@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix skos: . @prefix emmo: . @prefix rdfs: . @prefix term: . @base . rdf:type owl:Ontology ; owl:versionIRI ; owl:imports ; term: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)."@en ; term:contributor "SINTEF"@en ; term:creator "Francesca L. Bleken"@en , "Jesper Friis"@en ; term:publisher "EMMC ASBL"@en ; term:title "Atomistic"@en ; rdfs:comment """Contacts: Jesper Friis SINTEF email: jesper.friis@sintef.no Francesca L. Bleken SINTEF email: francesca.l.bleken@sintef.no"""@en , "The EMMO requires FaCT++ reasoner plugin in order to visualize allinferences and class hierarchy (ctrl+R hotkey in Protege)."@en , "This ontology is generated with data from the ASE Python package."@en ; owl:versionInfo "0.0.1"@en ; "https://creativecommons.org/licenses/by/4.0/legalcode"@en . ################################################################# # Annotation properties ################################################################# ### https://w3id.org/emmo#EMMO_21ae69b4_235e_479d_8dd8_4f756f694c1b rdf:type owl:AnnotationProperty . ### https://w3id.org/emmo#EMMO_5525a055_dda5_4556_8b91_f0d22fa676cc rdf:type owl:AnnotationProperty . ### https://w3id.org/emmo#EMMO_de178b12_5d35_4bca_8efa_a4193162571d rdf:type owl:AnnotationProperty . ################################################################# # Object Properties ################################################################# ### https://w3id.org/emmo/domain/atomistic#EMMO_c2da4973_b83d_4581_a4b4_87ab401b8f5b :EMMO_c2da4973_b83d_4581_a4b4_87ab401b8f5b rdf:type owl:ObjectProperty ; rdfs:subPropertyOf ; rdfs:domain ; rdfs:range ; skos:prefLabel "hasSpecies"@en ; "Relates a material to the species it is made of."@en ; "Intended for documeting what kind of atoms a material is made of."@en . ### https://w3id.org/emmo/domain/atomistic#42812fef-145a-56e9-9c18-72bd32214455 rdf:type owl:ObjectProperty ; rdfs:subPropertyOf ; rdfs:domain ; skos:prefLabel "hasEigenvalue"@en ; "Relates a mathematical (or physical) operator to its eigenvalue."@en . ################################################################# # Classes ################################################################# ### https://w3id.org/emmo/domain/atomistic#EMMO_070efd9c_b971_44ee_bd45_8c548a80a65d :EMMO_070efd9c_b971_44ee_bd45_8c548a80a65d rdf:type owl:Class ; rdfs:subClassOf :EMMO_3cd827b2_e9c6_4d08_a215_d22fd2a46298 ; skos:example "LAMMPS"@en ; skos:prefLabel "ForceFieldSimulationSoftware"@en ; "Forcefield-based simulation software."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_0f0feb84-14ef-4def-babb-718c9244f098 :EMMO_0f0feb84-14ef-4def-babb-718c9244f098 rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "ElectronicState"@en ; "A specific electronic state of a quantum system. Often defined by its wavefunction."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_1338c034-b1cb-478e-a60b-816b96280ac6 :EMMO_1338c034-b1cb-478e-a60b-816b96280ac6 rdf:type owl:Class ; rdfs:subClassOf :EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 ; skos:prefLabel "Functional"@en ; skos:altLabel "DFTFunctional"@en ; skos:example "LDA, GGA, GW"@en ; "A functional that approximates the exchange-correlation of the electron density of the chosen system."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_197db0fe-da46-4969-9410-4d5089e941ec :EMMO_197db0fe-da46-4969-9410-4d5089e941ec rdf:type owl:Class ; rdfs:subClassOf :EMMO_0f0feb84-14ef-4def-babb-718c9244f098 ; skos:prefLabel "SaddlePoint"@en ; "A critical point on a potential energy surface representing a transition state in a chemical reaction."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 :EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "AtomisticComputationMathematical"@en ; "Mathematicals used by an atomistic computational software, often defined as a setting in the input file."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_2be6633a-e701-41a7-a42b-0e89f262d82c :EMMO_2be6633a-e701-41a7-a42b-0e89f262d82c rdf:type owl:Class ; rdfs:subClassOf :EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f ; skos:prefLabel "NWChemGeometryOptimization"@en ; "Geometry optimisation performed with NWChem"@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_3cd827b2_e9c6_4d08_a215_d22fd2a46298 :EMMO_3cd827b2_e9c6_4d08_a215_d22fd2a46298 rdf:type owl:Class ; rdfs:subClassOf ; skos:example "NWChem - a physical based software that implements both DFT and higher order QM methods."@en ; skos:prefLabel "AtomisticSimulationSoftware"@en ; "The superclass of physical-based electronic and forcefield simulation softwares."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_429430f4_00e9_4157_a636_6cf798139e40 :EMMO_429430f4_00e9_4157_a636_6cf798139e40 rdf:type owl:Class ; rdfs:subClassOf :EMMO_3cd827b2_e9c6_4d08_a215_d22fd2a46298 ; skos:example "VASP, Quantum ESPRESSO, NWChem "@en ; skos:prefLabel "DFTSimulationSoftware"@en ; "DFT-based simulation software."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_42f4778d-5d87-4d1f-86cb-46cd02693733 :EMMO_42f4778d-5d87-4d1f-86cb-46cd02693733 rdf:type owl:Class ; rdfs:subClassOf :EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 ; skos:prefLabel "SolvationModelSolvent"@en ; "A solvent used in the solvation model, typically identified with a chemical name."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_47d1df6d-c997-4dc4-a0ae-3bcee7f92f02 :EMMO_47d1df6d-c997-4dc4-a0ae-3bcee7f92f02 rdf:type owl:Class ; rdfs:subClassOf :EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 ; skos:prefLabel "SolvationModel"@en ; "A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_52a6103f_86a4_4710_9028_a49b4cef858e :EMMO_52a6103f_86a4_4710_9028_a49b4cef858e rdf:type owl:Class ; rdfs:subClassOf :EMMO_5ddbdd13-b5ba-4101-8b13-4ab06b5173eb ; skos:prefLabel "DFTComputation"@en ; "A computation that solves the Kohn-Sham equation (using DFT)."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_5ddbdd13-b5ba-4101-8b13-4ab06b5173eb :EMMO_5ddbdd13-b5ba-4101-8b13-4ab06b5173eb rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "ElectronicComputation"@en ; "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."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f :EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f rdf:type owl:Class ; rdfs:subClassOf :EMMO_5ddbdd13-b5ba-4101-8b13-4ab06b5173eb ; skos:prefLabel "NWChemComputation"@en ; "Electronic computation performed with the NWChem software." . ### https://w3id.org/emmo/domain/atomistic#EMMO_807b8909-f44c-43de-b7cc-45d1abd515eb :EMMO_807b8909-f44c-43de-b7cc-45d1abd515eb rdf:type owl:Class ; rdfs:subClassOf :EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f ; skos:prefLabel "NWChemDFTModuleCOSMO"@en ; "NWChem comutation that includes cosmo as solvation model."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_a8d08da5-cc89-4a50-83c1-e7f11e718bb5 :EMMO_a8d08da5-cc89-4a50-83c1-e7f11e718bb5 rdf:type owl:Class ; rdfs:subClassOf :EMMO_0f0feb84-14ef-4def-babb-718c9244f098 ; skos:prefLabel "GroundState"@en ; "he lowest-energy quantum state of a physical system."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_abdf0104-0349-4c60-b4b8-91161660b2f4 :EMMO_abdf0104-0349-4c60-b4b8-91161660b2f4 rdf:type owl:Class ; rdfs:subClassOf :EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 ; skos:prefLabel "BasisSet"@en ; "A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations."@en . ### https://w3id.org/emmo/domain/atomistic#EMMO_f2dca06b-5987-4ff7-ac9e-9772b59b5c42 :EMMO_f2dca06b-5987-4ff7-ac9e-9772b59b5c42 rdf:type owl:Class ; rdfs:subClassOf :EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f ; skos:altLabel "NWChemFinite-differenceHessian"@en ; skos:prefLabel "NWChemFiniteDifferenceHessian"@en ; "A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis."@en . ### https://w3id.org/emmo/domain/atomistic#acaafcb6-b65f-5996-93ed-2f486f5f2b30 :acaafcb6-b65f-5996-93ed-2f486f5f2b30 rdf:type owl:Class ; rdfs:subClassOf :c4dd4450-cc80-5de4-a8d6-db0651115a2c ; skos:prefLabel "TimeIndependentSchrodingerEquation"@en ; "TimeIndependentSchrödingerEquation"@en ; """If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form."""@en . ### https://w3id.org/emmo/domain/atomistic#b65fe3b6-8477-5508-a066-2f7edcf25126 :b65fe3b6-8477-5508-a066-2f7edcf25126 rdf:type owl:Class ; rdfs:subClassOf :acaafcb6-b65f-5996-93ed-2f486f5f2b30 , [ rdf:type owl:Restriction ; owl:onProperty ; owl:someValuesFrom ] ; rdfs:comment "This is the equation that is solved with density functional theory." ; skos:prefLabel "KohnShamEquation"@en ; "The Schrödinger equation for a fictious \"Kohn-Sham\" system of non-interacting electrons that generates the same charge density as the real interacting system."@en . ### https://w3id.org/emmo/domain/atomistic#c4dd4450-cc80-5de4-a8d6-db0651115a2c :c4dd4450-cc80-5de4-a8d6-db0651115a2c rdf:type owl:Class ; rdfs:subClassOf , [ rdf:type owl:Restriction ; owl:onProperty ; owl:someValuesFrom ] , [ rdf:type owl:Restriction ; owl:onProperty ; owl:someValuesFrom :df750ce7-fda1-5e9b-ba32-db96ec170577 ] , [ rdf:type owl:Restriction ; owl:onProperty ; owl:someValuesFrom ] ; skos:prefLabel "SchrodingerEquation"@en ; "SchrödingerEquation"@en ; """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."""@en ; "https://en.wikipedia.org/wiki/Schr%C3%B6dinger_equation" . ### https://w3id.org/emmo/domain/atomistic#df750ce7-fda1-5e9b-ba32-db96ec170577 :df750ce7-fda1-5e9b-ba32-db96ec170577 rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "WaveFunction"@en ; """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."""@en ; "https://en.wikipedia.org/wiki/Wave_function" ; "T0 L0 M0 I0 Θ0 N0 J0" . ### https://w3id.org/emmo/domain/atomistic#fac61002-4a3d-5810-a430-ad5dad69c9a0 :fac61002-4a3d-5810-a430-ad5dad69c9a0 rdf:type owl:Class ; rdfs:subClassOf :c4dd4450-cc80-5de4-a8d6-db0651115a2c ; skos:prefLabel "TimeDependentSchrodingerEquation"@en ; "TimeDependentSchrödingerEquation"@en ; "The full time-dependent Schrödinger equation."@en . ### https://w3id.org/emmo/domain/atomistic#08fd7117-66ac-5b6d-b65e-34a826675877 rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "PhysicalOperator"@en ; "A mathematical operator with a physical interpretation."@en . ### https://w3id.org/emmo/domain/atomistic#42244404-98d1-582a-8fc0-3cdd2a9b3df6 rdf:type owl:Class ; rdfs:subClassOf , , [ rdf:type owl:Restriction ; owl:onProperty ; owl:someValuesFrom ] ; skos:prefLabel "Hamiltonian"@en ; """An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system."""@en . ### https://w3id.org/emmo/domain/atomistic#83a69cf2-00c1-58b8-915b-76cb3549890a rdf:type owl:Class ; rdfs:subClassOf ; skos:prefLabel "DensityFunctionalTheory"@en ; """An efficient computional method for solving the many-electron (time-independent) Schrödinger equation."""@en . ################################################################# # Individuals ################################################################# ### https://w3id.org/emmo/domain/atomistic#acetonitrile :acetonitrile rdf:type owl:NamedIndividual , :EMMO_42f4778d-5d87-4d1f-86cb-46cd02693733 ; skos:prefLabel "acetonitrile"@en ; "The dielectric constant for acetonitrile."@en . ### https://w3id.org/emmo/domain/atomistic#aug-cc-pVDZ :aug-cc-pVDZ rdf:type owl:NamedIndividual , :EMMO_abdf0104-0349-4c60-b4b8-91161660b2f4 ; skos:prefLabel "aug-cc-pVDZ"@en ; "The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals."@en . ### https://w3id.org/emmo/domain/atomistic#b3lyp :b3lyp rdf:type owl:NamedIndividual , :EMMO_1338c034-b1cb-478e-a60b-816b96280ac6 ; skos:prefLabel "b3lyp"@en ; "The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional."@en . ### https://w3id.org/emmo/domain/atomistic#cosmo :cosmo rdf:type owl:NamedIndividual , :EMMO_47d1df6d-c997-4dc4-a0ae-3bcee7f92f02 ; skos:prefLabel "cosmo"@en ; "The cosmo solvatisation model."@en . ### https://w3id.org/emmo/domain/atomistic#pbe :pbe rdf:type owl:NamedIndividual , :EMMO_1338c034-b1cb-478e-a60b-816b96280ac6 ; skos:prefLabel "pbe"@en ; "The Predew-Burke-Ernzerhof exchange-correlation functional"@en . ### Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi