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.Comment: 9 pages, 9 figure

Negative-U properties for substitutional Au in Si

The isolated substitutional gold impurity in bulk silicon is studied in detail using electronic structure calculations based on density-functional theory. The defect system is found to be a non-spin-polarized negative-U centre, thus providing a simple solution to the long-standing debate over the electron paramagnetic resonance signal for gold in silicon. There is an excellent agreement (within 0.03 eV) between the well-established experimental donor and acceptor levels and the predicted stable charge state transition levels, allowing for the unambiguous assignment of the two experimental levels to the (1+/1-) and (1-/3-) transitions, respectively, in contrast to previously held assumptions about the system.Comment: 6 pages, 5 figure

On the properties of point defects in silicon nanostructures from ab initio calculations

In this thesis we apply a variety of computational methods based on density-functional theory (DFT) to the study of defect centres in bulk silicon and silicon nanostructures. Firstly, we discuss the system-size convergence of point defect properties in the supercell method for deep-level defects in bulk silicon; we consider both the vacancy and gold impurity. For the vacancy, we investigate systematically the main contributions to the finite size error that lead to the well-known slow convergence with respect to system size of defect properties, and demonstrate that different properties of interest can benefit from the use of different k-point sampling schemes. We also present a simple and accurate method for calculating the potential alignment correction to the valence band maximum of charged defect supercells by using maximally-localised Wannier functions, and show that the localised view of the electronic structure provided by them gives a clear description of the nature of the electronic bonding at the defect centre. For the gold impurity, we show that the system becomes a non-spin-polarised negative-U centre due to the effect of Jahn-Teller distortion, thus providing a simple explanation for the absent electron paramagnetic resonance signal for gold in silicon. The calculated transition levels are found to be in excellent agreement with experimental measurements. We then investigate the segregation of arsenic impurities in silicon close to an interface with amorphous silica. We employ a multiscale approach, generating a realistic disordered interface structure from Monte Carlo simulation, with a continuous random network model of the system parametrised from DFT. We calculate the segregation energy using DFT for a large number of substitutional sites encompassing all the oxidation states of silicon, and show that the results can be understood with a minimal model based only on the local strain and volume of the defect site.Open Acces

Twist-angle dependence of electron correlations in moir\'e graphene bilayers

Motivated by the recent observation of correlated insulator states and unconventional superconductivity in twisted bilayer graphene, we study the dependence of electron correlations on the twist angle and reveal the existence of strong correlations over a narrow range of twist-angles near the magic angle. Specifically, we determine the on-site and extended Hubbard parameters of the low-energy Wannier states using an atomistic quantum-mechanical approach. The ratio of the on-site Hubbard parameter and the width of the flat bands, which is an indicator of the strength of electron correlations, depends sensitively on the screening by the semiconducting substrate and the metallic gates. Including the effect of long-ranged Coulomb interactions significantly reduces electron correlations and explains the experimentally observed sensitivity of strong correlation phenomena on twist angle.Comment: 17 pages, 6 figure

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.Comment: 10 pages, 6 figure

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

On the properties of point defects in silicon nanostructures from ab initio calculations

In this thesis we apply a variety of computational methods based on density-functional theory (DFT) to the study of defect centres in bulk silicon and silicon nanostructures. Firstly, we discuss the system-size convergence of point defect properties in the supercell method for deep-level defects in bulk silicon; we consider both the vacancy and gold impurity. For the vacancy, we investigate systematically the main contributions to the finite size error that lead to the well-known slow convergence with respect to system size of defect properties, and demonstrate that different properties of interest can benefit from the use of different k-point sampling schemes. We also present a simple and accurate method for calculating the potential alignment correction to the valence band maximum of charged defect supercells by using maximally-localised Wannier functions, and show that the localised view of the electronic structure provided by them gives a clear description of the nature of the electronic bonding at the defect centre. For the gold impurity, we show that the system becomes a non-spin-polarised negative-U centre due to the effect of Jahn-Teller distortion, thus providing a simple explanation for the absent electron paramagnetic resonance signal for gold in silicon. The calculated transition levels are found to be in excellent agreement with experimental measurements. We then investigate the segregation of arsenic impurities in silicon close to an interface with amorphous silica. We employ a multiscale approach, generating a realistic disordered interface structure from Monte Carlo simulation, with a continuous random network model of the system parametrised from DFT. We calculate the segregation energy using DFT for a large number of substitutional sites encompassing all the oxidation states of silicon, and show that the results can be understood with a minimal model based only on the local strain and volume of the defect site.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Entropic bonding of the type 1 pilus from experiment and simulation.

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β -strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy experiments and steered molecular dynamics simulations (Alonso-Caballero et al. 2018 Nat. Commun. 9, 2758. (doi:10.1038/s41467-018-05107-6)). In this work, we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature