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Mejia-Rodriguez, Daniel

Publications and source records attributed to Mejia-Rodriguez, Daniel.

5 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Electronic structure simulations in the cloud computing environment

The transformative impact of modern computational paradigms and technologies, such as high-performance computing, quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages, such as NWChem, NWChemEx, SPEC, ExaChem, and FLOSIC codes on the Azure Quantum Element (AQE) Microsoft cloud services. We pay particular attention to the intricate workflows for performing composite chemistry simulations, associated data curation, and mechanisms for accuracy assessment, as defined by the enabling cloud Computational Chemistry as a Service (CCaaS). Our focus also extends to Arrows' automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities (LCFs).

computational chemistry, electronic structure, Clo↗
DOE OSTI2023

G 0 W 0 Ionization Potentials of First-Row Transition Metal Aqua Ions

Here, we report computations of the vertical ionization potentials within the GW approximation of the near-complete series of first-row transition metal (V–Cu) aqua ions in their most common oxidation states, i.e., V 3+ , Cr 3+ , Cr 2+ , Mn 2+ , Fe 3+ , Fe 2+ , Co 2+ , Ni 2+ , and Cu 2+ . The d-orbital occupancy of these systems spans a broad range from d 2 to d 9 . All of the structures were first optimized at the density functional theory level using a large cluster of explicit water molecules that are embedded in a continuum solvation model. Vertical ionization potentials were computed with the one-shot G 0 W 0 approach on a range of transition metal ion clusters (6, 18, 40, and 60 explicit water molecules), wherein the convergence with respect to the basis set size was evaluated using the systems with 40 water molecules. We assess the results using three different density functional approximations as starting points for the vertical ionization potential calculations, namely, G 0 W 0 @PBE, G 0 W 0 @PBE0, and G 0 W 0 @r 2 SCAN. While the predicted ground-state structures are similar to all three exchange-correlation functionals, the vertical ionization potentials were in closer agreement with experiment when using the G 0 W 0 @PBE0 and G 0 W 0 @r 2 SCAN approaches, with the r 2 SCAN-based calculations being significantly less expensive. Computed bond distances and vertical ionization potentials for all structures are in good agreement with available experimental data.

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

NWChem: Recent and Ongoing Developments

In this paper we summarize developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0). Specifically, we focus on functionalities, along with input blocks, that are currently accessible in the current stable release (NWChem 7.2) and master branches, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem GitHub repository, and containerization of NWChem executable images. In conclusion, some of the ongoing developments that will be available in the near future are also discussed.

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

pnnl/PTMPSI

PTM-Psi is a Python 3 package that combines several capabilities to streamline the workflow to interrogate the impact of PTMs on proteins using well-established software packages. The workflow of the PTM-Psi software package includes input files and launch instances from standard packages such as AlphaFold, NWChem, GROMACS, and the Autodock Suite

Mejia-Rodriguez, Daniel↗