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. https://creativecommons.org/licenses/by/4.0/ Atomistic Simulation Methods Ontology (ASMO) https://github.com/OCDO/asmo 1.0.0 Abril Azocar Guzman. (2024). Atomistic Simulation Methods Ontology. Zenodo. https://doi.org/10.5281/zenodo.10805591 Ontology Specification https://ror.org/05qj6w324 https://raw.githubusercontent.com/OCDO/.github/refs/heads/main/profile/ocdo_logo.png 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source 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. Asiyah Yu Lin, Jie Zheng, Yongqun He 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). definition 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. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. preferred label The preferred lexical label for a resource, in a given language. The relation between a computational sample and the calculated property. has calculated property The relation between an activity and the type of computation method employed. has computational method The relation between a Simulation activity and the input parameters used. has input parameter The relation between an activity and the interatomic potential used. has interatomic potential The relation between a Simulation activity and the output parameters used. has output parameter has plane The relation between an Energy Calculation activity and the relaxation degrees of freedom set as constraints in the calculation. has relaxation DOF The relation between a Shear spatial transformation and a specific plane within a material where shear deformation is applied. has shear plane The relation between a Simulation activity and the simulation parameters used (or physical quantities used as simulation parameters). has simulation parameter The relation between an activity and the statistical ensemble set in the simulation. has statistical ensemble The relation between an entity and the unit of the quantity. (e.g. eV for energy cutoff) has unit The relation between a Simulation activity and a simulation algorithm used or implemented as part of the simulation or calculation. uses simulation algorithm The relation between a calculated property and the activity through which it was obtained. was calculated by The relation between an entity and its vectors. has vector 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. actedOnBehalfOf starting-point agents-responsibility hadDelegate generated expanded entities-activities prov:generated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions. wasGeneratedBy influenced expanded agents-responsibility wasInfluencedBy A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven . used starting-point entities-activities wasUsedBy An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity. wasAssociatedWith starting-point agents-responsibility wasAssociateFor Attribution is the ascribing of an entity to an agent. wasAttributedTo starting-point agents-responsibility Attribution is the ascribing of an entity to an agent. contributed 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. wasDerivedFrom starting-point derivations 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. hadDerivation 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 starting-point entities-activities generated 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 <a href="#owl-profile">PROV-O OWL Profile</a>. wasInfluencedBy qualified agents-responsibility 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. influenced influencee: an identifier (o2) for an entity, activity, or agent; http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence influencer: an identifier (o1) for an ancestor entity, activity, or agent that the former depends on; http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence 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. wasInformedBy starting-point entities-activities informed hasXCFunctional represents the relationship between a density functional theory method and the exchange-correlation energy functionals it takes. has XC functional A data property linking an addition with the addend value. has addend A data property linking an exponentiation operation with the base value. has base A data property linking a subtraction with the difference value. has difference A data property linking a division with the dividend value. has dividend A data property linking a division with the divisor value. has divisor A data property linking an exponentiation operation with the exponent value. has exponent A data property linking a multiplication with the factor value. has factor A data property linking a subtraction with the minuend value. has minuend A data property linking a multiplication with the product value. has product A data property linking a division with the quotient value. has quotient A data property linking an entity with a reference (e.g. bibliographic) to another resource. has reference A data property linking a subtraction with the subtrahend value. has subtrahend A data property linking an addition with the sum value. has sum A data property linking an entity to its value. has value The time at which an activity ended. See also prov:startedAtTime. endedAtTime starting-point entities-activities 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. startedAtTime starting-point entities-activities It is the intent that the property chain holds: (prov:qualifiedStart o prov:atTime) rdfs:subPropertyOf prov:startedAtTime. The axial next-nearest neighbor Ising (ANNNI) model is a variant of the Ising model used to describe the behavior of magnetic materials. The ANNNI model includes interactions between next-nearest neighbors along one of the crystallographic axes of the lattice, in addition to the nearest-neighbor interactions considered in the standard Ising model. https://doi.org/10.1098/rspa.2020.0319 In the simplest case of the comparison in stability of fcc versus hcp lattices, fcc corresponds to the ‘ferromagnetic’ arrangement of spins and is stable in the Ising model for J > 0; and hcp is represented by ‘antiferromagnetic’ spin arrangement and is stable if J < 0. ANNNI Model Axial Next-Nearest-Neighbour Ising Model 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. Ab Initio Molecular Dynamics AIMD Ab initio MD An arithmetic operation by which the total or sum of two or more numbers is computed, symbolized by the plus symbol +. Addition Barostat is an algorithm used in molecular dynamics simulations to control system pressure. Barostat Bulk modulus is a property that quantifies a material's resistance to uniform compression. Bulk Modulus B K Calculated Property A calculated property is a property of a material resulting from a calculation or simulation. Compression Test Computational method is a method used to numerically solve mathematical models and study the behaviour of physical systems. Computational Method 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. Density Functional Theory DFT An arithmetic operation by which the quotient of two numbers (dividend and divisor) is computed, symbolized by / or ÷. Division Elastic Constant Elastic Tensor 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. https://doi.org/10.1103/PhysRevLett.50.1285 E(r) = \sum_i F_i (\rho_i(r_i)) + 1/2 \sum_{i,j} \varphi(r_{i,j}) Embedded Atom Model EAM Energy is a physical quantity characterizing the ability of a system to do work. https://doi.org/10.1351/goldbook.E02101 Energy https://qudt.org/vocab/quantitykind/Energy https://si-digital-framework.org/quantities/ENGY E 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 Calculation Energy cutoff is the input parameter that defines the maximum kinetic energy of plane waves included in the basis set for electronic structure calculations. Energy Cutoff 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. Equation of State Fit EOS Equation of State 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. Exponentiation Flow Stress Force is a physical quantity that represents an interaction that causes mass to accelerate. It is a vector quantity, having both magnitude and direction. https://doi.org/10.1351/goldbook.F02480 F = ma According to Newton's second law of motion, force is the product of mass and acceleration (F = ma). Force https://qudt.org/vocab/quantitykind/Force https://si-digital-framework.org/quantities/FORC F 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. Formation Energy Free Energy 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. Free Energy Calculation 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. G=H-TS Gibbs Free Energy G Helmholtz free energy is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature. F = U-TS Helmholtz Free Energy F Input Parameter is a parameter provided as input to the software tool performing the numerical calculations. Input Parameter 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. https://en.wikipedia.org/wiki/Interatomic_potential Interatomic Potential K-Point mesh type is an input parameter that indicates how the Bloch vectors (k points) used to sample the Brillouin zone are provided. KPoint Mesh Kinetic energy is the energy due to motion. https://doi.org/10.1351/goldbook.K03402 E_k = (mv^2)/2 Kinetic Energy 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. Kinetic Monte Carlo Method kMC Length is a physical quantity that measures the distance between two points. https://doi.org/10.1351/goldbook.L03498 Length is can also be understood to mean the longest dimension of an object. Length https://qudt.org/vocab/quantitykind/Length https://si-digital-framework.org/quantities/LENG l 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). https://doi.org/10.1021/acs.jctc.4c00135 E(r) = 4\epsilon[(\sigma/r)^{12}-(\sigma/r)^{6}] Lennard-Jones Potential 12-6 potential LJ potential 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. https://doi.org/10.1016/j.actamat.2021.116980 Some of the most commonly used MLIP are: Atomic Cluster Expansion (ACE), Moment Tensor Potential (MTP) and Neural Network Potential (NNP) Machine Learning Potential MLIP MLP Mass is a physical quantity that defines the amount of matter of a body. Mass is force divided by acceleration. https://doi.org/10.1351/goldbook.M03709 Mass https://qudt.org/vocab/quantitykind/Mass https://si-digital-framework.org/quantities/MASS m 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. https://en.wikipedia.org/wiki/Operation_(mathematics) Mathematical Operation http://purl.obolibrary.org/obo/NCIT_C54025 Modified Embedded Atom Model is an interatomic potential which extends EAM to include angular forces. https://doi.org/10.1103/PhysRevB.46.2727 Modified Embedded Atom Model MEAM 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’. https://doi.org/10.1038/npg.els.0003048 Molecular Dynamics MD 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. ISBN-13: 9780192524706 Force Field Molecular Force Field 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. Molecular Statics MS 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. Monte Carlo Method MC Monte Carlo Simulation An arithmetic operation by which the product of two numbers is computed, symbolized by x or *. http://purl.obolibrary.org/obo/NCIT_C90596 Multiplication Nanoindentation 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. Number Of Ionic Steps Output Parameter is a parameter resulting from a software tool performing the numerical calculations. Output Parameter Periodic boundary conditions (PBCs) are input parameters that define the directions in which the simulation cell is replicated to approximate an infinite system. Periodic Boundary Condition PBC Attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively. https://doi.org/10.1351/goldbook.Q04982 Physical Quantity Point defect creation is a type of structure manipulation to introduce a point defect, i.e. add, delete or substitute atoms. Point Defect Creation 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. ν = - transverse_strain / axial_strain Poisson's Ratio ν Potential energy is the energy of position or orientation in a field of force. https://doi.org/10.1351/goldbook.P04778 Potential Energy Pressure is a physical quantity that expresses the normal force acting on a surface divided by the area of that surface. https://doi.org/10.1351/goldbook.P04819 Pressure https://qudt.org/vocab/quantitykind/Pressure https://si-digital-framework.org/quantities/PRES P 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. Quasi-Harmonic Approximation 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. Relaxation Degrees of Freedom RelaxationDOF Rotation is a type of spatial transformation described by the motion of an object around a point or axis. Rotation Shear is a type of spatial transformation in which an object is distorted such that its shape changes while parallel lines remain parallel, but angles between them may change. This transformation shifts parts of the object in a specific direction, typically along one axis, while keeping the opposite axis fixed. Shear 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. Shear Modulus G Modulus of rigidity 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 A simulation algorithm is a computational method used to represent and approximate a system's behavior based on mathematical models and input parameters. Simulation Algorithm The simulation cell length refers to the length (dimension) of the simulation cell or box. Simulation Cell Length Box Length The simulation cell volume refers to the volume of the simulation cell or box. Simulation Cell Volume Simulation parameter is a parameter for a software tool to perform numerical calculations. Simulation Parameter Simulation run time is the actual elapsed time taken to execute a simulation on a computing system. Simulation Run Time 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. Simulation Time Spatial transformation is a type of structure manipulation to convert the coordinates of an image to the coordinates of a reference image. https://doi.org/10.1561/0600000009 The spatial transformations that involve translation or rotation are generally considered rigid body or Euclidean transformations, since the Euclidean distances within images are preserved. In contrast, the other ones are classified as non-rigid or elastic. Spatial Transformation Specific Heat Capacity 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. ISBN-13: 9780192524706 Statistical Ensemble 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). https://doi.org/10.1103/PhysRevB.31.5262 Stillinger-Weber Potential Strain Rate Stress Structure manipulation is an activity where methods are applied to a structure (e.g. atomic structure) to modify it. Structure Manipulation An arithmetic operation by which the removal of a number from another number or amount is computed, symbolized by the minus symbol -. Subtraction Temperature is a physical quantity that expresses the average measure of the kinetic energy of a system of particles. Temperature https://qudt.org/vocab/quantitykind/Temperature T Tensile Test Thermal Expansion Coefficient Thermodynamic free energy is the energy in a physical system that can be converted to do work. Thermodynamic Free Energy 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. Thermodynamic Integration Thermostat is an algorithm used in molecular dynamics simulations to control the system's temperature. Thermostat Time is a base quantity in the measuring system upon which SI is based used to sequence and measure duration of events. https://doi.org/10.1351/goldbook.T06375 Time https://qudt.org/vocab/quantitykind/Time https://si-digital-framework.org/quantities/TIME t 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 Time Step In mechanics, it is the sum of potential energy and kinetic energy. Total 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. Total Magnetic Moment Translation is a type of spatial transformation described by the motion of every point of an object by the same distance in a given direction. Translation Virial Pressure Volume is a physical quantity that measures the three-dimensional space contained within an object or shape. Volume https://qudt.org/vocab/quantitykind/Volume https://si-digital-framework.org/quantities/VOLU V Volume range is an input parameter that indicates the predefined limits for the system's volume variation in a simulation. Volume Range Yield Stress 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. Young’s Modulus E A computational sample is a representative system of a material for analysis through computational methods in the context of materials science. Computational Sample In mathematics, a plane is a two-dimensional space or flat surface that extends indefinitely. 𝑎 𝑥 + 𝑏 𝑦 + 𝑐 𝑧 + 𝑑 = 0 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. 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. Simulation Cell Box Supercell Vector is a quantity that has a magnitude and direction. Vector 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 \(Q = nU\). Unit Activity starting-point entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig 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. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Activity http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Activity Agent starting-point agents-responsibility 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. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Agent Entity starting-point entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-entity http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Entity Organization expanded agents-responsibility An organization is a social or legal institution such as a company, society, etc. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types Person expanded agents-responsibility Person agents are people. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types SoftwareAgent expanded agents-responsibility A software agent is running software. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types 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. Add Atom 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 Barostat 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. https://doi.org/10.1063/1.439486 Andersen Thermostat Atomic positions are allowed to change in the calculation. Atomic Position Relaxation 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 Barostat 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. https://doi.org/10.1007/978-94-009-6463-1_16 Berendsen Thermostat Equation of state proposed by Albert Francis Birch in 1947, based on the Murnaghan equation. https://doi.org/10.1103/PhysRev.71.809 https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state Birch-Murnaghan 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. https://doi.org/10.1063/1.2408420 Bussi-Donadio-Parrinello In the canonical ensemble the temperature, volume, and the number of particles of every species are kept constant. ISBN-13: 978-0323902922 Canonical Ensemble NVT ensemble Cell shape is allowed to change in the calculation. Cell Shape Relaxation Cell volume is allowed to change in the calculation. Cell Volume Relaxation Deletion of an atom to create a vacancy. Delete Atom An explicit k-point mesh refers to an input where the software will use exactly the points provided. Explicit KPoint Mesh A gamma-centered k-point mesh refers to a grid where the k-points are arranged symmetrically around the Gamma point (k = 0). Gamma-Centered KPoint Mesh In the grand canonical ensemble the temperature, volume, and the chemical potential are kept constant. ISBN-13: 978-0323902922 Grand Canonical Ensemble µVT ensemble In the isoenthalpic-isobaric ensemble the enthalpy, pressure, and the number of particles of every species are kept constant. ISBN-13: 978-0323902922 Isoenthalpic–Isobaric Ensemble NPH ensemble In the isothermal-isobaric ensemble the temperature, pressure, and the number of particles of every species are kept constant. ISBN-13: 978-0323902922 Isothermal–Isobaric Ensemble NPT ensemble 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 Langevin In the microcanonical ensemble the energy, volume, and the number of particles of every species are kept constant. ISBN-13: 978-0323902922 Microcanonical Ensemble NVE ensemble A Monkhorst-Pack k-point mesh refers to a regular grid of k-points for sampling the Brillouin zone. Monkhorst Pack KPoint Mesh 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 https://en.wikipedia.org/wiki/Murnaghan_equation_of_state Murnaghan 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. https://doi.org/10.1063%2F1.447334 https://doi.org/10.1103%2FPhysRevA.31.1695 Nose-Hoover 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. Parrinello-Rahman 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. Periodicity in X-direction Input parameter defining whether periodicity in the Y-axis of the simulation cell is enabled. In most cases, it refers to the use of periodic boundary conditions in molecular dynamics. Periodicity in Y-direction Input parameter defining whether periodicity in the Z-axis of the simulation cell is enabled. In most cases, it refers to the use of periodic boundary conditions in molecular dynamics. Periodicity in Z-direction Substitution of an atom to create an impurity. Substitute Atom EOS calculation using a third-order polynomial fit. 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. Velocity Rescaling Equation of state proposed by Pascal Vinet in 1987. It is a modification of the Birch–Murnaghan equation of state. https://doi.org/10.1103/PhysRevB.35.1945 https://en.wikipedia.org/wiki/Rose%E2%80%93Vinet_equation_of_state Vinet Rose–Vinet