Atomistic Simulation Methods Ontology (ASMO)
type: Ontology
version IRI: v0.2.0
abstract: The Atomistic Simulation Methods Ontology (ASMO) provides a formal vocabulary for describing computational methods used in atomistic simulations of materials. It covers density functional theory (DFT), molecular dynamics (MD), Monte Carlo (MC) methods, and related simulation techniques, including interatomic potentials, simulation parameters, and calculated physical properties. ASMO leverages the W3C Provenance Ontology (PROV-O) to represent simulation workflows, enabling interoperability with workflow management systems and FAIR data practices in computational materials science. ASMO is part of the Open Computational Data Ontology (OCDO) ecosystem.
Contributor: 0000-0002-5149-603X
Contributor: https://orcid.org/0000-0002-6776-1213
Contributor: https://orcid.org/0000-0003-0698-4891
created: 2024-03-11
creator: https://orcid.org/0000-0001-7564-7990
creator: https://orcid.org/0000-0001-9560-4728
description: ASMO is an ontology that aims to define the concepts needed to describe commonly used atomic scale simulation methods, i.e. density functional theory, molecular dynamics, Monte Carlo methods, etc. ASMO uses the Provenance Ontology (PROV-O) to describe the simulation process.
issued: 2024-03-11
License: https://creativecommons.org/licenses/by/4.0/
modified: 2026-03-06
doi: 10.5281/zenodo.10805591
prior version: v0.0.1
version info: 0.2.0
citation: Abril Azocar Guzman. (2024). Atomistic Simulation Methods Ontology. Zenodo. https://doi.org/10.5281/zenodo.10805591
code repository: https://github.com/OCDO/asmo
creative work status: Ontology Specification
funder: https://ror.org/05qj6w324

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: IAO_0000122
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
IAO_0000117: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
IAO_0000111: definition source
IAO_0000114: IAO_0000122
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
IAO_0000117: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

mathematical formula
type: AnnotationProperty
IAO_0000112: A normal distribution probability density function has a formula of: f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2))
definition: An annotation property that represents a mathematical formula.
IAO_0000117: Asiyah Yu Lin, Jie Zheng, Yongqun He

Contributor
type: AnnotationProperty
comment: Examples of a Contributor include a person, an organization, or a service. Typically, the name of a Contributor should be used to indicate the entity.
definition: An entity responsible for making contributions to the resource.
sub property of: contributor

Creator
type: AnnotationProperty
comment: Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
definition: An entity primarily responsible for making the resource.
sub property of: creator
sub property of: Contributor
range: Agent

Description
type: AnnotationProperty
comment: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
definition: An account of the resource.
sub property of: description

License
type: AnnotationProperty
definition: A legal document giving official permission to do something with the resource.
range: LicenseDocument

Title
type: AnnotationProperty
definition: A name given to the resource.
note: In current practice, this term is used primarily with literal values; however, there are important uses with non-literal values as well. As of December 2007, the DCMI Usage Board is leaving this range unspecified pending an investigation of options.
sub property of: title

alternative label
type: AnnotationProperty
comment: The range of skos:altLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: An alternative lexical label for a resource.
example: Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
sub property of: label

definition
type: AnnotationProperty
definition: A statement or formal explanation of the meaning of a concept.
sub property of: note

example
type: AnnotationProperty
definition: An example of the use of a concept.
sub property of: note

note
type: AnnotationProperty
definition: A general note, for any purpose.

preferred label
type: AnnotationProperty
comment: A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
comment: The range of skos:prefLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: The preferred lexical label for a resource, in a given language.
sub property of: label

has vector
type: ObjectProperty
range: Vector
definition: The relation between an entity and its vectors.

actedOnBehalfOf
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Agent
range: Agent
comment: An object property to express the accountability of an agent towards another agent. The subordinate agent acted on behalf of the responsible agent in an actual activity.
category: starting-point
component: agents-responsibility
inverse: hadDelegate
qualified form: Delegation
qualified form: qualifiedDelegation

generated
type: ObjectProperty
sub property of: influenced
inverse of: wasGeneratedBy
domain: Activity
range: Entity
category: expanded
component: entities-activities
editorial note: prov:generated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions.
inverse: wasGeneratedBy
shares definition with: Generation

influenced
type: ObjectProperty
inverse of: wasInfluencedBy
category: expanded
component: agents-responsibility
inverse: wasInfluencedBy
shares definition with: Influence

used
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Activity
range: Entity
comment: A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven .
category: starting-point
component: entities-activities
inverse: wasUsedBy
qualified form: Usage
qualified form: qualifiedUsage

wasAssociatedWith
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Activity
range: Agent
comment: An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity.
category: starting-point
component: agents-responsibility
inverse: wasAssociateFor
qualified form: Association
qualified form: qualifiedAssociation

wasAttributedTo
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Entity
range: Agent
comment: Attribution is the ascribing of an entity to an agent.
category: starting-point
component: agents-responsibility
definition: Attribution is the ascribing of an entity to an agent.
inverse: contributed
qualified form: Attribution
qualified form: qualifiedAttribution

Axiom
annotated source: wasAttributedTo
annotated property: subPropertyOf
annotated target: wasInfluencedBy
comment: Attribution is a particular case of trace (see http://www.w3.org/TR/prov-dm/#concept-trace), in the sense that it links an entity to the agent that ascribed it.
definition: IF wasAttributedTo(e2,ag1,aAttr) holds, THEN wasInfluencedBy(e2,ag1) also holds.

wasDerivedFrom
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Entity
range: Entity
comment: The more specific subproperties of prov:wasDerivedFrom (i.e., prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource) should be used when applicable.
category: starting-point
component: derivations
definition: A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity.
inverse: hadDerivation
qualified form: Derivation
qualified form: qualifiedDerivation

Axiom
annotated source: wasDerivedFrom
annotated property: subPropertyOf
annotated target: wasInfluencedBy
comment: Derivation is a particular case of trace (see http://www.w3.org/TR/prov-dm/#term-trace), since it links an entity to another entity that contributed to its existence.

wasGeneratedBy
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Entity
range: Activity
category: starting-point
component: entities-activities
inverse: generated
qualified form: Generation
qualified form: qualifiedGeneration

wasInfluencedBy
type: ObjectProperty
domain: Class
range: Class
comment: Because prov:wasInfluencedBy is a broad relation, its more specific subproperties (e.g. prov:wasInformedBy, prov:actedOnBehalfOf, prov:wasEndedBy, etc.) should be used when applicable.
comment: This property has multiple RDFS domains to suit multiple OWL Profiles. See PROV-O OWL Profile.
category: qualified
component: agents-responsibility
editorial note: The sub-properties of prov:wasInfluencedBy can be elaborated in more detail using the Qualification Pattern. For example, the binary relation :baking prov:used :spoon can be qualified by asserting :baking prov:qualifiedUsage [ a prov:Usage; prov:entity :spoon; prov:atLocation :kitchen ] . Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. prov:wasInfluencedBy should not be used without also using one of its subproperties.
inverse: influenced
qualified form: Influence
qualified form: qualifiedInfluence
shares definition with: Influence

Axiom
annotated source: wasInfluencedBy
annotated property: range
annotated target: Class
definition: influencer: an identifier (o1) for an ancestor entity, activity, or agent that the former depends on;
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence

Axiom
annotated source: wasInfluencedBy
annotated property: domain
annotated target: Class
definition: influencee: an identifier (o2) for an entity, activity, or agent;
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence

wasInformedBy
type: ObjectProperty
sub property of: wasInfluencedBy
domain: Activity
range: Activity
comment: An activity a2 is dependent on or informed by another activity a1, by way of some unspecified entity that is generated by a1 and used by a2.
category: starting-point
component: entities-activities
inverse: informed
qualified form: Communication
qualified form: qualifiedCommunication

has calculated property
type: ObjectProperty
domain: Computational Sample
range: Calculated Property
definition: The relation between a computational sample and the calculated property.

has computational method
type: ObjectProperty
domain: Activity
range: Computational Method
definition: The relation between an activity and the type of computation method employed.

has input parameter
type: ObjectProperty
sub property of: has simulation parameter
domain: Simulation
range: Input Parameter
definition: The relation between a Simulation activity and the input parameters used.

has interatomic potential
type: ObjectProperty
domain: Activity
range: Interatomic Potential
definition: The relation between an activity and the interatomic potential used.

has output parameter
type: ObjectProperty
sub property of: has simulation parameter
domain: Simulation
range: Output Parameter
definition: The relation between a Simulation activity and the output parameters used.

has relaxation DOF
type: ObjectProperty
domain: Energy Calculation
range: Relaxation Degrees of Freedom
definition: The relation between an Energy Calculation activity and the relaxation degrees of freedom set as constraints in the calculation.

has simulation parameter
type: ObjectProperty
domain: Simulation
range: Class
  union of: Physical Quantity
  union of: Simulation Parameter
definition: The relation between a Simulation activity and the simulation parameters used (or physical quantities used as simulation parameters).

has statistical ensemble
type: ObjectProperty
domain: Activity
range: Statistical Ensemble
definition: The relation between an activity and the statistical ensemble set in the simulation.

has unit
type: ObjectProperty
domain: Class
  union of: Calculated Property
  union of: Physical Quantity
  union of: Simulation Parameter
range: Unit
definition: The relation between an entity and the unit of the quantity. (e.g. eV for energy cutoff)

uses simulation algorithm
type: ObjectProperty
domain: Simulation
range: Simulation Algorithm
definition: The relation between a Simulation activity and a simulation algorithm used or implemented as part of the simulation or calculation.

was calculated by
type: ObjectProperty
domain: Calculated Property
domain: Physical Quantity
range: Activity
definition: The relation between a calculated property and the activity through which it was obtained.

has XC functional
type: ObjectProperty
domain: Density Functional Theory
range: Exchange Correlation Energy Functional
comment: hasXCFunctional represents the relationship between a density functional theory method and the exchange-correlation energy functionals it takes.

endedAtTime
type: DatatypeProperty
domain: Activity
range: dateTime
comment: The time at which an activity ended. See also prov:startedAtTime.
category: starting-point
component: entities-activities
editorial note: It is the intent that the property chain holds: (prov:qualifiedEnd o prov:atTime) rdfs:subPropertyOf prov:endedAtTime.
qualified form: End
qualified form: atTime

startedAtTime
type: DatatypeProperty
domain: Activity
range: dateTime
comment: The time at which an activity started. See also prov:endedAtTime.
category: starting-point
component: entities-activities
editorial note: It is the intent that the property chain holds: (prov:qualifiedStart o prov:atTime) rdfs:subPropertyOf prov:startedAtTime.
qualified form: Start
qualified form: atTime

has addend
type: DatatypeProperty
domain: Addition
range: float
definition: A data property linking an addition with the addend value.

has base
type: DatatypeProperty
domain: Exponentiation
range: float
definition: A data property linking an exponentiation operation with the base value.

has difference
type: DatatypeProperty
domain: Subtraction
range: float
definition: A data property linking a subtraction with the difference value.

has dividend
type: DatatypeProperty
domain: Division
range: float
definition: A data property linking a division with the dividend value.

has divisor
type: DatatypeProperty
domain: Division
range: float
definition: A data property linking a division with the divisor value.

has exponent
type: DatatypeProperty
domain: Exponentiation
range: float
definition: A data property linking an exponentiation operation with the exponent value.

has factor
type: DatatypeProperty
domain: Multiplication
range: float
definition: A data property linking a multiplication with the factor value.

has minuend
type: DatatypeProperty
domain: Subtraction
range: float
definition: A data property linking a subtraction with the minuend value.

has product
type: DatatypeProperty
domain: Multiplication
range: float
definition: A data property linking a multiplication with the product value.

has quotient
type: DatatypeProperty
domain: Division
range: float
definition: A data property linking a division with the quotient value.

has reference
type: DatatypeProperty
domain: Thing
range: anyURI
definition: A data property linking an entity with a reference (e.g. bibliographic) to another resource.

has subtrahend
type: DatatypeProperty
domain: Subtraction
range: float
definition: A data property linking a subtraction with the subtrahend value.

has sum
type: DatatypeProperty
domain: Addition
range: float
definition: A data property linking an addition with the sum value.

has value
type: DatatypeProperty
domain: Thing
range: float
definition: A data property linking an entity to its value.

Computational Sample
type: Class
definition: A computational sample is a representative system of a material for analysis through computational methods in the context of materials science.

Plane
type: Class
definition: In mathematics, a plane is a two-dimensional space or flat surface that extends indefinitely.
mathematical formula: 𝑎 𝑥 + 𝑏 𝑦 + 𝑐 𝑧 + 𝑑 = 0
comment: The equation of a plane is 𝑎 𝑥 + 𝑏 𝑦 + 𝑐 𝑧 + 𝑑 = 0 , where 𝑎 , 𝑏 , and 𝑐 are the components of the normal vector ⃑ 𝑛 = ( 𝑎 , 𝑏 , 𝑐 ) , which is perpendicular to the plane or any vector parallel to the plane.

Simulation Cell
type: Class
definition: A simulation cell is a representation of the structure or system to be simulated. It is often a three-dimensional box (although not necessarily), where information about the crystal structure and material is contained.
alternative label: Box
alternative label: Supercell

Vector
type: Class
definition: Vector is a quantity that has a magnitude and direction.

Unit
type: Class
description: A unit of measure, or unit, is a particular quantity value that has been chosen as a scale for measuring other quantities the same kind (more generally of equivalent dimension). For example, the meter is a quantity of length that has been rigorously defined and standardized by the BIPM (International Board of Weights and Measures). Any measurement of the length can be expressed as a number multiplied by the unit meter. More formally, the value of a physical quantity Q with respect to a unit (U) is expressed as the scalar multiple of a real number (n) and U, as \(Q = nU\).

Activity
type: Class
disjoint with: Entity
category: starting-point
component: entities-activities
constraints: http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
definition: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Activity
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Activity

Agent
type: Class
category: starting-point
component: agents-responsibility
definition: An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Agent

Entity
type: Class
category: starting-point
component: entities-activities
constraints: http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
definition: An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-entity
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Entity

Organization
type: Class
subclass of: Agent
category: expanded
component: agents-responsibility
definition: An organization is a social or legal institution such as a company, society, etc.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types

Person
type: Class
subclass of: Agent
category: expanded
component: agents-responsibility
definition: Person agents are people.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types

SoftwareAgent
type: Class
subclass of: Agent
category: expanded
component: agents-responsibility
definition: A software agent is running software.
dm: http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
n: http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types

Ab Initio Molecular Dynamics
type: Class
subclass of: Computational Method
definition: Ab Initio Molecular Dynamics is a computational method where finite-temperature dynamical trajectories are generated by using forces obtained directly from electronic structure calculations performed ‘‘on the fly’’ as the simulation proceeds.
alternative label: AIMD
alternative label: Ab initio MD

Addition
type: Class
subclass of: Mathematical Operation
definition: An arithmetic operation by which the total or sum of two or more numbers is computed, symbolized by the plus symbol +.

Barostat
type: Class
subclass of: Simulation Algorithm
definition: Barostat is an algorithm used in molecular dynamics simulations to control system pressure.

Bulk Modulus
type: Class
subclass of: Calculated Property
definition: Bulk modulus is a property that quantifies a material's resistance to uniform compression.
alternative label: B
alternative label: K

Calculated Property
type: Class
definition: A calculated property is a property of a material resulting from a calculation or simulation.

Compression Test
type: Class
subclass of: Simulation Algorithm

Computational Method
type: Class
definition: Computational method is a method used to numerically solve mathematical models and study the behaviour of physical systems.

Density Functional Theory
type: Class
subclass of: Computational Method
definition: Density functional theory is a computational method used to study the electronic structure and ground state of atoms, molecules, and, solids. This technique determines the properties of a many-electron system through functionals of the spatially dependent electron density.
alternative label: DFT

Division
type: Class
subclass of: Mathematical Operation
definition: An arithmetic operation by which the quotient of two numbers (dividend and divisor) is computed, symbolized by / or ÷.

Elastic Constant
type: Class
subclass of: Calculated Property

Elastic Tensor
type: Class
subclass of: Calculated Property

Embedded Atom Model
type: Class
subclass of: Interatomic Potential
definition: Embedded Atom Model is a many-body interatomic potential which contains two contributions to the potential energy: the embedding term, which describes the energy required to embed an atom into an electron cloud, and the pair-wise interaction.
definition source: https://doi.org/10.1103/PhysRevLett.50.1285
mathematical formula: E(r) = \sum_i F_i (\rho_i(r_i)) + 1/2 \sum_{i,j} \varphi(r_{i,j})
alternative label: EAM

Energy
type: Class
subclass of: Physical Quantity
definition: Energy is a physical quantity characterizing the ability of a system to do work.
definition source: https://doi.org/10.1351/goldbook.E02101
alternative label: E

Energy Calculation
type: Class
subclass of: Simulation
definition: Energy calculation is an activity where the energy of the system is computed within the given optimization constraints.
comment: This activity does not specify the way the energy is calculated, it can be used to refer to a rigid calculation or also to energy minimization or optimization. See RelaxationDOF class for specifics about the constraints.

Energy Cutoff
type: Class
subclass of: Input Parameter
definition: Energy cutoff is the input parameter that defines the maximum kinetic energy of plane waves included in the basis set for electronic structure calculations.

Equation of State Fit
type: Class
subclass of: Simulation Algorithm
definition: Equation of state is a relationship between the volume of a body and the pressure to which it is subjected. There are multiple proposed equations for fitting the values of the energy as a function of the volume obtained from ab-initio and molecular dynamics calculations.
alternative label: EOS
alternative label: Equation of State

Exponentiation
type: Class
subclass of: Mathematical Operation
definition: An arithmetic operation by which a number (the base) is raised to the power of another number (the exponent), symbolized by ** or ^. It represents repeated multiplication of the base by itself.

Flow Stress
type: Class
subclass of: Calculated Property
subclass of: Stress

Force
type: Class
subclass of: Physical Quantity
definition: Force is a physical quantity that represents an interaction that causes mass to accelerate. It is a vector quantity, having both magnitude and direction.
definition source: https://doi.org/10.1351/goldbook.F02480
mathematical formula: F = ma
comment: According to Newton's second law of motion, force is the product of mass and acceleration (F = ma).
alternative label: F

Formation Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Formation energy is a property that quantifies the energy required to create a defect, molecule, or material from its constituent atoms or molecules in their standard states.
comment: It is typically calculated as the difference between the total energy of the system containing the defect or structure and the total energy of the isolated constituent atoms or molecules.

Free Energy
type: Class
subclass of: Energy

Free Energy Calculation
type: Class
subclass of: Simulation
definition: Free energy calculation is an activity where the thermodynamic free energy of a system is computed, often under specific conditions such as constant temperature and pressure, to determine system stability or phase transitions.

Gibbs Free Energy
type: Class
subclass of: Thermodynamic Free Energy
definition: Gibbs free energy is a thermodynamic potential that measures the maximum amount of work that may be performed by a thermodynamically closed system at constant temperature and pressure.
mathematical formula: G=H-TS
alternative label: G

Helmholtz Free Energy
type: Class
subclass of: Thermodynamic Free Energy
definition: Helmholtz free energy is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature.
mathematical formula: F = U-TS
alternative label: F

Input Parameter
type: Class
subclass of: Simulation Parameter
definition: Input Parameter is a parameter provided as input to the software tool performing the numerical calculations.

Interatomic Potential
type: Class
definition: Interatomic potentials, in the context of computer simulations, are mathematical functions to calculate the potential energy of a system of atoms with given positions in space.
definition source: https://en.wikipedia.org/wiki/Interatomic_potential

KPoint Mesh
type: Class
subclass of: Input Parameter
definition: K-Point mesh type is an input parameter that indicates how the Bloch vectors (k points) used to sample the Brillouin zone are provided.

Kinetic Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Kinetic energy is the energy due to motion.
definition source: https://doi.org/10.1351/goldbook.K03402
mathematical formula: E_k = (mv^2)/2

Kinetic Monte Carlo Method
type: Class
subclass of: Monte Carlo Method
definition: Kinetic Monte Carlo Method is a variation of the Monte Carlo method, intended to simulate the time evolution of a process with known transition rates among states.
alternative label: kMC

Length
type: Class
subclass of: Physical Quantity
definition: Length is a physical quantity that measures the distance between two points.
definition source: https://doi.org/10.1351/goldbook.L03498
comment: Length is can also be understood to mean the longest dimension of an object.
alternative label: l

Lennard-Jones Potential
type: Class
subclass of: Interatomic Potential
definition: Lennard-Jones Potential is a general two-body interatomic potential, which separates the interaction between atoms into a repulsive part, r^(–n), and attractive part, r^(–m), with (n > m).
definition source: https://doi.org/10.1021/acs.jctc.4c00135
mathematical formula: E(r) = 4\epsilon[(\sigma/r)^{12}-(\sigma/r)^{6}]
alternative label: 12-6 potential
alternative label: LJ potential

Machine Learning Potential
type: Class
subclass of: Interatomic Potential
definition: Machine Learning Potential is an interatomic potential which maps the 3N-dimensional configurational space of the system onto its potential energy surface, represented by a discrete set of DFT energies included in the training dataset.
definition source: https://doi.org/10.1016/j.actamat.2021.116980
comment: Some of the most commonly used MLIP are: Atomic Cluster Expansion (ACE), Moment Tensor Potential (MTP) and Neural Network Potential (NNP)
alternative label: MLIP
alternative label: MLP

Mass
type: Class
subclass of: Physical Quantity
definition: Mass is a physical quantity that defines the amount of matter of a body. Mass is force divided by acceleration.
definition source: https://doi.org/10.1351/goldbook.M03709
alternative label: m

Mathematical Operation
type: Class
subclass of: Activity
definition: In mathematics, an operation is a function which takes zero or more input values (also called "operands" or "arguments") to a well-defined output value.
definition source: https://en.wikipedia.org/wiki/Operation_(mathematics)

Modified Embedded Atom Model
type: Class
subclass of: Interatomic Potential
definition: Modified Embedded Atom Model is an interatomic potential which extends EAM to include angular forces.
definition source: https://doi.org/10.1103/PhysRevB.46.2727
alternative label: MEAM

Molecular Dynamics
type: Class
subclass of: Computational Method
definition: Molecular dynamics is a computational method for simulation of complex systems, modelled at the atomic level. The equations of motion are solved numerically to follow the time evolution of the system, allowing the derivation of kinetic and thermodynamic properties of interest by means of ‘computer experiments’.
definition source: https://doi.org/10.1038/npg.els.0003048
alternative label: MD

Force Field
type: Class
subclass of: Interatomic Potential
definition: Molecular force field is a type of interatomic potential that contains the functional forms used to describe the intra- and inter-molecular potential energy of a collection of atoms, and the corresponding parameters that will determine the energy of a given configuration.
definition source: ISBN-13: 9780192524706
label: Molecular Force Field

Molecular Statics
type: Class
subclass of: Computational Method
definition: Molecular statics is a computational method that uses a constrained optimization technique to minimize the energy of the system at the atomic level. It is usually employed within a Molecular Dynamics framework.
alternative label: MS

Monte Carlo Method
type: Class
subclass of: Computational Method
definition: Monte Carlo Method is a computational method that models the probability of different outcomes. The system is evolved to a new state which is chosen from a randomly generated ensemble of possible future states. Then, using some criteria, this new state is accepted or rejected with a certain probability.
alternative label: MC
alternative label: Monte Carlo Simulation

Multiplication
type: Class
subclass of: Mathematical Operation
definition: An arithmetic operation by which the product of two numbers is computed, symbolized by x or *.
definition source: http://purl.obolibrary.org/obo/NCIT_C90596

Nanoindentation
type: Class
subclass of: Simulation Algorithm

Number Of Ionic Steps
type: Class
subclass of: Input Parameter
subclass of: Output Parameter
definition: Number of ionic steps is a simulation parameter that refers to the total iterations performed in a simulation to update atomic positions based on forces until convergence is reached.

Output Parameter
type: Class
subclass of: Simulation Parameter
definition: Output Parameter is a parameter resulting from a software tool performing the numerical calculations.

Periodic Boundary Condition
type: Class
subclass of: Input Parameter
definition: Periodic boundary conditions (PBCs) are input parameters that define the directions in which the simulation cell is replicated to approximate an infinite system.
alternative label: PBC

Physical Quantity
type: Class
definition: Attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively.
definition source: https://doi.org/10.1351/goldbook.Q04982

Point Defect Creation
type: Class
subclass of: Structure Manipulation
definition: Point defect creation is a type of structure manipulation to introduce a point defect, i.e. add, delete or substitute atoms.

Poisson's Ratio
type: Class
subclass of: Calculated Property
definition: Poisson's ratio is a dimensionless property that quantifies the Poisson effect, which describes the deformation (expansion or contraction) of a material in the direction perpendicular to the applied load. It is the ratio of the transverse strain to the axial strain in a material subjected to uniaxial stress.
mathematical formula: ν = - transverse_strain / axial_strain
alternative label: ν

Potential Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Potential energy is the energy of position or orientation in a field of force.
definition source: https://doi.org/10.1351/goldbook.P04778

Pressure
type: Class
subclass of: Physical Quantity
definition: Pressure is a physical quantity that expresses the normal force acting on a surface divided by the area of that surface.
definition source: https://doi.org/10.1351/goldbook.P04819
alternative label: P

Quasi-Harmonic Approximation
type: Class
subclass of: Simulation Algorithm
definition: The Quasi-Harmonic Approximation (QHA) is a phonon-based model that extends the harmonic approximation by treating vibrational frequencies as volume-dependent, thereby accounting for thermal effects such as thermal expansion.

Relaxation Degrees of Freedom
type: Class
definition: Relaxation Degrees of Freedom are the degrees of freedom allowed for the relaxation of the simulation cell in an atomistic simulation.
comment: The instances of this class indicate the type of relaxation allowed, i.e. relaxation of the atomic positions, cell volume and cell shape.
alternative label: RelaxationDOF

Shear Modulus
type: Class
subclass of: Calculated Property
definition: Shear modulus, also known as the modulus of rigidity, is a measure of a material's resistance to shear deformation. It is defined as the ratio of shear stress (force per unit area applied parallel to the surface) to shear strain in the linear elastic region of the material.
alternative label: G
alternative label: Modulus of rigidity

Simulation
type: Class
subclass of: Activity
definition: In computational materials science, a simulation refers to the production of a computer model of a material system, for the purpose of imitating a process over time.

Simulation Algorithm
type: Class
definition: A simulation algorithm is a computational method used to represent and approximate a system's behavior based on mathematical models and input parameters.

Simulation Cell Length
type: Class
subclass of: Calculated Property
subclass of: Length
definition: The simulation cell length refers to the length (dimension) of the simulation cell or box.
alternative label: Box Length

Simulation Cell Volume
type: Class
subclass of: Calculated Property
subclass of: Volume
definition: The simulation cell volume refers to the volume of the simulation cell or box.

Simulation Parameter
type: Class
definition: Simulation parameter is a parameter for a software tool to perform numerical calculations.

Simulation Run Time
type: Class
subclass of: Time
definition: Simulation run time is the actual elapsed time taken to execute a simulation on a computing system.

Simulation Time
type: Class
subclass of: Time
definition: Simulation time is the time that progresses within a simulation, independent of real-world time, used to model and analyze the simulated system's behavior.

Specific Heat Capacity
type: Class
subclass of: Calculated Property

Statistical Ensemble
type: Class
definition: Statistical Ensemble is a collection of points in phase space. The points are distributed according to a probability density, which is determined by the chosen fixed macroscopic parameters (NPT, NVT, etc.). Each point represents a typical system at any particular instant of time.
definition source: ISBN-13: 9780192524706

Stillinger-Weber Potential
type: Class
subclass of: Interatomic Potential
definition: Stillinger-Weber Potential is an interatomic potential comprising both two- and three-atom contributions to describe interactions in solid and liquid forms of Si (and other diamond structures).
definition source: https://doi.org/10.1103/PhysRevB.31.5262

Strain Rate
type: Class
subclass of: Input Parameter

Stress
type: Class
subclass of: Physical Quantity

Structure Manipulation
type: Class
subclass of: Activity
definition: Structure manipulation is an activity where methods are applied to a structure (e.g. atomic structure) to modify it.

Subtraction
type: Class
subclass of: Mathematical Operation
definition: An arithmetic operation by which the removal of a number from another number or amount is computed, symbolized by the minus symbol -.

Temperature
type: Class
subclass of: Physical Quantity
definition: Temperature is a physical quantity that expresses the average measure of the kinetic energy of a system of particles.
alternative label: T

Tensile Test
type: Class
subclass of: Simulation Algorithm

Thermal Expansion Coefficient
type: Class
subclass of: Calculated Property

Thermodynamic Free Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Thermodynamic free energy is the energy in a physical system that can be converted to do work.

Thermodynamic Integration
type: Class
subclass of: Simulation Algorithm
definition: Thermodynamic integration is a numerical method used to compute free energy differences between two states by integrating the average derivative of the system's energy with respect to a coupling parameter along a reversible path connecting the states.
comment: It is commonly used in molecular simulations to calculate free energies of solvation, binding, or phase transitions.

Thermostat
type: Class
subclass of: Simulation Algorithm
definition: Thermostat is an algorithm used in molecular dynamics simulations to control the system's temperature.

Time
type: Class
subclass of: Physical Quantity
definition: Time is a base quantity in the measuring system upon which SI is based used to sequence and measure duration of events.
definition source: https://doi.org/10.1351/goldbook.T06375
alternative label: t

Time Step
type: Class
subclass of: Input Parameter
definition: Time step is an input parameter that indicates a discrete interval of simulated time used to update system state in molecular dynamics or other time-dependent simulations

Total Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: In mechanics, it is the sum of potential energy and kinetic energy.

Total Magnetic Moment
type: Class
subclass of: Calculated Property
definition: Total magnetic moment is a property that quantifies the overall strength and direction of the magnetic field produced by a system, calculated as the vector sum of all individual magnetic moments contributed by its atoms, ions, or molecules.

Virial Pressure
type: Class
subclass of: Calculated Property
subclass of: Pressure

Volume
type: Class
subclass of: Physical Quantity
definition: Volume is a physical quantity that measures the three-dimensional space contained within an object or shape.
alternative label: V

Volume Range
type: Class
subclass of: Input Parameter
definition: Volume range is an input parameter that indicates the predefined limits for the system's volume variation in a simulation.

Yield Stress
type: Class
subclass of: Calculated Property
subclass of: Stress

Young’s Modulus
type: Class
subclass of: Calculated Property
definition: Young's modulus is a property that quantifies the stiffness of a material, defined as the ratio of tensile stress (force per unit area) to tensile strain (proportional deformation in length) in the linear elastic region of a material's stress-strain curve.
alternative label: E

Exchange Correlation Energy Functional
type: Class
comment: An ExchangeCorrelationEnergyFunctional is a functional to compute the exchange correlation energy.

Generalized Gradient Approximation
type: Class
subclass of: Exchange Correlation Energy Functional
comment: A GeneralizedGradientApproximation is a classification of exchange correlation energy functionals that only use the local value of the electronic density and its gradient.

Hybrid Functional
type: Class
subclass of: Exchange Correlation Energy Functional
comment: A hybrid functional is a classification of exchange correlation energy functionals that combine exact exchange from HartreeFock theory with another exchange correlation energy approximation.

Hybrid Generalized Gradient Approximation
type: Class
subclass of: Hybrid Functional
comment: A hybrid generalized gradient approximation is a classification of exchange correlation energy functionals that combine exact exchange from Hartree–Fock theory with generalized gradient approximation.

Hybrid Meta Generalized Gradient Approximation
type: Class
subclass of: Hybrid Functional
comment: A hybrid meta generalized gradient approximation is a classification of exchange correlation energy functionals that combine exact exchange from Hartree–Fock theory with meta generalized gradient approximation.

Local Density Approximation
type: Class
subclass of: Exchange Correlation Energy Functional
comment: A LDA is a classification of exchange correlation energy functionals that only use the local value of the electronic density.

Meta Generalized Gradient Approximation
type: Class
subclass of: Exchange Correlation Energy Functional
comment: A MetaGeneralizedGradientApproximation is a classification of exchange correlation energy functionals that only use the local value of the electronic density and its gradient and the Kohn–Sham orbital kinetic energy density.

Add Atom
type: NamedIndividual
type: Point Defect Creation
definition: Substitution of an atom to create an impurity.

Andersen Barostat
type: NamedIndividual
type: Barostat
definition: The Andersen barostat is a barostat method that couples the system to a pressure bath by introducing an extra degree of freedom (a "piston") to adjust the simulation box volume isotropically.

Andersen Thermostat
type: NamedIndividual
type: Thermostat
definition: The Andersen thermostat is a stochastic thermostat method that maintains the system's temperature by simulating random collisions with a fictitious heat bath. During these collisions, the momentum of randomly selected particles is instantaneously reassigned according to the Boltzmann distribution at the target temperature, controlled by a collision frequency parameter. This approach introduces temperature fluctuations while ensuring thermal equilibrium with the desired temperature.
definition source: https://doi.org/10.1063/1.439486

Atomic Position Relaxation
type: NamedIndividual
type: Relaxation Degrees of Freedom
definition: Atomic positions are allowed to change in the calculation.

Berendsen Barostat
type: NamedIndividual
type: Barostat
definition: The Berendsen barostat is a barostat method that controls system pressure by scaling the simulation box volume (and thus atomic coordinates) based on the difference between current and target pressures. It weakly couples the system to an external pressure bath for smooth equilibration.

Berendsen Thermostat
type: NamedIndividual
type: Thermostat
definition: The Berendsen thermostat is a thermostat algorithm that adjusts the velocities of particles to control the system's temperature by rescaling them at each time step. It uses a damping parameter to determine how quickly the temperature approaches a desired value, allowing for a smooth temperature transition.
definition source: https://doi.org/10.1007/978-94-009-6463-1_16

Birch-Murnaghan
type: NamedIndividual
type: Equation of State Fit
definition: Equation of state proposed by Albert Francis Birch in 1947, based on the Murnaghan equation.
definition source: https://doi.org/10.1103/PhysRev.71.809
definition source: https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state

Bussi-Donadio-Parrinello
type: NamedIndividual
type: Thermostat
definition: The Bussi-Donadio-Parrinello (BDP) thermostat, also known as canonical sampling through velocity rescaling (CSVR), is a thermostat algorithm designed to maintain a constant temperature while ensuring proper sampling of the canonical ensemble. This method extends the Berendsen thermostat by stochastically rescaling the velocities of particles, allowing the kinetic energy to fluctuate around a target value derived from the canonical equilibrium distribution.
definition source: https://doi.org/10.1063/1.2408420

Canonical Ensemble
type: NamedIndividual
type: Statistical Ensemble
definition: In the canonical ensemble the temperature, volume, and the number of particles of every species are kept constant.
definition source: ISBN-13: 978-0323902922
alternative label: NVT ensemble

Cell Shape Relaxation
type: NamedIndividual
type: Relaxation Degrees of Freedom
definition: Cell shape is allowed to change in the calculation.

Cell Volume Relaxation
type: NamedIndividual
type: Relaxation Degrees of Freedom
definition: Cell volume is allowed to change in the calculation.

Delete Atom
type: NamedIndividual
type: Point Defect Creation
definition: Deletion of an atom to create a vacancy.

Explicit KPoint Mesh
type: NamedIndividual
type: KPoint Mesh
definition: An explicit k-point mesh refers to an input where the software will use exactly the points provided.

Gamma-Centered KPoint Mesh
type: NamedIndividual
type: KPoint Mesh
definition: A gamma-centered k-point mesh refers to a grid where the k-points are arranged symmetrically around the Gamma point (k = 0).

Grand Canonical Ensemble
type: NamedIndividual
type: Statistical Ensemble
definition: In the grand canonical ensemble the temperature, volume, and the chemical potential are kept constant.
definition source: ISBN-13: 978-0323902922
alternative label: µVT ensemble

Isoenthalpic–Isobaric Ensemble
type: NamedIndividual
type: Statistical Ensemble
definition: In the isoenthalpic-isobaric ensemble the enthalpy, pressure, and the number of particles of every species are kept constant.
definition source: ISBN-13: 978-0323902922
alternative label: NPH ensemble

Isothermal–Isobaric Ensemble
type: NamedIndividual
type: Statistical Ensemble
definition: In the isothermal-isobaric ensemble the temperature, pressure, and the number of particles of every species are kept constant.
definition source: ISBN-13: 978-0323902922
alternative label: NPT ensemble

Langevin
type: NamedIndividual
type: Thermostat
definition: Langevin thermostat is a thermostat, which mimics the coupling of the system of interest to a thermal bath by modifying Newton's equations of motion in two ways: first, a ‘random force’ term is introduced: this is the stochastic element of the algorithm. Second, a deterministic ‘frictional force’ is added, proportional to particle velocities. The strength of these terms, and the prescribed temperature, are connected by the fluctuation–dissipation theorem.
definition source: "Computer Simulation of Liquids", ISBN-13 : ‎978-0198556459

Microcanonical Ensemble
type: NamedIndividual
type: Statistical Ensemble
definition: In the microcanonical ensemble the energy, volume, and the number of particles of every species are kept constant.
definition source: ISBN-13: 978-0323902922
alternative label: NVE ensemble

Monkhorst Pack KPoint Mesh
type: NamedIndividual
type: KPoint Mesh
definition: A Monkhorst-Pack k-point mesh refers to a regular grid of k-points for sampling the Brillouin zone.

Murnaghan
type: NamedIndividual
type: Equation of State Fit
definition: Equation of state proposed by Francis D. Murnaghan in 1944. The Murnaghan equation is derived, under certain assumptions, from the equations of continuum mechanics. It involves two adjustable parameters: the modulus of incompressibility K0 and its first derivative with respect to the pressure, K′0, both measured at ambient pressure.
definition source: https://en.wikipedia.org/wiki/Murnaghan_equation_of_state
definition source: "Finite Deformation of an Elastic Solid", Applied mathematics series, ISSN 0272-1643

Nose-Hoover
type: NamedIndividual
type: Thermostat
definition: The Nosé–Hoover thermostat is a deterministic algorithm for constant-temperature molecular dynamics simulations. Nosé–Hoover thermostat maintains constant-temperature condition (canonical ensemble) by connecting the system to a heat bath through an additional degree of freedom.
definition source: https://doi.org/10.1063%2F1.447334
definition source: https://doi.org/10.1103%2FPhysRevA.31.1695

Parrinello-Rahman
type: NamedIndividual
type: Barostat
definition: The Parrinello-Rahman barostat is a barostat method that controls system pressure by allowing both the volume and shape of the simulation box to fluctuate.

Periodicity in X-direction
type: NamedIndividual
type: Periodic Boundary Condition
definition: Input parameter defining whether periodicity in the X-axis of the simulation cell is enabled.
comment: In most cases, it refers to the use of periodic boundary conditions in molecular dynamics.

Periodicity in Y-direction
type: NamedIndividual
type: Periodic Boundary Condition
definition: Input parameter defining whether periodicity in the Y-axis of the simulation cell is enabled.
comment: In most cases, it refers to the use of periodic boundary conditions in molecular dynamics.

Periodicity in Z-direction
type: NamedIndividual
type: Periodic Boundary Condition
definition: Input parameter defining whether periodicity in the Z-axis of the simulation cell is enabled.
comment: In most cases, it refers to the use of periodic boundary conditions in molecular dynamics.

Substitute Atom
type: NamedIndividual
type: Point Defect Creation
definition: Substitution of an atom to create an impurity.

Third-order polynomial fit
type: NamedIndividual
type: Equation of State Fit
definition: EOS calculation using a third-order polynomial fit.

Velocity Rescaling
type: NamedIndividual
type: Thermostat
definition: Velocity rescaling is a simple thermostat method used in molecular dynamics simulations to maintain a constant temperature by adjusting particle velocities at each time step. It resets the temperature of a group of atoms by explicitly rescaling their velocities.

Vinet
type: NamedIndividual
type: Equation of State Fit
definition: Equation of state proposed by Pascal Vinet in 1987. It is a modification of the Birch–Murnaghan equation of state.
definition source: https://doi.org/10.1103/PhysRevB.35.1945
definition source: https://en.wikipedia.org/wiki/Rose%E2%80%93Vinet_equation_of_state
alternative label: Rose–Vinet