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Liu, Hongbin

Publications and source records attributed to Liu, Hongbin.

12 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

High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference validation

Quantum chemical calculations on atomistic systems have evolved into a standard approach to studying molecular matter. These calculations often involve a significant amount of manual input and expertise, although most of this effort could be automated, which would alleviate the need for expertise in software and hardware accessibility. Here, we present the AutoRXN workflow, an automated workflow for exploratory high-throughput electronic structure calculations of molecular systems, in which (i) density functional theory methods are exploited to deliver minimum and transition-state structures and corresponding energies and properties, (ii) coupled cluster calculations are then launched for optimized structures to provide more accurate energy and property estimates, and (iii) multi-reference diagnostics are evaluated to back check the coupled cluster results and subject them to automated multi-configurational calculations for potential multi-configurational cases. All calculations are carried out in a cloud environment and support massive computational campaigns. Key features of all components of the AutoRXN workflow are autonomy, stability, and minimum operator interference. We highlight the AutoRXN workflow with the example of an autonomous reaction mechanism exploration of the mode of action of a homogeneous catalyst for the asymmetric reduction of ketones.

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

Metabolic activity and community structure of prokaryotes associated with particles in the twilight zone of the South China Sea

The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs) in the larger particles along the water depths, might be due to the fast sinking and major contribution of carbon flux of the larger particles from the euphotic layer. In addition to polymers as the major carbon source, carbohydrates and amino acids were preferentially used by microbial community at the upper and lower boundary, respectively. This could potentially be attributed to the metabolic capabilities of attached microbial groups in different particles, and reflected the initial preference of the carbon source by the natural microbes in the twilight zone as well. The microbial structure and carbon metabolic profiles could be complemented with metatranscriptomic analysis in future studies to augment the understanding of the complex carbon cycling pathways in the twilight zone.

Liu, Hao↗
DOE OSTI2021

Toward quantum computing for high-energy excited states in molecular systems: quantum phase estimations of core-level states

This paper explores the utility of the quantum phase estimation (QPE) in calculating high-energy excited states characterized by promotions of electrons occupying inner energy shells. These states have been intensively studied over the last few decades especially in supporting the experimental effort at light sources. Results obtained with the QPE are compared with various high-accuracy many-body techniques developed to describe core-level states. The feasibility of the quantum phase estimator in identifying classes of challenging shake-up states characterized by the presence of higher-order excitation effects is also discussed.

Bauman, Nicholas P.↗
DOE OSTI2019

Design and Evaluation of the LAr Trigger Digitizer Board in the ATLAS Phase-I Upgrade

The Phase-I upgrade of the trigger readout electronics for the ATLAS Liquid Argon (LAr) calorimeters will be installed during the second long shutdown of the Large Hadron Collider (LHC) in 2019-2020 which will enable enhanced instantaneous luminosities during LHC Run 3 from 2021 through 2023. In this trigger upgrade, so-called supercells are introduced to provide higher granularity, higher resolution and longitudinal shower shape information from the LAr calorimeters to the Level-1 trigger processors. A new LAr Trigger Digitizer Board (LTDB) will process and digitize up to 320 channels of supercell signals, and transmit them via 40 fiber optical links to the back end where the data are further processed and transmitted to the trigger processors. Five pairs of bidirectional GBT links are used for slow control and monitoring between LTDB and the Front-End LInk eXchange (FELIX) in the ATLAS Trigger and Data Acquisition (TDAQ) system. Here, the LTDB also outputs 64 summed analog legacy signals to the current Tower Builder Board via a new baseplane. A test system for the production of 124 LTDBs has been developed, supporting configuration and calibration of all ASICs

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Time-Dependent Complete Active Space Embedded in Polarizable Force Field

Electron correlation and environmental effects play important roles in electron dynamics and spectroscopic observables of chemical systems in condensed phase. In this paper, we present a time-dependent complete active space configuration interaction (TD-CASCI) approach embedded in a polaraizable force filed, MMPol. The present implementation of TD-CASCI/MMPol utilizes a direct matrix-vector contraction, allowing studies of large systems. This scheme is used to study the solvatochromic shift of coumarin 153 in methanol. The TD-CASCI/MMPol approach captures the double excitation character in the excited state wave function and accurately predicts the solvatochromic red-shift of coumarin 153 dye within the experimental range, outperforming linear response time-dependent density functional theory. The effect of using different reference orbitals for the TD-CASCI/MMPol simulation is also investigated, highlighting the need for an unbiased treatment of all electronic states in the energy range of interest.

Liu, Hongbin↗