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.
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.
Atomistic Simulation Methods Ontology (ASMO)
Abril Azocar Guzman. (2024). Atomistic Simulation Methods Ontology. Zenodo. https://doi.org/10.5281/zenodo.10805591
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
definition source
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
A normal distribution probability density function has a formula of: f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2))
An annotation property that represents a mathematical formula.
mathematical formula
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.
Contributor
An entity responsible for making contributions to the resource.
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.
Creator
An entity primarily responsible for making the resource.
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.
Description
An account of the resource.
License
A legal document giving official permission to do something with the resource.
Title
A name given to the resource.
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.
The range of skos:altLabel is the class of RDF plain literals.
skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
alternative label
An alternative lexical label for a resource.
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).
A statement or formal explanation of the meaning of a concept.
example
An example of the use of a concept.
A general note, for any purpose.
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.
The range of skos:prefLabel is the class of RDF plain literals.
preferred label
The preferred lexical label for a resource, in a given language.
The relation between an entity and its vectors.
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.
prov:generated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions.
A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven .
An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity.
Attribution is the ascribing of an entity to an agent.
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.
IF wasAttributedTo(e2,ag1,aAttr) holds, THEN wasInfluencedBy(e2,ag1) also holds.
The more specific subproperties of prov:wasDerivedFrom (i.e., prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource) should be used when applicable.
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.
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.
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.
This property has multiple RDFS domains to suit multiple OWL Profiles. See PROV-O OWL Profile.
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.
influencer: an identifier (o1) for an ancestor entity, activity, or agent that the former depends on;
influencee: an identifier (o2) for an entity, activity, or agent;
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.
The relation between a computational sample and the calculated property.
The relation between an activity and the type of computation method employed.
The relation between a Simulation activity and the input parameters used.
The relation between an activity and the interatomic potential used.
The relation between a Simulation activity and the output parameters used.
The relation between an Energy Calculation activity and the relaxation degrees of freedom set as constraints in the calculation.
The relation between a Simulation activity and the simulation parameters used (or physical quantities used as simulation parameters).
The relation between an activity and the statistical ensemble set in the simulation.
The relation between an entity and the unit of the quantity. (e.g. eV for energy cutoff)
The relation between a Simulation activity and a simulation algorithm used or implemented as part of the simulation or calculation.
The relation between a calculated property and the activity through which it was obtained.
hasXCFunctional represents the relationship between a density functional theory method and the exchange-correlation energy functionals it takes.
has XC functional
The time at which an activity ended. See also prov:startedAtTime.
It is the intent that the property chain holds: (prov:qualifiedEnd o prov:atTime) rdfs:subPropertyOf prov:endedAtTime.
The time at which an activity started. See also prov:endedAtTime.
It is the intent that the property chain holds: (prov:qualifiedStart o prov:atTime) rdfs:subPropertyOf prov:startedAtTime.
A data property linking an addition with the addend value.
A data property linking an exponentiation operation with the base value.
A data property linking a subtraction with the difference value.
A data property linking a division with the dividend value.
A data property linking a division with the divisor value.
A data property linking an exponentiation operation with the exponent value.
A data property linking a multiplication with the factor value.
A data property linking a subtraction with the minuend value.
A data property linking a multiplication with the product value.
A data property linking a division with the quotient value.
A data property linking an entity with a reference (e.g. bibliographic) to another resource.
A data property linking a subtraction with the subtrahend value.
A data property linking an addition with the sum value.
A data property linking an entity to its value.
A computational sample is a representative system of a material for analysis through computational methods in the context of materials science.
In mathematics, a plane is a two-dimensional space or flat surface that extends indefinitely.
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.
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.
Vector is a quantity that has a magnitude and direction.
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 \(Q = nU\).
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.
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.
An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
An organization is a social or legal institution such as a company, society, etc.
Person agents are people.
A software agent is running software.
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.
An arithmetic operation by which the total or sum of two or more numbers is computed, symbolized by the plus symbol +.
Barostat is an algorithm used in molecular dynamics simulations to control system pressure.
Bulk modulus is a property that quantifies a material's resistance to uniform compression.
A calculated property is a property of a material resulting from a calculation or simulation.
Computational method is a method used to numerically solve mathematical models and study the behaviour of physical systems.
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.
An arithmetic operation by which the quotient of two numbers (dividend and divisor) is computed, symbolized by / or ÷.
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.
Energy is a physical quantity characterizing the ability of a system to do work.
Energy calculation is an activity where the energy of the system is computed within the given optimization constraints.
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 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 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.
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.
Force is a physical quantity that represents an interaction that causes mass to accelerate. It is a vector quantity, having both magnitude and direction.
According to Newton's second law of motion, force is the product of mass and acceleration (F = ma).
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.
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 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 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.
Helmholtz free energy is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature.
Input Parameter is a parameter provided as input to the software tool performing the numerical calculations.
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.
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 is the energy due to motion.
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.
Length is a physical quantity that measures the distance between two points.
Length is can also be understood to mean the longest dimension of an object.
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).
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.
Some of the most commonly used MLIP are: Atomic Cluster Expansion (ACE), Moment Tensor Potential (MTP) and Neural Network Potential (NNP)
Mass is a physical quantity that defines the amount of matter of a body. Mass is force divided by acceleration.
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.
Modified Embedded Atom Model is an interatomic potential which extends EAM to include angular forces.
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’.
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.
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.
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.
An arithmetic operation by which the product of two numbers is computed, symbolized by x or *.
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 is a parameter resulting from a software tool performing the numerical calculations.
Periodic boundary conditions (PBCs) are input parameters that define the directions in which the simulation cell is replicated to approximate an infinite system.
Attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively.
Point defect creation is a type of structure manipulation to introduce a point defect, i.e. add, delete or substitute atoms.
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.
Potential energy is the energy of position or orientation in a field of force.
Pressure is a physical quantity that expresses the normal force acting on a surface divided by the area of that surface.
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 are the degrees of freedom allowed for the relaxation of the simulation cell in an atomistic simulation.
The instances of this class indicate the type of relaxation allowed, i.e. relaxation of the atomic positions, cell volume and cell shape.
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.
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.
A simulation algorithm is a computational method used to represent and approximate a system's behavior based on mathematical models and input parameters.
The simulation cell length refers to the length (dimension) of the simulation cell or box.
The simulation cell volume refers to the volume of the simulation cell or box.
Simulation parameter is a parameter for a software tool to perform numerical calculations.
Simulation run time is the actual elapsed time taken to execute a simulation on a computing system.
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.
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.
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).
Structure manipulation is an activity where methods are applied to a structure (e.g. atomic structure) to modify it.
An arithmetic operation by which the removal of a number from another number or amount is computed, symbolized by the minus symbol -.
Temperature is a physical quantity that expresses the average measure of the kinetic energy of a system of particles.
Thermodynamic free energy is the energy in a physical system that can be converted to do work.
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.
It is commonly used in molecular simulations to calculate free energies of solvation, binding, or phase transitions.
Thermostat is an algorithm used in molecular dynamics simulations to control the system's temperature.
Time is a base quantity in the measuring system upon which SI is based used to sequence and measure duration of events.
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
In mechanics, it is the sum of potential energy and kinetic energy.
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.
Volume is a physical quantity that measures the three-dimensional space contained within an object or shape.
Volume range is an input parameter that indicates the predefined limits for the system's volume variation in a simulation.
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.
An ExchangeCorrelationEnergyFunctional is a functional to compute the exchange correlation energy.
Exchange Correlation Energy Functional
A GeneralizedGradientApproximation is a classification of exchange correlation energy functionals that only use the local value of the electronic density and its gradient.
Generalized Gradient Approximation
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 Functional
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 Generalized Gradient Approximation
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.
Hybrid Meta Generalized Gradient Approximation
A LDA is a classification of exchange correlation energy functionals that only use the local value of the electronic density.
Local Density Approximation
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.
Meta Generalized Gradient Approximation
Substitution of an atom to create an impurity.
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.
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.
Atomic positions are allowed to change in the calculation.
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.
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.
Equation of state proposed by Albert Francis Birch in 1947, based on the Murnaghan equation.
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.
In the canonical ensemble the temperature, volume, and the number of particles of every species are kept constant.
Cell shape is allowed to change in the calculation.
Cell volume is allowed to change in the calculation.
Deletion of an atom to create a vacancy.
An explicit k-point mesh refers to an input where the software will use exactly the points provided.
A gamma-centered k-point mesh refers to a grid where the k-points are arranged symmetrically around the Gamma point (k = 0).
In the grand canonical ensemble the temperature, volume, and the chemical potential are kept constant.
In the isoenthalpic-isobaric ensemble the enthalpy, pressure, and the number of particles of every species are kept constant.
In the isothermal-isobaric ensemble the temperature, pressure, and the number of particles of every species are kept constant.
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.
"Computer Simulation of Liquids", ISBN-13 : ‎978-0198556459
In the microcanonical ensemble the energy, volume, and the number of particles of every species are kept constant.
A Monkhorst-Pack k-point mesh refers to a regular grid of k-points for sampling the Brillouin zone.
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.
"Finite Deformation of an Elastic Solid", Applied mathematics series, ISSN 0272-1643
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.
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.
Input parameter defining whether periodicity in the X-axis of the simulation cell is enabled.
In most cases, it refers to the use of periodic boundary conditions in molecular dynamics.
Input parameter defining whether periodicity in the Y-axis of the simulation cell is enabled.
Input parameter defining whether periodicity in the Z-axis of the simulation cell is enabled.
EOS calculation using a third-order polynomial fit.
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.
Equation of state proposed by Pascal Vinet in 1987. It is a modification of the Birch–Murnaghan equation of state.