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QMCPACK is an open-source production level many-body ab initio Quantum Monte Carlo code for computing the electronic structure of atoms, molecules, and solids with full performance portable GPU support.
The first continuum gyrokinetic calculations of electrostatic ion scale turbulence are presented for the case of a diverted tokamak geometry. The simulation model solves the long-wavelength limit of the full-F gyrokinetic equation for ion species coupled to the quasi-neutrality equation for electrostatic potential variations, where a fluid model is used for an electron response. Furthermore, in order to facilitate simulations of highly-anisotropic microturbulence in the presence of strong magnetic shear and a magnetic X-point, a numerical algorithm utilizing a locally field-aligned multiblock coordinate system has been developed and implemented in the 5D finite-volume code COGENT. In this approach, the toroidal direction is divided into blocks, such that within each block, the cells are field-aligned and a non-matching grid interface is allowed at block boundaries. The toroidal angle corresponds to the “coarse” field-aligned coordinate, whereas the poloidal cross section, comprised of the radial and poloidal directions, is finely gridded to resolve short-scale perpendicular turbulence structures and to support accurate re-mapping (interpolation) at block boundaries. The 5D simulations explore cross-separatrix ion scale turbulence in the presence of a self-consistent radial electric field and address the effects of magnetic-shear stabilization in the X-point region.
In this study, a new conversion electron detector has been commissioned at the ATLAS/ CARIBU facility at Argonne National Laboratory. The LSU-Argonne Conversion Electron Spectrometer (LACES) is a LN 2 -cooled Si(Li) detector system designed to be incorporated into a decay station that comprises the dedicated HPGe clover array with a box geometry (X -Array) and the Scintillator and Tape Using Radioactive Nuclei (SATURN) device. This integration enables simultaneous measurements of conversion electrons and gamma-rays in decay experiments, yielding novel information on transition multipolarities, electric monopole transitions, and isomeric states that decay mostly via conversion electrons. A measurement of the energy resolution of LACES yielded 2.3-keV FWHM at 975 keV for electrons and 1.3-keV FWHM at 75 keV for X-rays. A detailed study of the absolute detection efficiency (at 5 mm from the source) was performed, where this quantity was determined experimentally in the range of electron transition energies between 25.5 keV and 1047.8 keV and subsequently simulated using the GEANT4 code. Measurement and simulations are found to be in excellent agreement. A precise characterization, for this type of detector system, of the absolute detection efficiency for such a wide energy range is reported for the first time.
The real-space Green's function code FEFF has been extensively developed and used for calculations of X-ray and related spectra, including X-ray absorption (XAS), X-ray emission (XES), inelastic X-ray scattering, and electron energy-loss spectra. The code is particularly useful for the analysis and interpretation of the XAS fine-structure (EXAFS) and the near-edge structure (XANES) in materials throughout the periodic table. Nevertheless, many applications, such as non-equilibrium systems, and the analysis of ultra-fast pump–probe experiments, require extensions of the code including finite-temperature and auxiliary calculations of structure and vibrational properties. To enable these extensions, we have developed in tandem a new version FEFF10 and new FEFF -based workflows for the Corvus workflow manager, which allow users to easily augment the capabilities of FEFF10 via auxiliary codes. This coupling facilitates simplified input and automated calculations of spectra based on advanced theoretical techniques. The approach is illustrated with examples of high-temperature behavior, vibrational properties, many-body excitations in XAS, super-heavy materials, and fits of calculated spectra to experiment.
Magnetically driven implosions involving a liner collapsing onto a target are inherently vulnerable to the magneto-Rayleigh–Taylor instability (MRTI). Among the various approaches proposed to achieve fusion conditions within the target, the staged Z-pinch (SZP) concept employs a high-Z liner, the advantages of which remain an active area of investigation. Consequently, ongoing design optimization efforts are essential, while critical physical processes such as magnetic field (B-field) diffusion and radiation transport increase the complexity of required simulations. In this study, we utilize the new capabilities of the FLASH code to simulate in 2D, for the first time using this code, staged Z-pinch configurations (designated SZP1 and SZP1*), focusing on their stability. First, a comparison of simulation results with theoretical predictions of MRTI growth provide new insights into the often-overlooked influences of high mesh resolution and initial perturbation seeding on instability dynamics. These findings then lead to a discussion on potential improvements for future SZP experiments. These include the use of an axial B-field stabilization and the optimization of radiation transport processes during the implosion. The results presented herein establish the framework for simulating multi-dimensional Z pinches using the FLASH code and pave the way for the development of innovative experimental configurations leveraging its advanced simulation capabilities.
Polarization lifetime for He3 using two and six snakes are studied using the T-BMT Spin Resonance Tracker code. This code integrates a reduced spinor form of the T-BMT equation including only several spin resonances and the kinematics of synchrotron motion. It was previously benchmarked against RHIC polarization lifetime under the two snake system *. * Phys. Rev.Accel. Beams 22 (2019) 9, 091001
The Oak Ridge National Laboratory (ORNL) shutdown dose rate (SDDR) code suite calculates gamma dose rates at a location of interest due to activation of materials. The code suite is based on the rigorous two-step (R2S) method that involves two radiation transport calculations: (1) neutron radiation transport to determine neutron fluxes in the material for which activation calculations will be performed and (2) gamma radiation transport to determine dose rates at a location of interest, due to material activation. The ORNL SDDR code suite is used to determine an importance function that characterizes the neutron’s importance to the final SDDR when the Monte Carlo radiation transport method is used. This report demonstrates how the ORNL SDDR code suite is implemented through the following codes: Monte Carlo N-Particle (MCNP) code Version 5-1.60, Oak Ridge Isotope Generator (ORIGEN), MSX suite of utilities, Neutron Activation Gamma Source Sampler (NAGSS), and Automated Variance Reduction Generator (ADVANTG). For this demonstration, the International Thermonuclear Experimental Reactor (ITER) SDDR benchmark problem is used and the dose rate result is compared to previously published work.
This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and optimizers that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started ). The library is organized hierarchically, enabling users to employ the abstraction level most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users.
The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.
Electronic structure calculations based on density functional theory (DFT) give quantitatively accurate predictions of properties of most materials containing light elements. For heavy materials, and in particular for f -electron systems, DFT based methods can fail both qualitatively and quantitatively for two distinct reasons: their failure to describe confinement effects arising from localized f -electron behavior and their incomplete or approximate treatment of relativity. In addition, different methods for incorporating relativistic effects, which give identical results in most light materials, can give different predictions in heavy elements. In order to develop a quantitative capability for calculating the properties of these materials, it is essential to separate the predictions of the underlying equations from the uncertainty introduced in approximations used in computation. Working toward that goal, here we have developed a code, called dirac-fp , which is based directly on solving the Dirac-Kohn-Sham equations and uses the full-potential linear muffin-tin orbital (FP-LMTO) approach to electronic structure. In order to assess the performance of dirac-fp , we perform calculations on three different face-centered cubic materials using different approximate treatments of relativity: the scalar relativistic (SR) approach commonly used in most solid-state DFT codes, the scalar relativistic plus spin-orbit coupling corrections (SR+SO) approach which includes spin-orbit coupling self-consistently using the SR states inside the muffin tins, and the Dirac-Kohn-Sham (Dirac) approach implemented in dirac-fp . Performing calculations on thorium, in which relativistic effects should be strong, aluminum, in which relativistic effects should be negligible, and gold, in which relativistic effects play an intermediate role, we find that the Dirac approach is able to provide theoretically consistent results in the electronic structure and ground-state properties across all three materials.
The Defense Programs Package (DPP)-3 is to be certified by the National Nuclear Security Administration (NNSA) Packaging and Transportation Division (PTD). Certification is based on successful physical testing of the package, and six certification test units (CTUs) have been subjected to the normal conditions of transport (NCT) and hypothetical accident conditions (HAC) outlined in Title 10 of the Code of Federal Regulations Part 71 (10 CFR 71). During regulatory testing of one of the CTUs, the drum lid closure bolt closest to the impact surface failed during the HAC 30-ft side drop. One of the testing goals for this CTU was to minimize the thermal pathway from the drum exterior shell to the containment vessel (CV) flange and O-rings, leading to the maximum damage scenario in preparation for thermal testing at 1475 °F. Therefore, the puncture bar impact proceeded as originally planned by striking the side wall of the package exterior closest to the location of the CV flange. This puncture bar impact did not attempt to exploit the region of the failed drum lid closure bolt to potentially cause more damage to the package. After the conclusion of regulatory testing, the DPP-3 package finite element model was used to numerically evaluate the effects of puncture bar impacts to the drum exterior in the vicinity of the failed drum lid closure bolt to further demonstrate the robustness of the DPP-3 design. Three alternate puncture bar impact locations and orientations were evaluated to demonstrate that these puncture bar impacts would not substantially reduce the effectiveness of the DPP-3 packaging. This paper describes the supplemental finite element models performed and structural analysis results that demonstrate the alternate HAC 40-in. puncture bar impact tests would have no deleterious effect on the performance of the DPP-3.
In this research, we derive equations for solving for the stationary points of the DLPNO–CCSD Lagrangian, in the t 1 -transformed formalism introduced earlier and as currently implemented in the P SI 4 quantum chemistry software package. These lambda equations in the local pair natural orbital basis allow for the evaluation of CCSD(T) Λ energetics with linear-scaling computational effort, also known as the asymmetric triples correction. This DLPNO–CCSD(T) Λ method allows for accurate triples contributions to be computed for larger molecules, especially in cases that CCSD(T) is known to be insufficient, such as with multireference systems and bond-breaking systems. We showcase the accuracy of our code on reaction energies, barrier heights, and noncovalent interaction energies. Also showcased are the capabilities of our code by evaluating DLPNO–CCSD(T) Λ energetics on large noncovalent dimers up to 112 atoms, as well as a rhodium catalyst complex containing 66 atoms.
A set of magnetic diagnostics has been designed, manufactured, and calibrated for the first operational phase of the small aspect ratio tokamak. The sensor suite comprises of Rogowski coils; 2D magnetic probes; and poloidal, saddle, and diamagnetic flux loops. Here, a set of continuous Rogowski coils has been manufactured for the measurement of plasma current and induced eddy currents in conductive elements. A set of flux loops and magnetic probes will be used as input for the reconstruction of the magnetohydrodynamic equilibrium. The quantity and position of these sensors have been verified to be sufficient with synthetic equilibrium reconstructions using the equilibrium fitting code and baseline scenarios computed with the Fiesta code. These sensors will also be used as input for the real-time control system, and magnetic probes will be used for the detection of plasma instabilities. The calibration procedure for the magnetic probes is described, and the results are shown. The signal conditioning and data acquisition systems are described.
Isomeric states and associated collective structures have been studied up to high spin in 198,200,202 Hg using multinucleon transfer reactions and the Gammasphere array. A coupled rotational band, with possible four-quasiparticle character, is established in 198 Hg. Sequences built on two-quasiparticle, positive- and negative-parity levels are assigned to 202 Hg. New isomers in 202 Hg with I π = (7 – ) and (9 – ), and T 1/2 = 10.4(4) ns and 1.4(3) ns, respectively, have been identified. A half-life of 1.0(3) ns is established for the I π = 12 + state in 200 Hg. B(E2) values deduced from isomeric transitions in Hg isotopes indicate that, while collectivity near the ground state gradually diminishes from N = 112 to N = 124, it is found to increase for the 12 + and 9 – states up to N = 118, followed by a reduction for higher neutron numbers. Calculations using the ultimate cranker code provide insight into the variation of deformation with spin and allow for an understanding of observed band crossings. As a result, the evolution of collectivity with spin, and along the isotopic chain, is described.
The Fast Flux Test Facility (FFTF) at the Hanford site in Washington was designed by the Westinghouse Electric Corporation for the U.S. Department of Energy. FFTF was a 400 MW thermal, oxide-fueled, liquid sodium cooled test reactor, built to assist development and testing of advanced fuels and materials for fast breeder reactors. After reaching criticality in 1980, FFTF operated until 1992, providing the U.S. Department of Energy (DOE) with the means to test fuels, materials, and other components in a fast neutron flux environment. In July 1986, a series of unprotected transients (with the plant protection system intentionally disabled) were performed in FFTF as part of the passive safety demonstration program. Among these were thirteen loss of flow without scram (LOFWOS) tests. The goals of this program included confirming the liquid metal reactor safety margins, providing data for computer code validation, and demonstrating the inherent and passive safety benefits of specific design features. The test defined in this benchmark is LOFWOS Test #13, which was initiated at 50% power and 100% flow with the pump pony motors turned off. This benchmark specification is intended to support collaborative efforts within international partnerships on the validation of simulation tools and models in the area of Sodium-cooled Fast Reactor (SFR) safety. Validated tools and models are needed to evaluate SFR inherent safety characteristics and assess the impact of passive design features in response to accident initiators. Comparisons with experimental data and the results of safety analyses from other groups create unique opportunities to improve predictive capabilities of computational codes and methods for SFR modeling and simulation. The conditions of the LOFWOS test along with the feedback from FFTF’s limited free bow core restraint system and the novel passive reactivity control Gas-Expansion Modules (GEMs) pose a very challenging and uniquely valuable benchmark exercise.
Environmentally friendly amino-acid salt solutions are used for the absorption of carbon dioxide from concentrated flue-gas streams via chemical absorption. Process intensification reduces operating and capital costs by combining chemical reactions and separation operations. Here, we present a new process-intensification approach that combines the CO 2 capture and the amino-acid regeneration steps into a single process carried out in a slurry three-phase reactor. The absorbed CO 2 precipitates as a solid carbonated guanidine compound. The cycle is completed by separation of the solid precipitate to strip the CO 2 and regenerate the guanidine compound, while the liquid solution is recycled to the slurry reactor. The process was studied by modifying a model developed by the authors for a gas-liquid bubble column without the presence of the guanidine compound. The guanidine precipitation reaction was accounted for using kinetic parameters calculated by the authors in another study. The proposed model was implemented by modifying an existing computer code used for the simulation of gas-liquid bubble columns. The calculated results showed that the proposed cycle can significantly reduce energy, equipment, and operating costs and can make an important contribution to developing a competitive cost-effective large-scale process for CO 2 capture.
Experiments in L- and H-mode plasmas performed on the DIII-D tokamak explored ion cyclotron emission (ICE) propagation via the recently upgraded ICE diagnostic. The distance between the plasma and the outer wall was scanned to alter the evanescent region, which was seen to impact the detection of runaway electron-driven whistler modes in a comparable frequency range to typical ICE harmonics (f≳10fci) [Heidbrink et al., Plasma Phys. Controlled Fusion 61, 014007 (2018)]. In L-mode plasmas, core ICE did not exhibit clear trends as the plasma-wall distance was altered. Instead, inadvertent changes to the fast ion density correlated with different ICE fine structures; the most spectral bands (spaced ∼150–200 kHz apart) were observed at the highest fast ion density, and a just single band when nfast decreased by ∼ 40%. The full-wave Petra-M code simulated core ICE propagation through the plasma and to ICE probes, agreeing with experimental findings that these are likely compressional fast waves, which propagate to probe locations with no dependence on plasma-wall gap. Edge ICE in H-mode plasmas was similarly unaffected by plasma-wall distance. Unlike in core ICE cases, there were negligible changes to the edge fast ion distribution and edge bulk plasma profiles. However, changes in ELM frequency seemed most closely tied to ICE behavior. Ultimately, core and edge ICE did not exhibit clear dependencies on the plasma-wall distance, and ICE harmonics were observed with even the largest plasma-wall gaps. This independence bodes well for similar diagnostics in future tokamaks, which might be placed further from high radiation areas without adversely impacting measurement capabilities.
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.