Electronic Structure Code Research Articles

Investigating robustness of interatomic potentials with universal interface

We present a set of Python routines to perform basic tests of classical atomistic potentials and their example applications. These routines are implemented using universal Atomic Simulation Environment (ASE) and LAMMPS molecular dynamics code. ASE is utilized to create atomic configurations, to write input scripts for LAMMPS, and to read results from output files. Evaluated properties are formation energies and volumes of simple point defects (vacancies, substitutions, and interstitials), formation energies of basic surfaces, heats of formation of simple binary compounds, and elastic constants. The flexibility of LAMMPS allows easy switching between different semi-empirical potentials, while the universality of ASE allows to compare results with a variety of electronic structure codes.

Structural evolution of amino acid crystals under stress from a non-empirical density functional

Use of the non-local correlation functional vdW-DF (from ‘van der Waals density functional’; Dion M et al 2004 Phys. Rev. Lett. 92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10 GPa—with and without van der Waals interactions—and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3 GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.

What Is the Best DFT Functional for Vibronic Calculations? A Comparison of the Calculated Vibronic Structure of the S1–S0 Transition of Phenylacetylene with Cavity Ringdown Band Intensities

The sensitivity of vibronic calculations to electronic structure methods and basis sets is explored and compared to accurate relative intensities of the vibrational bands of phenylacetylene in the S(1)(A(1)B(2)) ← S(0)(X(1)A(1)) transition. To provide a better measure of vibrational band intensities, the spectrum was recorded by cavity ringdown absorption spectroscopy up to energies of 2000 cm(-1) above the band origin in a slit jet sample. The sample rotational temperature was estimated to be about 30 K, but the vibrational temperature was higher, permitting the assignment of many vibrational hot bands. The vibronic structure of the electronic transition was simulated using a combination of time-dependent density functional theory (TD-DFT) electronic structure codes, Franck-Condon integral calculations, and a second-order vibronic model developed previously [Johnson, P. M.; Xu, H. F.; Sears, T. J. J. Chem. Phys. 2006, 125, 164331]. The density functional theory (DFT) functionals B3LYP, CAM-B3LYP, and LC-BLYP were explored. The long-range-corrected functionals, CAM-B3LYP and LC-BLYP, produced better values for the equilibrium geometry transition moment, but overemphasized the vibronic coupling for some normal modes, while B3LYP provided better-balanced vibronic coupling but a poor equilibrium transition moment. Enlarging the basis set made very little difference. The cavity ringdown measurements show that earlier intensities derived from resonance-enhanced multiphoton ionization (REMPI) spectra have relative intensity errors.

Libxc: A library of exchange and correlation functionals for density functional theory

The central quantity of density functional theory is the so-called exchange–correlation functional. This quantity encompasses all non-trivial many-body effects of the ground-state and has to be approximated in any practical application of the theory. For the past 50 years, hundreds of such approximations have appeared, with many successfully persisting in the electronic structure community and literature. Here, we present a library that contains routines to evaluate many of these functionals (around 180) and their derivatives.Program summaryProgram title: LIBXCCatalogue identifier: AEMU_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMU_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU Lesser General Public License version 3No. of lines in distributed program, including test data, etc.: 87455No. of bytes in distributed program, including test data, etc.: 945365Distribution format: tar.gzProgramming language: C with Fortran bindings.Computer: All.Operating system: All.RAM: N.A.Classification: 7.3, 16.1.Nature of problem: Evaluation of the exchange–correlation energy functional and its derivatives. This is a fundamental part of any atomic, molecular, or solid-state code that uses density-functional theory.Solution method: The values of the energy functional and its derivatives are given in a real grid of mesh points.Running time: Typically much smaller than the remainder of the electronic structure code. The running time has a natural linear scaling with the number of grid points.

A first-principle study of the magnetic, electronic and elastic properties of the hypothetical YFe5 compound

We present a DFT-based study of the magnetic properties, electronic structure and bulk modulus of YFe5 at ambient and higher hydrostatic pressures. The LSDA and GGA approximations, as implemented in the electronic structure code FPLO-09, are used throughout the scalar relativistic calculation in this work. Charge and spin density maps using the WIEN2k are also reported for the equilibrium lattice constants. Our study shows that the magnetic phase of this hypothetical compound is more stable than the nonmagnetic phase, and that the application of pressure on magnetic YFe5 has a prominent effect on its magnetic and electronic properties, e.g. the reduction of the magnetic moment and finally the disappearance of ferromagnetism.

Ab-initio approach to study hydrogen diffusion in 9Cr steels

We calculate the equilibrium energies and migration barriers of Fe, Cr and H interstitial defects in α-FeX(X=Cr). We use the ab-initio electronic structure code, SIESTA, coupled to the monomer method to find activated states (or migration barriers), in order to study atomic defects diffusion. Ab-initio calculations reveal that in the presence of Cr the H migration barriers are higher than in pure α-Fe. On the other hand, our permeation tests on 9%Cr–91%Fe alloys reveal a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure, annealed iron. Focusing on our experimental results, we explore very simple model of new H trapping sites and possible migration paths that can explain the experimental observations.

Simulation of spin-polarized scanning tunneling microscopy on complex magnetic surfaces: Case of a Cr monolayer on Ag(111)

We propose an atom-superposition-based method for simulating spin-polarized scanning tunneling microscopy (SP-STM) from first principles. Our approach provides bias-dependent STM images in high spatial resolution, with the capability of using either constant current or constant height modes of STM. In addition, topographic and magnetic contributions can clearly be distinguished, which are directly comparable to results of SP-STM experiments in the differential magnetic mode. Advantages of the proposed method are that it is computationally cheap, it is easy to parallelize, and it can employ the results of any ab initio electronic structure code. Its capabilities are illustrated for the prototype frustrated hexagonal antiferromagnetic system, Cr monolayer on Ag(111) in a noncollinear magnetic ${120}^{\ensuremath{\circ}}$ N\'eel state. We show evidence that the magnetic contrast is sensitive to the tip electronic structure, and this contrast can be reversed depending on the bias voltage.

Coverage effects in the adsorption of H2 on Pd(100) studied by ab initio molecular dynamics simulations

The interaction of hydrogen with palladium surfaces represents one of the model systems for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently it has become possible, based on advances in the electronic structure codes and improvements in the computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Here, I present ab initio molecular dynamics (AIMD) simulations based on periodic density functional theory (DFT) calculations of the adsorption of H(2) on hydrogen-precovered Pd(100) for a broad variety of different hydrogen coverage structures. The stability of the adsorbate structures and the adsorption dynamics are analyzed in detail. Calculated sticking probabilities are larger than expected for pure site-blocking consistent with experimental results. It turns out that the adsorption dynamics on the strongly corrugated surfaces depends sensitively on the dynamic response of the substrate atoms upon the impact of the impinging H(2) molecules. In addition, for some structures the adsorption probability was evaluated as a function of the kinetic energy. Adsorbate structures corresponding to the same coverage but with different arrangements of the adsorbed atoms can lead to a qualitatively different dependence of the adsorption probability on the kinetic energy changing also the order of the preferred structures, as far as the adsorption is concerned, as a function of the kinetic energy. This indicates that dynamical effects such as steering and dynamical trapping play an important role in the adsorption on these precovered substrates.

Calculation of dissociating autoionizing states using the block diagonalization method: Application to N2H

We report the calculation of preliminary potential surfaces necessary to treat dissociative recombination (DR) of electrons with N2H+. We performed multi-reference, configuration interaction calculations with a large active space for N2H+ and N2H, using the GAMESS electronic structure code. Rydberg-valence coupling is strong in N2H, and a systematic procedure is desirable to isolate the appropriate dissociating, autoionizing states. We used the block diagonalization method, which requires only modest additional effort beyond the standard methodology. We treated both linear and bent geometries of the molecules, with N2 fixed at its equilibrium separation. The results indicate that the crossing between the dissociating neutral curve and the initial ion potential is not favorably located, suggesting that the direct mechanism for DR will be small. Dynamics calculations using the multi-configuration, time-dependent Hartree (MCTDH) method confirm this conclusion.

Optimized energy landscape exploration using the ab initio based activation-relaxation technique

Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

Contribution of molecular dynamics simulations and ab initiocalculations to the interpretation of Mg K-edge experimental XANES inK2O–MgO–3SiO2 glass

The structural environment of Mg in a K-bearing silicate glass of compositionK2MgSi3O8 is investigated by x-ray absorption near-edge structure (XANES) spectroscopy at the MgK-edge. XANES calculations are performed using a plane-wave electronic structure code,and a structural model obtained by classical molecular dynamics coupled to ab initiorelaxation. Bond valence theory is used to validate plausible environments within thestructural models. Comparison between the experimental and calculated spectra enables usto conclude that the Mg atoms are located in distorted tetrahedral sites. Sitedistortions are found to be correlated to the theoretical shift of the XANES edgeposition.

Automated quantum conductance calculations using maximally-localised Wannier functions

A robust, user-friendly, and automated method to determine quantum conductance in quasi-one-dimensional systems is presented. The scheme relies upon an initial density-functional theory calculation in a specific geometry after which the ground-state eigenfunctions are transformed to a maximally-localised Wannier function (MLWF) basis. In this basis, our novel algorithms manipulate and partition the Hamiltonian for the calculation of coherent electronic transport properties within the Landauer–Buttiker formalism. Furthermore, we describe how short-ranged Hamiltonians in the MLWF basis can be combined to build model Hamiltonians of large (>10,000 atom) disordered systems without loss of accuracy. These automated algorithms have been implemented in the Wannier90 code (Mostofi et al., 2008) [1], which is interfaced to a number of electronic structure codes such as Quantum-ESPRESSO, AbInit, Wien2k, SIESTA and FLEUR. We apply our methods to an Al atomic chain with a Na defect, an axially heterostructured Si/Ge nanowire and to a spin-polarised defect on a zigzag graphene nanoribbon.

First principles calculation of finite temperature magnetism in Fe and Fe3C

Density functional calculations have proven to be a useful tool in the study of ground state properties of many materials. The investigation of finite temperature magnetism, on the other hand, has to rely usually on the usage of empirical models that allow the large number of evaluations of the systems Hamiltonian that are required to obtain the phase space sampling needed to obtain the free energy, specific heat, magnetization, susceptibility, and other quantities as function of temperature. We have demonstrated a solution to this problem that harnesses the computational power of today’s large massively parallel computers by combining a classical Wang–Landau Monte-Carlo calculation [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with our first principles multiple scattering electronic structure code [Y. Wang et al., Phys. Rev. Lett. 75, 2867 (1995)] that allows the energy calculation of constrained magnetic states [M. Eisenbach et al., Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (ACM, New York, 2009)]. We present our calculations of finite temperature properties of Fe and Fe3C using this approach and we find the Curie temperatures to be 980 and 425K, respectively.

Implementation of GPU-FFT into Planewave Based First Principles Calculation Method

We present an implementation of a GPU based FFT routine (Graphics Processing Unit based Fast Fourier Transformation) into a CPU based ab initio periodic DFT (Density Functional Theory) calculation code. The FFT calculation in the CPU based DFT codes is the most time-consuming part; for the 128 silicon system, the fraction of time of a CPU FFT calculation amounts to 0.64 of the whole periodic DFT calculation. The replacement of a double precision FFT in the periodic PWscf code with a single precision FFT gives no appreciable differences in both the numerical total energies and the interatomic forces, guaranteeing the use of a single precision GPU based FFT, CUFFT, for the code. The use of the CUFFT reduces the fraction to 0.20 of the whole PWscf code; the replacement speedups a factor of 2.2 for single CPU system. The use of the multi-CPU system with the GPU FFT accelerates by 2.2f, where f is the acceleration factor of the multi-CPU system. The single precision GPU calculation is implementable in any self-consistent electronic structure code, except for the eigensolver part in the DFT codes.

Scientific Computing in the Cloud

We investigate the feasibility of high performance scientific computation using cloud computers as an alternative to traditional computational tools. The availability of these large, virtualized pools of compute resources raises the possibility of a new compute paradigm for scientific research with many advantages. For research groups, cloud computing provides convenient access to reliable, high performance clusters and storage, without the need to purchase and maintain sophisticated hardware. For developers, virtualization allows scientific codes to be optimized and pre-installed on machine images, facilitating control over the computational environment. Preliminary tests are presented for serial and parallelized versions of the widely used x-ray spectroscopy and electronic structure code FEFF on the Amazon Elastic Compute Cloud, including CPU and network performance.

ESTEST: a framework for the validation and verification of electronic structure codes

We present a framework for the verification and validation (V&V) of electronic structure simulation software. Electronic structure computations involve numerous parameters and approximations that determine their accuracy and reliability. As a large number of simulation data coming from several electronic structure codes are becoming available, the associated V&V process is becoming increasingly complex. We introduce ESTEST as a framework for facilitating the verification and validation of electronic structure computations. ESTEST software enables the V&V, comparison and sharing of simulation data by constructing a unified representation of code outputs, populating and organizing a query database with these representations and interfacing the data through a web service that offers ways to search, view, compare, visualize and post-process the data. We present examples of V&V as well as comparison and analysis from our implementation, and justify the details of each of the innovative features of this software. The present implementation supports electronic structure codes such as Qbox, Quantum Espresso, ABINIT, and the Exciting code. An online demonstration is available at http://estest.ucdavis.edu.

Electronic structure packages: Two implementations of the projector augmented wave (PAW) formalism

The projector augmented wave (PAW) formalism developed by Blöchl [Phys. Rev. B 50 (1994) 17953] is an accurate and efficient pseudopotential-like scheme for electronic structure calculations within density functional theory and is now implemented in several electronic structure codes. Some of these codes use an implementation of the formalism developed by Kresse et al. [Phys. Rev. B 59 (1999) 1758] which differs slightly from the original Blöchl formalism and which can lead to different electronic structure results. In this paper, we analyze and illustrate the difference between the Blöchl and Kresse PAW formulations.

ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces

The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

Ab Initio Molecular Dynamics Simulations of the Adsorption of H2 on Palladium Surfaces

The interaction of hydrogen with palladium surfaces represents a model system for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently has it become possible, based on advances in electronic structure codes and improvements in computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Herein, recent ab initio molecular dynamics studies are discussed that address the adsorption dynamics of hydrogen molecules on hydrogen- and sulfur-precovered Pd surfaces. In addition, the relaxation dynamics of the hydrogen atoms after the dissociation on clean Pd(100) are presented.

Low spin moment due to hidden multipole order from spin-orbital ordering in LaFeAsO

This work presents new development and applications of ab-initio simulation tools for material science. Focus lies on materials with strong electronic correlation and strong spin-orbit coupling. Improvements on methods for solving the impurity problem in LDA+DMFT is presented, as well as a reliant method for charge self-consistency in a LMTO based electronic structure code. A new adaptive scheme for Brillouin zone integration is developed, where we show a strong reduction of numerical noise compared to standard techniques. A reformulation of the standard LDA+U method aiming to reduce the number of free parameters is introduced. Fast and realistic reduction of the number of free parameters provides the possibility of high throughput calculations and enabled us to study a large number of compounds. An analysis method for polarization in terms of coupled multipoles, and their corresponding energy contributions is developed and applied. This led to the formulation of Katt's rules, a set of rules complementary to Hund's rules. Katt's rules applies for occupying the orbitals of an electronic shell with strong spin-orbit coupling. The analysis is also used to investigate the unconventional Uranium based superconductors URu2Si2, UPt3, UPd2Al3 and UNi2Al3, as well as the high temperature superconductor LaOFeAs. We also investigate the non-magnetic delta-phase of Plutonium, providing insight to the electronic structure and the branching ratios of 4d to 5f transitions seen in photo emission spectra.The influence of surface reconstruction on the magneto crystalline anisotropy is investigated in multilayer Fe/ZnSe, showing that Fe deposited on an unreconstructed interface strongly reduces the uniaxial component of the MAE. We provide a detailed understanding of the magnetic properties of Fe2P, opening possible routes for enhancing the MAE in this system. A general route to strong MAE in nano-laminates is presented, we apply this to propose a candidate with extremely strong anisotropy energy density, 5Fe/2W1-xReX for x=[0.6-0.8].