::ofstream > &	operator<< (Archive< std::ofstream > &archive, const Atom &atom)
Archive< std::ifstream > &	operator>> (Archive< std::ifstream > &archive, Atom &atom)
void	to_json (nlohmann::json &, const Atom &)
void	from_json (const nlohmann::json &, Atom &)

Detailed Description

Represents an atom in the simulation system.

The Atom struct encapsulates the properties and behaviors of an individual atom within the simulation. It includes positional data, velocity, gradient, charge, scaling factors for van der Waals and Coulomb interactions, and identifiers for molecule, type, component, and group associations. The struct provides constructors for initializing atoms and methods to adjust scaling parameters dynamically. Atom class type should have exactly a size of 128 bytes (4 times double4).

Constructor & Destructor Documentation

Atom() [1/3]

Atom::Atom ( )

defaultnoexcept

Default constructor for the Atom struct.

Initializes an Atom object with default values.

Atom() [2/3]

Atom::Atom ( double3  position, double  charge, double  scalingVDW, double  scalingCoulomb, std::uint32_t  moleculeId, std::uint16_t  type, std::uint8_t  componentId, std::uint8_t  groupId, std::uint8_t  isFractional  )

inline

Constructs an Atom with specified parameters.

Initializes an Atom with the provided position, charge, scaling factors, molecule ID, type, component ID, and group ID.

Parameters

position	The initial position of the atom.
charge	The electric charge of the atom.
scalingVDW	Scaling factor for van der Waals interactions.
scalingCoulomb	Scaling factor for Coulomb interactions.
moleculeId	Identifier for the molecule.
type	Type identifier of the atom.
componentId	Component identifier within the system.
groupId	Group identifier, defaults to false.

Atom() [3/3]

Atom::Atom ( double3  position, double  charge, double  lambda, std::uint32_t  moleculeId, std::uint16_t  type, std::uint8_t  componentId, std::uint8_t  groupId, std::uint8_t  isFractional  )

inline

Constructs an Atom with lambda-dependent scaling.

Initializes an Atom with position, charge, and scaling factors determined by the provided lambda value. Also sets molecule ID, type, component ID, and group ID.

Parameters

position	The initial position of the atom.
charge	The electric charge of the atom.
lambda	The scaling parameter for interactions.
moleculeId	Identifier for the molecule.
type	Type identifier of the atom.
componentId	Component identifier within the system.
groupId	Group identifier, defaults to false.

Member Function Documentation

repr()

std::string Atom::repr ( ) const

inline

Returns a string representation of the Atom.

Generates a string that includes the position coordinates and identifiers associated with the atom.

Returns

A string representing the Atom.

setScaling()

void Atom::setScaling ( double  lambda )

inline

Sets the scaling factors based on lambda.

Adjusts the scaling factors for van der Waals and Coulomb interactions linearly based on the provided lambda value. Scaling for van der Waals is active from 0 to 0.5, and Coulomb scaling is active from 0.5 to 1.0.

Parameters

lambda

The scaling parameter.

setScalingFullyOff()

void Atom::setScalingFullyOff ( )

inline

Fully deactivates scaling factors.

Sets both van der Waals and Coulomb scaling factors to 0.0, fully deactivating the interactions.

setScalingFullyOn()

void Atom::setScalingFullyOn ( )

inline

Fully activates scaling factors.

Sets both van der Waals and Coulomb scaling factors to 1.0, fully activating the interactions.

setScalingToInteger()

void Atom::setScalingToInteger ( )

inline

Sets scaling factors to integer values.

Sets both van der Waals and Coulomb scaling factors to 1.0 and resets the group ID to 0.

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

• src/raspakit/atom.ixx