description
a general annotation that provides extra context, clarifications, or useful background information
a note that helps to clarify the meaning and/or the use of a concept
q critical alert about potential dangers, system failures, or serious misuse of a concept.
warning
a best practice or helpful suggestion related to the concept.
tip
a moderate-level advisory about possible pitfalls, errors, or inefficiencies
caution
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.
A mathematical operator with a physical interpretation.
PhysicalOperator
An operator corresponding to the sum of the kinetic energies plus the potential energies for all the particles in the system.
Hamiltonian
An efficient computional method for solving the many-electron (time-independent) Schrödinger equation.
DensityFunctionalTheory
Forcefield-based simulation software.
ForceFieldSimulationSoftware
LAMMPS
A specific electronic state of a quantum system. Often defined by its wavefunction.
ElectronicState
A functional that approximates the exchange-correlation of the electron density of the chosen system.
Functional
DFTFunctional
Hybrid functionals
LDA, GGA, GW
A critical point on a potential energy surface representing a transition state in a chemical reaction.
SaddlePoint
Mathematicals used by an atomistic computational software, often defined as a setting in the input file.
AtomisticComputationMathematical
Geometry optimisation performed with NWChem
NWChemGeometryOptimization
This is not necessarily an optimisation to the ground state, as can also be a saddle point.
The superclass of physical-based electronic and forcefield simulation softwares.
AtomisticSimulationSoftware
NWChem - a physical based software that implements both DFT and higher order QM methods.
Relates a mathematical (or physical) operator to its eigenvalue.
hasEigenvalue
DFT-based simulation software.
DFTSimulationSoftware
VASP, Quantum ESPRESSO, NWChem
The software is not restricted to only DFT, i.e. also MP2 simulations are avilable in NWChem
A solvent used in the solvation model, typically identified with a chemical name.
SolvationModelSolvent
A mathematical model that allows the quantum chemistry calculations to include the interactions between solvents and the quantum solute implicitly.
SolvationModel
A computation that solves the Kohn-Sham equation (using DFT).
DFTComputation
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.
ElectronicComputation
Electronic computation performed with the NWChem software.
NWChemComputation
NWChem computation that includes cosmo as solvation model.
NWChemDFTModuleCOSMO
The lowest-energy quantum state of a physical system.
GroundState
Be aware that a locally found minimum is not necessarily the ground state.
A collection of mathematical functions used to represent molecular orbitals in quantum chemical calculations.
BasisSet
Relates a material to the species it is made of.
Intended for documeting what kind of atoms a material is made of.
hasSpecies
A numerically evaluated Hessian matrix computed using finite-difference methods within the NWChem software suite. May be used for frequency analysis.
NWChemFiniteDifferenceHessian
NWChemFinite-differenceHessian
If the external potential does not depende on time, the Schrödinger equation can be reduced to this time-independent form.
TimeIndependentSchrodingerEquation
TimeIndependentSchrödingerEquation
The dielectric constant for acetonitrile.
acetonitrile
The Dunning correlation-consistent polarized basis set with double-zeta for the valence orbitals.
aug-cc-pVDZ
The Becke, 3-parameter, Lee-Yang-Parr hybrid exchange-correlation functional.
b3lyp
The Schrödinger equation for a fictious "Kohn-Sham" system of non-interacting electrons that generates the same charge density as the real interacting system.
This is the equation that is solved with density functional theory.
KohnShamEquation
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.
SchrodingerEquation
SchrödingerEquation
chemicalFormula
The chemical formula of the species.
The cosmo solvatisation model.
cosmo
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.
WaveFunction
The full time-dependent Schrödinger equation.
TimeDependentSchrodingerEquation
TimeDependentSchrödingerEquation
hasNumberOfAtoms
Number of atoms in the species.
The Predew-Burke-Ernzerhof exchange-correlation functional
pbe