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At least 325 records · Page 18

dCache: Inter-disciplinary storage system

The dCache project provides open-source software deployed internationally to satisfy ever more demanding storage requirements. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, data sharing over wide area networks, efficient access from HPC clusters and long term data persistence on a tertiary storage. Though it was originally developed for the HEP experiments, today it is used by various scientific communities, including astrophysics, biomed, life science, which have their specific requirements. In this paper we describe some of the new requirements as well as demonstrate how dCache developers are addressing them.

Mkrtchyan, Tigran↗

Concept, implementation and commissioning of the automation system for the accelerator module test facility AMTF

The European XFEL project launched on June 5, 2007 will require about 103 accelerator modules as a main part of the XFEL linear accelerator. All superconducting components constituting the accelerator module like cavities and magnets have to be tested before the assembly. For the tests of the individual cavities and the complete modules an XFEL Accelerator Module Test Facility (AMTF) has been erected at DESY. The process control system EPICS (Experimental Physics and Industrial Control System) is used to control and operate the cryogenic plant and all its subcomponents. A complementary component of EPICS is the Open Source software suit CSS (Control System Studio). CSS is an integrated engineering, maintenance and operating tool for EPICS. CSS enables local and remote operating and monitoring of the complete system and thus represents the human machine interface. More than 250 PROFIBUS nodes work at the accelerator module test facility. DESY installed an extensive diagnostic and condition monitoring system. With these diagnostic tools it is possible to examine the correct installation and configuration of all PROFIBUS nodes in real time. The condition monitoring system based on FDT/DTM technology shows the state of the PROFIBUS devices at a glance. This information can be used for preventive maintenance which is mandatory for continuous operation of the AMTF facility. The poster will describe all steps form engineering to implementation and commissioning.

43 PARTICLE ACCELERATORS↗

Embedded image processing engine using ARM cortex-M4 based STM32F407 microcontroller

Due to advancement in low cost, easily available, yet powerful hardware and revolution in open source software, urge to make newer, more interactive machines and electronic systems have increased manifold among engineers. To make system more interactive, designers need easy to use sensor systems. Giving the boon of vision to machines was never easy, though it is not impossible these days; it is still not easy and expensive. This work presents a low cost, moderate performance and programmable Image processing engine. This Image processing engine is able to capture real time images, can store the images in the permanent storage and can perform preprogrammed image processing operations on the captured images.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Heliostat Aiming Strategies for Arbitrary Flux Profiles for High Temperature Gas-Based Receivers

High temperature gas-based receivers are seen as one potential path toward achieving the next generation of concentrated solar power tower systems. A key challenge associated with high temperature, high pressure heat transfer fluids is the lifetime of receiver containment materials. Achieving the desired lifetime while also designing an efficient receiver requires implementation of unique flux profiles, tailored to place high fluxes at cold fluid injection points. An aimpoint selection methodology was developed in the present study to allow user-defined flux profiles to be prescribed for a receiver. The methodology was implemented in NREL's open-source software SolarPILOT, modifying the existing “image size priority” aimpoint strategy. A case study for a tubular gas-based receiver is presented, examining the effect of various parameters on the ability to replicate the desired flux profile.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genetic algorithm-based geometry calibration for dynamic compression x-ray diffraction experiments

An important component of dynamic compression x-ray diffraction (XRD) experiment analysis is geometry calibration: proper data interpretation requires knowledge of the precise detector position and orientation and, if the experiment involves a single-crystal sample, knowledge of the lattice orientation. The determination of these parameters in the arbitrary three-dimensional (3D) scattering geometries often present in dynamic compression facilities is challenging, as the associated optimization problem can be highly nonlinear, nonsmooth, and discontinuous. We present a genetic algorithm-based approach for performing dynamic compression XRD calibrations that overcomes these obstacles. We provide details regarding the image processing, algorithm implementation, and open-source software deployment and demonstrate the capability of the approach to calibrate the detector and crystal parameters in 3D geometries. Notably, we demonstrate the solver’s capacity to find the crystal orientation without a priori rotation constraints.

Brown, Nathan P. [Sandia National Laboratories (SN↗

Rejoinder

We are grateful for the many insightful comments provided by the discussants. One team politely pointed out oversights in our literature review and the subsequent omission of a formidable comparator. Another made an important clarification about when a more aggressive variation (the so-called NoMax) would perform poorly. A third team offered enhancements to the framework, including a derivation of closed-form expressions and a more aggressive updating scheme; these enhancements were supported by an empirical study comparing new alternatives with old. The last team suggested hybridizing the statistical augmented Lagrangian (AL) method with modern stochastic search. Here we present our responses to these contributions and detail some improvements made to our own implementations in light of them. We conclude with some thoughts on statistical optimization using surrogate modeling and open-source software.

97 MATHEMATICS AND COMPUTING↗

CONSTRUCTING A FLEXIBLE LIKELIHOOD FUNCTION FOR SPECTROSCOPIC INFERENCE

We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically addresses the common problem of mismatches in model spectral line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line “outliers.” By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high-resolution V-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate-resolution K-band spectrum of Gliese 51, an M5 field dwarf.

79 ASTRONOMY AND ASTROPHYSICS↗

MODULES FOR EXPERIMENTS IN STELLAR ASTROPHYSICS (MESA): BINARIES, PULSATIONS, AND EXPLOSIONS

We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing transfer and loss of mass and angular momentum, greatly enhancing the prior ability to model binary evolution. New MESA capabilities in fully coupled calculation of nuclear networks with hundreds of isotopes now allow MESA to accurately simulate the advanced burning stages needed to construct supernova progenitor models. Implicit hydrodynamics with shocks can now be treated with MESA, enabling modeling of the entire massive star lifecycle, from pre-main-sequence evolution to the onset of core collapse and nucleosynthesis from the resulting explosion. Coupling of the GYRE non-adiabatic pulsation instrument with MESA allows for new explorations of the instability strips for massive stars while also accelerating the astrophysical use of asteroseismology data. We improve the treatment of mass accretion, giving more accurate and robust near-surface profiles. A new MESA capability to calculate weak reaction rates “on-the-fly” from input nuclear data allows better simulation of accretion induced collapse of massive white dwarfs and the fate of some massive stars. We discuss the ongoing challenge of chemical diffusion in the strongly coupled plasma regime, and exhibit improvements in MESA that now allow for the simulation of radiative levitation of heavy elements in hot stars. We close by noting that the MESA software infrastructure provides bit-for-bit consistency for all results across all the supported platforms, a profound enabling capability for accelerating MESA's development.

79 ASTRONOMY AND ASTROPHYSICS↗

PIV/BOS synthetic image generation in variable density environments for error analysis and experiment design

In this work, we present an image generation methodology based on ray tracing that can be used to render realistic images of Particle Image Velocimetry (PIV) and Background Oriented Schlieren (BOS) experiments in the presence of density/refractive index gradients. This methodology enables the simulation of aero-thermodynamics experiments for experiment design, error, and uncertainty analysis. Images are generated by emanating light rays from the particles or dot pattern, and propagating them through the density gradient field and the optical elements, up to the camera sensor. The rendered images are realistic, and can replicate the features of a given experimental setup, like optical aberrations and perspective effects, which can be deliberately introduced for error analysis. We demonstrate this methodology by simulating a BOS experiment with a known density field obtained from direct numerical simulations (DNS) of homogeneous buoyancy driven turbulence, and comparing the light ray displacements from ray tracing to results from BOS theory. The light ray displacements show good agreement with the reference data. This methodology provides a framework for further development of simulation tools for use in experiment design and development of image analysis tools for PIV and BOS applications. Finally, an implementation of the proposed methodology in a Python-CUDA program is made available as an open source software for researchers.

47 OTHER INSTRUMENTATION↗

A Monte Carlo model for 3D grain evolution during welding

Welding is one of the most wide-spread processes used in metal joining. However, there are currently no open-source software implementations for the simulation of microstructural evolution during a weld pass. Here we describe a Potts Monte Carlo based model implemented in the SPPARKS kinetic Monte Carlo computational framework. The model simulates melting, solidification and solid-state microstructural evolution of material in the fusion and heat-affected zones of a weld. The model does not simulate thermal behavior, but rather utilizes user input parameters to specify weld pool and heat-affect zone properties. Weld pool shapes are specified by Bezier curves, which allow for the specification of a wide range of pool shapes. Pool shapes can range from narrow and deep to wide and shallow representing different fluid flow conditions within the pool. Surrounding temperature gradients are calculated with the aide of a closest point projection algorithm. Furthermore, the model also allows simulation of pulsed power welding through time-dependent variation of the weld pool size. Example simulation results and comparisons with laboratory weld observations demonstrate microstructural variation with weld speed, pool shape, and pulsed-power.

36 MATERIALS SCIENCE↗

Characterizing structural features of two-dimensional particle systems through Voronoi topology

This paper introduces a new approach toward characterizing local structural features of two-dimensional particle systems. The approach can accurately identify and characterize defects in high-temperature crystals, distinguish a wide range of nominally disordered systems, and robustly describe complex structures such as grain boundaries. This paper also introduces two-dimensional functionality into the open-source software program VoroTop which automates this analysis. This software package is built on a recently-introduced multithreaded version of V ORO ++, enabling the analysis of systems with billions of particles on high-performance computer architectures.

36 MATERIALS SCIENCE↗

Extending Supernova Spectral Templates for Next-generation Space Telescope Observations

Empirical models of supernova (SN) spectral energy distributions (SEDs) are widely used for SN survey simulations and photometric classifications. The existing library of SED models has excellent optical templates, but limited, poorly constrained coverage of ultraviolet (UV) and infrared (IR) wavelengths. However, both regimes are critical for the design and operation of future SN surveys, particularly at IR wavelengths that will be accessible with the James Webb Space Telescope and the Wide-Field Infrared Survey Telescope. We create a public repository of improved empirical SED templates using a sampling of Type Ia and core-collapse (CC) photometric light curves to extend the Type Ia parameterized SALT2 model and a set of SN Ib, SN Ic, and SN II SED templates into the UV and near-IR. We apply this new repository of extrapolated SN SED models to examine how future surveys can discriminate between CC and Type Ia SNe at UV and IR wavelengths, and present an open-source software package written in Python, SNSEDextend, that enables users to generate their own extrapolated SEDs.

79 ASTRONOMY AND ASTROPHYSICS↗

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

59 BASIC BIOLOGICAL SCIENCES↗

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

Abstract Summary Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. Availability and implementation VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. Supplementary information Supplementary data is available at Bioinformatics online.

Libin, Pieter J. K. (ORCID:000000033906758X)↗