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SODA Synthesizer: an Open-source, Multi-level, Modular, Extensible Compiler from High-level Frameworks to Silicon
The SODA Synthesizer is an open-source modular, end-to-end hardware compiler framework. The SODA frontend, developed in MLIR, performs system-level design, code partitioning, and high-level optimizations to prepare the specifications for the hardware synthesis. The backend is based on a state-of-the-art high-level synthesis tool, and generates the final hardware design. The backend can interface with logic synthesis tools for field programmable gate arrays or with commercial and open-source logic synthesis tools for application-specific integrated circuits. We discuss the opportunities and challenges in integrating with commercial and open-source tools both at the frontend and backend, and the unique opportunities that an open-source hardware design ecosystem provides.
OpenMP Kernel Language Extensions for Performance Portable GPU Codes
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Efficient and Extensible Quasi-Explicit Modular Nonlinear Multiscale Battery Model: GH-MSMD
Complex physics and long computation time hinder the adoption of computer aided engineering models in the design of large-format battery cells and systems. A modular, efficient battery simulation model -- the multiscale multidomain (MSMD) model -- was previously introduced to aid the scale-up of Li-ion material and electrode designs to complete cell and pack designs, capturing electrochemical interplay with 3-D electronic current pathways and thermal response. Here, this paper enhances the computational efficiency of the MSMD model using a separation of time-scales principle to decompose model field variables. The decomposition provides a quasi-explicit linkage between the multiple length-scale domains and thus reduces time-consuming nested iteration when solving model equations across multiple domains. In addition to particle-, electrode- and cell-length scales treated in the previous work, the present formulation extends to bus bar- and multi-cell module-length scales. We provide example simulations for several variants of GH electrode-domain models.
CHAI and RAJA Extensions
CHAI and RAJA provide an excellent base on which to build portable codes. CARE expands that functionality, adding new features such as loop fusion capability and a portable interface for many numerical algorithms. It provides all the basics for anyone wanting to write portable code.
HPXr, HPX with Resilience Extension
This software is extended from HPX, open source software (the copyright belongs to Louisiana State University). SAND2019-5457 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Interpretable, Extensible Linear Regression Model for Electron Density Prediction
This code allows us to generate a model to predict ground state electron densities directly from atomic structure thereby bypassing the need to perform direct DFT calculations. It is based on many body correlation descriptors defined in https://arxiv.org/abs/2004.14442 (IM release numbers: LLNL-JRNL- 808791 and LLNL-JRNL-840698). The code reads in electron densities, in CHGCAR format used by the DFT code VASP, calculates many-body correlation descriptors based on atoms surrounding a grid point and then uses linear regression to obtain the fitting parameters.
Decadal Variability of Upper-Ocean Heat Content Associated with Meridional Shifts of Western Boundary Current Extensions in the North Pacific
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Extension of Complex Refractive Index Measurements to the Near-Infrared for Liquids: Methodology and Uncertainty Analysis
Optical identification of liquid droplets, aerosols, or thin films is important for many applications. While reference spectra are sometimes available for such measurements, they are not always applicable to the observed spectrum or the given sample morphology. Reference spectra for many forms can be modeled, however, if the n/k vectors (real and imaginary refractive indices) are available. In previous work we have reported protocols to determine the n/k vectors for dozens of liquids, primarily in the mid-infrared (MIR) spectral range from 7500 to 400 cm –1 . In this work we extend the spectral range into the near-infrared (NIR) region, demonstrating a method to measure and merge the data sets to create composite n/k data ranging from 10 000 to 400 cm –1 (1.0 to 25 µm) with absorbance fidelity spanning over four orders of magnitude, and vastly improved signal-to-noise in the NIR. The precision of the composite data is evaluated for three different liquids, focusing primarily on the steps for converting the raw absorbance spectra to k values. The variability in both MIR and NIR data as well as in the final n/k vectors is also investigated for several liquids. For typical liquids, the overall variability (reported as 2σ) in the final n and k-vectors is determined to be ∼0.4% and 3%, respectively. Finally, the derived n/k data are used to calculate absorbance spectra for aerosol droplets, showing marginal variability due to the typical measurement errors in the final n/k vectors.
An extension of the OpenModelica compiler for using Modelica models in a discrete event simulation
In this article, a new back-end and run-time system is described for the OpenModelica compiler. This new back-end transforms a Modelica model into a module for the adevs discrete event simulation package, thereby extending adevs to encompass complex, hybrid dynamical systems. The new run-time system that has been built within the adevs simulation package supports models with state-events and time-events and that comprise differential-algebraic systems with high index. Finally, although the procedure for effecting this transformation is based on adevs and the Discrete Event System Specification, it can be adapted to any discrete event simulation package.
Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae
Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages.
Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha
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Extension of the PINN diffusion model to k-eigenvalue problems
This paper extends our recent work on the Physics-Informed Neural Networks (PINN) approach for the fixed source diffusion models and applies it to the diffusion theory based k-eigenvalue problems. To make the PINN equitable for the eigenvalue problems, we introduce a novel integral regularization term to the loss function in the framework, and allow the direct inference of the principal eigenvalue and the associated eigenfunction. The regularization term enforces a pre-defined value on the integration of the model predictions, and this value can be directly related to a physical property of the system. We also introduce an additional learnable parameter to approximate the principal eigenvalue. As a proof of principle, we solve the one-group two-dimensional k-eigenvalue neutron diffusion equation in this work. We then provide two numerical examples to demonstrate the applicability of the PINN approach. In each example, we solve the k-eigenvalue diffusion equation in a multi-region configuration constrained with a set of Robin boundary conditions for generality. We use a FEM solution based on the power-iteration method to verify the results of the PINN solution. The results showed relative percentage error in the predicted eigenvalue of about 0.77% and about 1.2% for example 1 and example 2, respectively. The mean absolute error in the predicted flux for example 1 is ∼ 0.002 and for example 2 is ∼ 0.0024. These results indicate some preliminary successes of the PINN application to k-eigenvalue problems. (authors)
Bandwidth extension and conversion efficiency improvements beyond phase matching limitations using cavity-enhanced OPCPA
The conversion efficiency and phase matching bandwidth of ultrafast optical parametric amplification (OPA) are constrained by the dispersion and nonlinear coefficient of the employed crystal as well as pulse shaping effects. In our work we show that an enhancement cavity resonant with the pump seeded at the full repetition rate of the pump laser can automatically reshape the small-signal gain in optical parametric chirped-pulse amplification (OPCPA) to achieve close-to-optimal operation. This new method termed cavity-enhanced OPCPA or C-OPCPA significantly increases both the gain bandwidth and the conversion efficiency, in addition to boosting gain for high-repetition-rate amplification. The goal in C-OPCPA is to arrive at a condition of impedance matching at all temporal coordinates, such that, in the absence of linear losses, all the incident pump power is dissipated in the nonlinear loss element, i.e., converted to signal and idler. The use of a low finesse enhancement cavity resonant with a low average power (<1W) and a high repetition rate (78MHz) pump source is shown to achieve more than 50% conversion efficiency into signal and idler from the coupled pump in an optical parametric process, whereas an equivalent amount of pump power in a single-pass configuration leads to negligible conversion. Additionally, the gain bandwidth is extended by a factor of 3-4 beyond the phase-matching limit. Our empirical observations are corroborated by a numerical analysis of depletion optimizing the single-pass case, which assesses the underlying impedance matching that is responsible for the observed performance improvements.
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
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