arXiv subjects

Emanuel A. Lazar

Publications and source records attributed to Emanuel A. Lazar.

At least 19 recordsLinked to original sources

arXiv2024

Characterizing structural features of two-dimensional particle systems through Voronoi topology

This paper introduces a new approach toward characterizing local structural features of two-dimensional particle systems. The approach can accurately identify and characterize defects in high-temperature crystals, distinguish a wide range of nominally disordered systems, and robustly describe complex structures such as grain boundaries. This paper also introduces two-dimensional functionality into the open-source software program VoroTop which automates this analysis. This software package is built on a recently-introduced multithreaded version of VORO++, enabling the analysis of systems with billions of particles on high-performance computer architectures.

cond-mat.mtrl-sci↗

arXiv2023

Pair correlation function based on Voronoi topology

The pair correlation function (PCF) has proven an effective tool for analyzing many physical systems due to its simplicity and its applicability to simulated and experimental data. However, as an averaged quantity, the PCF can fail to capture subtle structural differences in particle arrangements, even when those differences can have a major impact on system properties. Here, we use Voronoi topology to introduce a discrete version of the PCF that highlights local inter-particle topological configurations. The advantages of the Voronoi PCF are demonstrated in several examples including crystalline, hyperuniform, and active systems showing clustering and giant number fluctuations.

cond-mat.dis-nn↗

arXiv2023

An extension to VORO++ for multithreaded computation of Voronoi cells

VORO++ is a software library written in C++ for computing the Voronoi tessellation, a technique in computational geometry that is widely used for analyzing systems of particles. VORO++ was released in 2009 and is based on computing the Voronoi cell for each particle individually. Here, we take advantage of modern computer hardware, and extend the original serial version to allow for multithreaded computation of Voronoi cells via the OpenMP application programming interface. We test the performance of the code, and demonstrate that we can achieve parallel efficiencies greater than 95% in many cases. The multithreaded extension follows standard OpenMP programming paradigms, allowing it to be incorporated into other programs. We provide an example of this using the VoroTop software library, performing a multithreaded Voronoi cell topology analysis of up to 102.4 million particles.

physics.comp-ph↗

arXiv2023

Identification of high-reliability regions of machine learning predictions in materials science using transparent conducting oxides and perovskites as examples

Progress in the application of machine learning (ML) methods to materials design is hindered by the lack of understanding of the reliability of ML predictions, in particular for the application of ML to small data sets often found in materials science. Using ML prediction for transparent conductor oxide formation energy and band gap, dilute solute diffusion, and perovskite formation energy, band gap and lattice parameter as examples, we demonstrate that 1) analysis of ML results by construction of a convex hull in feature space that encloses accurately predicted systems can be used to identify regions in feature space for which ML predictions are highly reliable 2) analysis of the systems enclosed by the convex hull can be used to extract physical understanding and 3) materials that satisfy all well-known chemical and physical principles that make a material physically reasonable are likely to be similar and show strong relationships between the properties of interest and the standard features used in ML. We also show that similar to the composition-structure-property relationships, inclusion in the ML training data set of materials from classes with different chemical properties will not be beneficial and will slightly decrease the accuracy of ML prediction and that reliable results likely will be obtained by ML model for narrow classes of similar materials even in the case where the ML model will show large errors on the dataset consisting of several classes of materials. Our work suggests that analysis of the error distributions of ML predictions will be beneficial for the further development of the application of ML methods in material science.

cond-mat.mtrl-sci↗

arXiv2022

Voronoi cell analysis: The shapes of particle systems

Many physical systems can be studied as collections of particles embedded in space, evolving through deterministic evolution equations. Natural questions arise concerning how to characterize these arrangements - are they ordered or disordered? If they are ordered, how are they ordered and what kinds of defects do they possess? Originally introduced to study problems in pure mathematics, Voronoi tessellations have become a powerful and versatile tool for analyzing countless problems in pure and applied physics. In this paper we explain the basics of Voronoi tessellations and the shapes they produce, and describe how they can be used to study many physical systems.

physics.comp-ph↗

arXiv2020

Voronoi chains, blocks, and clusters in perturbed square lattices

Perturbed lattices provide simple models for studying many physical systems. In this paper we study the distribution of Voronoi chains, blocks, and clusters with prescribed combinatorial features in the perturbed square lattice, generalizing earlier work. In particular, we obtain analytic results for the presence of hexagonally-ordered regions within a square-ordered phase. Connections to high-temperature crystals and to non-equilibrium phase transitions are considered. In an appendix, we briefly consider the site-percolation threshold for this system.

cond-mat.stat-mech↗

arXiv2020

Distribution of Topological Types in Grain-Growth Microstructures

An open question in studying normal grain growth concerns the asymptotic state to which microstructures converge. In particular, the distribution of grain topologies is unknown. We introduce a thermodynamic-like theory to explain these distributions in two- and three-dimensional systems. In particular, a bending-like energy $E_i$ is associated to each grain topology $t_i$, and the probability of observing that particular topology is proportional to $\frac{1}{s(t_i)}e^{-βE_i}$, where $s(t_i)$ is the order of an associated symmetry group and $β$ is a thermodynamic-like constant. We explain the physical origins of this approach, and provide numerical evidence in support.

cond-mat.mtrl-sci↗

arXiv2019

Topological extension of the isomorph theory based on the Shannon entropy

Isomorph theory is one of the promising theories to understand the quasi-universal relationship between thermodynamic, dynamic and structural characteristics. Based on the hidden scale invariance of the inverse power law potentials, it rationalizes the excess entropy scaling law of dynamic properties. This work aims to show that this basic idea of isomorph theory can be extended by examining the microstructural features of the system. Using the topological framework in conjunction with the entropy calculation algorithm, we demonstrate that Voronoi entropy, a measure of the topological diversity of single atoms, provides a scaling law for the transport properties of soft-sphere fluids, which is comparable to the frequently used excess entropy scaling. By examining the relationship between the Voronoi entropy and the solid-like fraction of simple fluids, we suggest that the Frenkel line, a rigid-nonrigid crossover line, {be} a topological isomorphic line where the scaling relation qualitatively changes.

cond-mat.stat-mech↗

arXiv2018

Topological generalization of the rigid-nonrigid transition in soft-sphere and hard-sphere fluids

A fluid particle changes its dynamics from diffusive to oscillatory as the system density increases up to the melting density. Hence, the notion of the Frenkel line was introduced to demarcate the fluid region into rigid and nonrigid liquid subregions based on the collective particle dynamics. In this work, we apply a topological framework to locate the Frenkel lines of the soft-sphere and the hard-sphere models relying on the system configurations. The topological characteristics of the ideal gas and the maximally random jammed state are first analyzed, then the classification scheme designed in our earlier work is applied. The classification result shows that the fraction of solid-like atoms increases from zero to one in the rigid liquid region. The dependence of the solid-like fraction on the bulk density is understood based on the theory of fluid polyamorphism. The percolation behavior of solid-like clusters is described based on the fraction of solid-like molecules in an integrated manner. The crossover densities are obtained by examining the percolation of solid-like clusters. The resultant crossover densities of soft-sphere fluids converge to that of hard-sphere fluid. Hence, the topological method successfully highlights the generality of the Frenkel line.

cond-mat.soft↗

arXiv2018

Topological Characterization of Rigid-Nonrigid Transition across the Frenkel Line

The dynamics of supercritical fluids, a state of matter beyond the gas-liquid critical point, changes from diffusive to oscillatory motions at high pressure. This transition is believed to occur across a locus of thermodynamic states called the Frenkel line. The Frenkel line has been extensively investigated from the viewpoint of the dynamics, but its structural meaning is not still well understood. This letter interprets the mesoscopic picture of the Frenkel line entirely based on a topological and geometrical framework. This discovery makes it possible to understand the mechanism of rigid/non-rigid transition based not on the dynamics of individual atoms, but on their instantaneous configurations. The topological classification method reveals that the percolation of solid-like structures occurs above the rigid-nonrigid crossover densities.

cond-mat.stat-mech↗

arXiv2018

VoroTop: Voronoi Cell Topology Visualization and Analysis Toolkit

This paper introduces a new open-source software program called VoroTop, which uses Voronoi topology to analyze local structure in atomic systems. Strengths of this approach include its abilities to analyze high-temperature systems and to characterize complex structure such as grain boundaries. This approach enables the automated analysis of systems and mechanisms previously not possible.

cond-mat.mtrl-sci↗

arXiv2017

Roundness of grains in cellular microstructures

Many physical systems are composed of polyhedral cells of varying sizes and shapes. These structures are simple in the sense that no more than three faces meet at an edge and no more than four edges meet at a vertex. This means that individual cells can usually be considered as simple, three-dimensional polyhedra. This paper is concerned with determining the distribution of combinatorial types of such polyhedral cells. We introduce the terms \emph{fundamental} and \emph{vertex-truncated} types and apply these concepts to the grain growth microstructure as a testing ground. For these microstructures we demonstrate that most grains are of particular fundamental types, whereas the frequency of vertex-truncated types decreases exponentially with the number of truncations. This can be explained by the evolutionary process through which grain growth structures are formed, and in which energetically unfavorable surfaces are quickly eliminated. Furthermore, we observe that these grain types are `round' in a combinatorial sense: there are no `short' separating cycles that partition the polyhedra into two parts of similar sizes. A particular microstructure derived from the Poisson--Voronoi initial condition is identified as containing an unusually large proportion of round grains. This Round microstructure has an average of $14.036$ faces per grain, and is conjectured to be more resistant to topological change than the steady-state grain growth microstructure.

cond-mat.mtrl-sci↗

arXiv2015

On fiber diameters of continuous maps

We present a surprisingly short proof that for any continuous map $f : \mathbb{R}^n \rightarrow \mathbb{R}^m$, if $n>m$, then there exists no bound on the diameter of fibers of $f$. Moreover, we show that when $m=1$, the union of small fibers of $f$ is bounded; when $m>1$, the union of small fibers need not be bounded. Applications to data analysis are considered.

math.MG↗

arXiv2015

Statistical Topology of Perturbed Two-Dimensional Lattices

The Voronoi cell of any atom in a lattice is identical. If atoms are perturbed from their lattice coordinates, then the topologies of the Voronoi cells of the atoms will change. We consider the distribution of Voronoi cell topologies in two-dimensional perturbed systems. These systems can be thought of as simple models of finite-temperature crystals. We give analytical results for the distribution of Voronoi topologies of points in two-dimensional Bravais lattices under infinitesimal perturbations and present a discussion with numerical results for finite perturbations.

cond-mat.stat-mech↗

arXiv2015

A Topological Framework for Local Structure Analysis in Condensed Matter

Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems.

cond-mat.other↗

arXiv2015

Geometric and topological properties of the canonical grain growth microstructure

Many physical systems can be modeled as large sets of domains "glued" together along boundaries - biological cells meet along cell membranes, soap bubbles meet along thin films, countries meet along geopolitical boundaries, and metallic crystals meet along grain interfaces. Each class of microstructures results from a complex interplay of initial conditions and particular evolutionary dynamics. The statistical steady-state microstructure resulting from isotropic grain growth of a polycrystalline material is canonical in that it is the simplest example of a cellular microstructure resulting from a gradient flow of a simple energy, directly proportional to the total length or area of all cell boundaries. As many properties of polycrystalline materials depend on their underlying microstructure, a more complete understanding of the grain growth steady-state can provide insight into the physics of a broad range of everyday materials. In this paper we report geometric and topological features of these canonical two- and three-dimensional steady-state microstructures obtained through large, accurate simulations of isotropic grain growth.

cond-mat.mtrl-sci↗

arXiv2014

Selectively Localized Wannier Functions

Since the seminal work of Marzari and Vanderbilt, maximally localized Wannier functions have become widely used as a real-space representation of the electronic structure of periodic materials. In this paper we introduce selectively localized Wannier functions which extend the method of Marzari and Vanderbilt in two important ways. First, our method allows us to focus on localizing a subset of orbitals of interest. Second, our method allows us to fix centers of these orbitals, and ensure the preservation of the point-group symmetry. These characteristics are important when Wannier functions are used in methodologies that go beyond density functional theory by treating a local subspace of the Hamiltonian more effectively. Application of our method to GaAs, SrMnO$_3$, and Co demonstrates that selectively localized Wannier functions can offer improvements over the maximally localized Wannier function technique.

cond-mat.str-el↗

arXiv2014

Statistical Topology of Three-Dimensional Poisson-Voronoi Cells and Cell Boundary Networks

Voronoi tessellations of Poisson point processes are widely used for modeling many types of physical and biological systems. In this paper, we analyze simulated Poisson-Voronoi structures containing a total of 250,000,000 cells to provide topological and geometrical statistics of this important class of networks. We also report correlations between some of these topological and geometrical measures. Using these results, we are able to corroborate several conjectures regarding the properties of three-dimensional Poisson-Voronoi networks and refute others. In many cases, we provide accurate fits to these data to aid further analysis. We also demonstrate that topological measures represent powerful tools for describing cellular networks and for distinguishing among different types of networks.

physics.comp-ph↗