Fabiano Corsetti

Room temperature compressibility and diffusivity of liquid water from first principles.

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid.

Structural and configurational properties of nanoconfined monolayer ice from first principles

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Optimal finite-range atomic basis sets for liquid water and ice.

Finite-range numerical atomic orbitals are the basis functions of choice for several first principles methods, due to their flexibility and scalability. Generating and testing such basis sets, however, remains a significant challenge for the end user. We discuss these issues and present a new scheme for generating improved polarization orbitals of finite range. We then develop a series of high-accuracy basis sets for the water molecule, and report on their performance in describing the monomer and dimer, two phases of ice, and liquid water at ambient and high density. The tests are performed by comparison with plane-wave calculations, and show the atomic orbital basis sets to exhibit an excellent level of transferability and consistency. The highest-order bases (quadruple-ζ) are shown to give accuracies comparable to a plane-wave kinetic energy cutoff of at least ~1000 eV for quantities such as energy differences and ionic forces, as well as achieving significantly greater accuracies for total energies and absolute pressures.

System-size convergence of point defect properties: The case of the silicon vacancy

We present a comprehensive study of the vacancy in bulk silicon in all its charge states from 2+ to 2-, using a supercell approach within plane-wave density-functional theory, and systematically quantify the various contributions to the well-known finite size errors associated with calculating formation energies and stable charge state transition levels of isolated defects with periodic boundary conditions. Furthermore, we find that transition levels converge faster with respect to supercell size when only the Gamma-point is sampled in the Brillouin zone, as opposed to a dense k-point sampling. This arises from the fact that defect level at the Gamma-point quickly converges to a fixed value which correctly describes the bonding at the defect centre. Our calculated transition levels with 1000-atom supercells and Gamma-point only sampling are in good agreement with available experimental results. We also demonstrate two simple and accurate approaches for calculating the valence band offsets that are required for computing formation energies of charged defects, one based on a potential averaging scheme and the other using maximally-localized Wannier functions (MLWFs). Finally, we show that MLWFs provide a clear description of the nature of the electronic bonding at the defect centre that verifies the canonical Watkins model.

Stroboscopic wave-packet description of nonequilibrium many-electron problems.

We introduce the construction of an orthogonal wave-packet basis set, using the concept of stroboscopic time propagation, tailored to the efficient description of nonequilibrium extended electronic systems. Thanks to three desirable properties of this basis, significant insight is provided into nonequilibrium processes (both time-dependent and steady-state), and reliable physical estimates of various many-electron quantities such as density, current, and spin polarization can be obtained. Use of the wave-packet basis provides new results for time-dependent switching-on of the bias in quantum transport, and for current-induced spin accumulation at the edge of a 2D doped semiconductor caused by edge-induced spin-orbit interaction.

Enhanced Configurational Entropy in High-Density Nanoconfined Bilayer Ice

A novel kind of crystal order in high-density nanoconfined bilayer ice is proposed from molecular dynamics and density-functional theory simulations. A first-order transition is observed between a low-temperature proton-ordered solid and a high-temperature proton-disordered solid. The latter is shown to possess crystalline order for the oxygen positions, arranged on a close-packed triangular lattice with AA stacking. Uniquely among the ice phases, the triangular bilayer is characterized by two levels of disorder (for the bonding network and for the protons) which results in a configurational entropy twice that of bulk ice.

Electronic stopping power in a narrow band gap semiconductor from first principles

The direction and impact parameter dependence of electronic stopping power, along with its velocity threshold behavior, is investigated in a prototypical small-band-gap semiconductor. We calculate the electronic stopping power of H in Ge, a semiconductor with relatively low packing density, using time-evolving time-dependent density-functional theory. The calculations are carried out in channeling conditions with different impact parameters and in different crystal directions for projectile velocities ranging from 0.05 to 0.6 atomic units. The satisfactory comparison with available experiments supports the results and conclusions beyond experimental reach. The calculated electronic stopping power is found to differ in different crystal directions; however, strong impact parameter dependence is observed only in one of these directions. The distinct velocity threshold observed in experiments is well reproduced, and its nontrivial relation with the band gap follows a perturbation theory argument surprisingly well. This simple model is also successful in explaining why different density functionals give the same threshold even with substantially different band gaps.

Performance Analysis of Electronic Structure Codes on HPC Systems: A Case Study of SIESTA

We report on scaling and timing tests of the SIESTA electronic structure code for ab initio molecular dynamics simulations using density-functional theory. The tests are performed on six large-scale supercomputers belonging to the PRACE Tier-0 network with four different architectures: Cray XE6, IBM BlueGene/Q, BullX, and IBM iDataPlex. We employ a systematic strategy for simultaneously testing weak and strong scaling, and propose a measure which is independent of the range of number of cores on which the tests are performed to quantify strong scaling efficiency as a function of simulation size. We find an increase in efficiency with simulation size for all machines, with a qualitatively different curve depending on the supercomputer topology, and discuss the connection of this functional form with weak scaling behaviour. We also analyze the absolute timings obtained in our tests, showing the range of system sizes and cores favourable for different machines. Our results can be employed as a guide both for running SIESTA on parallel architectures, and for executing similar scaling tests of other electronic structure codes.

The orbital minimization method for electronic structure calculations with finite-range atomic basis sets

Abstract The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn–Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better than diagonalization depending on the details of the OMM implementation. Finally, we discuss the possibility of making use of the natural sparsity of the operator matrices for this type of basis, leading to a method that scales linearly with basis size.

Knock-on damage in bilayer graphene: Indications for a catalytic pathway

We study by high-resolution transmission electron microscopy the structural response of bilayer graphene to electron irradiation with energies below the knock-on damage threshold of graphene. We observe that one type of divacancy, which we refer to as the butterfly defect, is formed for radiation energies and doses for which no vacancies are formed in clean monolayer graphene. By using first principles calculations based on density-functional theory, we analyze two possible causes related with the presence of a second layer that could explain the observed phenomenon: an increase of the defect stability or a catalytic effect during its creation. For the former, the obtained formation energies of the defect in monolayer and bilayer systems show that the change in stability is negligible. For the latter, ab initio molecular dynamics simulations indicate that the threshold energy for direct expulsion does not decrease in bilayer graphene as compared with monolayer graphene, and we demonstrate the possibility of creating divacancies through catalyzed intermediate states below this threshold energy. The estimated cross section agrees with what is observed experimentally. Therefore, we show the possibility of a catalytic pathway for creating vacancies under electron radiation below the expulsion threshold energy.