Robust Structural Identification via Polyhedral Template Matching
arXiv:1603.05143 · doi:10.1088/0965-0393/24/5/055007
Abstract
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common Neighbour Analysis, rely on interatomic distances (or thresholds thereof) to classify atomic structure. As a consequence they are sensitive to strain and thermal displacements, and preprocessing such as quenching or temporal averaging of the atomic positions is necessary to provide reliable identifications. We propose a new method, Polyhedral Template Matching (PTM), which classifies structures according to the topology of the local atomic environment, without any ambiguity in the classification, and with greater reliability than e.g. Common Neighbour Analysis in the presence of thermal fluctuations. We demonstrate that the method can reliably be used to identify structures even in simulations near the melting point, and that it can identify the most common ordered alloy structures as well. In addition, the method makes it easy to identify the local lattice orientation in polycrystalline samples, and to calculate the local strain tensor. An implementation is made available under a Free and Open Source Software license.
20 pages, 14 figures. Revised version: algorithm improved slightly
References in corpus (3)
Cited by in corpus (94)
- Homogeneous ice nucleation in an ab initio machine learning model of water
- Inverse methods for design of soft materials
- Uncovering the effects of interface-induced ordering of liquid on crystal growth using machine learning
- Dissecting functional degradation in NiTi shape-memory-alloys containing amorphous regions via atomistic simulations
- Atomistic deformation behavior of single and twin crystalline Cu nanopillars with preexisting dislocations
- Unsupervised machine learning for detection of phase transitions in off-lattice systems I. Foundations
- Examination of computed aluminum grain boundary structures and interface energies that span the 5D space of crystallographic character
- Thermostat Influence on the Structural Development and Material Removal during Abrasion of Nanocrystalline Ferrite
- VoroTop: Voronoi Cell Topology Visualization and Analysis Toolkit
- Quantifying Dynamic Tilting in Halide Perovskites: Chemical Trends and Local Correlations
- Probing the atomically diffuse interfaces in core-shell nanoparticles in three dimensions
- Non-classical nucleation pathways in stacking-disordered crystals
- A first-principles machine-learning force field for heterogeneous ice nucleation on microcline feldspar
- Unsupervised learning of atomic environments from simple features
- Grain-resolved kinetics and rotation during grain growth of nanocrystalline Aluminium by molecular dynamics
- Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence
- Quantifying Disorder One Atom at a Time Using an Interpretable Graph Neural Network Paradigm
- Determining the three-dimensional atomic structure of a metallic glass
- Phase glides and self-organization of atomically abrupt interfaces out of stochastic disorder in -GaO
- Atomistic simulations of the deformation behavior of an Nb nanowire embedded in a NiTi shape memory alloy
- Interaction of prismatic screw dislocations with the interface side face in Ti alloys
- A Molecular Dynamics Study of Laser-Excited Gold
- Pattern formation during deformation of metallic nanolaminates
- A taxonomy of grain boundary migration mechanisms via displacement texture characterization
- Shock-induced melting and crystallization in titanium irradiated by ultrashort laser pulse
- Automated Identification and Tracking of Deformation Twin Structures in Molecular Dynamics Simulations
- Nonequilibrium chemical short-range order in metallic alloys
- Kinetic phase diagram for nucleation and growth of competing crystal polymorphs in charged colloidal suspensions
- Segregation and Ordering of Light Interstitials (B, C, H, and N) in Cr-Ni Alloys: Implications for Grain Boundary Stability in Superalloy Design
- Embracing the chaos: Alloying adds stochasticity to twin embryo growth
- Atomistic simulations of ductile failure in a b.c.c. high entropy alloy
- Atomistic modeling of metal-nonmetal interphase boundary diffusion
- Unravelling densification during sintering by multiscale modelling of grain motion
- Core-softened water-alcohol mixtures: the solute-size effects
- Manifestation of dipole-induced disorder in self-assembly of ferroelectric and ferromagnetic nanocubes
- Sim2Ls: FAIR simulation workflows and data
- Effect of the atomic structure of complexions on the active disconnection mode during shear-coupled grain boundary motion
- Materials Fingerprinting Classification
- Picosecond-scale Heterogeneous Melting of Metals at Extreme Non-equilibrium States
- Impact of Surface Adsorbates and Dimensionality on Templating of Halide Perovskites
- Predicting elastic and plastic properties of small iron polycrystals by machine learning
- Grain boundary interstitial segregation in substitutional binary alloys
- Crystal structure identification with 3D convolutional neural networks with application to high-pressure phase transitions in SiO
- Melting Temperature of Iron Under the Earth's Inner Core Condition from Deep Machine Learning
- The Role of Pressure in Inverse Design for Assembly
- Revealing the Low Temperature Phase of FAPbI using A Machine-Learned Potential
- Effect of Samarium doping on the nucleation of fcc-Aluminum in undercooled liquids
- Competing interactions near the liquid-liquid phase transition of core-softened water/methanol mixtures
- Uncharacteristic second order martensitic transformation in metals via epitaxial stress fields
- Atomistic-informed phase field modeling of magnesium twin growth by disconnections
- Solid-amorphous transition is related to the waterlike anomalies in a fluid without liquid-liquid phase transition
- Atomistic simulation of martensite microstructural evolution during temperature driven transition in pure titanium
- Stable nanofacets in [111] tilt grain boundaries of face-centered cubic metals
- Tunability of martensitic behavior through coherent nanoprecipitates and other nanostructures
- Grain boundary segregation prediction with a dual-solute model
- Bayesian inference of composition-dependent phase diagrams
- A feasibility analysis towards the simulation of hysteresis with spin-lattice dynamics
- Classification of atomic environments via the Gromov-Wasserstein distance
- Atomistic modeling of diffusion processes at Al(Si)/Si(111) interphase boundaries obtained by vapor deposition
- A neutron tomography study: probing the spontaneous crystallization of randomly packed granular assemblies
- Metallization of colloidal crystals
- Exploring the impact of Ti/Al on L12 nanoprecipitation and deformation behavior in CoNiFeAlTi multi-principal element alloys through atomistic simulations
- Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point
- Maximum volume simplex method for automatic selection and classification of atomic environments and environment descriptor compression
- Tuning martensitic transformations via coherent second phases in nanolaminates using free energy landscape engineering
- A detailed examination of polysilicon resistivity incorporating the grain size distribution
- A local orientational order parameter for systems of interacting particles
- Devitrification of the Kob-Andersen glass former: Competition with the locally favored structure
- Understanding the two-step nucleation of iron at Earth's inner core conditions: a comparative molecular dynamics study
- Faceting transition in aluminum as a grain boundary phase transition
- Role of electronic thermal transport in amorphous metal recrystallization: a molecular dynamics study
- Preferential Composition during Nucleation and Growth in Multi-Principal Elements Alloys
- Bayesian Optimization of Metastable Nickel Formation During the Spontaneous Crystallization under Extreme Conditions
- Learning from metastable grain boundaries
- 3D Visualization Reveals the Cooling Rate Dependent Crystallization near a Wall in Dense Microgel Systems
- Crystal nucleation rates in one-component Yukawa systems
- Simulations of Nanocrystalline Iron Formation under High Shear Strain
- Radiation damage and phase stability of AlCrCuFeNi alloys using a machine-learned interatomic potential
- Disconnection formation via segregation-induced grain boundary phase transitions
- Designing binary mixtures of colloidal particles with simple interactions that assemble complex crystals
- Kinetic phase diagram for two-step nucleation in colloid-polymer mixtures
- Probing trade-off between critical size and velocity in cold-spray: An atomistic simulation
- Structural dynamics of a model of amorphous silicon
- Crystal Nucleation in Eutectic Al-Si Alloys by Machine-Learned Molecular Dynamics
- Systematic Study of Machine Learning Classification Algorithms of Zeolitic Imidazolate Framework Polymorphs
- Thermal conductivities of monolayer graphene oxide from machine learning molecular dynamics simulations
- Core structure of dislocations in ordered ferromagnetic FeCo
- Unsupervised Machine-Learning Pipeline for Data-Driven Defect Detection and Characterisation: Application to Displacement Cascades
- Finely Tunable Thermal Expansion of NiTi by Stress-Induced Martensitic Transformation and Thermomechanical Training
- Robust recognition and exploratory analysis of crystal structures via Bayesian deep learning
- Predicting co-segregation in alloys with solute-solute interactions
- Lattice Matching Dictates the Growth Mode and Quality of Deuterium Crystallization in Confined Spherical Shells
- Energy-Conserving Contact Dynamics of Nonspherical Rigid-Body Particles
- Nonequilibrium Processes in Repulsive Binary Mixtures