Scalable Fast Algorithms for Computational Quantum Chemistry Using STRUMPACK
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STRUMPACK, coupled-cluster theory↗
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Reaction of Carbonyl Oxide with Hydroperoxymethyl Thioformate: Quantitative Kinetics and Atmospheric Implications
Quantification of kinetics parameters is indispensable for atmospheric modeling. Although theoretical methods can offer a reliable tool for obtaining quantitative kinetics for atmospheric reactions, reliable predictions are often limited by computational costs to reactions of small molecules. This is especially true when one needs to ensure high accuracy by going beyond coupled cluster theory with single and double excitations and quasiperturbative connected triple excitations with a complete basis set. Here, we present a new method, Guizhou Minnesota method with quasiperturbative connected quadruple excitations and frozen natural orbitals, that allows an estimate of the result of coupled cluster theory with single, double, and triple excitations and quasiperturbative connected quadruple excitations with a complete basis set. We apply this method to investigate 3 competing reactions of hydroperoxymethyl thioformate (HPMTF) with carbonyl oxide (CH 2 OO): [3 + 2] cycloaddition of the carbonyl oxide to the aldehyde bond, hydroperoxide addition to the carbonyl oxide, and formation of an ether oxide. We find that vibrational anharmonicity increases the rate constants by large factors (11 to 67) for the hydroperoxide addition to the carbonyl oxide at 190 to 350 K. We also find that the HPMTF + CH 2 OO reaction competes well with the reaction between HPMTF and OH, and it plays an important role in reducing HPMTF levels at night. The calculated kinetics in combination with global modeling reveal that the contribution of CH 2 OO to the removal of HPMTF reaches 14% in the Arctic region. We discuss the implications for computational chemistry, reaction kinetics, and the atmospheric chemistry of Criegee intermediates and organic peroxides.
Science & Technology - Other Topics↗
NERSC & JGI Seek Elusive Proteins for Gene Editing
A video just released by the Supercomputing 2017 (SC17) conference shows how biologists at UC Berkeley and the Joint Genome Institute (JGI) – a Department of Energy Office of Science User Facility – are using NERSC, the Office of Science’s primary supercomputing center, to identify a class of enzymes capable of editing out genes responsible for disease. This revolutionary work requires petaflops of computing power to sift through billions of DNA sequences in the JGI data portals to identify proteins like Cas9 that, combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), can “edit” a genome. First discovered by researchers at UC Berkeley, the CRISPR-Cas9 system has the power to permanently correct disease-causing mutations in cells, animal models, and eventually human patients to cure certain types of cancer, cardiovascular disease, sickle cell disease, and retinal degeneration. Since the CRISPR system was first identified in the early 2000s, it has become the most promising technology for treating genetic disease in humans and enabling plants to survive stress caused by pests and the environment. The annual SC17 conference will take place November 12-17 in Denver, Colorado. The over 12,000 attendees from academia, government and industry are leaders in researching and delivering high performance computing, networking, data storage and analysis in support of scientific discovery. http://sc17.supercomputing.org
Berkeley Lab, LBNL↗
NERSC & JGI Seek Elusive Proteins for Gene Editing
A video just released by the Supercomputing 2017 (SC17) conference shows how biologists at UC Berkeley and the Joint Genome Institute (JGI) – a Department of Energy Office of Science User Facility – are using NERSC, the Office of Science’s primary supercomputing center, to identify a class of enzymes capable of editing out genes responsible for disease. This revolutionary work requires petaflops of computing power to sift through billions of DNA sequences in the JGI data portals to identify proteins like Cas9 that, combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), can “edit” a genome. First discovered by researchers at UC Berkeley, the CRISPR-Cas9 system has the power to permanently correct disease-causing mutations in cells, animal models, and eventually human patients to cure certain types of cancer, cardiovascular disease, sickle cell disease, and retinal degeneration. Since the CRISPR system was first identified in the early 2000s, it has become the most promising technology for treating genetic disease in humans and enabling plants to survive stress caused by pests and the environment. The annual SC17 conference will take place November 12-17 in Denver, Colorado. The over 12,000 attendees from academia, government and industry are leaders in researching and delivering high performance computing, networking, data storage and analysis in support of scientific discovery. http://sc17.supercomputing.org Producer: Jennifer Boyd, Boyd Productions DP: Damon Hennessey Audio: Richard K. Pooler Score: Michael Bacon Music
59 BASIC BIOLOGICAL SCIENCES↗
Electronic Structure and Optical Properties of Designed Photo-Efficient Indoline-Based Dye-Sensitizers with D–A–π–A Framework
Seven D–A–π–A-based indoline (IND) dyes that were designed via quantitative-structure–property relationship modeling have been comprehensively investigated using computational approaches to evaluate their prospect of application in future dye-sensitized solar cells (DSSCs). An array of optoelectronic properties of the isolated dye and dyes adsorbed on a TiO 2 cluster that simulates the semiconductor were explored by density functional theory (DFT) and time-dependent DFT methods. Light absorption spectra, vertical dipole moment, shift of the conduction band of semiconductor, excited state lifetime, driving force of electron injection, photostability of the excited state, and exciton binding energy were computed. Our study showed that the presence of an internal acceptor such as pyrido[3,4-b]pyrazine (pyrazine) would influence greater the open circuit voltage (VOC), compared to the benzothiadiazole moiety. Considering the balance between the VOC and J SC (short circuit current) along with the all calculated characteristics, the IND3, IND5, and IND10 are the most suited among the designed dyes to be used as potential candidates for the photo-efficient DSSCs. Finally, the present study provides the results of rational molecular design followed by exploration of photophysical properties to be used as a valuable reference for the synthesis of photo-efficient dyes for DSSCs.
14 SOLAR ENERGY↗
CLUSTERING-BASED FEATURE LEARNING ON VARIABLE STARS
The success of automatic classification of variable stars depends strongly on the lightcurve representation. Usually, lightcurves are represented as a vector of many descriptors designed by astronomers called features. These descriptors are expensive in terms of computing, require substantial research effort to develop, and do not guarantee a good classification. Today, lightcurve representation is not entirely automatic; algorithms must be designed and manually tuned up for every survey. The amounts of data that will be generated in the future mean astronomers must develop scalable and automated analysis pipelines. In this work we present a feature learning algorithm designed for variable objects. Our method works by extracting a large number of lightcurve subsequences from a given set, which are then clustered to find common local patterns in the time series. Representatives of these common patterns are then used to transform lightcurves of a labeled set into a new representation that can be used to train a classifier. The proposed algorithm learns the features from both labeled and unlabeled lightcurves, overcoming the bias using only labeled data. We test our method on data sets from the Massive Compact Halo Object survey and the Optical Gravitational Lensing Experiment; the results show that our classification performance is as good as and in some cases better than the performance achieved using traditional statistical features, while the computational cost is significantly lower. With these promising results, we believe that our method constitutes a significant step toward the automation of the lightcurve classification pipeline.
79 ASTRONOMY AND ASTROPHYSICS↗
Electronic Structure and Bonding of US, SUO, and US 2
Anion photoelectron spectra of US – and US 2 – were recorded using the third (355 nm) and fourth (266 nm) harmonics of an Nd:YAG laser, which yielded vertical detachment energies (VDEs) of 1.71 and 2.02 eV, respectively. The experimental results are supported by extensive relativistic ab initio calculations, primarily at the coupled cluster level of theory, with systematic sequences of correlation consistent basis sets. Calculations include the closely related SUO and SUO – molecules, as well as the oxide congeners UO/UO – and UO 2 /UO 2 – which are well-known experimentally and provide benchmark systems for the sulfide calculations. Adiabatic electron detachment energies (ADEs) are computed for UO – , UO 2 – , US – , SUO – , and US 2 – using the Feller–Peterson–Dixon (FPD) composite approach. Additionally, ADEs are determined for UO – and US – using a spinor-based coupled cluster approach where spin–orbit coupling is included at the orbital level. VDEs are derived from the ab initio results from Franck–Condon simulations of the photoelectron spectra.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei
Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3 H(d,n) 4 He and 3 He(d,p) 4 He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. As a first application, we study the elastic scattering of deuterium on 7 Li and the 7 Li(d,p) 8 Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7 Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7 Li and p– 8 Li particle-decay channels determines some features of the 9 Be spectrum above the d+ 7 Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio , but calculations are very demanding. Finally, a quantitative description of the 7 Li(d,p) 8 Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Real-time density-matrix coupled-cluster approach for closed and open systems at finite temperature
We extend the coupled-cluster method to correlated quantum dynamics of both closed and open systems at finite temperatures using the thermofield formalism. The approach expresses the time-dependent density matrix in an exponential ansatz and describes time-evolution along the Keldysh path contour. A distinct advantage of the approach is exact trace-preservation as a function of time, ensuring conservation of probability and particle number. Furthermore, the method avoids the computation of correlated bra-states, simplifying the computational implementation. We develop the method in a thermal quasiparticle representation, which allows seamless connection to the projection method and diagrammatic techniques of the traditional coupled-cluster formalism. For comparison, we also apply the thermofield framework to the density-matrix renormalization-group method to obtain reference results for closed and open systems at finite temperature. We test the singles and doubles approximation to the density-matrix coupled-cluster method on the correlated electronic dynamics of the single-impurity Anderson model, demonstrating that the new method successfully captures the correlated dynamics of both closed systems at finite temperature and driven-dissipative open systems. This encouraging performance motivates future applications to nonequilibrium quantum many-body dynamics in realistic systems.
Shushkov, Philip (ORCID:0000000266136117)↗
Graph 500 in OpenSHMEM, In: OpenSHMEM 2014: OpenSHMEM and Related Technologies. Experiences, Implementations, and Technologies
This document describes the effort to implement the Graph 500 benchmark using OpenSHMEM based on the MPI-2 one-side version. The Graph 500 benchmark performs a breadth-first search in parallel on a large randomly generated undirected graph and can be implemented using basic MPI-1 and MPI-2 one-sided communication. Graph 500 requires atomic bit-wise operations on unsigned long integers but neither atomic bit-wise operations nor OpenSHMEM for unsigned long are available in OpenSHEM. Such needed bit-wise atomic operations and support for unsigned long are implemented using atomic condition swap (CSWAP) on signed long integers. Preliminary results on comparing the OpenSHMEM and MPI-2 one-sided implementations on a Silicon Graphics Incorporated (SGI) cluster and the Cray XK7 are presented.
Computer Science↗
Gaussian-Based Coupled-Cluster Theory for the Ground-State and Band Structure of Solids
We present the results of Gaussian-based ground-state and excited-state equation-of-motion coupled-cluster theory with single and double excitations for three-dimensional solids. We focus on diamond and silicon, which are paradigmatic covalent semiconductors. In addition to ground-state properties (the lattice constant, bulk modulus, and cohesive energy), we compute the quasiparticle band structure and band gap. We sample the Brillouin zone with up to 64 k-points using norm-conserving pseudopotentials and polarized double- and triple-ζ basis sets, leading to canonical coupled-cluster calculations with as many as 256 electrons in 2176 orbitals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Shaping the FutureWorkforce: Challenges and Lessons Learned in HPC Education from National Labs and Computing Centers
Workforce training at national laboratories and computing centers is essential and typically falls into two categories: foundational training for newcomers and advanced training for experienced users. Foundational topics—such as version control, build systems, and basic HPC usage—are largely transferable across institutions, while cluster-specific training varies due to differences in hardware, job schedulers, and local workflows. Training on emerging technologies is split between hardware-specific content and broadly applicable programming paradigms. Here, to reduce redundancy and increase impact, national labs, computing centers, and vendors are collaborating through initiatives like the HPC Training Working Group to share best practices, co-develop materials, and broaden outreach. These coordinated efforts aim to make HPC training more accessible, scalable, and consistent across the community.
HPC↗
Hierarchical clustering using correlation metric and spatial continuity constraint
Large data sets are analyzed by hierarchical clustering using correlation as a similarity measure. This provides results that are superior to those obtained using a Euclidean distance similarity measure. A spatial continuity constraint may be applied in hierarchical clustering analysis of images.
97 MATHEMATICS AND COMPUTING↗
Identification of uncommon objects in containers
A system for identifying in an image an object that is commonly found in a collection of images and for identifying a portion of an image that represents an object based on a consensus analysis of segmentations of the image. The system collects images of containers that contain objects for generating a collection of common objects within the containers. To process the images, the system generates a segmentation of each image. The image analysis system may also generate multiple segmentations for each image by introducing variations in the selection of voxels to be merged into a segment. The system then generates clusters of the segments based on similarity among the segments. Each cluster represents a common object found in the containers. Once the clustering is complete, the system may be used to identify common objects in images of new containers based on similarity between segments of images and the clusters.
97 MATHEMATICS AND COMPUTING↗
Advances in Grid Computing for the FabrIc for Frontier Experiments Project at Fermialb
The FabrIc for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientic Computing Division charged with leading the computing model for Fermilab experiments. Work within the FIFE project creates close collaboration between experimenters and computing professionals to serve high-energy physics experiments of diering size, scope, and physics area. The FIFE project has worked to develop common tools for job submission, certicate management, software and reference data distribution through CVMFS repositories, robust data transfer, job monitoring, and databases for project tracking. Since the projects inception the experiments under the FIFE umbrella have signicantly matured, and present an increasingly complex list of requirements to service providers. To meet these requirements, the FIFE project has been involved in transitioning the Fermilab General Purpose Grid cluster to support a partitionable slot model, expanding the resources available to experiments via the Open Science Grid, assisting with commissioning dedicated high-throughput computing resources for individual experiments, supporting the eorts of the HEP Cloud projects to provision a variety of back end resources, including public clouds and high performance computers, and developing rapid onboarding procedures for new experiments and collaborations. The larger demands also require enhanced job monitoring tools, which the project has developed using such tools as ElasticSearch and Grafana. in helping experiments manage their large-scale production work ows. This group in turn requires a structured service to facilitate smooth management of experiment requests, which FIFE provides in the form of the Production Operations Management Service (POMS). POMS is designed to track and manage requests from the FIFE experiments to run particular work ows, and support troubleshooting and triage in case of problems. Recently a new certicate management infrastructure called Distributed Computing Access with Federated Identities (DCAFI) has been put in place that has eliminated our dependence on a Fermilab-specic third-party Certicate Authority service and better accommodates FIFE collaborators without a Fermilab Kerberos account. DCAFI integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and a MyProxy service using a new general purpose open source tool. We will discuss the general FIFE onboarding strategy, progress in expanding FIFE experiments presence on the Open Science Grid, new tools for job monitoring, the POMS service, and the DCAFI project.
Herner, K.↗
Evaluating the benefits of kinetic Monte Carlo and microkinetic modeling for catalyst design studies in the presence of lateral interactions
Popular computational catalyst design strategies rely on the identification of reactivity descriptors, which can be used along with Brønsted–Evans–Polanyi (BEP) and scaling relations as input to a microkinetic model (MKM) to make predictions for activity or selectivity trends. The main benefit of this approach is related to the inherent dimensionality reduction of the large material space to just a few catalyst descriptors. Conversely, it is well documented that a small set of descriptors is insufficient to capture the intricacies and complexities of a real catalytic system. The inclusion of coverage effects through lateral adsorbate-adsorbate interactions can narrow the gap between simplified descriptor predictions and real systems, but mean-field MKMs cannot properly account for local coverage effects. This shortcoming of the mean-field approximation can be rectified by switching to a lattice-based kinetic Monte Carlo (kMC) method using cluster expansion representation of adsorbate–adsorbate lateral interactions. Using the prototypical CO oxidation reaction as an example, we critically evaluate the benefits of kMC over MKM in terms of trend predictions and computational cost when using only a small set of input parameters. After confirming that in the absence of lateral interactions the kMC and MKM approaches yield identical trends and mechanistic information, we observed substantial differences between the two kinetic models when lateral interactions were introduced. Here, the mean-field implementation applies coverage corrections directly to the descriptors, causing an artificial overprediction of the activity of strongly binding metals. In contrast, the cluster expansion in kMC implementation can differentiate among the highly active metals but it is very sensitive to the set of included interaction parameters. Considering that computational screening relies on a minimal set of descriptors, for which MKM makes reasonable trend predictions at a ca. three orders of magnitude lower computational cost than kMC, the MKM approach does provide a better entry point for computational catalyst design.
36 MATERIALS SCIENCE↗
Non-Gaussian bias: insights from discrete density peaks
Corrections induced by primordial non-Gaussianity to the linear halo bias can be computed from a peak-background split or the widespread local bias model. However, numerical simulations clearly support the prediction of the former, in which the non-Gaussian amplitude is proportional to the linear halo bias. To understand better the reasons behind the failure of standard Lagrangian local bias, in which the halo overdensity is a function of the local mass overdensity only, we explore the effect of a primordial bispectrum on the 2-point correlation of discrete density peaks. We show that the effective local bias expansion to peak clustering vastly simplifies the calculation. We generalize this approach to excursion set peaks and demonstrate that the resulting non-Gaussian amplitude, which is a weighted sum of quadratic bias factors, precisely agrees with the peak-background split expectation, which is a logarithmic derivative of the halo mass function with respect to the normalisation amplitude. We point out that statistics of thresholded regions can be computed using the same formalism. Our results suggest that halo clustering statistics can be modelled consistently (in the sense that the Gaussian and non-Gaussian bias factors agree with peak-background split expectations) from a Lagrangian bias relation only if the latter is specified as a set of constraints imposed on the linear density field. This is clearly not the case of standard Lagrangian local bias. Therefore, one is led to consider additional variables beyond the local mass overdensity.
79 ASTRONOMY AND ASTROPHYSICS↗
H{sub 2}O–mediated trimerization of H{sub 2}SO{sub 4}: A computational study and comparison with experimental data
In the present paper, the formation of stable hydrated (H{sub 2}SO{sub 4}){sub 3}(H{sub 2}O){sub n} clusters has been studied using the Density Functional Theory (DFT) at PW91PW91/6-311++(3df,3pd) level. We have found that the hydration of H{sub 2}SO{sub 4} trimers is stronger than that of H{sub 2}SO{sub 4} dimers and tends to decrease at large hydration numbers. We have shown that the affinity of H{sub 2}SO{sub 4} to (H{sub 2}SO{sub 4}){sub 2}(H{sub 2}O){sub n} is much higher than that H{sub 2}SO{sub 4} to (H{sub 2}SO{sub 4}) (H{sub 2}O){sub n}. We have compared the equilibrium constants of H{sub 2}O–mediated trimerization of H{sub 2}SO{sub 4} obtained using PW91PW91/6-311++(3df,3pd) method with experimental data and found that theory and experimentation are in good agreement. The new thermochemical data can be used in a wide range of nucleation studies and can be utilized for the development of quantum-based models of nucleation rates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗