Kurt Stokbro

Bio: Kurt Stokbro is an academic researcher from Synopsys. The author has contributed to research in topics: Density functional theory & Scanning tunneling microscope. The author has an hindex of 37, co-authored 117 publications receiving 9177 citations. Previous affiliations of Kurt Stokbro include University of Copenhagen & Technical University of Denmark.

Density-functional method for nonequilibrium electron transport

Abstract: We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (i) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects.

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

Abstract: QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented,a#13; the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings,a#13; simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more.a#13; Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation detailsa#13; not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.a#13;

Theory of rectification in tour wires: the role of electrode coupling.

Abstract: We report first-principles studies of electronic transport and rectification in molecular wires attached to gold electrodes. Our ab initio calculation gives an accurate description of the voltage drop as well as the broadening and alignment of the molecular levels in the metal-molecule-metal complex. We find that the operation range and rectification in such strongly chemisorbed molecules is limited by the width of the transmission resonances and their proximity to the Fermi level.

Improved initial guess for minimum energy path calculations

Abstract: A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fundamentals of zinc oxide as a semiconductor

Abstract: In the past ten years we have witnessed a revival of, and subsequent rapid expansion in, the research on zinc oxide (ZnO) as a semiconductor. Being initially considered as a substrate for GaN and related alloys, the availability of high-quality large bulk single crystals, the strong luminescence demonstrated in optically pumped lasers and the prospects of gaining control over its electrical conductivity have led a large number of groups to turn their research for electronic and photonic devices to ZnO in its own right. The high electron mobility, high thermal conductivity, wide and direct band gap and large exciton binding energy make ZnO suitable for a wide range of devices, including transparent thin-film transistors, photodetectors, light-emitting diodes and laser diodes that operate in the blue and ultraviolet region of the spectrum. In spite of the recent rapid developments, controlling the electrical conductivity of ZnO has remained a major challenge. While a number of research groups have reported achieving p-type ZnO, there are still problems concerning the reproducibility of the results and the stability of the p-type conductivity. Even the cause of the commonly observed unintentional n-type conductivity in as-grown ZnO is still under debate. One approach to address these issues consists of growing high-quality single crystalline bulk and thin films in which the concentrations of impurities and intrinsic defects are controlled. In this review we discuss the status of ZnO as a semiconductor. We first discuss the growth of bulk and epitaxial films, growth conditions and their influence on the incorporation of native defects and impurities. We then present the theory of doping and native defects in ZnO based on density-functional calculations, discussing the stability and electronic structure of native point defects and impurities and their influence on the electrical conductivity and optical properties of ZnO. We pay special attention to the possible causes of the unintentional n-type conductivity, emphasize the role of impurities, critically review the current status of p-type doping and address possible routes to controlling the electrical conductivity in ZnO. Finally, we discuss band-gap engineering using MgZnO and CdZnO alloys.

Handbook of Chemistry and Physics

Abstract: There is a special reason for reviewing this book at this time: it is the 50th edition of a compendium that is known and used frequently in most chemical and physical laboratories in many parts of the world. Surely, a publication that has been published for 56 years, withstanding the vagaries of science in this century, must have had something to offer. There is another reason: while the book is a standard fixture in most chemical and physical laboratories, including those in medical centers, it is not as frequently seen in the laboratories of physician's offices (those either in solo or group practice). I believe that the Handbook can be useful in those laboratories. One of the reasons, among others, is that the various basic items of information it offers may be helpful in new tests, either physical or chemical, which are continuously being published. The basic information may relate

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Abstract: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr_2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

The Atomic Simulation Environment - A Python library for working with atoms

Abstract: The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.