Reference Index#
Atomistic#
Classes#
AtomisticComputationMathematical#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_29fd60b8-b709-4bc9-8e0e-19498abb5da0 |
| Annotations | |
|---|---|
| prefLabel | AtomisticComputationMathematical |
| elucidation | Mathematicals used by an atomistic computational software, often defined as a setting in the input file. |
| Formal description | |
| Subclass Of | Mathematical |
| Subclasses | SolvationModel, Functional, SolvationModelSolvent, BasisSet |
AtomisticSimulationSoftware#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_3cd827b2_e9c6_4d08_a215_d22fd2a46298 |
| Annotations | |
|---|---|
| prefLabel | AtomisticSimulationSoftware |
| elucidation | The superclass of physical-based electronic and forcefield simulation softwares. |
| Formal description | |
| Subclass Of | PhysicalBasedSimulationSoftware |
| Subclasses | ForceFieldSimulationSoftware, DFTSimulationSoftware |
Example
NWChem - a physical based software that implements both DFT and higher order QM methods.
BasisSet#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_abdf0104-0349-4c60-b4b8-91161660b2f4 |
| Annotations | |
|---|---|
| prefLabel | BasisSet |
| elucidation | A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations. |
| Formal description | |
| Subclass Of | AtomisticComputationMathematical |
DFTComputation#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_52a6103f_86a4_4710_9028_a49b4cef858e |
| Annotations | |
|---|---|
| prefLabel | DFTComputation |
| elucidation | A computation that solves the Kohn-Sham equation (using DFT). |
| Formal description | |
| Subclass Of | ElectronicComputation |
DFTSimulationSoftware#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_429430f4_00e9_4157_a636_6cf798139e40 |
| Annotations | |
|---|---|
| prefLabel | DFTSimulationSoftware |
| elucidation | DFT-based simulation software. |
| Formal description | |
| Subclass Of | AtomisticSimulationSoftware |
Example
VASP, Quantum ESPRESSO, NWChem
Note
The software is not restricted to only DFT, i.e. also MP2 simulations are avilable in NWChem
DensityFunctionalTheory#
| IRI | https://w3id.org/emmo/domain/atomistic#83a69cf2-00c1-58b8-915b-76cb3549890a |
| Annotations | |
|---|---|
| prefLabel | DensityFunctionalTheory |
| elucidation | An efficient computional method for solving the many-electron (time-independent) Schrödinger equation. |
| Formal description | |
| Subclass Of | ElectronicModel |
ElectronicComputation#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_5ddbdd13-b5ba-4101-8b13-4ab06b5173eb |
| Annotations | |
|---|---|
| prefLabel | ElectronicComputation |
| elucidation | 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. |
| Formal description | |
| Subclass Of | PhysicsMathematicalComputation |
| Subclasses | NWChemComputation, DFTComputation |
ElectronicState#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_0f0feb84-14ef-4def-babb-718c9244f098 |
| Annotations | |
|---|---|
| prefLabel | ElectronicState |
| elucidation | A specific electronic state of a quantum system. Often defined by its wavefunction. |
| Formal description | |
| Subclass Of | TemporalTile |
| Subclasses | GroundState, SaddlePoint |
ForceFieldSimulationSoftware#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_070efd9c_b971_44ee_bd45_8c548a80a65d |
| Annotations | |
|---|---|
| prefLabel | ForceFieldSimulationSoftware |
| elucidation | Forcefield-based simulation software. |
| Formal description | |
| Subclass Of | AtomisticSimulationSoftware |
Example
LAMMPS
Functional#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_1338c034-b1cb-478e-a60b-816b96280ac6 |
| Annotations | |
|---|---|
| prefLabel | Functional |
| altLabel | DFTFunctional |
| elucidation | A functional that approximates the exchange-correlation of the electron density of the chosen system. |
| Formal description | |
| Subclass Of | AtomisticComputationMathematical |
Example
Hybrid functionals
LDA, GGA, GW
GroundState#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_a8d08da5-cc89-4a50-83c1-e7f11e718bb5 |
| Annotations | |
|---|---|
| prefLabel | GroundState |
| elucidation | The lowest-energy quantum state of a physical system. |
| Formal description | |
| Subclass Of | ElectronicState |
Caution
Be aware that a locally found minimum is not necessarily the ground state.
Hamiltonian#
| IRI | https://w3id.org/emmo/domain/atomistic#42244404-98d1-582a-8fc0-3cdd2a9b3df6 |
| Annotations | |
|---|---|
| prefLabel | Hamiltonian |
| elucidation | An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system. |
| Formal description | |
| Subclass Of | Referent, PhysicalOperator |
| Restrictions |
|
KohnShamEquation#
| IRI | https://w3id.org/emmo/domain/atomistic#b65fe3b6-8477-5508-a066-2f7edcf25126 |
| Annotations | |
|---|---|
| prefLabel | KohnShamEquation |
| elucidation | The Schrödinger equation for a fictious "Kohn-Sham" system of non-interacting electrons that generates the same charge density as the real interacting system. |
| Formal description | |
| Subclass Of | TimeIndependentSchrodingerEquation |
| Restrictions | |
NWChemComputation#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_78e3ce89-632d-4a3e-a194-a051df2f5d5f |
| Annotations | |
|---|---|
| prefLabel | NWChemComputation |
| elucidation | Electronic computation performed with the NWChem software. |
| Formal description | |
| Subclass Of | ElectronicComputation |
| Subclasses | NWChemFiniteDifferenceHessian, NWChemGeometryOptimization, NWChemDFTModuleCOSMO |
NWChemDFTModuleCOSMO#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_807b8909-f44c-43de-b7cc-45d1abd515eb |
| Annotations | |
|---|---|
| prefLabel | NWChemDFTModuleCOSMO |
| elucidation | NWChem computation that includes cosmo as solvation model. |
| Formal description | |
| Subclass Of | NWChemComputation |
NWChemFiniteDifferenceHessian#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_f2dca06b-5987-4ff7-ac9e-9772b59b5c42 |
| Annotations | |
|---|---|
| prefLabel | NWChemFiniteDifferenceHessian |
| altLabel | NWChemFinite-differenceHessian |
| elucidation | A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis. |
| Formal description | |
| Subclass Of | NWChemComputation |
NWChemGeometryOptimization#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_2be6633a-e701-41a7-a42b-0e89f262d82c |
| Annotations | |
|---|---|
| prefLabel | NWChemGeometryOptimization |
| elucidation | Geometry optimisation performed with NWChem |
| Formal description | |
| Subclass Of | NWChemComputation |
Warning
This is not necessarily an optimisation to the ground state, as can also be a saddle point.
PhysicalOperator#
| IRI | https://w3id.org/emmo/domain/atomistic#08fd7117-66ac-5b6d-b65e-34a826675877 |
| Annotations | |
|---|---|
| prefLabel | PhysicalOperator |
| elucidation | A mathematical operator with a physical interpretation. |
| Formal description | |
| Subclass Of | MathematicalOperator |
| Subclasses | Hamiltonian |
SaddlePoint#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_197db0fe-da46-4969-9410-4d5089e941ec |
| Annotations | |
|---|---|
| prefLabel | SaddlePoint |
| elucidation | A critical point on a potential energy surface representing a transition state in a chemical reaction. |
| Formal description | |
| Subclass Of | ElectronicState |
SchrodingerEquation#
| IRI | https://w3id.org/emmo/domain/atomistic#c4dd4450-cc80-5de4-a8d6-db0651115a2c |
| Annotations | |
|---|---|
| prefLabel | SchrodingerEquation |
| altLabel | SchrödingerEquation |
| elucidation | 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. |
| wikipediaReference | https://en.wikipedia.org/wiki/Schr%C3%B6dinger_equation |
| illustration |  |
| Formal description | |
| Subclass Of | PhysicsEquation |
| Subclasses | TimeIndependentSchrodingerEquation, TimeDependentSchrodingerEquation |
| Restrictions |
|
SolvationModel#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_47d1df6d-c997-4dc4-a0ae-3bcee7f92f02 |
| Annotations | |
|---|---|
| prefLabel | SolvationModel |
| elucidation | A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly. |
| Formal description | |
| Subclass Of | AtomisticComputationMathematical |
SolvationModelSolvent#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_42f4778d-5d87-4d1f-86cb-46cd02693733 |
| Annotations | |
|---|---|
| prefLabel | SolvationModelSolvent |
| elucidation | A solvent used in the solvation model, typically identified with a chemical name. |
| Formal description | |
| Subclass Of | AtomisticComputationMathematical |
TimeDependentSchrodingerEquation#
| IRI | https://w3id.org/emmo/domain/atomistic#fac61002-4a3d-5810-a430-ad5dad69c9a0 |
| Annotations | |
|---|---|
| prefLabel | TimeDependentSchrodingerEquation |
| altLabel | TimeDependentSchrödingerEquation |
| elucidation | The full time-dependent Schrödinger equation. |
| Formal description | |
| Subclass Of | SchrodingerEquation |
TimeIndependentSchrodingerEquation#
| IRI | https://w3id.org/emmo/domain/atomistic#acaafcb6-b65f-5996-93ed-2f486f5f2b30 |
| Annotations | |
|---|---|
| prefLabel | TimeIndependentSchrodingerEquation |
| altLabel | TimeIndependentSchrödingerEquation |
| elucidation | If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form. |
| Formal description | |
| Subclass Of | SchrodingerEquation |
| Subclasses | KohnShamEquation |
WaveFunction#
| IRI | https://w3id.org/emmo/domain/atomistic#df750ce7-fda1-5e9b-ba32-db96ec170577 |
| Annotations | |
|---|---|
| prefLabel | WaveFunction |
| elucidation | 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. |
| wikipediaReference | https://en.wikipedia.org/wiki/Wave_function |
| Formal description | |
| Subclass Of | ISQDimensionlessQuantity |
Object Properties#
hasEigenvalue#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_42812fef-145a-56e9-9c18-72bd32214455 |
| Annotations | |
|---|---|
| prefLabel | hasEigenvalue |
| elucidation | Relates a mathematical (or physical) operator to its eigenvalue. |
| Formal description | |
| Subproperty Of | ObjectProperty, hasProperty |
| Domain | MathematicalOperator |
hasSpecies#
| IRI | https://w3id.org/emmo/domain/atomistic#EMMO_c2da4973_b83d_4581_a4b4_87ab401b8f5b |
| Annotations | |
|---|---|
| prefLabel | hasSpecies |
| elucidation | Relates a material to the species it is made of. |
| Formal description | |
| Subproperty Of | ObjectProperty, hasRole |
| Domain | ChemicallyDefinedMaterial |
| Range | MolecularEntity |
Note
Intended for documeting what kind of atoms a material is made of.
Data Properties#
hasNumberOfAtoms#
| IRI | https://w3id.org/emmo/domain/atomistic#hasNumberOfAtoms |
| Annotations | |
|---|---|
| prefLabel | hasNumberOfAtoms |
| Formal description | |
| Subproperty Of | DatatypeProperty |
| Domain | MolecularEntity |
| Range | xsd:int |
Annotation Properties#
chemicalFormula#
| IRI | https://w3id.org/emmo/domain/atomistic#chemicalFormula |
| Annotations | |
|---|---|
| prefLabel | chemicalFormula |
| Formal description | |
| Subproperty Of | AnnotationProperty |
Individuals#
acetonitrile#
| IRI | https://w3id.org/emmo/domain/atomistic#acetonitrile |
| Annotations | |
|---|---|
| prefLabel | acetonitrile |
| elucidation | The dielectric constant for acetonitrile. |
| Formal description | |
| Instance of | SolvationModelSolvent |
aug-cc-pVDZ#
| IRI | https://w3id.org/emmo/domain/atomistic#aug-cc-pVDZ |
| Annotations | |
|---|---|
| prefLabel | aug-cc-pVDZ |
| elucidation | The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals. |
| Formal description | |
| Instance of | BasisSet |
b3lyp#
| IRI | https://w3id.org/emmo/domain/atomistic#b3lyp |
| Annotations | |
|---|---|
| prefLabel | b3lyp |
| elucidation | The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional. |
| Formal description | |
| Instance of | Functional |
cosmo#
| IRI | https://w3id.org/emmo/domain/atomistic#cosmo |
| Annotations | |
|---|---|
| prefLabel | cosmo |
| elucidation | The cosmo solvatisation model. |
| Formal description | |
| Instance of | SolvationModel |
pbe#
| IRI | https://w3id.org/emmo/domain/atomistic#pbe |
| Annotations | |
|---|---|
| prefLabel | pbe |
| elucidation | The Predew-Burke-Ernzerhof exchange-correlation functional |
| Formal description | |
| Instance of | Functional |