Algorithm
type: Class
comment: The algorithm used in a computational method

Angle
type: Class
subclass of: TopologicalEntities
comment: The angle between two atoms

Atom
type: Class
subclass of: StructuralEntity
subclass of: Class
  intersection of: Restriction
    on property: atomic number
    qualified cardinality: 1
    on data range: integer
  intersection of: Restriction
    on property: symbol
    qualified cardinality: 1
    on data range: string
disjoint with: MolecularAggregate
disjoint with: MolecularSystem
disjoint with: Particle
disjoint with: StructuralUnit
disjoint with: Structure
comment: An elementary constituent of matter, made of a nucleus and electrons

Barostat
type: Class
subclass of: ExternalCoupling
disjoint with: Thermostat
comment: A method for coupling the particles in a molecular dynamics simulation to an external barostat for controlling pressure

BondedPotential
type: Class
subclass of: MolecularMechanics
disjoint with: NonBondedPotential
comment: The bonded terms of an interaction potential in simulations

CartesianCoordinates
type: Class
subclass of: Coordinates
disjoint with: SphericalCoordinates
comment: The cartesian coordinates of an object in 3D space with respect to a reference system

ChemicalProperty
type: Class
subclass of: Property
comment: A chemical property of a material

ComputationalMethod
type: Class
comment: A specific computational method for simulating the properties or the behavior of a material or materials

Coordinates
type: Class
comment: The spatial coordinates of a structural entity

Crystal
type: Class
subclass of: Structure
comment: A material structure with periodicity in space in one, two or three dimensions

DFT
type: Class
subclass of: QuantumMechanics
comment: A computational method for evaluating interaction potentials based on density functional theory

ElectricalMethod
type: Class
subclass of: ExperimentalMethod
comment: An electrical experimental method or procedure

ElectroMagneticProperty
type: Class
subclass of: Property
comment: An electromagnetic property of a material

Experiment
type: Class
comment: An experimental operation/procedure or a set of experimental operations/procedures for determining or measuring the properties or the behavior of a material or materials

ExperimentalMethod
type: Class
comment: A specific experimental method for determining or measuring the properties or the behavior of a material or materials

ExternalCoupling
type: Class
comment: A method used to couple particles in a molecular dynamics simulation to an external reference systems

FourBody
type: Class
subclass of: PotentialComponents
comment: A 4-body interaction potential term

HarteeFock
type: Class
subclass of: QuantumMechanics
comment: A computational method for evaluating interaction potentials based on the Hartree-Fock theory

Integrator
type: Class
comment: The integrator of the equation of motions in molecular dynamics simulations

InteractionPotential
type: Class
comment: The interaction potential used in a specific computational method

LatticeParameters
type: Class
comment: The parameters of a lattice in a periodic structure

Material
type: Class
comment: A portion of physical matter

MechanicalProperty
type: Class
subclass of: Property
comment: A mechanical property of a material

MolecularAggregate
type: Class
subclass of: Structure
subclass of: Restriction
  on property: has subunit
  some values from: MolecularSystem
disjoint with: MolecularSystem
disjoint with: Particle
disjoint with: StructuralUnit
comment: A material composed of aggregates of molecules of the same kind or of different kind

MolecularDynamics
type: Class
subclass of: Algorithm
comment: A computational tool or algorithm for molecular dynamics simulation

MolecularMechanics
type: Class
subclass of: InteractionPotential
comment: A potential based on molecular mechanics

MolecularSystem
type: Class
subclass of: StructuralEntity
disjoint with: Particle
disjoint with: StructuralUnit
disjoint with: Structure
comment: A chemically well-defined system made up of atoms kept together by chemical bonds

NPT
type: Class
subclass of: SimulationEnsembles
comment: The constant-pressure constant-temperature (isothermal-isobaric) simulation ensemble in molecular dynamics

NVE
type: Class
subclass of: SimulationEnsembles
comment: The constant-energy (microcanonical) simulation ensemble in molecular dynamics

NVT
type: Class
subclass of: SimulationEnsembles
comment: The constant-temperature (canonical) simulation ensemble in molecular dynamics

NonBondedPotential
type: Class
subclass of: MolecularMechanics
comment: The non bonded terms of an interaction potential in simulations

OpticalMethod
type: Class
subclass of: ExperimentalMethod
comment: An optical experimental method or procedure

Optimizer
type: Class
subclass of: Algorithm
comment: A computational tool or algorithm for structural optimization

Orientation
type: Class
comment: The orientation of a system in 3D space with respect to a reference orientation

Particle
type: Class
subclass of: StructuralEntity
disjoint with: StructuralUnit
disjoint with: Structure
comment: A pseudo-particle used in simulations

PotentialComponents
type: Class
comment: The components of an interaction potentials

Property
type: Class
subclass of: Restriction
  on property: unit
  qualified cardinality: 1
  on data range: string
subclass of: Restriction
  on property: value
  qualified cardinality: 1
  on data range: float
comment: A chemico-physical property of a material or materials

QuantumMechanics
type: Class
subclass of: InteractionPotential
comment: A potential based on quantum mechanics

Quaternion
type: Class
subclass of: Orientation
disjoint with: RotationMatrix
comment: The quaternion coordinate vector of a system in 3D space with respect to a reference orientation

RotationMatrix
type: Class
subclass of: Orientation
comment: The matrix representing the rotation of a system in 3D space with respect to a reference orientation

Simulation
type: Class
comment: A computational operation/procedure or a set of computational operations/procedures for simulating the properties or the behavior of a material or materials

SimulationEnsembles
type: Class
comment: The thermodynamic ensemble in which a molecular dynamics simulation is performed

SphericalCoordinates
type: Class
subclass of: Coordinates
comment: The spherical coordinates of an object in 3D space with respect to a reference system

StructuralEntity
type: Class
comment: A structural unit in which a structure can be decomposed into

StructuralUnit
type: Class
subclass of: StructuralEntity
disjoint with: Structure
comment: A chemically well-defined structural unit, for example a functional group, constituting

Structure
type: Class
comment: The structure of a material or materials

StructureManipulation
type: Class
subclass of: Algorithm
comment: An algorithm or tool for the manipulation of a structure

TOF
type: Class
subclass of: ElectricalMethod
comment: A time-of-flight experimental method

Thermostat
type: Class
subclass of: ExternalCoupling
comment: A method for coupling the particles in a molecular dynamics simulation to an external thermostat for controlling temperature

ThreeBody
type: Class
subclass of: PotentialComponents
comment: A 3-body interaction potential term

TwoBody
type: Class
subclass of: PotentialComponents
comment: A 2-body interaction potential term

continuant
type: Class
subclass of: Experiment
id: BFO:0000002

process
type: Class
subclass of: Experiment
id: BFO:0000015

continuant fiat boundary
type: Class
subclass of: Experiment
id: BFO:0000140

hydrogen1
type: NamedIndividual
type: Atom
has coordinates: hydrogen1 cartesian coordinates
has coordinates: hydrogen1 spherical coordinates
is part of: water molecule1
atomic number: 1
symbol: H

hydrogen1 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 1.0
y: 1.0
z: 1.0

hydrogen1 spherical coordinates
type: NamedIndividual
type: SphericalCoordinates
azimuthal angle: 0.1
polar angle: 0.1
radial distance: 1.0

hydrogen2
type: NamedIndividual
type: Atom
has coordinates: hydrogen2 cartesian coordinates
has coordinates: hydrogen2 spherical coordinates
is part of: water molecule1
atomic number: 1
symbol: H

hydrogen2 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 2.0
y: 2.0
z: 2.0

hydrogen2 spherical coordinates
type: NamedIndividual
type: SphericalCoordinates
azimuthal angle: 0.2
polar angle: 0.2
radial distance: 1.0

hydrogen3
type: NamedIndividual
type: Atom
has coordinates: hydrogen3 cartesian coordinates
is part of: water molecule2
atomic number: 1
symbol: H

hydrogen3 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 11.0
y: 11.0
z: 11.0

hydrogen4
type: NamedIndividual
type: Atom
has coordinates: hydrogen4 cartesian coordinates
is part of: water molecule2
atomic number: 1
symbol: H

hydrogen4 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 12.0
y: 12.0
z: 12.0

oxygen1
type: NamedIndividual
type: Atom
has coordinates: oxygen1 cartesian coordinates
has coordinates: oxygen1 spherical coordinates
is part of: water molecule1
atomic number: 8
symbol: O

oxygen1 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 0.0
y: 0.0
z: 0.0

oxygen1 spherical coordinates
type: NamedIndividual
type: SphericalCoordinates
azimuthal angle: 0.0
polar angle: 0.0
radial distance: 1.0

oxygen2
type: NamedIndividual
type: Atom
has coordinates: oxygen2 cartesian coordinates
is part of: water molecule2
atomic number: 8
symbol: O

oxygen2 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 10.0
y: 10.0
z: 10.0

water1
type: NamedIndividual
type: Material
purpose: Solvent

water aggregate1
type: NamedIndividual
type: MolecularAggregate
has subunit: water molecule1
has subunit: water molecule2
number of molecules: 2

water molecule1 cartesian coordinates
type: NamedIndividual
type: CartesianCoordinates
x: 0.5
y: 0.5
z: 0.5