arXiv subjects

David Williams-Young

Publications and source records attributed to David Williams-Young.

3 recordsLinked to original sources

arXiv2023

Using Diffusion Maps to Analyze Reaction Dynamics for a Hydrogen Combustion Benchmark Dataset

We use local diffusion maps to assess the quality of two types of collective variables (CVs) for a recently published hydrogen combustion benchmark dataset~\cite{guan2022benchmark} that contains ab initio molecular dynamics trajectories and normal modes along minimum energy paths. This approach was recently advocated in~\cite{tlldiffmap20} for assessing CVs and analyzing reactions modeled by classical molecular dynamics simulations. We report the effectiveness of this approach to molecular systems modeled by quantum ab initio molecular dynamics. In addition to assessing the quality of CVs, we also use global diffusion maps to perform committor analysis as proposed in~\cite{tlldiffmap20}. We show that the committor function obtained from the global diffusion map allows us to identify transition regions of interest in several hydrogen combustion reaction channels.

physics.chem-ph↗

arXiv2021

The Effect of Geometry, Spin and Orbital Optimization in Achieving Accurate, Fully-Correlated Results for Iron-Sulfur Cubanes

Iron-sulfur clusters comprise an important functional motif of the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from fully-correlated calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. To provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of cubane-based clusters using two complementary, fully-correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (< 1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the lowest singlet and the highest spin states is strongly geometry dependent, changing by an order of magnitude upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap by a factor of two compared to typical mean-field orbital approaches. Our results clearly demonstrate the need for performing highly correlated calculations to unveil the challenging electronic structure of these complex catalytic centers.

physics.chem-ph↗

arXiv2019

On the Efficacy and High-Performance Implementation of Quaternion Matrix Multiplication

Quaternion symmetry is ubiquitous in the physical sciences. As such, much work has been afforded over the years to the development of efficient schemes to exploit this symmetry using real and complex linear algebra. Recent years have also seen many advances in the formal theoretical development of explicitly quaternion linear algebra with promising applications in image processing and machine learning. Despite these advances, there do not currently exist optimized software implementations of quaternion linear algebra. The leverage of optimized linear algebra software is crucial in the achievement of high levels of performance on modern computing architectures, and thus provides a central tool in the development of high-performance scientific software. In this work, a case will be made for the efficacy of high-performance quaternion linear algebra software for appropriate problems. In this pursuit, an optimized software implementation of quaternion matrix multiplication will be presented and will be shown to outperform a vendor tuned implementation for the analogous complex matrix operation. The results of this work pave the path for further development of high-performance quaternion linear algebra software which will improve the performance of the next generation of applicable scientific applications.

cs.MS↗