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.

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

Point defects and impurities strongly affect the physical properties of materials and have a decisive impact on their performance in applications. First-principles calculations have emerged as a powerful approach that complements experiments and can serve as a predictive tool in the identification and characterization of defects. The theoretical modeling of point defects in crystalline materials by means of electronic-structure calculations, with an emphasis on approaches based on density functional theory (DFT), is reviewed. A general thermodynamic formalism is laid down to investigate the physical properties of point defects independent of the materials class (semiconductors, insulators, and metals), indicating how the relevant thermodynamic quantities, such as formation energy, entropy, and excess volume, can be obtained from electronic structure calculations. Practical aspects such as the supercell approach and efficient strategies to extrapolate to the isolated-defect or dilute limit are discussed. Recent advances in tractable approximations to the exchange-correlation functional ($\mathrm{DFT}+U$, hybrid functionals) and approaches beyond DFT are highlighted. These advances have largely removed the long-standing uncertainty of defect formation energies in semiconductors and insulators due to the failure of standard DFT to reproduce band gaps. Two case studies illustrate how such calculations provide new insight into the physics and role of point defects in real materials.

First-principles calculations for point defects in solids

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, Delta SCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.

https://iopscience.iop.org/article/10.1088/0953-8984/22/25/253202/pdf

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.

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Perspective on density functional theory

https://th.fhi-berlin.mpg.de/site/uploads/Publications/CPC-180-2175-2009.pdf

Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals

The low-index surfaces of Au and Pt all tend to reconstruct, a fact that is of key importance in many nanostructure, catalytic, and electrochemical applications Remarkably, some significant questions regarding their structural energies remain even today, specifically for the large-scale quasihexagonally reconstructed (100) surfaces: rather dissimilar reconstruction energies for Au and Pt in available experiments and experiment and theory do not match for Pt We here show by all-electron density functional theory that only large enough ``$(5\ifmmode\times\else\texttimes\fi{}N)$'' approximant supercells capture the qualitative reconstruction energy trend between Au(100) and Pt(100), in contrast to what is often done in the theoretical literature Their magnitudes are then in fact similar and closer to the measured value for Pt(100); our calculations achieve excellent agreement with known geometric characteristics and provide direct evidence for the electronic reconstruction driving force

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Large-scale surface reconstruction energetics of Pt(100) and Au(100) by all-electron density functional theory

We have performed first principles calculations to investigate the structure and electronic properties of several different Si–HfOx interfaces. The atomic structure has been obtained by growing HfOx layer by layer on top of the Si(100) surface and repeatedly annealing the structure using ab initio molecular dynamics. The interfaces are characterized via their geometric and electronic properties, and also using electron transport calculations implementing a finite element based Green’s function method. We find that in all interfaces, oxygen diffuses towards the interface to form a silicon dioxide layer. This results in the formation of dangling Hf bonds in the oxide, which are saturated either by hafnium diffusion or Hf–Si bonds. The generally poor performance of these interfaces suggests that it is important to stabilize the system with respect to lattice oxygen diffusion.

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Paula Havu

Papers

Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals

Large-scale surface reconstruction energetics of Pt(100) and Au(100) by all-electron density functional theory

Interfacial oxide growth at silicon/high-k oxide interfaces: First principles modeling of the Si-HfO2 interface

Erratum: Spin-dependent electron transport through a magnetic resonant tunneling diode [Phys. Rev. B 71, 235301 (2005)]