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This is prototype code that implements many of the concepts in our invention, "The CORAL Framework for FAIR Data Management and Analysis" (ROI 2019-123, attached). The code includes a back end module that interfaces with third party open source software (ArangoDB), and a front end user interface (UI) that allows user interaction with the software through a web interface.
This is prototype code that implements many of the concepts in our invention, "The CORAL Framework for FAIR Data Management and Analysis" (ROI 2019-123, attached). The code includes a back end module that interfaces with third party open source software (ArangoDB), and a front end user interface (UI) that allows user interaction with the software through a web interface.
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 python routines are outlined in detail to perform the methods and results in the manuscript under review in the journal Geophysical Research Letters titled “Seismic features predict ground motions during repeating caldera collapse sequence” with LA-UR-23-33345. All routines are written in open source python and were applied to publicly available data sets. The codes formats the data into the appropriate structure required to train a boosted tree regression model. Other codes produce figure results.
The objective of this project over the years has been to develop novel quantum chemical methods and employ them to study the chemistry of systems containing actinides, and transactinides. We have focused on their electronic and spectroscopic properties, their reactivity and utilization as single molecule magnets. We have developed wave-function based methods that are optimal to treat strongly correlated systems, namely systems with many electronic configurations that are all important and should be treated on an equal foot. Moreover, relativistic effects have to be included in the model, with special focus on spin-orbit coupling. We have derived our theories and developed our codes and made them available to the community as parts of open source packages. We have modelled systems in collaboration with experimentalists in the program, so that we could address some of the questions that are relevant to this community. We have also worked in collaboration with people at Lawrence Livermore National Laboratories on a project on super-heavy atoms. We hope that our theoretical predictions will inspire novel experiments. We have trained about 10 students/postdocs during this period, which are now faculty, researchers at national laboratories and in companies.
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.
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.
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.
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 present work addresses the need for an efficient, versatile, accurate and open-source numerical tool to be used during the design stage of wave energy converters (WECs). The device considered here is the heaving point-absorber developed and tested by Sandia National Laboratories. The smoothed particle hydrodynamics (SPH) method, as implemented in DualSPHysics, is proposed since its meshless approach presents some important advantages when simulating floating devices. The dynamics of the power take-off system are also modelled by coupling DualSPHysics with the multi-physics library Project Chrono. A satisfactory matching between experimental and numerical results is obtained for: (i) the heave response of the device when forced via its actuator; (ii) the vertical forces acting on the fixed device under regular waves and; (iii) the heave response of the WEC under the action of both regular waves and the actuator force. This proves the ability of the numerical approach proposed to simulate accurately the fluid–structure interaction along with the WEC’s closed-loop control system. In addition, radiation models built from the experimental and WAMIT results are compared with DualSPHysics by plotting the intrinsic impedance in the frequency domain, showing that the SPH method can be also employed for system identification.
Here we introduce an open-source package called QTraj that solves the Lindblad equation for heavy-quarkonium dynamics using the quantum trajectories algorithm. The package allows users to simulate the suppression of heavy-quarkonium states using externally-supplied input from 3+1D hydrodynamics simulations. The code uses a split-step pseudo-spectral method for updating the wave-function between jumps, which is implemented using the open-source multi-threaded FFTW3 package. This allows one to have manifestly unitary evolution when using real-valued potentials. In this paper, we provide detailed documentation of QTraj 1.0, installation instructions, and present various tests and benchmarks of the code.
The ARPA-E Grid Optimization (GO) Competition Challenge 1, from 2018 to 2019, focused on the basic Security Constrained AC Optimal Power Flow problem (SCOPF) for a single time period. The Challenge utilized sets of unique datasets generated by the ARPA-E GRID DATA program. Each dataset consisted of a collection of power system network models of different sizes with associated operating scenarios (snapshots in time defining instantaneous power demand, renewable generation, generator and line availability, etc.). The datasets were of two types: Real-Time, which included starting-point information, and Online, which did not. Week-Ahead data is also provided for some cases but was not used in the Competition. Although most datasets were synthetic and generated by GRIDDATA, a few came from industry and were only used in the Final Event. All synthetic Input Data and Team Results for the GO Competition Challenge 1 for the Sandbox, Trial Events 1 to 3, and the Final Event along with problem, format, scoring and rules descriptions are available here. Data for industry scenarios will not be made public. Challenge 1, a minimization problem, required two computational steps. Solver 1 or Code 1 solved the base SCOPF problem under a strict wall clock time limit, as would be the case in industry, and reported the base case operating point as output, which was used to compute the Objective Function value that was used as the scenario score. The feasibility of the solution was provided by the Solver 2 or Code 2, which solves the power flow problem for all contingencies based on the results from Solver 1. This is not normally done in industry, so the time limits were relaxed. In fact, there were no time limits for Trial Event 1. This proved to be a mistake, with some codes running for more than 90 hours, and a time limit of 2 seconds per contingency was imposed for all other events. Entrants were free to use their own Solver 2 or use an open-source version provided by the Competition. Containers, such as Docker, were considered to improve the portability of codes, but none that could reliably support a multi-node parallel computing environment, e.g., MPI, could be found. For more information on the competition and challenge see the "GO Competition Challenge 1 Information" and "GO Competition Challenge 1 Additional Information" resources below.
Performing a variety of numerical computations efficiently and, at the same time, in a portable fashion requires both an overarching design followed by a number of implementation strategies. All of these are exemplified below as we present transitioning the PLASMA numerical library from relying on dependence-driven large tasks to achieving utilization of fine grain tasking and offload to hardware accelerators while keeping its core dependence sets: OpenMP source code pragmas and runtime for most system-level functionality and basic low-level numerical kernels provided directly by hardware vendors or open source projects with vendor contributions. We also present new algorithmic methods and their efficient parallel implementations including fine grained tasking for eigen-spectrum slicing and offload for mixed-precision eigenvalue refinement. We provide performance, scaling, and numerical results showing sizable gains over the available solutions from either the open source and vendor-provided packages.
This work aims to improve the ability of particle accelerator researchers to develop high-performance accelerator cavity designs by creating an overall multiphysics framework that integrates and couples existing application codes. This framework will allow accelerator researchers to build multiphysics models that will optimize cavity design, improve understanding of whole-device performance, and reduce the development and fabrication costs of accelerator research. We utilize the open-source VizSchema data standard as an intermediate data structure interface layer to standardize interfaces between individual application codes. VizScema is extensively documented online, and plugins for VizSchema are available for popular visualization packages, including VisIt and ParaView. Currently, the work focuses on coupling the EM field solver COMSOL and the electron gun code MICHELLE to allow COMSOL field-solve results to be seamlessly used by MICHELLE for particle-solve. Later work will extend this integration to include other fields, particles, and thermodynamics simulation codes.
We present Stellar Population Interface for Stellar Evolution and Atmospheres (SPISEA), an open-source Python package that simulates simple stellar populations. The strength of SPISEA is its modular interface which offers the user control of 13 input properties including (but not limited to) the initial mass function, stellar multiplicity, extinction law, and the metallicity-dependent stellar evolution and atmosphere model grids used. The user also has control over the initial–final mass relation in order to produce compact stellar remnants (black holes, neutron stars, and white dwarfs). We demonstrate several outputs produced by the code, including color–magnitude diagrams, HR-diagrams, luminosity functions, and mass functions. SPISEA is object-oriented and extensible, and we welcome contributions from the community. The code and documentation are available on GitHub (https://github.com/astropy/SPISEA) and ReadtheDocs (https://spisea.readthedocs.io/en/latest/), respectively.
We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of a core library with standard mass spectrometry utilities greatly facilitates fast software development. Here, we present a Python library, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python with minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multi-omics domain. The free and open source mzapy is built with extensibility in mind, and future development will support cloud computing and artificial intelligence/machine learning applications. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.
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We introduce the first version of GPU4P Y SCF, a module that provides GPU acceleration of methods in P Y SCF. As a core functionality, this provides a GPU implementation of two-electron repulsion integrals (ERIs) for contracted basis sets comprising up to g functions using the Rys quadrature. As an illustration of how this can accelerate a quantum chemistry workflow, we describe how to use the ERIs efficiently in the integral-direct Hartree–Fock build and nuclear gradient construction. Benchmark calculations show a significant speedup of 2 orders of magnitude with respect to the multithreaded CPU Hartree–Fock code of P Y SCF and the performance comparable to other open-source GPU-accelerated quantum chemical packages, including GAMESS and QUICK, on a single NVIDIA A100 GPU.