arXiv subjects

J. Bernholc

Publications and source records attributed to J. Bernholc.

14 recordsLinked to original sources

arXiv2025

pyRMG: A Framework for High-Throughput, Large-Cell DFT Calculations on Supercomputers

Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density functional theory (DFT) code's grid-decomposition approach scales nearly linearly with the number of GPUs, even for simulations exceeding thousands of atoms. This scalability makes RMG a compelling tool for high-throughput DFT studies of materials that would otherwise be bottlenecked in other codes (for example, by global Fast Fourier Transforms in plane-wave DFT). However, the limited workflow infrastructure for RMG has thus far constrained its adoption to a small user community. In this work, we present pyRMG, a Python package designed to streamline the setup and execution of RMG DFT calculations. Built on the pymatgen and ASE computational materials science Python packages, pyRMG automates input generation and convergence checking, and integrates with modern job schedulers (e.g., Flux) on leadership-class platforms such as Frontier and Perlmutter. We demonstrate pyRMG for a high-throughput study of interfacial strain and twist-angle effects in lattice-matched, 2D Bi$_2$Se$_3$/NbSe$_2$ heterostructures, which offers chemical insights into this system and shows that RMG-based workflows can converge with limited user intervention.

cond-mat.mtrl-sci↗

arXiv2023

Adaptive Finite Differencing in High Accuracy Electronic Structure Calculations

A new method for implementing the kinetic energy operator for real-space, grid-based electronic structure codes is developed. It is based on multi-order Adaptive Finite Differencing (AFD) and uses atomic pseudo orbitals produced by the corresponding pseudopotential codes to optimize the standard finite difference (SFD) operators for improved accuracy. Results are presented for a variety of test systems and Bravais lattice types, including the well-known Delta test for 71 elements in the periodic table, the Mott insulator NiO, and borax decahydrate, which contains covalent, ionic, and hydrogen bonds. The tests show that an 8th-order AFD operator leads to the same average Delta value as that achieved by plane-wave codes and is typically far more accurate and a much lower computational cost than a 12th-order SFD operator. The scalability of real-space electronic calculations is demonstrated for a 2,016-atom NiO cell, for which the computational time decreases nearly linearly when scaled from 18 to 144 CPU-GPU nodes.

physics.comp-ph↗

arXiv2020

Study of anharmonicity in Zirconium Hydrides using inelastic neutron scattering and ab-initio computer modeling

The anharmonic phenomena in Zirconium Hydrides and Deuterides, including ε-ZrH2, γ-ZrH, and γ-ZrD, have been investigated from aspects of inelastic neutron scattering (INS) and lattice dynamics calculations within the framework of density functional theory (DFT). The observed multiple sharp peaks below harmonic multi-phonon bands in the experimental spectra of all three materials did not show up in the simulated INS spectra based on the harmonic approximation, indicating the existence of strong anharmonicity in those materials and the necessity of further explanations. We present a detailed study on the anharmonicity of zirconium hydrides/deuterides by exploring the 2D potential energy surface of hydrogen/deuterium atoms, and solving the corresponding 2D single-particle Schrodinger equation to get the eigenfrequencies. The obtained results well describe the experimental INS spectra and show harmonic behavior in the fundamental modes and strong anharmonicity at higher energies.

cond-mat.mtrl-sci↗

arXiv2018

Direct writing of heterostructures in single atomically precise graphene nanoribbons

Precision control of interfacial structures and electronic properties is the key to the realization of functional heterostructures. Here, utilizing the scanning tunneling microscope (STM) both as a manipulation and characterization tool, we demonstrate the fabrication of a heterostructure in a single atomically precise graphene nanoribbon (GNR) and report its electronic properties. The heterostructure is made of a seven-carbon-wide armchair GNR and a lower band gap intermediate ribbon synthesized bottom-up from a molecular precursor on an Au substrate. The short GNR segments are directly written in the ribbon with an STM tip to form atomic precision intraribbon heterostructures. Based on STM studies combined with density functional theory calculations, we show that the heterostructure has a type-I band alignment, with manifestations of quantum confinement and orbital hybridization. Our finding demonstrates a feasible strategy to create a double barrier quantum dot structure with atomic precision for novel functionalities, such as negative differential resistance devices in GNR-based nanoelectronics.

cond-mat.mes-hall↗

arXiv2018

Design of Atomically Precise Nanoscale Negative Differential Resistance Devices

Down-scaling device dimensions to the nanometer range raises significant challenges to traditional device design, due to potential current leakage across nanoscale dimensions and the need to maintain reproducibility while dealing with atomic-scale components. Here we investigate negative differential resistance (NDR) devices based on atomically precise graphene nanoribbons. Our computational evaluation of the traditional double-barrier resonant tunneling diode NDR structure uncovers important issues at the atomic scale, concerning the need to minimize the tunneling current between the leads while achieving high peak current. We propose a new device structure consisting of multiple short segments that enables high current by the alignment of electronic levels across the segments while enlarging the tunneling distance between the leads. The proposed structure can be built with atomic precision using a scanning tunneling microscope (STM) tip during an intermediate stage in the synthesis of an armchair nanoribbon. An experimental evaluation of the band alignment at the interfaces and an STM image of the fabricated active part of the device are also presented. This combined theoretical-experimental approach opens a new avenue for the design of nanoscale devices with atomic precision.

cond-mat.mes-hall↗

arXiv2015

Parallel implementation of electronic structure eigensolver using a partitioned folded spectrum method

A parallel implementation of an eigensolver designed for electronic structure calculations is presented. The method is applicable to computational tasks that solve a sequence of eigenvalue problems where the solution for a particular iteration is similar but not identical to the solution from the previous iteration. Such problems occur frequently when performing electronic structure calculations in which the eigenvectors are solutions to the Kohn-Sham equations. The eigenvectors are represented in some type of basis but the problem sizes are normally too large for direct diagonalization in that basis. Instead a subspace diagonalization procedure is employed in which matrix elements of the Hamiltonian operator are generated and the eigenvalues and eigenvectors of the resulting reduced matrix are obtained using a standard eigensolver from a package such as LAPACK or SCALAPACK. While this method works well and is widely used, the standard eigensolvers scale poorly on massively parallel computer systems for the matrix sizes typical of electronic structure calculations. We present a new method that utilizes a partitioned folded spectrum scheme (PFSM) that takes into account the iterative nature of the problem and performs well on massively parallel systems. Test results for a range of problems are presented that demonstrate an equivalent level of accuracy when compared to the standard eigensolvers, while also executing up to an order of magnitude faster. Unlike O(N) methods, the technique works equally well for metals and systems with unoccupied orbitals as for insulators and semiconductors. Timing and accuracy results are presented for a range of systems, including a 512 atom diamond cell, a cluster of 13 C60 molecules, bulk copper, a 216 atom silicon cell with a vacancy, using 40 unoccupied states/atom, and a 4000 atom aluminum supercell.

physics.comp-ph↗

arXiv2010

Quantum-interference-controlled three-terminal molecular transistors based on a single ring-shaped-molecule connected to graphene nanoribbon electrodes

We study all-carbon-hydrogen molecular transistors where zigzag graphene nanoribbons play the role of three metallic electrodes connected to a ring-shaped 18-annulene molecule. Using the nonequilibrium Green function formalism combined with density functional theory, recently extended to multiterminal devices, we show that the proposed nanostructures exhibit exponentially small transmission when the source and drain electrodes are attached in a configuration that ensures destructive interference of electron paths around the ring. The third electrode, functioning either as an attached infinite-impedance voltage probe or as an "air-bridge" top gate covering half of molecular ring, introduces dephasing that brings the transistor into the "on" state with its transmission in the latter case approaching the maximum limit for a single conducting channel device. The current through the latter device can also be controlled in the far-from-equilibrium regime by applying a gate voltage.

cond-mat.mes-hall↗

arXiv2010

Band gap control of small bundles of carbon nanotubes using applied electric fields: A density functional theory study

Electrostatic screening between carbon nanotubes (CNTs) in a small CNT bundle leads to a switching behavior induced by electric field perpendicular to the bundle axis. Using a first-principles method, we investigate the electronic structures of bundles consisting of two or three CNTs and the effects of the electric field applied perpendicular to the bundle axis. The applied field causes band gap closure in semiconducting bundles, while a gap opening occurs in metallic ones, which enables considerable modulation of bundle conductivity. The modulation effect originates from symmetry breaking due to electrostatic screening between the adjacent tube walls.

cond-mat.mes-hall↗

arXiv2009

First-principles methodology for quantum transport in multiterminal junctions

We present a generalized approach for computing electron conductance and I-V characteristics in multiterminal junctions from first-principles. Within the framework of Keldysh theory, electron transmission is evaluated employing an O(N) method for electronic-structure calculations. The nonequilibrium Green function for the nonequilibrium electron density of the multiterminal junction is computed self-consistently by solving Poisson equation after applying a realistic bias. We illustrate the suitability of the method on two examples of four-terminal systems, a radialene molecule connected to carbon chains and two crossed carbon chains brought together closer and closer. We describe charge density, potential profile, and transmission of electrons between any two terminals. Finally, we discuss the applicability of this technique to study complex electronic devices.

cond-mat.mtrl-sci↗

arXiv2009

Electron transport in multi-terminal molecular device

The electron transport properties of a four-terminal molecular device are computed within the framework of density functional theory and non-equilibrium Keldysh theory. The additional two terminals lead to new properties, including a pronounced negative differential resistance not present in a two-terminal setup, and a pseudo-gating effect. In general, quantum interference between the four terminals and the central molecule leads to a complex non-linear behavior, dependent on the alignment of individual molecular states under bias and their coupling to the leads.

cond-mat.mes-hall↗

arXiv2003

Mn Interstitial Diffusion in (Ga,Mn)As

We present a combined theoretical and experimental study of the ferromagnetic semiconductor (Ga,Mn)As which explains the remarkably large changes observed on low temperature annealing. Careful control of the annealing conditions allows us to obtain samples with ferromagnetic transition temperatures up to 159 K. Ab initio calculations, and resistivity measurements during annealing, show that the observed changes are due to out-diffusion of Mn interstitials towards the surface, governed by an energy barrier of about 0.7-0.8 eV. The Mn interstitial is a double donor resulting in compensation of charge carriers and suppression of ferromagnetism. Electric fields induced by high concentrations of substitutional Mn acceptors have a significant effect on the diffusion.

cond-mat.mtrl-sci↗

arXiv2003

Spontaneous polarization and piezoelectricity in boron nitride nanotubes

Ab initio calculations of the spontaneous polarization and piezoelectric properties of boron nitride nanotubes show that they are excellent piezoelectric systems with response values larger than those of piezoelectric polymers. The intrinsic chiral symmetry of the nanotubes induces an exact cancellation of the total spontaneous polarization in ideal, isolated nanotubes of arbitrary indices. Breaking of this symmetry by inter-tube interaction or elastic deformations induces spontaneous polarization comparable to those of wurtzite semiconductors.

cond-mat.mtrl-sci↗

arXiv1996

Multigrid Methods in Electronic Structure Calculations

We describe a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods provide effective convergence acceleration and preconditioning on all length scales, thereby permitting efficient calculations for ill-conditioned systems with long length scales or high energy cut-offs. We discuss specific implementations of multigrid and real-space algorithms for electronic structure calculations, including an efficient multigrid-accelerated solver for Kohn-Sham equations, compact yet accurate discretization schemes for the Kohn-Sham and Poisson equations, optimized pseudo\-potentials for real-space calculations, efficacious computation of ionic forces, and a complex-wavefunction implementation for arbitrary sampling of the Brillioun zone. A particular strength of a real-space multigrid approach is its ready adaptability to massively parallel computer architectures, and we present an implementation for the Cray-T3D with essentially linear scaling of the execution time with the number of processors. The method has been applied to a variety of periodic and non-periodic systems, including disordered Si, a N impurity in diamond, AlN in the wurtzite structure, and bulk Al. The high accuracy of the atomic forces allows for large step molecular dynamics; e.g., in a 1 ps simulation of Si at 1100 K with an ionic step of 80 a.u., the total energy was conserved within 27 microeV per atom.

mtrl-th↗

arXiv1995

Large Scale Electronic Structure Calculations with Multigrid Acceleration

We have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. The technique has been applied to systems containing up to 100 atoms, including a highly elongated diamond cell, an isolated C$_{60}$ molecule, and a 32-atom cell of GaN with the Ga d-states in valence. The method is well suited for implementation on both vector and massively parallel architectures.

mtrl-th↗