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).
SINTEF
Francesca L. Bleken
Jesper Friis
EMMC ASBL
Atomistic
Contacts: Jesper Friis SINTEF email: jesper.friis@sintef.no Francesca L. Bleken SINTEF email: francesca.l.bleken@sintef.no
The EMMO requires FaCT++ reasoner plugin in order to visualize allinferences and class hierarchy (ctrl+R hotkey in Protege).
This ontology is generated with data from the ASE Python package.
hasSpecies
Relates a material to the species it is made of.
Intended for documeting what kind of atoms a material is made of.
hasEigenvalue
Relates a mathematical (or physical) operator to its eigenvalue.
LAMMPS
ForceFieldSimulationSoftware
Forcefield-based simulation software.
ElectronicState
A specific electronic state of a quantum system. Often defined by its wavefunction.
Functional
DFTFunctional
LDA, GGA, GW
A functional that approximates the exchange-correlation of the electron density of the chosen system.
SaddlePoint
A critical point on a potential energy surface representing a transition state in a chemical reaction.
AtomisticComputationMathematical
Mathematicals used by an atomistic computational software, often defined as a setting in the input file.
NWChemGeometryOptimization
Geometry optimisation performed with NWChem
NWChem - a physical based software that implements both DFT and higher order QM methods.
AtomisticSimulationSoftware
The superclass of physical-based electronic and forcefield simulation softwares.
VASP, Quantum ESPRESSO, NWChem
DFTSimulationSoftware
DFT-based simulation software.
SolvationModelSolvent
A solvent used in the solvation model, typically identified with a chemical name.
SolvationModel
A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly.
DFTComputation
A computation that solves the Kohn-Sham equation (using DFT).
ElectronicComputation
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
Electronic computation performed with the NWChem software.
NWChemDFTModuleCOSMO
NWChem comutation that includes cosmo as solvation model.
GroundState
he lowest-energy quantum state of a physical system.
BasisSet
A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations.
NWChemFinite-differenceHessian
NWChemFiniteDifferenceHessian
A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis.
TimeIndependentSchrodingerEquation
TimeIndependentSchrödingerEquation
If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form.
This is the equation that is solved with density functional theory.
KohnShamEquation
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
SchrödingerEquation
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.
WaveFunction
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.
TimeDependentSchrodingerEquation
TimeDependentSchrödingerEquation
The full time-dependent Schrödinger equation.
PhysicalOperator
A mathematical operator with a physical interpretation.
Hamiltonian
An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system.
DensityFunctionalTheory
An efficient computional method for solving the many-electron (time-independent) Schrödinger equation.
acetonitrile
The dielectric constant for acetonitrile.
aug-cc-pVDZ
The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals.
b3lyp
The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional.
cosmo
The cosmo solvatisation model.
pbe
The Predew-Burke-Ernzerhof exchange-correlation functional