13 papers · ranked by Valyu relevance
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
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Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher + 3 more
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting…
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Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
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The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
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This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Peter Kraus, Edan Bainglass, Francisco F. Ramirez, Enea Svaluto-Ferro + 7 more
Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by a full control of the data gathering process. In this work, we demonstrate tooling which bridges these two aspects, and illustrate its use in a case study of automated battery cycling. We…
Pavel Pokhilko, Evgeny Epifanovsky, Anna I. Krylov
Using single precision floating point representation reduces the size of data and computation time by a factor of two relative to double precision conventionally used in electronic structure programs. For large-scale calculations, such as those encountered in many-body theories, reduced memory footprint alleviates…
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Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…