42 research outputs found
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