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Atomistic Simulation Methods Ontology (ASMO)

This version:
http://purls.helmholtz-metadaten.de/asmo/v1.0.0
Revision:
1.0.0
Authors:
https://orcid.org/0000-0001-7564-7990
Contributors:
https://orcid.org/0000-0001-9560-4728
https://orcid.org/0000-0002-5149-603X
https://orcid.org/0000-0002-6776-1213
https://orcid.org/0000-0003-0698-4891
See also:
https://github.com/OCDO/asmo
Funder:
https://ror.org/05qj6w324
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://creativecommons.org/licenses/by/4.0/
Visualization:
Visualize with WebVowl
Cite as:
Abril Azocar Guzman. (2024). Atomistic Simulation Methods Ontology. Zenodo. https://doi.org/10.5281/zenodo.10805591
Provenance of this page
Pre-release

Atomistic Simulation Methods Ontology (ASMO): Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Named Individuals

Atomistic Simulation Methods Ontology (ASMO): Description back to ToC

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.

Cross-reference for Atomistic Simulation Methods Ontology (ASMO) classes, object properties and data properties back to ToC

This section provides details for each class and property defined by Atomistic Simulation Methods Ontology (ASMO).

Classes

Ab Initio Molecular Dynamicsc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/AbInitioMolecularDynamics

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.
has super-classes
Computational Method c

Activityc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Activity

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.
Is defined by
http://www.w3.org/ns/prov-o#
has sub-classes
Mathematical Operation c, Simulation c, Structure Manipulation c
is in domain of
endedAtTime dp, generated op, has computational method op, has interatomic potential op, has statistical ensemble op, startedAtTime dp, used op, wasAssociatedWith op, wasInformedBy op
is in range of
was calculated by op, wasGeneratedBy op, wasInformedBy op
is disjoint with
Entity c

Additionc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Addition

An arithmetic operation by which the total or sum of two or more numbers is computed, symbolized by the plus symbol +.
has super-classes
Mathematical Operation c
is in domain of
has addend dp, has sum dp

Agentc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Agent

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.
Is defined by
http://www.w3.org/ns/prov-o#
has sub-classes
Organization c, Person c, SoftwareAgent c
is in domain of
actedOnBehalfOf op
is in range of
actedOnBehalfOf op, wasAssociatedWith op, wasAttributedTo op

ANNNI Modelc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ANNNImodel

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.
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.
Source
https://doi.org/10.1098/rspa.2020.0319
has super-classes
Simulation Algorithm c

Barostatc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Barostat

Barostat is an algorithm used in molecular dynamics simulations to control system pressure.
has super-classes
Simulation Algorithm c
has members
Andersen Barostat ni, Berendsen Barostat ni, Parrinello-Rahman ni

Bulk Modulusc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/BulkModulus

Bulk modulus is a property that quantifies a material's resistance to uniform compression.
has super-classes
Calculated Property c

Calculated Propertyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/CalculatedProperty

A calculated property is a property of a material resulting from a calculation or simulation.
has sub-classes
Bulk Modulus c, Formation Energy c, Poisson's Ratio c, Shear Modulus c, Total Magnetic Moment c, Young’s Modulus c
is in domain of
was calculated by op

Computational Methodc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ComputationalMethod

Computational method is a method used to numerically solve mathematical models and study the behaviour of physical systems.
has sub-classes
Ab Initio Molecular Dynamics c, Density Functional Theory c, Molecular Dynamics c, Molecular Statics c, Monte Carlo Method c
is in range of
has computational method op

Density Functional Theoryc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/DensityFunctionalTheory

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.
has super-classes
Computational Method c
is in domain of
has XC functional op

Divisionc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Division

An arithmetic operation by which the quotient of two numbers (dividend and divisor) is computed, symbolized by / or ÷.
has super-classes
Mathematical Operation c
is in domain of
has dividend dp, has divisor dp, has quotient dp

Embedded Atom Modelc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/EmbeddedAtomModel

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.
Source
https://doi.org/10.1103/PhysRevLett.50.1285
has super-classes
Interatomic Potential c

Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Energy

Energy is a physical quantity characterizing the ability of a system to do work.
Source
https://doi.org/10.1351/goldbook.E02101
has super-classes
Physical Quantity c
has sub-classes
Formation Energy c, Free Energy c, Kinetic Energy c, Potential Energy c, Thermodynamic Free Energy c, Total Energy c

Energy Calculationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/EnergyCalculation

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.
has super-classes
Simulation c
is in domain of
has relaxation DOF op

Energy Cutoffc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/EnergyCutoff

Energy cutoff is the input parameter that defines the maximum kinetic energy of plane waves included in the basis set for electronic structure calculations.
has super-classes
Input Parameter c

Entityc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Entity

An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
Is defined by
http://www.w3.org/ns/prov-o#
is in domain of
wasAttributedTo op, wasDerivedFrom op, wasGeneratedBy op
is in range of
generated op, used op, wasDerivedFrom op
is disjoint with
Activity c

Equation of State Fitc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/EquationOfStateFit

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.
has super-classes
Simulation Algorithm c
has members
Birch-Murnaghan ni, Murnaghan ni, Third-order polynomial fit ni, Vinet ni

Exchange Correlation Energy Functionalc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/ExchangeCorrelationEnergyFunctional

An ExchangeCorrelationEnergyFunctional is a functional to compute the exchange correlation energy.
has sub-classes
Generalized Gradient Approximation c, Hybrid Functional c, Local Density Approximation c, Meta Generalized Gradient Approximation c
is in range of
has XC functional op

Exponentiationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Exponentiation

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.
has super-classes
Mathematical Operation c
is in domain of
has base dp, has exponent dp

Forcec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Force

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).
Source
https://doi.org/10.1351/goldbook.F02480
has super-classes
Physical Quantity c

Force Fieldc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MolecularForceField

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.
Source
ISBN-13: 9780192524706
has super-classes
Interatomic Potential c

Formation Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/FormationEnergy

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.
has super-classes
Calculated Property c, Energy c

Free Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/FreeEnergy

has super-classes
Energy c

Free Energy Calculationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/FreeEnergyCalculation

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.
has super-classes
Simulation c

Generalized Gradient Approximationc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/GeneralizedGradientApproximation

A GeneralizedGradientApproximation is a classification of exchange correlation energy functionals that only use the local value of the electronic density and its gradient.
has super-classes
Exchange Correlation Energy Functional c

Gibbs Free Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/GibbsFreeEnergy

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.
has super-classes
Thermodynamic Free Energy c

Helmholtz Free Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/HelmholtzFreeEnergy

Helmholtz free energy is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature.
has super-classes
Thermodynamic Free Energy c

Hybrid Functionalc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/HybridFunctional

A hybrid functional is a classification of exchange correlation energy functionals that combine exact exchange from HartreeFock theory with another exchange correlation energy approximation.
has super-classes
Exchange Correlation Energy Functional c
has sub-classes
Hybrid Generalized Gradient Approximation c, Hybrid Meta Generalized Gradient Approximation c

Hybrid Generalized Gradient Approximationc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/HybridGeneralizedGradientApproximation

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.
has super-classes
Hybrid Functional c

Hybrid Meta Generalized Gradient Approximationc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/HybridMetaGeneralizedGradientApproximation

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.
has super-classes
Hybrid Functional c

Input Parameterc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/InputParameter

Input Parameter is a parameter provided as input to the software tool performing the numerical calculations.
has super-classes
Simulation Parameter c
has sub-classes
Energy Cutoff c, KPoint Mesh c, Number Of Ionic Steps c, Periodic Boundary Condition c, Time Step c, Volume Range c
is in range of
has input parameter op

Interatomic Potentialc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/InteratomicPotential

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.
Source
https://en.wikipedia.org/wiki/Interatomic_potential
has sub-classes
Embedded Atom Model c, Force Field c, Lennard-Jones Potential c, Machine Learning Potential c, Modified Embedded Atom Model c, Stillinger-Weber Potential c
is in range of
has interatomic potential op

Kinetic Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/KineticEnergy

Kinetic energy is the energy due to motion.
Source
https://doi.org/10.1351/goldbook.K03402
has super-classes
Energy c

Kinetic Monte Carlo Methodc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/KineticMonteCarloMethod

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.
has super-classes
Monte Carlo Method c

KPoint Meshc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/KPointMesh

K-Point mesh type is an input parameter that indicates how the Bloch vectors (k points) used to sample the Brillouin zone are provided.
has super-classes
Input Parameter c
has members
Explicit KPoint Mesh ni, Gamma-Centered KPoint Mesh ni, Monkhorst Pack KPoint Mesh ni

Lengthc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Length

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.
Source
https://doi.org/10.1351/goldbook.L03498
has super-classes
Physical Quantity c

Lennard-Jones Potentialc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Lennard-JonesPotential

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).
Source
https://doi.org/10.1021/acs.jctc.4c00135
has super-classes
Interatomic Potential c

Local Density Approximationc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/LocalDensityApproximation

A LDA is a classification of exchange correlation energy functionals that only use the local value of the electronic density.
has super-classes
Exchange Correlation Energy Functional c

Machine Learning Potentialc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MachineLearningPotential

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)
Source
https://doi.org/10.1016/j.actamat.2021.116980
has super-classes
Interatomic Potential c

Massc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Mass

Mass is a physical quantity that defines the amount of matter of a body. Mass is force divided by acceleration.
Source
https://doi.org/10.1351/goldbook.M03709
has super-classes
Physical Quantity c

Mathematical Operationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MathematicalOperation

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.
Source
https://en.wikipedia.org/wiki/Operation_(mathematics)
has super-classes
Activity c
has sub-classes
Addition c, Division c, Exponentiation c, Multiplication c, Subtraction c

Meta Generalized Gradient Approximationc back to ToC or Class ToC

IRI: https://w3id.org/mdo/calculation/MetaGeneralizedGradientApproximation

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.
has super-classes
Exchange Correlation Energy Functional c

Modified Embedded Atom Modelc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ModifiedEmbeddedAtomModel

Modified Embedded Atom Model is an interatomic potential which extends EAM to include angular forces.
Source
https://doi.org/10.1103/PhysRevB.46.2727
has super-classes
Interatomic Potential c

Molecular Dynamicsc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MolecularDynamics

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’.
Source
https://doi.org/10.1038/npg.els.0003048
has super-classes
Computational Method c

Molecular Staticsc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MolecularStatics

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.
has super-classes
Computational Method c

Monte Carlo Methodc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MonteCarloMethod

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.
has super-classes
Computational Method c
has sub-classes
Kinetic Monte Carlo Method c

Multiplicationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Multiplication

An arithmetic operation by which the product of two numbers is computed, symbolized by x or *.
Source
http://purl.obolibrary.org/obo/NCIT_C90596
has super-classes
Mathematical Operation c
is in domain of
has factor dp, has product dp

Number Of Ionic Stepsc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps

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.
has super-classes
Input Parameter c, Output Parameter c

Organizationc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Organization

An organization is a social or legal institution such as a company, society, etc.
Is defined by
http://www.w3.org/ns/prov-o#
has super-classes
Agent c

Output Parameterc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/OutputParameter

Output Parameter is a parameter resulting from a software tool performing the numerical calculations.
has super-classes
Simulation Parameter c
has sub-classes
Number Of Ionic Steps c
is in range of
has output parameter op

Periodic Boundary Conditionc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PeriodicBoundaryCondition

Periodic boundary conditions (PBCs) are input parameters that define the directions in which the simulation cell is replicated to approximate an infinite system.
has super-classes
Input Parameter c
has members
Periodicity in X-direction ni, Periodicity in Y-direction ni, Periodicity in Z-direction ni

Personc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Person

Person agents are people.
Is defined by
http://www.w3.org/ns/prov-o#
has super-classes
Agent c

Physical Quantityc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PhysicalQuantity

Attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively.
Source
https://doi.org/10.1351/goldbook.Q04982
has sub-classes
Energy c, Force c, Length c, Mass c, Pressure c, Temperature c, Time c, Volume c
is in domain of
was calculated by op

Planec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/cmso/Plane

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.
is in range of
has plane op

Point Defect Creationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PointDefectCreation

Point defect creation is a type of structure manipulation to introduce a point defect, i.e. add, delete or substitute atoms.
has super-classes
Structure Manipulation c
has members
Add Atom ni, Delete Atom ni, Substitute Atom ni

Poisson's Ratioc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PoissonsRatio

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.
has super-classes
Calculated Property c

Potential Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PotentialEnergy

Potential energy is the energy of position or orientation in a field of force.
Source
https://doi.org/10.1351/goldbook.P04778
has super-classes
Energy c

Pressurec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Pressure

Pressure is a physical quantity that expresses the normal force acting on a surface divided by the area of that surface.
Source
https://doi.org/10.1351/goldbook.P04819
has super-classes
Physical Quantity c

Quasi-Harmonic Approximationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/QuasiHarmonicApproximation

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.
has super-classes
Simulation Algorithm c

Relaxation Degrees of Freedomc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/RelaxationDOF

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.
is in range of
has relaxation DOF op
has members
Atomic Position Relaxation ni, Cell Shape Relaxation ni, Cell Volume Relaxation ni

Rotationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Rotation

Rotation is a type of spatial transformation described by the motion of an object around a point or axis.
has super-classes
Spatial Transformation c

Shearc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Shear

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.
has super-classes
Spatial Transformation c
is in domain of
has plane op

Shear Modulusc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ShearModulus

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.
has super-classes
Calculated Property c

Simulationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Simulation

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.
has super-classes
Activity c
has sub-classes
Energy Calculation c, Free Energy Calculation c
is in domain of
has input parameter op, has output parameter op, has simulation parameter op, uses simulation algortihm op

Simulation Algorithmc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SimulationAlgorithm

A simulation algorithm is a computational method used to represent and approximate a system's behavior based on mathematical models and input parameters.
has sub-classes
ANNNI Model c, Barostat c, Equation of State Fit c, Quasi-Harmonic Approximation c, Thermodynamic Integration c, Thermostat c
is in range of
uses simulation algortihm op

Simulation Cellc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/cmso/SimulationCell

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 Parameterc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SimulationParameter

Simulation parameter is a parameter for a software tool to perform numerical calculations.
has sub-classes
Input Parameter c, Output Parameter c

Simulation Run Timec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SimulationRunTime

Simulation run time is the actual elapsed time taken to execute a simulation on a computing system.
has super-classes
Time c

Simulation Timec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SimulationTime

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.
has super-classes
Time c

SoftwareAgentc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#SoftwareAgent

A software agent is running software.
Is defined by
http://www.w3.org/ns/prov-o#
has super-classes
Agent c

Spatial Transformationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SpatialTransformation

Spatial transformation is a type of structure manipulation to convert the coordinates of an image to the coordinates of a reference image.
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.
Source
https://doi.org/10.1561/0600000009
has super-classes
Structure Manipulation c
has sub-classes
Rotation c, Shear c, Translation c

Statistical Ensemblec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/StatisticalEnsemble

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.
Source
ISBN-13: 9780192524706
is in range of
has statistical ensemble op
has members
Canonical Ensemble ni, Grand Canonical Ensemble ni, Isoenthalpic–Isobaric Ensemble ni, Isothermal–Isobaric Ensemble ni, Microcanonical Ensemble ni

Stillinger-Weber Potentialc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/StillingerWeberPotential

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).
Source
https://doi.org/10.1103/PhysRevB.31.5262
has super-classes
Interatomic Potential c

Structure Manipulationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/StructureManipulation

Structure manipulation is an activity where methods are applied to a structure (e.g. atomic structure) to modify it.
has super-classes
Activity c
has sub-classes
Point Defect Creation c, Spatial Transformation c

Subtractionc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Subtraction

An arithmetic operation by which the removal of a number from another number or amount is computed, symbolized by the minus symbol -.
has super-classes
Mathematical Operation c
is in domain of
has difference dp, has minuend dp, has subtrahend dp

Temperaturec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Temperature

Temperature is a physical quantity that expresses the average measure of the kinetic energy of a system of particles.
has super-classes
Physical Quantity c

Thermodynamic Free Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ThermodynamicFreeEnergy

Thermodynamic free energy is the energy in a physical system that can be converted to do work.
has super-classes
Energy c
has sub-classes
Gibbs Free Energy c, Helmholtz Free Energy c

Thermodynamic Integrationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ThermodynamicIntegration

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.
has super-classes
Simulation Algorithm c

Thermostatc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Thermostat

Thermostat is an algorithm used in molecular dynamics simulations to control the system's temperature.
has super-classes
Simulation Algorithm c
has members
Andersen Thermostat ni, Berendsen Thermostat ni, Bussi-Donadio-Parrinello ni, Langevin ni, Nose-Hoover ni, Velocity Rescaling ni

Timec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Time

Time is a base quantity in the measuring system upon which SI is based used to sequence and measure duration of events.
Source
https://doi.org/10.1351/goldbook.T06375
has super-classes
Physical Quantity c
has sub-classes
Simulation Run Time c, Simulation Time c

Time Stepc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/TimeStep

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
has super-classes
Input Parameter c

Total Energyc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/TotalEnergy

In mechanics, it is the sum of potential energy and kinetic energy.
has super-classes
Energy c

Total Magnetic Momentc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/TotalMagneticMoment

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.
has super-classes
Calculated Property c

Translationc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Translation

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.
has super-classes
Spatial Transformation c

Unitc back to ToC or Class ToC

IRI: http://qudt.org/schema/qudt/Unit

Is defined by
http://qudt.org/2.1/schema/qudt
is in range of
has unit op

Vectorc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/cmso/Vector

Vector is a quantity that has a magnitude and direction.
is in range of
has vector op

Volumec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Volume

Volume is a physical quantity that measures the three-dimensional space contained within an object or shape.
has super-classes
Physical Quantity c

Volume Rangec back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/VolumeRange

Volume range is an input parameter that indicates the predefined limits for the system's volume variation in a simulation.
has super-classes
Input Parameter c

Young’s Modulusc back to ToC or Class ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/YoungsModulus

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.
has super-classes
Calculated Property c

Object Properties

actedOnBehalfOfop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#actedOnBehalfOf

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.
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Agent c
has range
Agent c

generatedop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#generated

Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
influenced op
has domain
Activity c
has range
Entity c
is inverse of
wasGeneratedBy op

has computational methodop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasComputationalMethod

The relation between an activity and the type of computation method employed.
has domain
Activity c
has range
Computational Method c

has input parameterop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasInputParameter

The relation between a Simulation activity and the input parameters used.
has super-properties
has simulation parameter op
has domain
Simulation c
has range
Input Parameter c

has interatomic potentialop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasInteratomicPotential

The relation between an activity and the interatomic potential used.
has domain
Activity c
has range
Interatomic Potential c

has output parameterop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasOutputParameter

The relation between a Simulation activity and the output parameters used.
has super-properties
has simulation parameter op
has domain
Simulation c
has range
Output Parameter c

has planeop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasPlane

has domain
Shear c
has range
Plane c

has relaxation DOFop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasRelaxationDOF

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

has simulation parameterop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasSimulationParameter

The relation between a Simulation activity and the simulation parameters used (or physical quantities used as simulation parameters).
has sub-properties
has input parameter op, has output parameter op
has domain
Simulation c
has range
Physical Quantity c or Simulation Parameter c

has statistical ensembleop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasStatisticalEnsemble

The relation between an activity and the statistical ensemble set in the simulation.
has domain
Activity c
has range
Statistical Ensemble c

has unitop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasUnit

The relation between an entity and the unit of the quantity. (e.g. eV for energy cutoff)
has domain
Calculated Property c or Physical Quantity c or Simulation Parameter c
has range
Unit c

has vectorop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/cmso/hasVector

The relation between an entity and its vectors.
has domain
Spatial Transformation c or Simulation Cell c
has range
Vector c

has XC functionalop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/calculation/hasXCFunctional

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

influencedop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#influenced

Is defined by
http://www.w3.org/ns/prov-o#
has sub-properties
generated op
is inverse of
wasInfluencedBy op

usedop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#used

A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven .
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Activity c
has range
Entity c

uses simulation algortihmop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/usesSimulationAlgortihm

The relation between a Simulation activity and a simulation algorithm used or implemented as part of the simulation or calculation.
has domain
Simulation c
has range
Simulation Algorithm c

was calculated byop back to ToC or Object Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/wasCalculatedBy

The relation between a calculated property and the activity through which it was obtained.
has domain
Calculated Property c
Physical Quantity c
has range
Activity c

wasAssociatedWithop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasAssociatedWith

An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity.
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Activity c
has range
Agent c

wasAttributedToop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasAttributedTo

Attribution is the ascribing of an entity to an agent.
Attribution is the ascribing of an entity to an agent.
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Entity c
has range
Agent c

wasDerivedFromop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasDerivedFrom

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.
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Entity c
has range
Entity c

wasGeneratedByop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasGeneratedBy

Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Entity c
has range
Activity c
is inverse of
generated op

wasInfluencedByop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasInfluencedBy

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.
Is defined by
http://www.w3.org/ns/prov-o#
has sub-properties
actedOnBehalfOf op, used op, wasAssociatedWith op, wasAttributedTo op, wasDerivedFrom op, wasGeneratedBy op, wasInformedBy op
has domain
has range
is inverse of
influenced op

wasInformedByop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasInformedBy

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.
Is defined by
http://www.w3.org/ns/prov-o#
has super-properties
wasInfluencedBy op
has domain
Activity c
has range
Activity c

Data Properties

endedAtTimedp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/prov#endedAtTime

The time at which an activity ended. See also prov:startedAtTime.
Is defined by
http://www.w3.org/ns/prov-o#
has domain
Activity c
has range
date time

has addenddp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasAddend

A data property linking an addition with the addend value.
has domain
Addition c
has range
float

has basedp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasBase

A data property linking an exponentiation operation with the base value.
has domain
Exponentiation c
has range
float

has differencedp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasDifference

A data property linking a subtraction with the difference value.
has domain
Subtraction c
has range
float

has dividenddp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasDividend

A data property linking a division with the dividend value.
has domain
Division c
has range
float

has divisordp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasDivisor

A data property linking a division with the divisor value.
has domain
Division c
has range
float

has exponentdp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasExponent

A data property linking an exponentiation operation with the exponent value.
has domain
Exponentiation c
has range
float

has factordp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasFactor

A data property linking a multiplication with the factor value.
has domain
Multiplication c
has range
float

has minuenddp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasMinuend

A data property linking a subtraction with the minuend value.
has domain
Subtraction c
has range
float

has productdp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasProduct

A data property linking a multiplication with the product value.
has domain
Multiplication c
has range
float

has quotientdp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasQuotient

A data property linking a division with the quotient value.
has domain
Division c
has range
float

has referencedp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasReference

A data property linking an entity with a reference (e.g. bibliographic) to another resource.
has domain
thing c
has range
anyURI

has subtrahenddp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasSubtrahend

A data property linking a subtraction with the subtrahend value.
has domain
Subtraction c
has range
float

has sumdp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasSum

A data property linking an addition with the sum value.
has domain
Addition c
has range
float

has valuedp back to ToC or Data Property ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/hasValue

A data property linking an entity to its value.
has domain
thing c
has range
float

startedAtTimedp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/prov#startedAtTime

The time at which an activity started. See also prov:endedAtTime.
Is defined by
http://www.w3.org/ns/prov-o#
has domain
Activity c
has range
date time

Named Individuals

Add Atomni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/AddAtom

Substitution of an atom to create an impurity.
belongs to
Point Defect Creation c

Andersen Barostatni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/AndersenBarostat

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.
belongs to
Barostat c

Andersen Thermostatni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/AndersenThermostat

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.
Source
https://doi.org/10.1063/1.439486
belongs to
Thermostat c

Atomic Position Relaxationni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/AtomicPositionRelaxation

Atomic positions are allowed to change in the calculation.
belongs to
Relaxation Degrees of Freedom c

Berendsen Barostatni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/BerendsenBarostat

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.
belongs to
Barostat c

Berendsen Thermostatni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/BerendsenThermostat

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.
Source
https://doi.org/10.1007/978-94-009-6463-1_16
belongs to
Thermostat c

Birch-Murnaghanni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/BirchMurnaghan

Equation of state proposed by Albert Francis Birch in 1947, based on the Murnaghan equation.
Source
https://doi.org/10.1103/PhysRev.71.809
https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state
belongs to
Equation of State Fit c

Bussi-Donadio-Parrinelloni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/BussiDonadioParrinello

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.
Source
https://doi.org/10.1063/1.2408420
belongs to
Thermostat c

Canonical Ensembleni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/CanonicalEnsemble

In the canonical ensemble the temperature, volume, and the number of particles of every species are kept constant.
Source
ISBN-13: 978-0323902922
belongs to
Statistical Ensemble c

Cell Shape Relaxationni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/CellShapeRelaxation

Cell shape is allowed to change in the calculation.
belongs to
Relaxation Degrees of Freedom c

Cell Volume Relaxationni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/CellVolumeRelaxation

Cell volume is allowed to change in the calculation.
belongs to
Relaxation Degrees of Freedom c

Delete Atomni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/DeleteAtom

Deletion of an atom to create a vacancy.
belongs to
Point Defect Creation c

Explicit KPoint Meshni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ExplicitKPointMesh

An explicit k-point mesh refers to an input where the software will use exactly the points provided.
belongs to
KPoint Mesh c

Gamma-Centered KPoint Meshni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/GammaCenteredKPointMesh

A gamma-centered k-point mesh refers to a grid where the k-points are arranged symmetrically around the Gamma point (k = 0).
belongs to
KPoint Mesh c

Grand Canonical Ensembleni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/GrandCanonicalEnsemble

In the grand canonical ensemble the temperature, volume, and the chemical potential are kept constant.
Source
ISBN-13: 978-0323902922
belongs to
Statistical Ensemble c

Isoenthalpic–Isobaric Ensembleni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/IsoenthalpicIsobaricEnsemble

In the isoenthalpic-isobaric ensemble the enthalpy, pressure, and the number of particles of every species are kept constant.
Source
ISBN-13: 978-0323902922
belongs to
Statistical Ensemble c

Isothermal–Isobaric Ensembleni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/IsothermalIsobaricEnsemble

In the isothermal-isobaric ensemble the temperature, pressure, and the number of particles of every species are kept constant.
Source
ISBN-13: 978-0323902922
belongs to
Statistical Ensemble c

Langevinni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Langevin

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.
Source
"Computer Simulation of Liquids", ISBN-13 : ‎978-0198556459
belongs to
Thermostat c

Microcanonical Ensembleni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MicrocanonicalEnsemble

In the microcanonical ensemble the energy, volume, and the number of particles of every species are kept constant.
Source
ISBN-13: 978-0323902922
belongs to
Statistical Ensemble c

Monkhorst Pack KPoint Meshni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/MonkhorstPackKPointMesh

A Monkhorst-Pack k-point mesh refers to a regular grid of k-points for sampling the Brillouin zone.
belongs to
KPoint Mesh c

Murnaghanni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Murnaghan

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.
Source
https://en.wikipedia.org/wiki/Murnaghan_equation_of_state
"Finite Deformation of an Elastic Solid", Applied mathematics series, ISSN 0272-1643
belongs to
Equation of State Fit c

Nose-Hooverni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/NoseHoover

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.
Source
https://doi.org/10.1063%2F1.447334
https://doi.org/10.1103%2FPhysRevA.31.1695
belongs to
Thermostat c

Parrinello-Rahmanni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ParrinelloRahman

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.
belongs to
Barostat c

Periodicity in X-directionni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PeriodicityInXdirection

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.
belongs to
Periodic Boundary Condition c

Periodicity in Y-directionni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PeriodicityInYdirection

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.
belongs to
Periodic Boundary Condition c

Periodicity in Z-directionni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/PeriodicityInZdirection

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.
belongs to
Periodic Boundary Condition c

Substitute Atomni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/SubstituteAtom

Substitution of an atom to create an impurity.
belongs to
Point Defect Creation c

Third-order polynomial fitni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/ThirdOrderPolynomialFit

EOS calculation using a third-order polynomial fit.
belongs to
Equation of State Fit c

Velocity Rescalingni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/VelocityRescaling

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.
belongs to
Thermostat c

Vinetni back to ToC or Named Individual ToC

IRI: http://purls.helmholtz-metadaten.de/asmo/Vinet

Equation of state proposed by Pascal Vinet in 1987. It is a modification of the Birch–Murnaghan equation of state.
Source
https://doi.org/10.1103/PhysRevB.35.1945
https://en.wikipedia.org/wiki/Rose%E2%80%93Vinet_equation_of_state
belongs to
Equation of State Fit c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.