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Semi-stochastic full configuration interaction quantum Monte Carlo: Developments and application
We expand upon the recent semi-stochastic adaptation to full configuration interaction quantum Monte Carlo (FCIQMC). We present an alternate method for generating the deterministic space without a priori knowledge of the wave function and present stochastic efficiencies for a variety of both molecular and lattice systems. The algorithmic details of an efficient semi-stochastic implementation are presented, with particular consideration given to the effect that the adaptation has on parallel performance in FCIQMC. We further demonstrate the benefit for calculation of reduced density matrices in FCIQMC through replica sampling, where the semi-stochastic adaptation seems to have even larger efficiency gains. We then combine these ideas to produce explicitly correlated corrected FCIQMC energies for the beryllium dimer, for which stochastic errors on the order of wavenumber accuracy are achievable.
Verification and Performance Impact of the New Parallel MCNP6.3 Particle Track Output Capability for Subcritical Multiplication Simulations
The MCNP6® code, version 6.3, has several new features that are intended to ultimately replace legacy features that are now marked for deprecation. One of these features is the new particle track output (PTRAC) format and capability, where the legacy PTRAC capability still exists alongside the modern PTRAC capability in MCNP6.3. While the MCNP6.3 code has been extensively verified and validated for many applications, the PTRAC feature is not exercised in any of the typical verification and validation (V&V) applications studied during the course of a typical MCNP code release. The primary goal of this paper is to verify that the legacy and modern PTRAC feature produces equivalent results for subcritical multiplication benchmarks previously studied. In the process of verifying that the simulated benchmark results are equivalent, the computational performance is compared between the legacy and modern PTRAC uses. In addition to verification of the update, which is important to the community as a whole, this effort also supports advances in the simulation of recent subcritical neutron noise measurements that require higher computational effort per second of real-time measurement than that of systems typically measured.
The LISE package: solvers for static and time-dependent superfluid local density approximation equations in three dimensions
Nuclear implementation of the density functional theory (DFT) is at present the only microscopic framework applicable to the whole nuclear landscape. The extension of DFT to superfluid systems in the spirit of the Kohn-Sham approach, the superfluid local density approximation (SLDA) and its extension to time-dependent situations, time-dependent superfluid local density ap- proximation (TDSLDA), have been extensively used to describe various static and dynamical problems in nuclear physics, neutron star crust, and cold atom systems. In this paper, we present the codes that solve the static and time-dependent SLDA equations in three-dimensional coordinate space without any symmetry restriction. These codes are fully parallelized with the message passing interface (MPI) library and take advantage of graphic processing units (GPU) for accelerating execution. The dynamic codes have checkpoint/restart capabilities and for initial conditions one can use any generalized Slater determinant type of wave function. The code can describe a large number of physical problems: nuclear fission, collisions of heavy ions, the interaction of quantized vor- tices with nuclei in the nuclear star crust, excitation of superfluid fermion systems by time dependent external fields, quantum shock waves, domain wall generation and propagation, the dynamics of the Anderson-Bogoliubov-Higgs mode, dynamics of fragmented condensates, vortex rings dynamics, generation and dynamics of quantized vortices, their crossing and recombinations and the incipient phases of quantum turbulence.
RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM)
Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, we devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative amounts of analytes in two samples, a mixture is prepared from aliquots of the samples, and the samples and the mixture are analyzed in parallel according to the intended workflow. Processing of the resulting data using the REQUIEM algorithm yields unbiased analyte fold-changes and associated statistics, allowing several types of errors to be diagnosed or eliminated. Extensive simulations and analysis of carefully prepared standard samples demonstrated the rigorous foundations of REQUIEM. We applied REQUIEM to several real-world analytical techniques and workflows, notably to tandem mass spectrometry analysis by using isomeric oligosaccharides as test analytes. Finally, we conclude that REQUIEM can reveal inaccuracies in the data that are difficult to identify by using traditional approaches.
Domain decomposition in time for PDE-constrained optimization
Here, PDE-constrained optimization problems have a wide range of applications, but they lead to very large and ill-conditioned linear systems, especially if the problems are time dependent. In this paper we outline an approach for dealing with such problems by decomposing them in time and applying an additive Schwarz preconditioner in time, so that we can take advantage of parallel computers to deal with the very large linear systems. We then illustrate the performance of our method on a variety of problems.
Cylindrical Confinement of Nanocolloidal Cholesteric Liquid Crystal
The organization of nanocolloidal liquid crystals in constrained geometries has fundamental and practical importance, since under confinement, liquid crystals contain stable topological defects that can serve as templates for nanoparticle organization. Three-dimensional confinement of cholesteric (Ch) liquid crystals formed by cellulose nanocrystals (CNCs) have been extensively studied; however, their two-dimensional confinement remains underinvestigated. In this work, we report the results of systematic experimental studies of two-dimensional confinement of Ch–CNC liquid crystal in cylindrical capillaries with varying inner diameters. Confinement resulted in phase separation of the Ch–CNC liquid crystal into a Ch shell formed by concentric CNC pseudolayers with the helicoidal axis perpendicular to the inner surface of the capillary walls, and a micrometer-diameter isotropic core thread running parallel to the long axis of the capillary. The morphology of the confined Ch–CNC liquid crystal varied when progressively increasing the degree confinement. Finally, we show that phase separation of the Ch–CNC liquid crystal into a Ch shell and an isotropic core is preserved in flexible capillary tubing, suggesting the applicability of this system for the fabrication of flexible optical waveguides.
First-Principles-Based Study of the Decomposition of Phenol and Hydroquinone on Pt(111) Combined with Quantitative Information from XPS Spectra to Address the Impact of Coverage and Number of Hydroxyl Functional Groups
A combined first-principles-based and experimental X-ray photoelectron spectroscopy approach was used to investigate the thermal decomposition of two model biofuel compounds, phenol and hydroquinone, on Pt(111) at both low and high coverages. The DFT-based approach yields adsorption geometries and energies, activation barriers and core-level binding energy shifts for C 1s and O 1s. Increasing the coverage in the theoretical model leads to slight shifts in core-level binding energies─toward higher values for C 1s and lower values for O 1s. It also alters the energy profiles of the decomposition reaction pathway, resulting in weaker adsorption energies and changes in both reaction and activation barriers. At low temperatures, we observe a multilayer for phenol and hydroquinone upon adsorption, with desorption occurring at 200 and 270 K, respectively. Following desorption of the multilayer, decomposition proceeds via initial O–H bond scission, followed by two parallel pathways involving either C–H or C–C bond scission, whereby in the case of phenol C–H bond scission occurs first. Here, we further provide characteristic core level binding energies by theoretical calculations that are subsequently used in experimental analyses, establishing a reference database for key spectra of phenolic functionalities applicable to a range of catalytic reactions.
Initial position optimization in molecular dynamics simulations for a Coulomb system
A new algorithm for molecular dynamics (MD) simulations is developed to optimize plasma particle distributions at given initial temperatures. By combining velocity scaling and reassignment, the method effectively eliminates the initial rise and oscillation in temperatures observed with randomly distributed positions. These rises and oscillations are undesired numerical artifacts observed in conventional plasma MD simulations, arising from unoptimized particle positions. The algorithm demonstrates temperature relaxation without initial rises or oscillations, as well as precise flow velocity relaxation, enabling accurate measurement of relaxation times. The code is accelerated using graphics processing units for parallel processing, enhancing the study of plasma dynamics. The proposed method for distributing physically valid particles in MD simulations enables accurate studies of intrinsic collision processes in plasmas, including the dynamics of strongly coupled plasmas, plasma–wave interactions, and transport phenomena in magnetized plasmas. The paper concludes with a discussion of potential applications and future enhancements to the algorithm.
Imaging anisotropic vortex dynamics in FeSe
Strong vortex pinning in FeSe could be useful for technological applications and could provide clues about the coexistence of superconductivity and nematicity. To characterize the pinning of individual, isolated vortices, we simultaneously apply a local magnetic field and image the vortex motion with scanning SQUID susceptibility. We find that the pinning is highly anisotropic: the vortices move easily along directions that are parallel to the orientations of twin domain walls and pin strongly in a perpendicular direction. These results are consistent with a scenario in which the anisotropy arises from vortex pinning on domain walls and quantify the dynamics of individual vortex pinning in FeSe.
Mapping of exhaust gas recirculation and combustion-residual backflow in the intake ports of a heavy-duty diesel engine using a multiplexed multi-species absorption spectroscopy sensor [Mapping of EGR and combustion residual backflow in the intake ports of a heavy duty diesel engine using a multiplexed multi-species absorption spectroscopy sensor]
Here, the combustion-residual backflow into the intake ports of a commercial diesel engine (Cummins ISX series) was spatiotemporally mapped using a multiplexed multi-species absorption spectroscopy sensor system; the resulting cycle- and cylinder-resolved measurements are applicable for assessing cylinder charge uniformity, control strategies, and computational fluid dynamics tools. On-engine measurements were made using four compact (3/8 in Outside Diameter) stainless steel probes which enabled simultaneous multi-point measurements, required minimal engine hardware modification, and featured a novel tip design for measurement of gas flows parallel to the probe axis. Three sensor probes were used to perform simultaneous backflow measurements in intake runners corresponding to three of the six engine cylinders, and a fourth probe was installed in the intake manifold plenum for tracking dynamics introduced by an external exhaust gas recirculation mixer. Near-crank-angle resolved measurements (5 kHz, that is, 1.2 crank angle resolution at 1000 RPM) were performed during steady-state engine operation at various levels of external exhaust gas recirculation to measure the gas properties and penetration distance of the backflow into the intake runners on a cylinder- and cycle-basis. Validation of computational fluid dynamics model results is also presented to demonstrate the utility of such measurements in advancing engine research.
Enabling real-time adaptation of machine learning models at x-ray Free Electron Laser facilities with high-speed training optimized computational hardware
The emergence of novel computational hardware is enabling a new paradigm for rapid machine learning model training. For the Department of Energy’s major research facilities, this developing technology will enable a highly adaptive approach to experimental sciences. In this manuscript we present the per-epoch and end-to-end training times for an example of a streaming diagnostic that is planned for the upcoming high-repetition rate x-ray Free Electron Laser, the Linac Coherent Light Source-II. We explore the parameter space of batch size and data parallel training across multiple Graphics Processing Units and Reconfigurable Dataflow Units. We show the landscape of training times with a goal of full model retraining in under 15 min. Although a full from scratch retraining of a model may not be required in all cases, we nevertheless present an example of the application of emerging computational hardware for adapting machine learning models to changing environments in real-time, during streaming data acquisition, at the rates expected for the data fire hoses of accelerator-based user facilities.
The Athena++ Adaptive Mesh Refinement Framework: Design and Magnetohydrodynamic Solvers
The design and implementation of a new framework for adaptive mesh refinement calculations are described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list" that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both nonrelativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available.
Multi-petascale highly efficient parallel supercomputer
A Multi-Petascale Highly Efficient Parallel Supercomputer of 100 petaOPS-scale computing, at decreased cost, power and footprint, and that allows for a maximum packaging density of processing nodes from an interconnect point of view. The Supercomputer exploits technological advances in VLSI that enables a computing model where many processors can be integrated into a single Application Specific Integrated Circuit (ASIC). Each ASIC computing node comprises a system-on-chip ASIC utilizing four or more processors integrated into one die, with each having full access to all system resources and enabling adaptive partitioning of the processors to functions such as compute or messaging I/O on an application by application basis, and preferably, enable adaptive partitioning of functions in accordance with various algorithmic phases within an application, or if I/O or other processors are underutilized, then can participate in computation or communication nodes are interconnected by a five dimensional torus network with DMA that optimally maximize the throughput of packet communications between nodes and minimize latency.
Analysis of Plane-Parallel Electron Beam Propagation in Different Media by Numerical Simulation Methods
Simulation by the Monte Carlo method is widely used to calculate the character of ionizing radiation interaction with substance. A wide variety of programs based on the given method allows users to choose the most suitable package for solving computational problems. In turn, it is important to know exactly restrictions of numerical systems to avoid gross errors. Results of estimation of the feasibility of application of the program PCLab (Computer Laboratory, version 9.9) for numerical simulation of the electron energy distribution absorbed in beryllium, aluminum, gold, and water for industrial, research, and clinical beams are presented. The data obtained using programs ITS and Geant4 being the most popular software packages for solving the given problems and the program PCLab are presented in the graphic form. A comparison and an analysis of the results obtained demonstrate the feasibility of application of the program PCLab for simulation of the absorbed energy distribution and dose of electrons in various materials for energies in the range 1–20 MeV.
SU-D-213-05: Design, Evaluation and First Applications of a Off-Site State-Of-The-Art 3D Dosimetry System
Purpose: To design, construct and commission a prototype in-house three dimensional (3D) dose verification system for stereotatic body radiotherapy (SBRT) verification at an off-site partner institution. To investigate the potential of this system to achieve sufficient performance (1mm resolution, 3% noise, within 3% of true dose reading) for SBRT verification. Methods: The system was designed utilizing a parallel ray geometry instigated by precision telecentric lenses and an LED 630nm light source. Using a radiochromic dosimeter, a 3D dosimetric comparison with our gold-standard system and treatment planning software (Eclipse) was done for a four-field box treatment, under gamma passing criteria of 3%/3mm/10% dose threshold. Post off-site installation, deviations in the system’s dose readout performance was assessed by rescanning the four-field box irradiated dosimeter and using line-profiles to compare on-site and off-site mean and noise levels in four distinct dose regions. As a final step, an end-to-end test of the system was completed at the off-site location, including CT-simulation, irradiation of the dosimeter and a 3D dosimetric comparison of the planned (Pinnacle{sup 3}) to delivered dose for a spinal SBRT treatment(12 Gy per fraction). Results: The noise level in the high and medium dose regions of the four field box treatment was relatively 5% pre and post installation. This reflects the reduction in positional uncertainty through the new design. This At 1mm dose voxels, the gamma pass rates(3%,3mm) for our in-house gold standard system and the off-site system were comparable at 95.8% and 93.2% respectively. Conclusion: This work will describe the end-to-end process and results of designing, installing, and commissioning a state-of-the-art 3D dosimetry system created for verification of advanced radiation treatments including spinal radiosurgery.
Exploring the scaling limitations of the variational quantum eigensolver with the bond dissociation of hydride diatomic molecules
Abstract Materials simulations involving strongly correlated electrons pose fundamental challenges to state‐of‐the‐art electronic structure methods but are hypothesized to be the ideal use case for quantum computing algorithms. To date, no quantum computer has simulated a molecule of a size and complexity relevant to real‐world applications, despite the fact that the variational quantum eigensolver (VQE) algorithm can predict chemically accurate total energies. Nevertheless, because of the many applications of moderately sized, strongly correlated systems, such as molecular catalysts, the successful use of the VQE stands as an important waypoint in the advancement toward useful chemical modeling on near‐term quantum processors. In this paper, we take a significant step in this direction. We lay out the steps, write, and run parallel code for an (emulated) quantum computer to compute the bond dissociation curves of the TiH, LiH, NaH, and KH diatomic hydride molecules using the VQE. TiH was chosen as a relatively simple chemical system that incorporates d orbitals and strong electron correlation. Because current VQE implementations on existing quantum hardware are limited by qubit error rates, the number of qubits available, and the allowable gate depth, recent studies using it have focused on chemical systems involving s and p block elements. Through VQE + UCCSD calculations of TiH, we evaluate the near‐term feasibility of modeling a molecule with d‐orbitals on real quantum hardware. We demonstrate that the inclusion of d‐orbitals and the use of the UCCSD ansatz, which are both necessary to capture the correct TiH physics, dramatically increase the cost of this problem. We estimate the approximate error rates necessary to model TiH on current quantum computing hardware using VQE + UCCSD and show them to likely be prohibitive until significant improvements in hardware and error correction algorithms are available.
Direct Exfoliation of Nanoribbons from Bulk van der Waals Crystals
Confinement of monolayers into quasi-1D atomically thin nanoribbons could lead to novel quantum phenomena beyond those achieved in their bulk and monolayer counterparts. However, current experimental availability of nanoribbon species beyond graphene is limited to bottom-up synthesis or lithographic patterning. Here, in this study, a versatile and direct approach is introduced to exfoliate bulk van der Waals crystals as nanoribbons. Akin to the Scotch tape exfoliation method for producing monolayers, this technique provides convenient access to a wide range of nanoribbons derived from their corresponding bulk crystals, including MoS 2 , WS 2 , MoSe 2 , WSe 2 , MoTe 2 , WTe 2 , ReS 2 , and hBN. The nanoribbons are predominantly monolayer, single-crystalline, parallel-aligned, flat, and exhibit high aspect ratios. The role of confinement, strain, and edge configuration of these nanoribbons is observed in their electrical, magnetic, and optical properties. This versatile exfoliation technique provides a universal route for producing a variety of nanoribbon materials and supports the study of their fundamental properties and potential applications.