ASMO — Atomistic Simulation Methods Ontology

ASMO — Atomistic Simulation Methods Ontology

Overview

ASMO describes how atomistic simulations are performed: the computational methods, algorithms, potentials, input parameters, and calculated properties. It complements CMSO (which describes what is being simulated — the material sample) by capturing the simulation methodology.

• IRI: http://purls.helmholtz-metadaten.de/asmo/
• Version: 1.0.0
• License: CC BY 4.0
• 105 classes | 25 object properties | 16 data properties

Note on named individuals: The ASMO documentation describes specific implementations (e.g., Nose-Hoover thermostat, Parrinello-Rahman barostat, NVT/NPT/NVE ensembles) as conceptual instances. However, the current OWL file does not declare these as owl:Class or owl:NamedIndividual. They are listed in the Usage Patterns section below for reference, but programmatic queries should use the parent classes (Thermostat, Barostat, Statistical Ensemble).

Domain Model

Simulation (Activity)
├── uses → Computational Method (DFT, MD, MC, Molecular Statics, AIMD)
├── uses → Interatomic Potential (LJ, EAM, MEAM, ML, Force Field, SW)
├── uses → Simulation Algorithm (Thermostat, Barostat, EOS Fitting, ...)
├── has → Statistical Ensemble
├── has → Input Parameter (Energy Cutoff, KPoint Mesh, Time Step, PBC)
├── has → Output Parameter
├── produces → Calculated Property (Energy, Moduli, Strain, Stress, ...)
└── acts on → Computational Sample (from CMSO)

Class Hierarchy

Computational Methods

Computational Method
├── Ab Initio Molecular Dynamics (AIMD)
├── Density Functional Theory (DFT)
├── Molecular Dynamics (MD)
├── Molecular Statics
└── Monte Carlo Method
    └── Kinetic Monte Carlo Method

Interatomic Potentials

Interatomic Potential
├── Embedded Atom Model (EAM)
├── Force Field
├── Lennard-Jones Potential
├── Machine Learning Potential
├── Modified Embedded Atom Model (MEAM)
└── Stillinger-Weber Potential

Simulation Algorithms

Simulation Algorithm
├── ANNNI Model
├── Barostat
├── Compression Test
├── Equation of State Fit
├── Nanoindentation
├── Quasi-Harmonic Approximation
├── Tensile Test
├── Thermodynamic Integration
└── Thermostat

Common implementations (described in ASMO documentation, not formal OWL classes):

• Thermostats: Andersen, Berendsen, Nose-Hoover, Langevin
• Barostats: Andersen, Berendsen, Parrinello-Rahman
• EOS models: Birch-Murnaghan, Murnaghan, Vinet, Rose

Statistical Ensembles

The Statistical Ensemble class has no formal subclasses in the OWL file. Common ensemble types described in the ASMO documentation:

• Microcanonical Ensemble (NVE)
• Canonical Ensemble (NVT)
• Isothermal-Isobaric Ensemble (NPT)
• Grand Canonical Ensemble

Calculated Properties

Calculated Property
├── Bulk Modulus
├── Elastic Constant
├── Elastic Tensor
├── Flow Stress
├── Formation Energy
├── Kinetic Energy
├── Poisson's Ratio
├── Potential Energy
├── Shear Modulus
├── Simulation Cell Length
├── Simulation Cell Volume
├── Specific Heat Capacity
├── Strain
├── Thermal Expansion Coefficient
├── Thermodynamic Free Energy
│   ├── Gibbs Free Energy
│   └── Helmholtz Free Energy
├── Total Energy
├── Total Magnetic Moment
├── Virial Pressure
├── Yield Stress
└── Young's Modulus

Physical Quantities

Physical Quantity
├── Energy
│   └── Free Energy
├── Force
├── Length
├── Mass
├── Pressure
├── Stress
├── Temperature
├── Time
│   ├── Simulation Run Time
│   └── Simulation Time
└── Volume

Input Parameters

Input Parameter
├── Energy Cutoff
├── KPoint Mesh
├── Number Of Ionic Steps
├── Periodic Boundary Condition
├── Strain Rate
├── Time Step
└── Volume Range

Exchange Correlation Functionals (from MDO)

Exchange Correlation Energy Functional
├── Generalized Gradient Approximation (GGA)
├── Hybrid Functional
│   ├── Hybrid Generalized Gradient Approximation
│   └── Hybrid Meta Generalized Gradient Approximation
├── Local Density Approximation (LDA)
└── Meta Generalized Gradient Approximation

Structure Manipulation

Structure Manipulation (Activity)
├── Point Defect Creation
└── Spatial Transformation
    ├── Rotation
    ├── Shear
    └── Translation

Mathematical Operations

Mathematical Operation (Activity)
├── Addition
├── Division
├── Exponentiation
├── Multiplication
└── Subtraction

Key Object Properties

Relationship to CMSO

ASMO imports from CMSO:

• Computational Sample — the material being simulated
• Simulation Cell — the periodic box
• Plane, Vector — geometric primitives

Typical usage pattern: CMSO describes the sample (crystal structure, composition, defects), ASMO describes what you do with it (DFT calculation, MD simulation with EAM potential).

Usage Patterns

DFT Energy Calculation

Simulation → Energy Calculation
  has computational method → Density Functional Theory
  has XC functional → Generalized Gradient Approximation (e.g., PBE)
  has input parameter → Energy Cutoff (500 eV)
  has input parameter → KPoint Mesh
  has calculated property → Total Energy
  has calculated property → Formation Energy

MD Simulation

Simulation
  has computational method → Molecular Dynamics
  has interatomic potential → Embedded Atom Model
  uses simulation algorithm → Thermostat (e.g., Nose-Hoover)
  uses simulation algorithm → Barostat (e.g., Parrinello-Rahman)
  has statistical ensemble → Statistical Ensemble (e.g., NPT)
  has input parameter → Time Step
  has calculated property → Kinetic Energy, Potential Energy

Elastic Constants Calculation

Simulation → Energy Calculation
  has computational method → Density Functional Theory
  has calculated property → Elastic Tensor
  has calculated property → Bulk Modulus
  has calculated property → Shear Modulus
  has calculated property → Young's Modulus
  has calculated property → Poisson's Ratio