Searcharxiv⌕ Search

arXiv subjects

S. Alireza Ghasemi

Publications and source records attributed to S. Alireza Ghasemi.

17 recordsLinked to original sources

Large Scale Structure Prediction of Near-Stoichiometric Magnesium Oxide Based on a Machine-Learned Interatomic Potential: Novel Crystalline Phases and Oxygen-Vacancy Ordering

Using a fast and accurate neural network potential we are able to systematically explore the energy landscape of large unit cells of bulk magnesium oxide with the minima hopping method. The potential is trained with a focus on the near-stoichiometric compositions, in particular on suboxides, i.e., Mg$_x$O$_{1-x}$ with $0.50<x<0.60$. Our extensive exploration demonstrates that for bulk stoichiometric compounds, there are several new low-energy rocksalt-like structures in which Mg atoms are octahedrally six--coordinated and form trigonal prismatic motifs with different stacking sequences. Furthermore, we find a dense spectrum of novel non-stoichiometric crystal phases of Mg$_x$O$_{1-x}$ for each composition of $x$. These structures are mostly similar to the rock salt structure with octahedral coordination and five--coordinated Mg atoms. Due to the removal of one oxygen atom, the energy landscape becomes more glass-like with oxygen-vacancy type structures that all lie very close to each other energetically. For the same number of magnesium and oxygen atoms our oxygen-deficient structures are lower in energy if the vacancies are aligned along lines or planes than rock salt structures with randomly distributed oxygen vacancies. We also found the putative global minima configurations for each composition of the non-stoichiometric suboxide structures. These structures are predominantly composed of (111) slabs of the rock salt structure which are terminated with Mg atoms at the top and bottom, and are stacked in different sequences along the $z$-direction. Like other Magnéli-type phases, these structures have properties that differ considerably from their stoichiometric counterparts such as low lattice thermal conductivity and high electrical conductivity.

cond-mat.mtrl-sci↗

An automated approach for developing neural network interatomic potentials with FLAME

The performance of machine learning interatomic potentials relies on the quality of the training dataset. In this work, we present an approach for generating diverse and representative training data points which initiates with \it{ab initio} calculations for bulk structures. The data generation and potential construction further proceed side-by-side in a cyclic process of training the neural network and crystal structure prediction based on the developed interatomic potentials. All steps of the data generation and potential development are performed with minimal human intervention. We show the reliability of our approach by assessing the performance of neural network potentials developed for two inorganic systems.

cond-mat.mtrl-sci↗

FLAME: a library of atomistic modeling environments

FLAME is a software package to perform a wide range of atomistic simulations for exploring the potential energy surfaces (PES) of complex condensed matter systems. The range of methods include molecular dynamics simulations to sample free energy landscapes, saddle point searches to identify transition states, and gradient relaxations to find dynamically stable geometries. In addition to such common tasks, FLAME implements a structure prediction algorithm based on the minima hopping method (MHM) to identify the ground state structure of any system given solely the chemical composition, and a framework to train a neural network potential to reproduce the PES from $\textit{ab initio}$ calculations. The combination of neural network potentials with the MHM in FLAME allows a highly efficient and reliable identification of the ground state as well as metastable structures of molecules and crystals, as well as of nano structures, including surfaces, interfaces, and two-dimensional materials. In this manuscript, we provide detailed descriptions of the methods implemented in the FLAME code and its capabilities, together with several illustrative examples.

physics.comp-ph↗

A two-dimensional hexagonal sheet of TiO$_2$

We report on the ab initio discovery of a novel putative ground state for quasi two-dimensional TiO$_2$ through a structural search using the minima hopping method with an artificial neural network potential. The structure is based on a honeycomb lattice and is energetically lower than the experimentally reported lepidocrocite sheet by 7~meV/atom, and merely 13~meV/atom higher in energy than the ground state rutile bulk structure. According to our calculations, the hexagonal sheet is stable against mechanical stress, it is chemically inert and can be deposited on various substrates without disrupting the structure. Its properties differ significantly from all known TiO$_2$ bulk phases with a large gap of 5.05~eV that can be tuned through strain engineering.

cond-mat.mtrl-sci↗

Highly accurate and efficient algorithm for electrostatic interaction of charged particles confined by metallic parallel plates

We present an accurate and efficient algorithm to calculate the electrostatic interaction of charged point particles with partially periodic boundary conditions that are confined along the nonperiodic direction by two metallic parallel plates. The method preserves the original boundary conditions and hence, it does not introduce any kind of artifacts. In addition, it enjoys the quasilinear complexity of $\mathcal{O}(N\ln(N))$, where $N$ being the number of particles in the simulation box. In fact, based on the superposition principle in electrostatics, the problem is split into two electrostatic problems where each one can be calculated by the appropriate Poisson solver. In this paper we apply the method to sodium chloride ultrathin films and investigate its dielectric response with respect to external bias voltage. We show how accurately in this method one can obtain the total charge induced on metallic boundaries to an arbitrary precision.

cond-mat.mtrl-sci↗

A fingerprint based metric for measuring similarities of crystalline structures

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell we introduce crystal fingerprints that can be calculated easily and allow to define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method is an useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms and high-throughput screenings.

physics.comp-ph↗

Interatomic potentials for ionic systems with density functional accuracy based on charge densities obtained by a neural network

Based on an analysis of the short range chemical environment of each atom in a system, standard machine learning based approaches to the construction of interatomic potentials aim at determining directly the central quantity which is the total energy. This prevents for instance an accurate description of the energetics of systems where long range charge transfer is important as well as of ionized systems. We propose therefore not to target directly with machine learning methods the total energy but an intermediate physical quantity namely the charge density, which then in turn allows to determine the total energy. By allowing the electronic charge to distribute itself in an optimal way over the system, we can describe not only neutral but also ionized systems with unprecedented accuracy. We demonstrate the power of our approach for both neutral and ionized NaCl clusters where charge redistribution plays a decisive role for the energetics. We are able to obtain chemical accuracy, i.e. errors of less than a milli Hartree per atom compared to the reference density functional results. The introduction of physically motivated quantities which are determined by the short range atomic environment via a neural network leads also to an increased stability of the machine learning process and transferability of the potential.

cond-mat.mtrl-sci↗

Stabilized Quasi-Newton Optimization of Noisy Potential Energy Surfaces

Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient, but also very reliable. Unfortunately computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a sever problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are superior to comparable existing methods.

physics.comp-ph↗

Metrics for measuring distances in configuration spaces

In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional configuration space. We show that these metrics correlate well with the RMSD between two configurations if this RMSD is obtained from a global minimization over all translations, rotations and permutations of atomic indices. We introduce a Monte Carlo approach to obtain this global minimum of the RMSD between configurations.

cond-mat.mtrl-sci↗

A Multi-scale Approach for Simulations of Kelvin Probe Force Microscopy with Atomic Resolution

The distance dependence and atomic-scale contrast observed in nominal contact potential difference (CPD) signals recorded by KPFM on surfaces of insulating and semiconducting samples, have stimulated theoretical attempts to explain such effects. We attack this problem in two steps. First, the electrostatics of the macroscopic tip-cantilever-sample system is treated by a finite-difference method on an adjustable nonuniform mesh. Then the resulting electric field under the tip apex is inserted into a series of atomistic wavelet-based density functional theory (DFT) calculations. Results are shown for a realistic neutral but reactive silicon nano-scale tip interacting with a NaCl(001) sample. Bias-dependent forces and resulting atomic displacements are computed to within an unprecedented accuracy. Theoretical expressions for amplitude modulation (AM) and frequency modulation (FM) KPFM signals and for the corresponding local contact potential differences (LCPD) are obtained by combining the macroscopic and atomistic contributions to the electrostatic force component generated at the voltage modulation frequency, and evaluated for several tip oscillation amplitudes A up to 10 nm. Being essentially constant over a few Volts, the slope of atomistic force versus bias is the basic quantity which determines variations of the atomic-scale LCPD contrast. Already above A = 0.1 nm, the LCPD contrasts in both modes exhibit almost the same spatial dependence as the slope. In the AM mode, this contrast is approximately proportional to $A^{-1/2}$, but remains much weaker than the contrast in the FM mode, which drops somewhat faster as A is increased. These trends are a consequence of the macroscopic contributions to the KPFM signal, which are stronger in the AM-mode and especially important if the sample is an insulator even at sub-nanometer separations where atomic-scale contrast appears.

cond-mat.mtrl-sci↗

The crystal structure of cold compressed graphite

Through a systematic structural search we found an allotrope of carbon with Cmmm symmetry which we predict to be more stable than graphite for pressures above 10 GPa. This material, which we refer to as Z-carbon, is formed by pure sp3 bonds and is the only carbon allotrope which provides an excellent match to unexplained features in experimental X-ray diffraction and Raman spectra of graphite under pressure. The transition from graphite to Z-carbon can occur through simple sliding and buckling of graphene sheets. Our calculations predict that Z-carbon is a transparent wide band gap semiconductor with a hardness comparable to diamond.

cond-mat.mtrl-sci↗

The effect of ionization on the global minima of small and medium sized silicon and magnesium clusters

We re-examine the question of whether the geometrical ground state of neutral and ionized clusters are identical. Using a well defined criterion for being "identical" together, the extensive sampling methods on a potential energy surface calculated by density functional theory, we show that the ground states are in general different. This behavior is to be expected whenever there are metastable configurations which are close in energy to the ground state, but it disagrees with previous studies.

physics.atm-clus↗

Structural Metastability of Endohedral Silicon Fullerenes

Endohedrally doped Si20 fullerenes appear as appealing building blocks for nanoscale materials. We investigate their structural stability with an unbiased and systematic global geometry optimization method within density-functional theory. For a wide range of metal doping atoms, it was sufficient to explore the Born Oppenheimer surface for only a moderate number of local minima to find structures that clearly differ from the initial endohedral cages, but are considerably more favorable in terms of energy. Previously proposed structures are thus all metastable.

cond-mat.mes-hall↗

The energy landscape of silicon systems and its description by force fields, tight binding schemes, density functional methods and Quantum Monte Carlo methods

The accuracy of the energy landscape of silicon systems obtained from various density functional methods, a tight binding scheme and force fields is studied. Quantum Monte Carlo results serve as quasi exact reference values. In addition to the well known accuracy of DFT methods for geometric ground states and metastable configurations we find that DFT methods give a similar accuracy for transition states and thus a good overall description of the energy landscape. On the other hand, force fields give a very poor description of the landscape that are in most cases too rugged and contain many fake local minima and saddle points or ones that have the wrong height.

physics.comp-ph↗

Structural stability of the $B_{80}$ fullerene against defect formation

Using a systematic search algorithm we identify several types of point defects in the boron fullerene with 80 atoms. All these point defect leave the cage structure intact. In addition the cage structure is also very stable with respect to elastic deformations and addition or removal of atoms.

cond-mat.mtrl-sci↗

A Particle-Particle, Particle-Density (P3D) algorithm for the calculation of electrostatic interactions of particles with slab-like geometry

We present a fast and accurate method to calculate the electrostatic energy and forces of interacting particles with the boundary conditions appropriate to surfaces, i.e periodic in the two directions parallel to the surface and free in the perpendicular direction. In the spirit of the Ewald method the problem is divided into a short range and long range part. The charge density responsible for the long range part is represented by plane waves in the periodic directions and by finite elements in the non-periodic direction. Our method has computational complexity of O(N_g log(N_g)) with a very small prefactor, where N_g is the number of grid points.

physics.comp-ph↗

Particle-Particle, Particle-Scaling function (P3S) algorithm for electrostatic problems in free boundary conditions

An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with the full O(N^2) direct summation than the Fast Multipole Method. The forces obtained by our algorithm are analytical derivatives of the energy which guarantees energy conservation during a molecular dynamics simulation. Our algorithm is very simple. An MPI parallelised version of the code can be downloaded under the GNU General Public License from the website of our group.

physics.comp-ph↗