Class Atom

java.lang.Object

org.episteme.natural.physics.classical.mechanics.Particle

org.episteme.natural.chemistry.Atom

All Implemented Interfaces:

Serializable, SpatialOctree.SpatialObject, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class Atom
extends Particle
implements ComprehensiveIdentification

An atom in a molecular structure. Extends Generic Linear Algebra Particle for physical simulation.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected final Map<String,Object>	traits

Constructor Summary

Constructors

Constructor	Description
Atom(Element element, Vector<Real> position)
Atom(Isotope isotope, Vector<Real> position)

Method Summary

Modifier and Type	Method	Description
void	addForce(Vector<Real> f)
void	clearForce()
Quantity<Length>	distanceTo(Atom other)	Distance to another atom.
Element	getElement()
Vector<Real>	getForce()
Quantity<ElectricCharge>	getFormalCharge()
Identification	getId()	Returns the unique identifier of this entity.
Isotope	getIsotope()
Map<String,Object>	getTraits()	Returns the traits map for this entity.
double	getX()	Returns the x-coordinate of this atom.
double	getY()	Returns the y-coordinate of this atom.
double	getZ()	Returns the z-coordinate of this atom.
void	setForce(Vector<Real> force)
void	setFormalCharge(Quantity<ElectricCharge> charge)
void	setIsotope(Isotope isotope)
String	toString()

Methods inherited from class Particle

distanceTo, getAcceleration, getMass, getMassValue, getPosition, getVelocity, kineticEnergy, setAcceleration, setAcceleration, setAcceleration, setPosition, setPosition, setVelocity, setVelocity, setVelocity, updatePosition, updateVelocity

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getName, getTrait, setName, setTrait

Field Details

traits

protected final Map<String,Object> traits

Constructor Details

Atom

public Atom(Element element,
 Vector<Real> position)

Atom

public Atom(Isotope isotope,
 Vector<Real> position)

Method Details

getElement

public Element getElement()

getForce

public Vector<Real> getForce()

setForce

public void setForce(Vector<Real> force)

addForce

public void addForce(Vector<Real> f)

clearForce

public void clearForce()

getFormalCharge

public Quantity<ElectricCharge> getFormalCharge()

setFormalCharge

public void setFormalCharge(Quantity<ElectricCharge> charge)

setIsotope

public void setIsotope(Isotope isotope)

getIsotope

public Isotope getIsotope()

getId

public Identification getId()

Description copied from interface: Identified

Returns the unique identifier of this entity.

Specified by:

getId in interface Identified<Identification>

Returns:

the identifier

getX

public double getX()

Returns the x-coordinate of this atom.

Specified by:

getX in interface SpatialOctree.SpatialObject

Overrides:

getX in class Particle

Returns:

the x-coordinate

getY

public double getY()

Returns the y-coordinate of this atom.

Specified by:

getY in interface SpatialOctree.SpatialObject

Overrides:

getY in class Particle

Returns:

the y-coordinate

getZ

public double getZ()

Returns the z-coordinate of this atom.

Specified by:

getZ in interface SpatialOctree.SpatialObject

Overrides:

getZ in class Particle

Returns:

the z-coordinate

getTraits

public Map<String,Object> getTraits()

Description copied from interface: ComprehensiveIdentification

Returns the traits map for this entity.

Specified by:

getTraits in interface Commented

Specified by:

getTraits in interface ComprehensiveIdentification

Returns:

the traits map

distanceTo

public Quantity<Length> distanceTo(Atom other)

Distance to another atom.

toString

public String toString()

Overrides:

toString in class Particle