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

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, 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, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. 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 details 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.Comment: Submitted to Journal of Physics: Condensed Matte

Modeling the iron oxides and oxyhydroxides for the prediction of environmentally sensitive phase transformations

Iron oxides and oxyhydroxides are challenging to model computationally as competing phases may differ in formation energies by only several kJ/mol, they undergo magnetization transitions with temperature, their structures may contain partially occupied sites or long-range ordering of vacancies, and some loose structures require proper description of weak interactions such as hydrogen bonding and dispersive forces. If structures and transformations are to be reliably predicted under different chemical conditions, each of these challenges must be overcome simultaneously, while preserving a high level of numerical accuracy and physical sophistication. Here we present comparative studies of structure, magnetization, and elasticity properties of iron oxides and oxyhydroxides using density functional theory calculations with plane-wave and locally-confined-atomic-orbital basis sets, which are implemented in VASP and SIESTA packages, respectively. We have selected hematite, maghemite, goethite, lepidocrocite, and magnetite as model systems from a total of 13 known iron oxides and oxyhydroxides; and use same convergence criteria and almost equivalent settings in order to make consistent comparisons. Our results show both basis sets can reproduce the energetic stability and magnetic ordering, and are in agreement with experimental observations. There are advantages to choosing one basis set over the other, depending on the intended focus. In our case, we find the method using PW basis set most appropriate, and combine our results to construct the first phase diagram of iron oxides and oxyhydroxides in the space of competing chemical potentials, generated entirely from first principlesComment: 46 pages - Accepted for publication in PRB (19 journal pages), January 201

Forces and atomic relaxations in the pSIC approach with ultrasoft pseudopotentials

We present the scheme that allows for efficient calculations of forces in the framework of pseudopotential self-interaction corrected (pSIC) formulation of the density functional theory. The scheme works with norm conserving and also with ultrasoft pseudopotentials and has been implemented in the plane-wave basis code {\sc quantum espresso}. We have performed tests of the internal consistency of the derived expressions for forces considering ZnO and CeO$_2$ crystals. Further, we have performed calculations of equilibrium geometry for LaTiO$_3$, YTiO$_3$, and LaMnO$_3$ perovskites and also for Re and Mn pairs in silicon. Comparison with standard DFT and DFT+U approaches shows that in the cases where spurious self-interaction matters, the pSIC approach predicts different geometry, very often closer to the experimental data.Comment: 11 pages, 2 figure

Functionalized nanopore-embedded electrodes for rapid DNA sequencing

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Green's Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.Comment: 12 pages, 5 figure

Algorithmic differentiation and the calculation of forces by quantum Monte Carlo

We describe an efficient algorithm to compute forces in quantum Monte Carlo using adjoint algorithmic differentiation. This allows us to apply the space warp coordinate transformation in differential form, and compute all the 3M force components of a system with M atoms with a computational effort comparable with the one to obtain the total energy. Few examples illustrating the method for an electronic system containing several water molecules are presented. With the present technique, the calculation of finite-temperature thermodynamic properties of materials with quantum Monte Carlo will be feasible in the near future.Comment: 32 pages, 4 figure, to appear in The Journal of Chemical Physic

A first principles study of wurtzite-structure MnO

We present results of a density functional theory study of MnO in the wurtzite structure. Our motivation is provided by recent experiments reporting ferromagnetism in Mn-doped wurtzite structure ZnO. We find that wurtzite MnO a) is not strongly energetically disfavored as compared with the ground state rocksalt MnO, b) shows strong magnetostructural coupling and c) has a piezoelectric response that is larger than that of ZnO. These predictions augur well for the creation of ferromagnetic piezoelectric semiconductor based on Mn-doped ZnO