kevinyager/SciTools
Collection of tools (Python scripts) for scientific experiments: SciAnalysis (analyze image-like data), SciControl (instrument control), and SciVis (visualize data).
Yager, Kevin [Brookhaven National Lab. (BNL), Upto↗
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Results for “PYTHON”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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ManiPIO - Manipulate Process I/O
SAND2021-15053 O ManiPIO is a Python-based tool used to test Programmable Logic Controllers (PLCs), Industrial Control Systems (ICS), and ICS networks. It reads an input script to construct complex Events on ICS networks and uses the ModBus communication standard to communicate. Users can use ManiPIO to construct complex timelines of ICS communication events to simulate any number of network-based scenarios. 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.
Hahn, Andrew↗
EXSCLAIM!
Due to recent improvements in image resolution and acquisition speed, materials microscopy is experiencing an explosion of published imaging data. The standard publication format, while sufficient for traditional data ingestion scenarios where a select number of images can be critically examined and curated manually, is not conducive tolarge-scale data aggregation or analysis, hindering data sharing and reuse. Most images in publications are presented as components of a larger figure with their explicit context buried in the main body or caption text, so even if aggregated, collections of images with weak or no digitized contextual labels have limited value. To solve the problem of curating labeled microscopy data from literature, we introduce the EXSCLAIM! Python toolkit for the automatic EXtraction, Separation, and Caption-based natural Language Annotation of IMages from scientific literature. The software is implemented through a three part pipeline: the JournalScraper, which searches the web and downloads figures and captions based on a user provided query, the CaptionDistributor, which separates caption text based on the subfigure each portion of the caption refers to, and the FigueSeparator, which separates figures into component subfigures and extracts other visual information. Also included is a Django user interface for exploring the resulting dataset.
CHAN, MARIA↗
PV DMFA [SWR-21-105]
The Photovoltaic Dynamic Material Flow Assessment (PV DMFA) model (also referred to here as “The model”) is a computational framework written in Python based on utility-scale PV electricity generation to quantify time-series stocks and flows of PV materials primarily in crystalline silicon PV technologies. The model evaluates cradle-to-cradle life cycle of utility-scale solar PV systems in the United States in the period 2000-2100. PV DMFA serves as a sustainability analysis tool to assess the impacts of different material circularity practices (i.e., reduce, reuse/refurbish, remanufacture, and recycle), PV module design shifts and sensitivity of material processing and technology related parameters to material installations, waste creation and raw material depletion in PV material supply chains. This tool enables advanced planning for future material needs and informs sustainable pathways for PV material management in the circular economy. This tool could be helpful to a wide range of stakeholders; Particularly, researchers and manufacturers looking for technoeconomic and/or environmental life cycle analysis (LCA) feedback for renewable energy (RE) systems.
Khalifa, SherifA.↗
Virtual Engineering (VE) (vebio)
The Virtual Engineering (VE, vebio) project provides a set of Python modules to enable users to connect mathematical models of unit operations to predict outcomes for an entire chemical process. This VE approach is currently being developed to support the beginning-to-end simulation of the low-temperature conversion of lignocellulosic biomass to a fuel precursor, but the underlying communication functions can be readily extended to connect models from other domains. The models and features currently included in the VE library include a models/simulations for pretreatment, enzymatic hydrolysis, and aerobic bioreaction.
Young, Ethan↗
Neural Networks for Supercapacitor Modeling
This software implements a one-dimensional model of a supercapacitor and calibrates it to experimental data. A system of coupled partial differential equation models the salt concentration and the ionic and electronic potentials. The term in the equation modeling the capacitance contains a neural network, whose parameters are optimized to fit the provided experimental data. The software is written in python using the open-source library JAX to calculate the gradients needed for the optimization.
Salazar de Troya, Miquel↗
In silico evolution of oscillatory gene dynamics formerly Code sharing for a manuscript to be submitted to the journal iScience
The disclosure is about the numerical simulations and visualization implemented in general-purpose language Python and C++. The simulations were in-silico evolution of hypothetical gene circuits that potentially admit oscillatory dynamics. The aim of the study, which was invited to be submitted to a special issue "Timekeeping, noise and development across kingdoms" in the journal iScience, is to demonstrate that in contrast to common belief, noise in gene expression dynamics could significantly facilitate the evolutionary process for searching oscillatory dynamics, which are essential for developing circadian rhythm in living organisms.
Lin, Yen Ting↗
MIDAS-DC-AC Tool: Fully Automating the Acquisition of AC Power Flow Solution (MIDAS-DC2AC)
MIDAS DC2AC is an automated tool for achieving a converged AC power flow solution from any dispatch, e.g., determined using DC power flow model based optimal power flow. The entire process is free of human interference. It is usually encountered in practice that, even with a DC power flow solution, acquiring the solved AC power flow solution, if exists, sometimes could be a challenging task, especially during the planning stage. It is also difficult to distinguish the unsolvable cases from diverging iterations. Manual adjustments to approach the desired power flow condition has been largely relied on in the past using lots of engineering heuristics. This tool provides a systematic way to first achieve a solvable AC power flow case by modifying the power flow condition, and then try to track the AC power flow solution while gradually removing the adopted changes. If all adopted changes can be completely removed, then the original AC power flow solution is obtained. Otherwise, insights for actionable controls are derived to help operation and planning. Currently, this tool has been implemented in Python using SIEMENS PTI PSS/E as power flow solver, where only adjusting generator terminal voltage set point is considered as an available means to try to turn an unsolved power flow to a solved one. In future, more means should be considered, including the operation of tap-changing transformers, switched shunts and redispatch of active power.
Tan, Jin↗
LAVA
We introduce LAVA, a general-purpose python toolkit to provide user-friendly and high throughput calculations for material properties using both LAMMPS and VASP. It contains a set of classes as well as pre-processing and post-processing functions to prepare, execute and extract information from LAMMPS/VASP simulations. An overview of the program structure is provided. The current version contains modules to calculate elastic and mechanical properties such as lattice constant, cohesive energy, cold curve, elastic constants, bulk and shear modulus, volume conserving/non-conserving deformation path, vacancy/interstitial formation energy, surface energy, stacking fault energy, melting point, radial distribution function, and thermal expansion.
Dang, Khanh↗
ML4PD (Machine Learning for High Throughput Process Design) [SWR-22-62]
ML4PD is a code base developed to use machine learning(ML)-based modular process units that can be combined to create whole process models. The package is developed within python and leverages tensorflow for the ML components.
Wilson, Nolan↗
ornladios/ADIOS2
ADIOS 2: The Adaptable Input Output (I/O) System version 2 is an open-source framework that addresses scientific data management challenges, e.g. scalable parallel I/O, as we approach the exascale era in high-performance computing (HPC). ADIOS 2 bindings are available in C++, C, Fortran, Python and can be used on supercomputers, personal computers, and cloud systems running on Linux, macOS and Windows. ADIOS 2 has out-of-the-box support for MPI and serial environments.
ECP↗
GridDS: Data Science Toolkit for Energy Grid Data
According to the U.S. Energy Information Administration (EIA), the demand for energy is expected to increase 50% by the year 20501. While energy standards, such as the Institute of Electrical and Electronics Engineers (IEEE) Standard 1547, (Basso 2015) and monitoring with wide area management systems (WAMS) (Liu 2017, Zhou 2016) have enabled large scale data collection and storage, the application of this data in mitigating costs associated with increased consumer demand is an ongoing focus for energy research. This ubiquitous data collection presents a promising opportunity for machine learning and data science to improve efficiency of distributed energy resources (DERs). The GridDS software toolkit is designed to leverage advanced metering infrastructure (AMI), outage management systems data (OMS), Supervisory control Data Acquisition (SCADA), and geographic information systems (GIS) to forecast future energy demands and detect incipient grid failures. GridDS is a python software library designed to be modular and generalizable to data recorded by DERs. In adapting to disparate datasets recorded by various WAMS, GridDS provides a range of unique functionality not presently implemented in current WAMS which have highly specific software infrastructure by design. GridDS functionality ranges from data specification and preparation, to training and validation for state of the art machine learning, to interactive data visualization. For data intake, GridDS combines: Pandera: a library for creating data specifications. TimeScaleDB: a postgresSQL database infrastructure for efficient storage of timeseries data. Dataset class: A custom dataset class / interface that ensures modularity between a range of synthetic and live recorded datasets. Is
Ladd, Alexander↗
dfdjaxGP
A small python package to fit Gaussian processes using Jax and leveraging the automatic differentiation in Jax to predict arbitrary derivatives from the GP. This package is meant to supplement the scientific community use of Gaussian process prediction with derivatives. The package is designed to smoothly work standalone or be used with the numpyro probabilistic programming language.
Grosskopf, Micheal↗
NISQ Benchmarking
Test suite of quantum algorithms for Noisy Intermediate Scale Quantum (NISQ) computers. The test suite includes benchmark-style code for quantum volume circuits (QV), fairness sampling circuits, quantum telecloning circuits, and other NISQ benchmark style algorithms on small problems (i.e., up to 100 qubits), such as Variational Quantum Eigensolver (VQE), Hamiltonian Simulation, and Grover unstructured search example circuits. These benchmark-style applications are implemented in quantum software packages, mostly IBM's QISKIT, but may include vendor-specific frameworks, such as PyQuil (for Rigetti) or Q\# for Microsoft, or CirQ (for Google) as the test suite grows with the vendor sample. The test suite also includes numerical simulation code for Quantum Alternating Operator Ansatz (QAOA) algorithms, VQE, Hamiltonian Simulation and search examples. Numerical simulation code simulates quantum computers on classical computers, which is only possible for small problem instances; the implementation framework of choice is typically within Python, using the numpy/scipy libraries as well as extensions to the Julia language.
Pelofske, Elijah↗
VICTOR-GS (Validation of Integrated Charging and TranspORtation infrastructure for Grid at Scale) [SWR-22-04]
VICTOR-GS is a site modeling and validation tool capable of assessing the performance benefits of different charging strategies for fleet depots. The model is written in OpenDSS and executed using a wrapper in Python. Outputs from the model include voltage distortion, current distortion, total harmonic distortion, flicker, and more.
Moniot, Matthew↗