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 ͑DFT͒ 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 states͒. 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 problem͒ 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: ͑i͒ single atom carbon wires connected to aluminum electrodes with extended or finite cross section, ͑ii͒ single atom gold wires, and finally ͑iii͒ large carbon nanotube systems with point defects.

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.

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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.

We present state-of-the-art first principles calculations for the IV characteristics of a donor-insulator-acceptor (DsigmaA) type molecular diode anchored with thiolate bonds to two gold electrodes. We find very poor diode characteristics of the device, and the origin of this is analyzed in terms of the bias-dependent electronic structure. At zero bias, the highest occupied molecular orbital (HOMO) is confined to the D part, and the lowest unoccupied molecular orbital (LUMO) is confined to the A part, while at 3.8 V the two states align, and this gives rise to an increasing current. The latter is a potential mechanism for rectification and may in some cases lead to favorable diode characteristics. We identify the origin of the vanishing rectification for the investigated molecule, and on the basis of this we suggest parameters which are important for successful chemical engineering of DsigmaA rectifiers.

We present density functional theory calculations of the phonon-limited mobility in n-type monolayer graphene, silicene and MoS2. The material properties, including the electron-phonon interaction, are calculated from first-principles. We provide a detailed description of the normalized full-band relaxation time approximation for the linearized Boltzmann transport equation (BTE) that includes inelastic scattering processes. The bulk electron-phonon coupling is evaluated by a supercell method. The method employed is fully numerical and does therefore not require a semianalytic treatment of part of the problem and, importantly, it keeps the anisotropy information stored in the coupling as well as the band structure. In addition, we perform calculations of the low-field mobility and its dependence on carrier density and temperature to obtain a better understanding of transport in graphene, silicene and monolayer MoS2. Unlike graphene, the carriers in silicene show strong interaction with the out-of-plane modes. We find that graphene has more than an order of magnitude higher mobility compared to silicene. For MoS2, we obtain several orders of magnitude lower mobilities in agreement with other recent theoretical results. The simulations illustrate the predictive capabilities of the newly implemented BTE solver applied in simulation tools based on first-principles and localized basis sets.

We report first-principles studies of electronic transport in monolayers of Tour wires functionalized with different side groups. An analysis of the scattering states and transmission eigenchannels suggests that the functionalization does not strongly affect the resonances responsible for current flow through the monolayer. However, functionalization has a significant effect on the interactions within the monolayer, so that monolayers with NO2 side groups exhibit local minima associated with twisted conformations of the molecules. We use our results to interpret observations of negative differential resistance and molecular memory in monolayers of NO2 functionalized molecules in terms of a twisting of the central ring induced by an applied bias potential.