arXiv subjects

Gábor Csányi

Publications and source records attributed to Gábor Csányi.

At least 91 records · Page 5Linked to original sources

arXiv2018

Equation of state of fluid methane from first principles with machine learning potentials

The predictive simulation of molecular liquids requires models that are not only accurate, but computationally efficient enough to handle the large systems and long time scales required for reliable prediction of macroscopic properties. We present a new approach to the systematic approximation of the first-principles potential energy surface (PES) of molecular liquids using the GAP (Gaussian Approximation Potential) framework. The approach allows us to create potentials at several different levels of accuracy in reproducing the true PES, which allows us to test the level of quantum chemistry that is necessary to accurately predict its macroscopic properties. We test the approach by building potentials for liquid methane (CH$_4$), which is difficult to model from first principles because its behavior is dominated by weak dispersion interactions with a significant many-body component. We find that an accurate, consistent prediction of its bulk density across a wide range of temperature and pressure requires not only many-body dispersion, but also quantum nuclear effects to be modeled accurately.

physics.chem-ph↗

arXiv2018

Growth Mechanism and Origin of High $sp^3$ Content in Tetrahedral Amorphous Carbon

We study the deposition of tetrahedral amorphous carbon (ta-C) films from molecular dynamics simulations based on a machine-learned interatomic potential trained from density-functional theory data. For the first time, the high $sp^3$ fractions in excess of 85% observed experimentally are reproduced by means of computational simulation, and the deposition energy dependence of the film's characteristics is also accurately described. High confidence in the potential and direct access to the atomic interactions allow us to infer the microscopic growth mechanism in this material. While the widespread view is that ta-C grows by "subplantation," we show that the so-called "peening" model is actually the dominant mechanism responsible for the high $sp^3$ content. We show that pressure waves lead to bond rearrangement away from the impact site of the incident ion, and high $sp^3$ fractions arise from a delicate balance of transitions between three- and fourfold coordinated carbon atoms. These results open the door for a microscopic understanding of carbon nanostructure formation with an unprecedented level of predictive power.

cond-mat.mtrl-sci↗

arXiv2018

Realistic atomistic structure of amorphous silicon from machine-learning-driven molecular dynamics

Amorphous silicon (a-Si) is a widely studied non-crystalline material, and yet the subtle details of its atomistic structure are still unclear. Here, we show that accurate structural models of a-Si can be obtained by harnessing the power of machine-learning algorithms to create interatomic potentials. Our best a-Si network is obtained by cooling from the melt in molecular-dynamics simulations, at a rate of 10$^{11}$ K/s (that is, on the 10 ns timescale). This structure shows a defect concentration of below 2% and agrees with experiments regarding excess energies, diffraction data, as well as $^{29}$Si solid-state NMR chemical shifts. We show that this level of quality is impossible to achieve with faster quench simulations. We then generate a 4,096-atom system which correctly reproduces the magnitude of the first sharp diffraction peak (FSDP) in the structure factor, achieving the closest agreement with experiments to date. Our study demonstrates the broader impact of machine-learning interatomic potentials for elucidating accurate structures and properties of amorphous functional materials.

cond-mat.mtrl-sci↗

arXiv2018

Gaussian approximation potential modeling of lithium intercalation in carbon nanostructures

We demonstrate how machine-learning based interatomic potentials can be used to model guest atoms in host structures. Specifically, we generate Gaussian approximation potential (GAP) models for the interaction of lithium atoms with graphene, graphite, and disordered carbon nanostructures, based on reference density-functional theory (DFT) data. Rather than treating the full Li--C system, we demonstrate how the energy and force differences arising from Li intercalation can be modeled and then added to a (prexisting and unmodified) GAP model of pure elemental carbon. Furthermore, we show the benefit of using an explicit pair potential fit to capture "effective" Li--Li interactions, to improve the performance of the GAP model. This provides proof-of-concept for modeling guest atoms in host frameworks with machine-learning based potentials, and in the longer run is promising for carrying out detailed atomistic studies of battery materials.

cond-mat.mtrl-sci↗

arXiv2018

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enable routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, BPNN-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.

physics.chem-ph↗

arXiv2017

Constant-pressure nested sampling with atomistic dynamics

The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are inefficient for condensed systems with general interactions where single-particle moves cannot be evaluated faster than the energy of the whole system. Here we enhance the method by using all-particle moves: either Galilean Monte Carlo or a total enthalpy Hamiltonian Monte Carlo algorithm, introduced in this paper. We show that these algorithms enable the determination of phase transition temperatures with equivalent accuracy to the previous method at $1/N$ of the cost for an $N$-particle system with general interactions, or at equal cost when single particle moves can be done in $1/N$ of the cost of a full $N$-particle energy evaluation.

cond-mat.stat-mech↗

arXiv2017

Data-driven learning of total and local energies in elemental boron

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated $β$-rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

cond-mat.mtrl-sci↗

arXiv2017

A Machine Learning Potential for Graphene

We present an accurate interatomic potential for graphene, constructed using the Gaussian Approximation Potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data - and amongst the empirical potentials themselves - the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

cond-mat.mtrl-sci↗

arXiv2017

Symmetry-Adapted Machine-Learning for Tensorial Properties of Atomistic Systems

Statistical learning methods show great promise in providing an accurate prediction of materials and molecular properties, while minimizing the need for computationally demanding electronic structure calculations. The accuracy and transferability of these models are increased significantly by encoding into the learning procedure the fundamental symmetries of rotational and permutational invariance of scalar properties. However, the prediction of tensorial properties requires that the model respects the appropriate geometric transformations, rather than invariance, when the reference frame is rotated. We introduce a formalism that can be used to perform machine-learning of tensorial properties of arbitrary rank for general molecular geometries. To demonstrate it, we derive a tensor kernel adapted to rotational symmetry, which is the natural generalization of the smooth overlap of atomic positions (SOAP) kernel commonly used for the prediction of scalar properties at the atomic scale. The performance and generality of the approach is demonstrated by learning the instantaneous electrical response of water oligomers of increasing complexity, from the isolated molecule to the condensed phase.

cond-mat.mtrl-sci↗

arXiv2017

Structural Simplicity as a Restraint on the Structure of Amorphous Silicon

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study we demonstrate that local 'structural simplicity', embodied by the degree to which atomic environments within a material are similar to each other, is powerful concept for rationalising the structure of canonical amorphous material amorphous silicon (a-Si). We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a-Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural homogeneity drives electronic homogeneity. That this method produces models of a-Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modelling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.

cond-mat.mtrl-sci↗

arXiv2017

Polytypism in the ground state structure of the Lennard-Jonesium

We present a systematic study of the stability of nineteen different periodic structures using the finite range Lennard-Jones potential model discussing the effects of pressure, potential truncation, cutoff distance and Lennard-Jones exponents. The structures considered are the hexagonal close packed (hcp), face centred cubic (fcc) and seventeen other polytype stacking sequences, such as dhcp and $9R$. We found that at certain pressure and cutoff distance values, neither fcc nor hcp is the ground state structure as previously documented, but different polytypic sequences. This behaviour shows a strong dependence on the way the tail of the potential is truncated.

cond-mat.mtrl-sci↗

arXiv2017

Discovering the Building Blocks of Atomic Systems using Machine Learning

Machine learning has proven to be a valuable tool to approximate functions in high-dimensional spaces. Unfortunately, analysis of these models to extract the relevant physics is never as easy as applying machine learning to a large dataset in the first place. Here we present a description of atomic systems that generates machine learning representations with a direct path to physical interpretation. As an example, we demonstrate its usefulness as a universal descriptor of grain boundary systems. Grain boundaries in crystalline materials are a quintessential example of a complex, high-dimensional system with broad impact on many physical properties including strength, ductility, corrosion resistance, crack resistance, and conductivity. In addition to modeling such properties, the method also provides insight into the physical "building blocks" that influence them. This opens the way to discover the underlying physics behind behaviors by understanding which building blocks map to particular properties. Once the structures are understood, they can then be optimized for desirable behaviors.

cond-mat.mtrl-sci↗

arXiv2016

Machine-learning based interatomic potential for amorphous carbon

We introduce a Gaussian approximation potential (GAP) for atomistic simulations of liquid and amorphous elemental carbon. Based on a machine-learning representation of the density-functional theory (DFT) potential-energy surface, such interatomic potentials enable materials simulations with close-to DFT accuracy but at much lower computational cost. We first determine the maximum accuracy that any finite-range potential can achieve in carbon structures; then, using a novel hierarchical set of two-, three-, and many-body structural descriptors, we construct a GAP model that can indeed reach the target accuracy. The potential yields accurate energetic and structural properties over a wide range of densities; it also correctly captures the structure of the liquid phases, at variance with state-of-the-art empirical potentials. Exemplary applications of the GAP model to surfaces of "diamond-like" tetrahedral amorphous carbon (ta-C) are presented, including an estimate of the amorphous material's surface energy, and simulations of high-temperature surface reconstructions ("graphitization"). The new interatomic potential appears to be promising for realistic and accurate simulations of nanoscale amorphous carbon structures.

cond-mat.mtrl-sci↗

arXiv2016

Determining pressure-temperature phase diagrams of materials

We extend the nested sampling algorithm to simulate materials under periodic boundary and constant pressure conditions, and show how it can be used to determine the complete equilibrium phase diagram, for a given potential energy function, efficiently and in a highly automated fashion. The only inputs required are the composition and the desired pressure and temperature ranges, in particular, solid-solid phase transitions are recovered without any a priori knowledge about the structure of solid phases. We benchmark and showcase the algorithm on the periodic Lennard-Jones system, aluminium and NiTi.

cond-mat.mtrl-sci↗

arXiv2014

The Adaptive Buffered Force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force QM/MM method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the adaptive buffered-force QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.

physics.chem-ph↗

arXiv2014

Accuracy and transferability of GAP models for tungsten

We introduce interatomic potentials for tungsten in the bcc crystal phase and its defects within the Gaussian Approximation Potential (GAP) framework, fitted to a database of first principles density functional theory (DFT) calculations. We investigate the performance of a sequence of models based on databases of increasing coverage in configuration space and showcase our strategy of choosing representative small unit cells to train models that predict properties only observable using thousands of atoms. The most comprehensive model is then used to calculate properties of the screw dislocation, including its structure, the Peierls barrier and the energetics of the vacancy-dislocation interaction. All software and raw data are available at www.libatoms.org.

cond-mat.mtrl-sci↗

arXiv2014

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

cond-mat.stat-mech↗

arXiv2014

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

cond-mat.stat-mech↗