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At least 415 records · Page 23

Python HITMIX

SAND2024-10158O Python HITMIX is a software package for computing hitting time moments of vertices in a graph. Hitting time moments can be used to rank the strengths of relationships between vertices in a graph. Examples are provided for computing and using hitting time moments on generic graphs and similarity graphs arising from the analysis of text documents in information retrieval applications. 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.

Dunlavy, Daniel↗

Efficient training of physics-informed neural networks

Open-source software package designed for the efficient training of Physics-Informed Neural Networks (PINNs) and their variants, integrating advanced methodologies such as adaptive weighting and adaptive sampling

Chen, Wenqian [Pacific Northwest National Laborato↗

MIJAMP

Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating false, under-, or overexplained motifs. MIJAMP can also report methylation data on a specific, user-defined motif.

Alexander, William↗

Computer Programs For Analysis Of Thermally Reactive Tracer Tests In Geothermal Reservoirs

The Tracer Analysis Toolbox (TAT) is a stand-alone executable software package that focuses on reservoir monitoring, using changes in concentration of thermally degrading tracers between and injection well and a production well to reflect the temperature-time histories along flow paths through the reservoir. By conducting such tests periodically, the thermal evolution of the flow paths connecting injection wells to production wells can be monitored. Because this approach is sensitive to temperature along the whole path, it can detect changes well before they occur at the distal end of the path (i.e., the production well). Thus, the thermally degrading tracer method provides early detection of thermal decline before it impacts that well. The goal of TAT is to simplify planning of a reactive tracer monitoring campaign and interpretation of results by providing: (1) tracer test planning and analysis tools to define the necessary kinetic parameters, injection concentrations, and other tracer parameters that are suitable for the expected reservoir residence time and temperature, (2) identification of tracers with suitable characteristics (defined by (1)) and (3) a suite of analysis programs to analyze tracer test results.

Plummer, MitchellAaron [Idaho National Laboratory ↗

Tardigrade-examples V0.2.0

Tardigrade-examples (LANL code O4735) is a repository of computational workflows that exercise the Tardigrade software package.

Allard, Thomas [Los Alamos National Laboratory]↗

CRISPR-CARB/nocap

Network Optimization and Causal Analysis of Perturb-seq (NOCAP) is a software package for causal inference of gene regulation networks using data from perturb-seq.

George, August↗

Zero-Order Reaction Kinetics v. 3.6

Zero-RK is a software package that simulates chemically reacting systems using sparse, preconditioned, adaptive matrix methods to achieve orders-of-magnitude reduction in simulation time while maintaining accurate results.

McNenly, MatthewJ [Lawrence Livermore National Lab↗

torc (Torc Workflow Management System) [SWR-24-127]

This software package orchestrates execution of a workflow of jobs on distributed computing resources. It is optimized for use on HPCs with Slurm, but also can be used in the cloud and on local computers. Please refer to the documentation at https://nrel.github.io/torc

Thom, Daniel [National Renewable Energy Laboratory↗

PRAQTICE

PRAQTICE (Python Repository for Advanced QCVV Tutorials and Interesting Characterization Experiments) is a software package containing advanced demonstrations of the implementation of quantum characterization, verification and validation protocols.

Ostrove, Corey [Sandia National Lab. (SNL-NM), Alb↗

The Satellite Image Simulation Toolkit

The Satellite Image Simulation Toolkit (SatIST) is a python software package designed to generate diverse and realistic satellite imaging scenarios. It serves as a toolkit for simulating data that supports the development and testing of algorithms used in satellite detection, calibration, and characterization. SIST provides a suite of simulation tools that allow users to replicate various satellite observation conditions, including sidereal and target tracking. By enabling the creation of scenarios that mimic real-world satellite operations, SIST facilitates advancements in satellite image data processing and the study of satellite behavior under different observational parameters.

Perloff, AlexxS [Lawrence Livermore National Labor↗

Seismic H2: Version 1.0

Seismic-H2 is an integrated software package for geological hydrogen reservoir simulation, optimization, and leakage monitoring. The package includes multiple components: (1) code used for modeling seismic wave propagation in 3D heterogeneous elastic media based on finite-difference method to support detection of geological hydrogen storage reservoir leakage; (2) 3D reservoir simulations of leaks from an underground reservoir and 3D simulations of saline aquifers and depleted gas reservoirs; (3) seismic monitoring costs of passive and active seismic monitoring required for UHS; (4) rock physics calculations and interpolations for converting the reservoir simulations from part (2) into the elastic media models in part (1); (5) pre-processing seismic data; and lastly (6), a GUI interface that combines these different components.

Creasy, Neala↗

SFold v0.1

This is a scientific software package to integrate Small Angle X-ray Scattering (SAXS) experimental data into OpenFold deep learning models to improve protein structure prediction.

Prince, Stephanie [Lawrence Berkeley National Labo↗

qcal v0.0.1

qcal is a software package for calibration, characterization, and benchmarking of quantum gates. It was developed to operate full-stack superconducting quantum systems at the Advanced Quantum Testbed.

Hashim, Akel [Lawrence Berkeley National Laborator↗

Cadmus v1.0

This software package is for distributed computation of persistent (co)homology. It is primarily intended for Topological Data Analysis (TDA) audience and scientists who use TDA methods and apply them to datasets that are too big to handle on a single machine. There are very few codes available for this; Cadmus outperforms DIPHA, if the user is interested in cohomology. The accompanying paper explaining the algorithm was accepted to ALENEX 26.

Nigmetov, Arnur [Lawrence Berkeley National Labora↗

AuroraGPT Data Collection Interface

SF-25-043 This software package facilitates data collection for the purpose of assessing the performance of LLMs on scientific topics

Underwood, Robert [Argonne National Laboratory (AN↗

pymcnp v1

This is a software package that makes it easier to handle MCNP, a neutron transport simulation toolkit, simulations. It helps with reading and writing output from MCNP and modifying the input files programmatically. Furthermore, it also allows the visualization of input geometry and of the results. Pymcnp provides access to these features using the Python programming language.

Persaud, Arun↗

NCCS High Performance GMRES Mixed Precision

HPG-MxP is a software package that performs a fixed number of multigrid preconditioned (using a Gauss-Seidel smoother) Generalized minimal residual (PGMRES) iterations in order to solve a possibly nonsymmetric large sparse linear system of equations. It is designed to be a benchmark to measure a computer's performance for sparse linear algebra workloads typical in scientific computing while allowing the use of mixed precision methods. The solution is required to have convergence characteristics and accuracy similar to double precision GMRES. It is based on the High Performance Conjugate Gradient Benchmark (HPCG) which restricts all implementations to use only the IEEE double precision format (FP64). The original implementation (https://github.com/hpg-mxp/hpg-mxp) was written by Ichitaro Yamazaki, Jennifer Loe, Christian Glusa, Sivasankaran Rajamanickam, Piotr Luszczek, and Jack Dongarra. Please refer to that repository for documentation on the original implementation. This version is maintained by the National Center for Computational Sciences at Oak Ridge National Laboratory. It is highly scalable and optimized for Oak Ridge Leadership Computing Facility (OLCF) systems, particularly Frontier.

Kashi, Aditya [Oak Ridge National Laboratory (ORNL↗

PyJMAK: An Open-Source Python Toolkit for Modeling Solid-State Metallurgical Phase Transformations

Accurate prediction of metallurgical phase transformations is an essential basis for autonomous optimization and rapid part qualification. Several methods can be used to estimate the evolution of phase fractions such as JMAK kinetics-based models, phase-field models, thermodynamic models, and data-driven machine learning models. Thermodynamic and phase-field-based methodologies solve multiphysics equations requiring numerous calibration parameters and significant computational resources. As a result, the computation domain is limited to a point or on order of micron-meters. The data-driven models rely on large datasets from experiments and simulations. While the JMAK model only provides information about phase fraction evolution, it can predict this evolution in near real-time using thermal history and thermodynamic data without restriction on the domain. JMAK models have been popularly used by researchers to model phase transformations occuring during additive manufacturing or over arbitrary temperature profiles. Commercial proprietary software such as Abaqus and Ansys or closed-source in-house implementations offer the ability to model JMAK based kinetics to predict phase transformation. However, these software packages are not open-source or freely available for use and development in conjunction with manufacturing machines, sensors, and machine learning algorithms. In addition, the use of the model is restricted by a license token. In contrast, given temperature profiles at multiple points in the domain, this Python-based PyJMAK model can compute phase evolution in parallel due to its stand-alone modular, voxel-based structure, and it can be executed on high-performance computing resources without any license restrictions.

Prabhune, Bhagya [Oak Ridge National Laboratory (O↗