An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes.Comment: SC17 conference paper, 12 pages, 7 figure

Knowledge is power: Quantum chemistry on novel computer architectures

In the first chapter of this thesis, a background of fundamental quantum chemistry concepts is provided. Chapter two contains an analysis of the performance and energy efficiency of various modern computer processor architectures while performing computational chemistry calculations. In chapter three, the processor architectural study is expanded to include parallel computational chemistry algorithms executed across multiple-node computer clusters. Chapter four describes a novel computational implementation of the fundamental Hartree-Fock method which significantly reduces computer memory requirements. In chapter five, a case study of quantum chemistry two-electron integral code interoperability is described. The final chapters of this work discuss applications of quantum chemistry. In chapter six, an investigation of the esterification of acetic acid on acid-functionalized silica is presented. In chapter seven, the application of ab initio molecular dynamics to study the photoisomerization and photocyclization of stilbene is discussed. Final concluding remarks are noted in chapter eight

Theoretical Study of Electron Transport and Trapping in Solvated Titanium Dioxide Nanoparticles

This thesis consists of two parts of work: the advances on the efficient and robust implementation of our quantum chemistry program Jaguar for large DFT calculations, and theoretical modeling of electron transport and trapping in solvated TiO_2 nanoparticles. In first half, We implemented an OpenMP/MPI hybrid parallelization implementation of the pseudospectral algorithm, developed a fragment based initial guess methodology which is suitable for addressing systems with significant delocalization, and improved numerical robustness with regard to the converged wavefunction. The parallel scalability is enhanced greatly from ∼16 to ∼128, which enables a hybrid-DFT calculation for a system with up to 5000 basis functions. Those advances enable Jaguar to be used in a wide range of materials science problems that previously were not accessible to our approach.In second half, by employing a large cluster, a hybrid DFT model (B3LYP), and a realistic treatment of solvent, we proposed an atomically detailed model for the electronic states involved in transport and trapping, and obtain good agreement with experiment for properties such as the energetics of the trapping states and the barriers to hopping conduction by electrons. The results suggest the existence of energetically shallow electron trapping states at (sub) surface region induced by the presence of small cations and the continuum solvent effect. The barrier heights imply that concerted ambipolar diffusion of the Li+/e − can occur under thermal activation, but it is energetically disfavored for proton/e− pair. Those results advance our understanding of the effect of the cation and solvent on the density of states (DOS) of electron traps, and establish the plausibility that ambipolar model plays a role in electron transport through TiO_2 film in DSSC

Complexity Reduction in Density Functional Theory: Locality in Space and Energy

We present recent developments of the NTChem program for performing large scale hybrid Density Functional Theory calculations on the supercomputer Fugaku. We combine these developments with our recently proposed Complexity Reduction Framework to assess the impact of basis set and functional choice on its measures of fragment quality and interaction. We further exploit the all electron representation to study system fragmentation in various energy envelopes. Building off this analysis, we propose two algorithms for computing the orbital energies of the Kohn-Sham Hamiltonian. We demonstrate these algorithms can efficiently be applied to systems composed of thousands of atoms and as an analysis tool that reveals the origin of spectral properties.Comment: Accepted Manuscrip

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Computation of optical properties of chromophores in different environments using QM/MM methods

Die theoretische Beschreibung der Wechselwirkung zwischen Molekülen und Licht kann herausfordernd sein, insbesondere dann, wenn es sich um flexible Farbstoffe in einer komplexen und dynamischen Umgebung handelt. Obgleich quantenmechanische (QM) Methoden den angeregten Zustand eines Moleküls beschreiben können, sind sie zu rechenaufwändig, um strukturelle Fluktuationen simulieren zu können. Darüber hinaus ist die mögliche Systemgröße, die beschrieben werden kann, durch die Rechenkosten begrenzt. Aus diesem Grund kommen für die Untersuchung von Farbstoffen in Proteinumgebung semiempirische und Multiskalenansätze ins Spiel. Die semiempirische Time-Dependent Long-range Corrected Density Functional Tight Binding (TD-LC-DFTB2) Methode wurde als effiziente Alternative zu ab initio Methoden oder der Dichtefunktionaltheorie in Bezug auf Geometrien im angeregten Zustand und Anregungsenergien getestet. Sie wurde in QM/MM Simulationen angewandt, in denen sie einen angeregten Fluorophor beschrieb, dessen Umgebung von einem klassischen Kraftfeld beschrieben wurde. Diese neue Strategie für die Untersuchung von Fluoreszenz wurde sorgfältig anhand von Literaturergebnissen bewertet, indem die Ergebnisse sowohl mit experimentellen als auch mit theoretischen Studien, die auf anderen Ansätzen basieren, verglichen wurden. Es wurde herausgefunden, dass TD-LC-DFTB2 im Allgemeinen Geometrien und Anregungsenergien von ausreichender Qualität liefert, aber es wurden auch einige Schwächen entdeckt. Außerdem wurde ein optischer Glukosesensor untersucht, der aus dem Glukosebindeprotein und einem angefügten Fluorophor besteht. Mit Hilfe von klassischen Molekulardynamiksimulationen (MD Simulationen) konnten Zusammenhänge zwischen der Anwesenheit von Glukose, den Proteinkonformationen und dem Aufenthaltsort des Farbstoffs gefunden werden. Daraus ergab sich ein starker Hinweis auf die Funktionsweise des Sensors. Schließlich wurde der Energietransfer in einem Pigment-Protein-Komplex untersucht. Der Fenna-Matthews-Olson-Komplex von Photosynthese betreibenden grünen Schwefelbakterien beinhaltet mehrere Bakteriochlorophyll a -- Pigmente in seinem Proteingerüst. Diese leiten die im Chlorosome gesammelte Anregungsenergie mit erstaunlicher Effizienz zum Reaktionszentrum weiter. Es wird Vorarbeit für eine Simulation der Exzitonenpropagation durch den Komplex gezeigt. Anregungsenergien und die Kopplungen zwischen den Pigmenten, das heißt die Elemente des exzitonischen Hamiltonoperators, wurden mit TD-LC-DFTB2 für Strukturen aus klassischen MD Simulationen berechnet. Dadurch wurde ein Eindruck zu deren Entwicklung über die Zeit und den Einfluss der Proteinumgebung gewonnen. Weiterhin wurden diese Daten genutzt, um neuronale Netze zu trainieren, die Anregungsenergien und Kopplungen noch schneller als TD-LC-DFTB2 vorhersagen können

Developments and applications of quantum chemistry : from novel electronic structure methods to conjugated optoelectronic materials

The work contained within this thesis encompasses a variety of different techniques to describe chemical systems of varying complexity, ranging from geometrically simple systems with an inherently correlated, and thus complex, electronic structure and vice versa. The stochastic technique of Monte-Carlo configuration interaction, which can generate properties of full configuration interaction (FCI) quality despite vast reduction in wavefunction size, was locally modified to involve a more systematic configuration selection regime, termed systematic-MCCI. A comparison of both approaches was undertaken on Ne, H2O, CO and Cr2 due to varying electronic structure in these systems; for comparison FCI and a novel pruned-FCI alternative was also included. It shall be demonstrated that the stochastic MCCI approach produced near optimal wavefunctions when compared to these systematically generated wavefunctions, with a far reduced computational cost. We then switch our attention to the modelling of chemical reaction pathways, specifically those undergoing an intramolecular Diels-Alder (IMD-A) cycloaddition process, using the high-accuracy thermochemistry method, CBS-QB3. It was observed that incorporation of a nitro group into the IMD-A substrate resulted in more exergonic reactions and lower activation barriers, when compared to non-substituted substrates, attributed to the enhanced positive charge stabilisation in the cycloadduct. The nature of the important frontier molecular orbital (FMO) interaction was also found to completely reverse upon nitration. The substitution of the dieneophile was tolerated to a much better degree in nitro bearing systems due to the increased distances between the bond forming carbons in the transition state. However, this nitration effect was not observed in highly polarity mismatched substrates. We also investigate if structureenergy correlations are present in a set of hetero IMD-A substrates, between the bond length contraction upon going from the transition state to the cycloadduct and the overall reaction free energy change and the retro IMD-A barrier. However, as will be discussed for the substrates of interest herein we observe very little correlation. In addition we explored the structure-energy correlation for the aforementioned nitro and non-nitrated IMD-A reactions but similar findings were observed. A density functional theory (DFT) study is then undertaken for a range of organic π-conjugated materials. We explore the ionisation potential of these materials with a comparison to recent experimental findings. As shall be discussed we observe good agreement with experiment, within 100 meV of the uncertainty range, for the computationally cheap approach of a single oligomer contained within an implicit solvent model when there is no known stacking within the polymer environment. However, if the thin film environment exhibits a degree of ordering this simple approach breaks down and more sophisticated models must be implemented. The thesis concludes with a molecular dynamics (MD) study of two simple π-organic conjugated materials using a recently parameterised force-field. The configurational landscape attained from the MD simulations are then explored with electronic structure methods and a brief statistical analysis undertaken

Structure and Bonding in DNA. Development and Application of Parallel and Order-N DFT Methods

Baerends, E.J. [Promotor]Snijders, J.G. [Promotor]Bickelhaupt, F.M. [Copromotor