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Richard, Ryan M.

Publications and source records attributed to Richard, Ryan M..

15 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

CMaize: Simplifying inter-package modularity from the build up

There is a growing desire for inter-package modularity within the chemistry software community to reuse encapsulated code units across a variety of software packages. Most comprehensive efforts at achieving inter-package modularity will quickly run afoul of a very practical problem, being able to cohesively build the modules. Writing and maintaining build systems has long been an issue for many scientific software packages that rely on compiled languages such as C/C++. The push for inter-package modularity compounds this issue by additionally requiring binary artifacts from disparate developers to interoperate at a binary level. Thankfully, the de facto build tool for C/C++, CMake, is more than capable of supporting the myriad of edge cases that complicate writing robust build systems. Unfortunately, writing and maintaining a robust CMake build system can be a laborious endeavor because CMake provides few abstractions to aid the developer. Further, the need to significantly simplify the process of writing robust CMake-based build systems, especially in inter-package builds, motivated us to write CMaize. In addition to describing the architecture and design of CMaize, the article also demonstrates how CMaize is used in production-level software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A Perspective on Sustainable Computational Chemistry Software Development and Integration

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

36 MATERIALS SCIENCE↗
DOE OSTI2023

CMakePPLang: An object-oriented extension to CMake

CMakePPLang is an object-oriented extension to the CMake language written entirely using the original CMake language, with the goal of making projects built on CMake easier to create and maintain. That said, CMakePPLang has different coding practices, paradigms, and standards than the original CMake language, much in the same way that C++ coding differs from C coding despite some level of interoperability. Currently, CMakePPLang is used within the CMakePP organization as the foundation for two in-progress projects: CMakeTest and CMaize. CMakeTest provides a solution for unit testing CMake and CMakePPLang code. CMaize is a CMake tool to simplify interoperability between projects and writing their build systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Roadmap on electronic structure codes in the exascale era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.

36 MATERIALS SCIENCE↗
DOE OSTI2023

PluginPlay: Enabling exascale scientific software one module at a time

For many computational chemistry packages, being able to efficiently and effectively scale across an exascale cluster is a heroic feat. Collective experience from the Department of Energy’s Exascale Computing Project suggests that achieving exascale performance requires far more planning, design, and optimization than scaling to petascale. In many cases, entire rewrites of software are necessary to address fundamental algorithmic bottlenecks. This in turn requires a tremendous amount of resources and development time, resources that cannot reasonably be afforded by every computational science project. It thus becomes imperative that computational science transition to a more sustainable paradigm. Key to such a paradigm is modular software. While the importance of modular software is widely recognized, what is perhaps not so widely appreciated is the effort still required to leverage modular software in a sustainable manner. The present manuscript introduces PluginPlay, https://github.com/NWChemEx-Project/PluginPlay, an inversion-of-control framework designed to facilitate developing, maintaining, and sustaining modular scientific software packages. Here this manuscript focuses on the design aspects of PluginPlay and how they specifically influence the performance of the resulting package. Although, PluginPlay serves as the framework for the NWChemEx package, PluginPlay is not tied to NWChemEx or even computational chemistry. We thus anticipate PluginPlay to prove to be a generally useful tool for a number of computational science packages looking to transition to the exascale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

CMinx: A CMake Documentation Generator

This manuscript introduces CMinx, a program for generating application programming interface (API) documentation written in the CMake language, and CMake modules in particular. Since most of CMinx’s intended audience is comprised of C/C++ developers, CMinx is designed to operate similar to Doxygen, the de facto C/C++ API documentation tool. Specifically, developers annotate their CMake source with “documentation” comments, which are traditional CMake block comments starting with an extra “[” character. The documentation comments, written in reST, describe to the reader how the functions, parameters, and variables should be used. Running CMinx on the annotated source code generates reST files containing the API documentation. The reST files can then be converted into static websites with tools such as Sphinx or easily converted to another format via Pandoc.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Developing a Computational Chemistry Framework for the Exascale Era

Within computational chemistry the NWChem package has arguably been the de facto standard for running high-accuracy numerical simulations on the most powerful supercomputers. In order to better address the challenges presented by emerging exascale architectures, the decision has been made to rewrite NWChem. Design of the resulting package, NWChemEx, has been driven by exascale computing; however, significant additional design considerations have arisen from the team's involvement with the Molecular Sciences Software Institute (MolSSI). MolSSI is a National Science Foundation initiative focused on establishing coding and data standards for the computational chemistry community. As a result, NWChemEx is built upon a general computational chemistry framework called the Simulation Development Environment (SDE) that is designed with a focus on extensibility and interoperability. The present manuscript describes the modular approach of the SDE and how it has been used to implement the self-consistent field algorithm within NWChemEx.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Understanding the many-body expansion for large systems. II. Accuracy considerations

To complement our study of the role of finite precision in electronic structure calculations based on a truncated many-body expansion (MBE, or “n-body expansion”), we examine the accuracy of such methods in the present work. Accuracy may be defined either with respect to a supersystem calculation computed at the same level of theory as the n-body calculations, or alternatively with respect to high-quality benchmarks. Both metrics are considered here. In applications to a sequence of water clusters, (H{sub 2}O){sub N=6−55} described at the B3LYP/cc-pVDZ level, we obtain mean absolute errors (MAEs) per H{sub 2}O monomer of ∼1.0 kcal/mol for two-body expansions, where the benchmark is a B3LYP/cc-pVDZ calculation on the entire cluster. Three- and four-body expansions exhibit MAEs of 0.5 and 0.1 kcal/mol/monomer, respectively, without resort to charge embedding. A generalized many-body expansion truncated at two-body terms [GMBE(2)], using 3–4 H{sub 2}O molecules per fragment, outperforms all of these methods and affords a MAE of ∼0.02 kcal/mol/monomer, also without charge embedding. GMBE(2) requires significantly fewer (although somewhat larger) subsystem calculations as compared to MBE(4), reducing problems associated with floating-point roundoff errors. When compared to high-quality benchmarks, we find that error cancellation often plays a critical role in the success of MBE(n) calculations, even at the four-body level, as basis-set superposition error can compensate for higher-order polarization interactions. A many-body counterpoise correction is introduced for the GMBE, and its two-body truncation [GMBCP(2)] is found to afford good results without error cancellation. Together with a method such as ωB97X-V/aug-cc-pVTZ that can describe both covalent and non-covalent interactions, the GMBE(2)+GMBCP(2) approach provides an accurate, stable, and tractable approach for large systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Finally, some specific chemical examples include calculations on the strongly correlated Cr 2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

computational modelling↗
DOE OSTI2014

Understanding the many-body expansion for large systems. I. Precision considerations

Electronic structure methods based on low-order “n-body” expansions are an increasingly popular means to defeat the highly nonlinear scaling of ab initio quantum chemistry calculations, taking advantage of the inherently distributable nature of the numerous subsystem calculations. Here, we examine how the finite precision of these subsystem calculations manifests in applications to large systems, in this case, a sequence of water clusters ranging in size up to (H{sub 2}O){sub 47}. Using two different computer implementations of the n-body expansion, one fully integrated into a quantum chemistry program and the other written as a separate driver routine for the same program, we examine the reproducibility of total binding energies as a function of cluster size. The combinatorial nature of the n-body expansion amplifies subtle differences between the two implementations, especially for n ⩾ 4, leading to total energies that differ by as much as several kcal/mol between two implementations of what is ostensibly the same method. This behavior can be understood based on a propagation-of-errors analysis applied to a closed-form expression for the n-body expansion, which is derived here for the first time. Discrepancies between the two implementations arise primarily from the Coulomb self-energy correction that is required when electrostatic embedding charges are implemented by means of an external driver program. For reliable results in large systems, our analysis suggests that script- or driver-based implementations should read binary output files from an electronic structure program, in full double precision, or better yet be fully integrated in a way that avoids the need to compute the aforementioned self-energy. Moreover, four-body and higher-order expansions may be too sensitive to numerical thresholds to be of practical use in large systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets

An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Approaching the complete-basis limit with a truncated many-body expansion

High-accuracy electronic structure calculations with correlated wave functions demand the use of large basis sets and complete-basis extrapolation, but the accuracy of fragment-based quantum chemistry methods has most often been evaluated using double-ζ basis sets, with errors evaluated relative to a supersystem calculation using the same basis set. Here, we examine the convergence towards the basis-set limit of two- and three-body expansions of the energy, for water clusters and ion–water clusters, focusing on calculations at the level of second-order Møller-Plesset perturbation theory (MP2). Several different corrections for basis-set superposition error (BSSE), each consistent with a truncated many-body expansion, are examined as well. We present a careful analysis of how the interplay of errors (from all sources) influences the accuracy of the results. We conclude that fragment-based methods often benefit from error cancellation wherein BSSE offsets both incompleteness of the basis set as well as higher-order many-body effects that are neglected in a truncated many-body expansion. An n-body counterpoise correction facilitates smooth extrapolation to the MP2 basis-set limit, and at n = 3 affords accurate results while requiring calculations in subsystems no larger than trimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2008

Evaluation of Vapor Pressure and Ultra-High Vacuum Tribological Properties of Ionic Liquids (2) Mixtures and Additives

Ionic liquids are salts, many of which are typically viscous fluids at room temperature. The fluids are characterized by negligible vapor pressures under ambient conditions. These properties have led us to study the effectiveness of ionic liquids containing both organic cations and anions for use as space lubricants. In the previous paper we have measured the vapor pressure and some tribological properties of two distinct ionic liquids under simulated space conditions. In this paper we will present vapor pressure measurements for two new ionic liquids and friction coefficient data for boundary lubrication conditions in a spiral orbit tribometer using stainless steel tribocouples. In addition we present the first tribological data on mixed ionic liquids and an ionic liquid additive. Post mortem infrared and Raman analysis of the balls and races indicates the major degradation pathway for these two organic ionic liquids is similar to those of other carbon based lubricants, i.e. deterioration of the organic structure into amorphous graphitic carbon. The coefficients of friction and lifetimes of these lubricants are comparable to or exceed these properties for several commonly used space oils.

Morales, Wilfredo↗