arXiv subjects

Irina V. Lebedeva

Publications and source records attributed to Irina V. Lebedeva.

At least 37 records · Page 2Linked to original sources

arXiv2020

The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure programs and redesign them as free, open-source libraries. They include "heavy-duty" ones with a high degree of parallelisation, and potential for adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers.

cond-mat.mtrl-sci↗

arXiv2020

Two phases with different domain wall networks and a reentrant phase transition in bilayer graphene under strain

The analytical two-chain Frenkel-Kontorova model is used to describe domain wall networks in bilayer graphene upon biaxial stretching of one of the layers. We show that the commensurate-incommensurate phase transition leading to formation of a regular triangular domain wall network at the relative biaxial elongation of $3.0\cdot 10^{-3}$ is followed by the transition to another incommensurate phase with a striped network at the elongation of $3.7\cdot 10^{-3}$. The reentrant transition to the phase with a triangular domain wall network is predicted for the elongation $\sim10^{-2}$.

cond-mat.mes-hall↗

arXiv2020

Energetics and Structure of Domain Wall Networks in Minimally Twisted Bilayer Graphene under Strain

The parameters of the triangular domain wall network in bilayer graphene with a simultaneously twisted and biaxially stretched bottom layer are studied using the two-chain Frenkel-Kontorova model. It is demonstrated that if the graphene layers are free to rotate, they prefer to stay co-aligned upon stretching the bottom layer and the regular triangular network of tensile domain walls is formed upon the commensurate-incommensurate phase transition. If the angle between the layers is fixed, the regular triangular network of shear domain walls is observed at zero elongation of the bottom layer. Upon stretching the bottom layer, however, the domain walls transform into the tensile ones and the size of the commensurate domains decreases. We also show that the parameters of the isosceles triangular domain wall network in twisted bilayer graphene under shear strain can be determined through purely geometrical considerations. Experimental analysis of the orientation of domain walls and period of the triangular network would, on the one hand, contribute to understanding of the interlayer interaction of graphene layers, and, on the other hand, serve for detection of relative strains and rotation between the layers. Vice versa external strains can be used to control the parameters of the triangular domain wall network and, therefore, electronic properties of twisted bilayer graphene.

cond-mat.mes-hall↗

arXiv2019

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems

Over the last years extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high-degree of precision. An appealing and challenging route towards engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, providing an unique framework allowing to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory framework. The present article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, like the new theoretical framework of quantum electrodynamics density-functional formalism (QEDFT) for the description of novel light-matter hybrid states. Those advances, and other being released soon as part of the Octopus package, will enable the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (QED-materials).

physics.comp-ph↗

arXiv2019

Commensurate-incommensurate phase transition and a network of domain walls in bilayer graphene with a biaxially stretched layer

The two-chain Frenkel-Kontorova model is applied for an analytical description of the energy and structure of the network of domain walls in bilayer graphene. Using this approach, the commensurate-incommensurate phase transition upon biaxial stretching of one of the graphene layers is considered. We demonstrate that formation of the equilateral triangular network of domain walls becomes energetically favourable above the critical relative biaxial elongation of the bottom layer of $3.0\cdot 10^{-3}$. It is shown that the optimal period of the triangular network of domain walls is inversely proportional to the difference between the biaxial elongation of the bottom layer and the critical elongation as long as it is much greater than the width of domain walls. Quantitative estimates of the contribution of a single dislocation node to the system energy and the period of the network of domain walls are obtained. Experimental measurements of the period could help to verify the energy of the fully incommensurate state (such as obtained by relative rotation of the layers) with respect to the commensurate one.

cond-mat.mes-hall↗

arXiv2019

Orbital magneto-optical response of periodic insulators from first principles

Magneto-optical response, i.e. optical response in the presence of a magnetic field, is commonly used for characterization of materials and in optical communications. However, quantum mechanical description of electric and magnetic fields in crystals is not straightforward as the position operator is ill defined. We present a reformulation of the density matrix perturbation theory for time-dependent electromagnetic fields under periodic boundary conditions, which allows us to treat the orbital magneto-optical response of solids at the \textit{ab initio} level. The efficiency of the computational scheme proposed is comparable to standard linear-response calculations of absorption spectra and the results of tests for molecules and solids agree with the available experimental data. A clear signature of the valley Zeeman effect is revealed in the continuum magneto-optical spectrum of a single layer of hexagonal boron nitride. The present formalism opens the path towards the study of magneto-optical effects in strongly driven low-dimensional systems.

cond-mat.mtrl-sci↗

arXiv2019

Elastic constants of graphene: Comparison of empirical potentials and DFT calculations

The capacity of popular classical interatomic potentials to describe elastic properties of graphene is tested. The Tersoff potential, Brenner reactive bond-order potentials REBO-1990, REBO-2000, REBO-2002 and AIREBO as well as LCBOP, PPBE-G, ReaxFF-CHO and ReaxFF-C2013 are considered. Linear and non-linear elastic response of graphene under uniaxial stretching is investigated by static energy calculations. The Young's modulus, Poisson's ratio and high-order elastic moduli are verified against the reference data available from experimental measurements and ab initio studies. The density functional theory calculations are performed to complement the reference data on the effective Young's modulus and Poisson's ratio at small but finite elongations. It is observed that for all the potentials considered, the elastic energy deviates remarkably from the simple quadratic dependence already at elongations of several percent. Nevertheless, LCBOP provides the results consistent with the reference data and thus realistically describes in-plane deformations of graphene. Reasonable agreement is also observed for the computationally cheap PPBE-G potential. REBO-2000, AIREBO and REBO-2002 give a strongly non-linear elastic response with a wrong sign of the third-order elastic modulus and the corresponding results are very far from the reference data. The ReaxFF potentials drastically overestimate the Poisson's ratio. Furthermore, ReaxFF-C2013 shows a number of numerical artefacts at finite elongations. The bending rigidity of graphene is also obtained by static energy calculations for large-diameter carbon nanotubes. The best agreement with the experimental and ab initio data in this case is achieved using the REBO-2000, REBO-2002 and ReaxFF potentials. Therefore, none of the considered potentials adequately describes both in-plane and out-of-plane deformations of graphene.

cond-mat.mes-hall↗

arXiv2018

Formation of nickel-carbon heterofullerenes under electron irradiation

A way to produce new metal-carbon nanoobjects by transformation of a graphene flake with an attached transition metal cluster under electron irradiation is proposed. The transformation process is investigated by molecular dynamics simulations by the example of a graphene flake with a nickel cluster. The parameters of the nickel-carbon potential (I. V. Lebedeva et al. J. Phys. Chem. C, 2012, 116, 6572) are modified to improve description of the balance between the fullerene elastic energy and graphene edge energies in this process. The metal-carbon nanoobjects formed are found to range from heterofullerenes with a metal patch to particles consisting of closed fullerene and metal clusters linked by chemical bonds. The atomic-scale transformation mechanism is revealed by the local structure analysis. The average time of formation of nanoobjects and their lifetime under electron irradiation are estimated for experimental conditions of high-resolution transmission electron microscope (HRTEM). The sequence of images of nanostructure evolution with time during its observation by HRTEM is also modelled. Furthermore, the possibility of batch production of studied metal-carbon nanoobjects and solids based on these nanoobjects is discussed.

cond-mat.mes-hall↗

arXiv2018

Long triple carbon chains formation by heat treatment of graphene nanoribbon: Molecular dynamics study with revised Brenner potential

The method for production of atomic chains by heating of graphene nanoribbons (GNRs) is proposed and studied by molecular dynamics simulations. The Brenner potential is revised to adequately describe formation of atomic chains, edges and vacancy migration in graphene. A fundamentally different behavior is observed for zigzag-edge GNRs with 3 and 4 atomic rows (3 and 4-ZGNRs) at 2500 K: formation of triple, double and single carbon chains with the length of hundreds of atoms in 3-ZGNRs and edge reconstruction with only short chains and GNR width reduction in 4-ZGNRs. The chain formation mechanism in 3-ZGNRs is revealed by analysis of bond reorganization reactions and is based on the interplay of two processes. The first one is breaking of bonds between 3 zigzag atomic rows leading to triple chain formation. The second one is bond breaking within the same zigzag atomic row, which occurs predominantly through generation of pentagons with subsequent bond breaking in pentagons and results in single or double chain formation. The DFT calculations of the barriers for relevant reactions are consistent with the mechanism proposed. The possibility of chain-based nanoelectronic devices with a controllable number of chains is discussed.

cond-mat.mes-hall↗

arXiv2018

Comparison of performance of van der Waals-corrected exchange-correlation functionals for interlayer interaction in graphene and hexagonal boron nitride

Exchange-correlation functionals with corrections for van der Waals interactions (PBE-D2, PBE-D3, PBE-D3(BJ), PBE-TS, optPBE-vdW and vdW-DF2) are tested for graphene and hexagonal boron nitride, both in the form of bulk and bilayer. The characteristics of the potential energy surface, such as the barrier to relative sliding of the layers and magnitude of corrugation, and physically measurable properties associated with relative in-plane and out-of-plane motion of the layers including the shear modulus and modulus for axial compression, shear mode frequency and frequency of out-of-plane vibrations are considered. The PBE-D3(BJ) functional gives the best results for the stackings of hexagonal boron nitride and graphite that are known to be ground-state from the experimental studies. However, it fails to describe the order of metastable states of boron nitride in energy. The PBE-D3 and vdW-DF2 functionals, which reproduce this order correctly, are identified as the optimal choice for general studies. The vdW-DF2 functional is preferred for evaluation of the modulus for axial compression and frequency of out-of-plane vibrations, while the PBE-D3 functional is somewhat more accurate in calculations of the shear modulus and shear mode frequency. The best description of the latter properties, however, is achieved also using the vdW-DF2 functional combined with consideration of the experimental interlayer distance. In the specific case of graphene, the PBE-D2 functional works very well and can be further improved by adjustment of the parameters.

cond-mat.mes-hall↗

arXiv2018

Structure and energetics of carbon, hexagonal boron nitride and carbon/hexagonal boron nitride single-layer and bilayer nanoscrolls

Single-layer and bilayer carbon and hexagonal boron nitride nanoscrolls as well as nanoscrolls made of bilayer graphene/hexagonal boron nitride heterostructure are considered. Structures of stable states of the corresponding nanoscrolls prepared by rolling single-layer and bilayer rectangular nanoribbons are obtained based on the analytical model and numerical calculations. The lengths of nanoribbons for which stable and energetically favorable nanoscrolls are possible are determined. Barriers to rolling of single-layer and bilayer nanoribbons into nanoscrolls and barriers to nanoscroll unrolling are calculated. Based on the calculated barriers nanoscroll lifetimes in the stable state are estimated. Elastic constants for bending of graphene and hexagonal boron nitride layers used in the model are found by density functional theory calculations.

cond-mat.mes-hall↗

arXiv2017

Stacking in incommensurate graphene/hexagonal-boron-nitride heterostructures based on ab initio study of interlayer interaction

The interlayer interaction in graphene/boron-nitride heterostructures is studied using density functional theory calculations with the correction for van der Waals interactions. It is shown that the use of the experimental interlayer distance allows to describe the potential energy surface at the level of more accurate but expensive computational methods. On the other hand, it is also demonstrated that the dependence of the interlayer interaction energy on the relative in-plane position of the layers can be fitted with high accuracy by a simple expression determined by the system symmetry. The use of only two independent parameters in such an approximation suggests that various physical properties of flat graphene/boron-nitride systems are interrelated and can be expressed through these two parameters. Here we estimate some of the corresponding physical properties that can be accessed experimentally, including the correction to the period of the Moiré superstructure for the highly incommensurate ground state of graphene/boron-nitride bilayer coming from the interlayer interaction, width of stacking dislocations in slightly incommensurate systems of boron nitride on stretched graphene and shear mode frequencies for commensurate graphene/boron-nitride systems, such as a flake on a layer. We propose that the commensurate-incommensurate phase transition can be observed in boron nitride on stretched graphene and experimental measurements of the corresponding critical strain can be also used to get an insight into graphene/boron-nitride interactions.

cond-mat.mes-hall↗

arXiv2017

Edge stacking dislocations in two-dimensional bilayers with a small lattice mismatch

Incomplete stacking dislocations are predicted to form at edges of the shorter upper layer in two-dimensional hexagonal bilayers upon stretching the longer bottom layer. A concept of the edge Burgers vector is introduced to describe such dislocations by analogy with the Burgers vector of standard bulk dislocations. Analytical solutions for the structure and energy of edge stacking dislocations in bilayer graphene are obtained depending on the magnitude of elongation and angles between the edge Burgers vector, direction of elongation and edge. The barrier for penetration of stacking dislocations inside the bilayer is estimated. The possibilities to measure the barrier to relative motion of graphene layers and strain of graphene on a substrate by observation of edge stacking dislocations are discussed.

cond-mat.mes-hall↗

arXiv2017

Transformation of amorphous carbon clusters to fullerenes

Transformation of amorphous carbon clusters into fullerenes under high temperature is studied using molecular dynamics simulations at microsecond times. Based on the analysis of both structure and energy of the system, it is found that fullerene formation occurs in two stages. Firstly, fast transformation of the initial amorphous structure into a hollow sp$^2$ shell with a few chains attached occurs with a considerable decrease of the potential energy and the number of atoms belonging to chains and to the amorphous domain. Then, insertion of remaining carbon chains into the sp$^2$ network takes place at the same time with the fullerene shell formation. Two types of defects remaining after the formation of the fullerene shell are revealed: 7-membered rings and single one-coordinated atoms. One of the fullerene structures obtained contains no defects at all, which demonstrates that defect-free carbon cages can be occasionally formed from amorphous precursors directly without defect healing. No structural changes are observed after the fullerene formation, suggesting that defect healing is a slow process in comparison with the fullerene shell formation. The schemes of the revealed reactions of chain atoms insertion into the fullerene shell just before its completion are presented. The results of the performed simulations are summarized within the paradigm of fullerene formation due to selforganization of the carbon system.

cond-mat.mes-hall↗

arXiv2017

Formation of nickel clusters wrapped in carbon cages: towards new endohedral metallofullerene synthesis

In spite of the high potential of endohedral metallofullerenes (EMFs) for application in biology, medicine and molecular electronics and recent efforts in EMF synthesis, the variety of EMFs accessible by conventional synthetic methods remains limited and does not include, for example, EMFs of late transition metals. We propose a method in which EMF formation is initiated by electron irradiation in aberration-corrected high-resolution transmission electron spectroscopy (AC-HRTEM) of a metal cluster surrounded by amorphous carbon inside a carbon nanotube serving as a nano-reactor and apply this method for synthesis of nickel EMFs. The use of ACHRTEM makes it possible not only to synthesize new, previously unattainable nanoobjects but also to study in situ the mechanism of structural transformations. Molecular dynamics simulations using the state-of-the-art approach for modeling the effect of electron irradiation are performed to rationalise the experimental observations and to link the observed processes with conditions of bulk EMF synthesis.

cond-mat.mes-hall↗

arXiv2016

Dislocations in stacking and commensurate-incommensurate phase transition in bilayer graphene and hexagonal boron nitride

Dislocations corresponding to a change of stacking in two-dimensional hexagonal bilayers, graphene and boron nitride, and associated with boundaries between commensurate domains are investigated using the two-chain Frenkel-Kontorova model on top of ab initio calculations. Structural transformations of bilayers in which the bottom layer is stretched and the upper one is left to relax freely are considered for gradually increased elongation of the bottom layer. Formation energies of dislocations, dislocation width and orientation of the boundary between commensurate domains are analyzed depending on the magnitude and direction of elongation. The second-order phase transition from the commensurate phase to the incommensurate one with multiple dislocations is predicted to take place at some critical elongation. The order parameter for this transition corresponds to the density of dislocations, which grows continuously upon increasing the elongation of the bottom layer above the critical value. In graphene and metastable boron nitride with the layers aligned in the same direction, where elementary dislocations are partial, this transition, however, is preceded by formation of the first dislocation at the elongation smaller than the critical one. The phase diagrams including this intermediate state are plotted in coordinates of the magnitude and direction of elongation of the bottom layer.

cond-mat.mes-hall↗

arXiv2016

Interlayer interaction and related properties of bilayer hexagonal boron nitride: ab initio study

Principal characteristics of interlayer interaction and relative motion of hexagonal boron nitride (h-BN) layers are investigated by the first-principles method taking into account van der Waals interactions. Dependences of the interlayer interaction energy on relative translational displacement of h-BN layers (potential energy surfaces) are calculated for two relative orientations of the layers, namely, for the layers aligned in the same direction and in the opposite directions upon relative rotation of the layers by 180 degrees. It is shown that the potential energy surfaces of bilayer h-BN can be approximated by the first Fourier components determined by symmetry. As a result, a wide set of physical qualintities describing relative motion of h-BN layers aligned in the same direction including barriers to their relative sliding and rotation, shear mode frequency and shear modulus are determined by a single parameter corresponding to the roughness of the potential energy surface, similar to bilayer graphene. The properties of h-BN layers aligned in the opposite directions are described by two such parameters. The possibility of partial and full dislocations in stacking of the layers is predicted for h-BN layers aligned in the same and opposite directions, respectively. The extended two-chain Frenkel-Kontorova model is used to estimate the width and formation energy of these dislocations on the basis of the calculated potential energy surfaces.

cond-mat.mes-hall↗

arXiv2014

Atomistic mechanism of carbon nanotube cutting catalyzed by nickel under the electron beam

The cutting of single-walled carbon nanotubes by an 80 keV electron beam catalyzed by nickel clusters is imaged in situ using aberration-corrected high-resolution transmission electron microscopy. Extensive molecular dynamics simulations within the CompuTEM approach provide insight into the mechanism of this process and demonstrate that the combination of irradiation and nickel catalyst is crucial for the cutting process to take place. The atomistic mechanism of cutting is revealed by detailed analysis of irradiation-induced reactions of bonds reorganization and atom ejection in the vicinity of the nickel cluster, showing a highly complex interplay of different chemical transformations catalysed by the metal cluster. One of the most prevalent pathways includes three consecutive stages: formation of polyyne carbon chains from carbon nanotube, dissociation of the carbon chains into single and pairs of adatoms adsorbed on the nickel cluster, and ejection of these adatoms leading to the cutting of nanotube. Significant variations in the atom ejection rate are discovered depending on the process stage and nanotube diameter. The revealed mechanism and kinetic characteristics of cutting process provide fundamental knowledge for the development of new methodologies for control and manipulation of carbon structures at the nanoscale.

cond-mat.mes-hall↗