Atomistic
type: Ontology
version IRI: atomistic
imports: dependencies
abstract: An EMMO-based domain ontology for atomistic and electronic modelling.Atomistic is released under the Creative Commons Attribution 4.0 International license (CC BY 4.0).
contributor: SINTEF
creator: Francesca L. Bleken
creator: Jesper Friis
publisher: EMMC ASBL
comment: Contacts: Jesper Friis SINTEF email: jesper.friis@sintef.no Francesca L. Bleken SINTEF email: francesca.l.bleken@sintef.no
comment: The EMMO requires FaCT++ reasoner plugin in order to visualize allinferences and class hierarchy (ctrl+R hotkey in Protege).
comment: This ontology is generated with data from the ASE Python package.
version info: 0.0.1
EMMO 5525a055 dda5 4556 8b91 f0d22fa676cc: https://creativecommons.org/licenses/by/4.0/legalcode

description
type: AnnotationProperty

note
type: AnnotationProperty
description: a general annotation that provides extra context, clarifications, or useful background information
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: a general annotation that provides extra context, clarifications, or useful background information

scopeNote
type: AnnotationProperty
description: a note that helps to clarify the meaning and/or the use of a concept
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: a note that helps to clarify the meaning and/or the use of a concept

warning
type: AnnotationProperty
description: q critical alert about potential dangers, system failures, or serious misuse of a concept.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: q critical alert about potential dangers, system failures, or serious misuse of a concept.

tip
type: AnnotationProperty
description: a best practice or helpful suggestion related to the concept.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: a best practice or helpful suggestion related to the concept.

caution
type: AnnotationProperty
description: a moderate-level advisory about possible pitfalls, errors, or inefficiencies
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: a moderate-level advisory about possible pitfalls, errors, or inefficiencies

chemicalFormula
type: AnnotationProperty
definition: The chemical formula of the species.

hasEigenvalue
type: ObjectProperty
description: Relates a mathematical (or physical) operator to its eigenvalue.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Relates a mathematical (or physical) operator to its eigenvalue.

hasSpecies
type: ObjectProperty
description: Relates a material to the species it is made of.
comment: Intended for documeting what kind of atoms a material is made of.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Relates a material to the species it is made of.
EMMO c7b62dd7 063a 4c2a 8504 42f7264ba83f: Intended for documeting what kind of atoms a material is made of.

hasNumberOfAtoms
type: DatatypeProperty
range: int
definition: Number of atoms in the species.

ForceFieldSimulationSoftware
type: Class
description: Forcefield-based simulation software.
example: LAMMPS
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Forcefield-based simulation software.

ElectronicState
type: Class
description: A specific electronic state of a quantum system. Often defined by its wavefunction.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A specific electronic state of a quantum system. Often defined by its wavefunction.

Functional
type: Class
description: A functional that approximates the exchange-correlation of the electron density of the chosen system.
alternative label: DFTFunctional
example: Hybrid functionals
example: LDA, GGA, GW
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A functional that approximates the exchange-correlation of the electron density of the chosen system.

SaddlePoint
type: Class
description: A critical point on a potential energy surface representing a transition state in a chemical reaction.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A critical point on a potential energy surface representing a transition state in a chemical reaction.

AtomisticComputationMathematical
type: Class
description: Mathematicals used by an atomistic computational software, often defined as a setting in the input file.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Mathematicals used by an atomistic computational software, often defined as a setting in the input file.

NWChemGeometryOptimization
type: Class
description: Geometry optimisation performed with NWChem
warning: This is not necessarily an optimisation to the ground state, as can also be a saddle point.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Geometry optimisation performed with NWChem

AtomisticSimulationSoftware
type: Class
description: The superclass of physical-based electronic and forcefield simulation softwares.
example: NWChem - a physical based software that implements both DFT and higher order QM methods.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The superclass of physical-based electronic and forcefield simulation softwares.

DFTSimulationSoftware
type: Class
description: DFT-based simulation software.
example: VASP, Quantum ESPRESSO, NWChem
note: The software is not restricted to only DFT, i.e. also MP2 simulations are avilable in NWChem
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: DFT-based simulation software.

SolvationModelSolvent
type: Class
description: A solvent used in the solvation model, typically identified with a chemical name.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A solvent used in the solvation model, typically identified with a chemical name.

SolvationModel
type: Class
description: A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly.

DFTComputation
type: Class
description: A computation that solves the Kohn-Sham equation (using DFT).
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A computation that solves the Kohn-Sham equation (using DFT).

ElectronicComputation
type: Class
description: Physics based calculation that solves the electronic states of a system. Can be either a simulation that treats the electronc explicitly or the electron density.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Physics based calculation that solves the electronic states of a system. Can be either a simulation that treats the electronc explicitly or the electron density.

NWChemComputation
type: Class
description: Electronic computation performed with the NWChem software.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Electronic computation performed with the NWChem software.

NWChemDFTModuleCOSMO
type: Class
description: NWChem computation that includes cosmo as solvation model.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: NWChem computation that includes cosmo as solvation model.

GroundState
type: Class
description: The lowest-energy quantum state of a physical system.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The lowest-energy quantum state of a physical system.
caution: Be aware that a locally found minimum is not necessarily the ground state.

BasisSet
type: Class
description: A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations.

NWChemFiniteDifferenceHessian
type: Class
description: A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis.
alternative label: NWChemFinite-differenceHessian
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis.

TimeIndependentSchrodingerEquation
type: Class
description: If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form.
alternative label: TimeIndependentSchrödingerEquation
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form.

KohnShamEquation
type: Class
subclass of: Restriction
description: The Schrödinger equation for a fictious "Kohn-Sham" system of non-interacting electrons that generates the same charge density as the real interacting system.
comment: This is the equation that is solved with density functional theory.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The Schrödinger equation for a fictious "Kohn-Sham" system of non-interacting electrons that generates the same charge density as the real interacting system.

SchrodingerEquation
type: Class
subclass of: Restriction
description: A linear partial differential equation describing the wave function of a quantum-mechanical system. The exact form of the Schrödinger equation depends on the physical situation. The most general form is the time-dependent Schrödinger equation.
alternative label: SchrödingerEquation
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A linear partial differential equation describing the wave function of a quantum-mechanical system. The exact form of the Schrödinger equation depends on the physical situation. The most general form is the time-dependent Schrödinger equation.
EMMO c84c6752 6d64 48cc 9500 e54a3c34898d: https://en.wikipedia.org/wiki/Schr%C3%B6dinger_equation

WaveFunction
type: Class
description: A mathematical description of the quantum state of an isolated quantum system. A wave function is a function of the degrees of freedom corresponding to some maximal set of commuting observables. Once such a representation is chosen, the wave function can be derived from the quantum state.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A mathematical description of the quantum state of an isolated quantum system. A wave function is a function of the degrees of freedom corresponding to some maximal set of commuting observables. Once such a representation is chosen, the wave function can be derived from the quantum state.
EMMO c84c6752 6d64 48cc 9500 e54a3c34898d: https://en.wikipedia.org/wiki/Wave_function

TimeDependentSchrodingerEquation
type: Class
description: The full time-dependent Schrödinger equation.
alternative label: TimeDependentSchrödingerEquation
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The full time-dependent Schrödinger equation.

PhysicalOperator
type: Class
description: A mathematical operator with a physical interpretation.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A mathematical operator with a physical interpretation.

Hamiltonian
type: Class
subclass of: Restriction
description: An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system.

DensityFunctionalTheory
type: Class
description: An efficient computional method for solving the many-electron (time-independent) Schrödinger equation.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: An efficient computional method for solving the many-electron (time-independent) Schrödinger equation.

acetonitrile
type: NamedIndividual
description: The dielectric constant for acetonitrile.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The dielectric constant for acetonitrile.

aug-cc-pVDZ
type: NamedIndividual
description: The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals.

b3lyp
type: NamedIndividual
description: The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional.

cosmo
type: NamedIndividual
description: The cosmo solvatisation model.
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The cosmo solvatisation model.

pbe
type: NamedIndividual
description: The Predew-Burke-Ernzerhof exchange-correlation functional
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The Predew-Burke-Ernzerhof exchange-correlation functional