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MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

Abstract Summary Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment. Availability and implementation This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

Biochemistry & Molecular Biology

ampworks: Battery analysis tools in Python [SWR-25-39]

Ampworks is a collection of tools designed to process experimental battery data with a focus on model-relevant analyses. It currently provides functions for incremental capacity analysis and GITT data processing, helping extract key properties for life and physics-based models (e.g., SPM and P2D). Some tools, like the incremental capacity analysis module, also include graphical user interfaces for ease of use. https://github.com/NREL/ampworks/ https://pypi.org/project/ampworks/

Randall, Corey [National Renewable Energy Laborato

PyTUQ: Python Toolkit for Uncertainty Quantification

SAND2025-03661O PyTUQ is a user-friendly software toolkit designed to help researchers and professionals understand and manage uncertainty in several scientific fields. By providing tools for analyzing how uncertainties affect outcomes, PyTUQ can be applied in areas such as energy production, and biology. Its unique approach allows users to make more informed decisions by assessing risks and improving predictions. Whether you're studying combustion processes or exploring complex biological systems, PyTUQ empowers you to gain deeper insights and enhance the reliability of your results. 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.

SciDAC

EVI-EnSitePy (Electric Vehicle Infrastructure – Energy Estimation and Site Optimization Tool in Python) [EVI-X Modeling Suite] [SWR-25-07]

EVI-EnSitePy is a comprehensive agent-based tool designed for the analysis and design of high-power charging sites, encompassing a wide array of site agents including Electric Vehicles (EVs), chargers, energy storage units (ESS), renewable energy resources (DER), and loads. This versatile tool offers diverse functionalities and a modular modeling approach, allowing detailed configuration of agents based on power ratings, port numbers, energy capacities, demand requirements, charger interfaces, and flexibility to customize the tool for project specific goals. By simulating agent interactions and employing various metrics, EVI-EnSitePy enables the assessment of site performance, exploration of energy management systems (EMS), and implementation of innovative EV charging policies. Utilizing EV charge schedules and arrival states, the tool performs thorough charging site simulations, with outputs consisting of agent and site-level power profiles and statistical metrics. Employing a tree graph structure, EVI-EnSitePy supports nested site structures and power distribution modeling. The tool's ability to generate charging schedules deterministically or via stochastic analysis further enhances its versatility. Through its features and capabilities, EVI-EnSitePy offers a powerful platform for informed decision-making in the realm of high-power charging site design and operation.

Jackson, Derek [National Renewable Energy Laborato

Python STXM Control (pystxmcontrol) v0.1

The software is a complete solution for controlling scanning microscopes. It provides a low level interface to device hardware via drivers, communication and coordination layers for managing scan execution and data acquisition, a graphical interface and scripting interface for user interaction. With optimized hardware drivers and low software overhead this software is 10 times faster than the legacy software it is replacing.

Shapiro, David [Lawrence Berkeley National Laborat

WFSUITE: A PYTHON SOFTWARE SUITE FOR X-RAY WAVEFRONT SENDING AND AT-WAVELENGTH METROLOGY

SF-26-025 WFSuite is a graphical and command-line toolkit for coded-mask-based X-ray wavefront sensing and phase reconstruction at synchrotron beamlines. It integrates analysis tools for both relative and absolute speckle-based measurements. In the relative metrology module, WFSuite implements Wavelet-transform-based X-ray Speckle Tracking (WXST) and Wavelet-transform-based Speckle Vector Tracking (WSVT) methods to retrieve differential phase and wavefront distortions by comparing speckle patterns recorded with and without the test sample. In the absolute phase module, WFSuite uses coded-mask speckle patterns and replaces the measured reference with a numerically simulated one, enablingsingle-shot wavefront reconstruction using either WXST or a neural-network-based method (SPINNet).

Rebuffi, Luca [Argonne National Laboratory (ANL),

wmpy-power: A Python package for process-based regional hydropower simulation

Hydropower is an important source of renewable energy in many parts of the world. The generation potential for a hydropower facility can vary greatly due to fluctuations in precipitation and snowmelt patterns impacting streamflow and reservoir storage. Human activities such as irrigation, manufacturing, and hydration can also influence water availability at nearby and downstream facilities. wmpy-power--the hydropower model described in this work--is process-based, leveraging explicit reservoir storage and release data to address impacts on hydropower from climate change and human adaptive behaviors to inform long-term planning and resource-adequacy considerations.

13 HYDRO ENERGY

DeepHyper: A Python Package for Massively Parallel Hyperparameter Optimization in Machine Learning

Machine learning models are increasingly applied across scientific disciplines, yet their effectiveness often hinges on heuristic decisions—such as data transformations, training strategies, and model architectures—that are not learned by the models themselves. Automating the selection of these heuristics and analyzing their sensitivity is crucial for building robust and efficient learning workflows. DeepHyper addresses this challenge by democratizing hyperparameter optimization, providing accessible tools to streamline and enhance machine learning workflows from a laptop to the largest supercomputer in the world. Building on top of hyperparameter optimization, it unlocks new capabilities around ensembles of models for improved accuracy and uncertainty quantification. All of these organized around efficient parallel computing.

ensemble

SSAPy - Space Situational Awareness for Python

SSAPy is a fast and flexible orbit modeling and analysis tool for orbits spanning from low-Earth into the cislunar regime. Orbits can be flexibly specified from common input formats such as Keplerian elements or two-line element (TLE) data files. SSAPy allows users to model satellites and specify parameters such as satellite area, mass, and drag coefficients. SSAPy includes a customizable force-propagation with a range of Earth, Lunar, radiation, atmospheric, and maneuvering models. SSAPy makes use of various community integration methods and can calculate time-evolved orbital quantities, including satellite magnitudes and state vectors. Users can specify various space- and ground-based observation models with support for multiple coordinate and reference frames. SSAPy also supports orbit analysis and propagation methods such as multiple hypothesis tracking and has built-in uncertainty quantification. The majority of SSAPy’s methods are vectorized and parallelizable, allowing for effective use of high-performance computer (HPC) systems. Finally, SSAPy has plotting functionality, allowing users to visualize orbits and trajectories. Examples are shown in Figure 1 and Figure 2.

97 MATHEMATICS AND COMPUTING

Terra-Populus v0.1: A Python Library for LandScan High-Definition Population Analysis and Modeling

The terra-populus library is designed for use by the LandScan HD technical team, offering a streamlined set of tools for generating and updating LandScan HD datasets from foundational building-level data, referred to as 'molecules,' provided by the building-level attribution team. This document serves as the primary technical documentation for terra-populus. Version 0.1 of the library includes the core modeling components necessary for LandScan HD production. It enables the generation of the LandScan HD Baseline dataset as well as corresponding confidence measures for the occupancy rates used. Parameters have been included for incorporating damaged building indicators and changes in population, to faciliate the creation of rapid updates for LandScan HD. Future iterations of terra-populus will introduce tools for creating a confidence index, and quantifying and propagating uncertainty, facilitating the creation of probabilistic LandScan HD outputs. This report provides an overview of the tools available in the library and the corresponding code implementations. One of the key advancements implemented in terra-populus is a redefinition of the atomic modeling unit for LandScan HD. Traditionally, the LandScan HD vector analytical framework has generated population estimates at the building sub-component (molecule) level. However, terra-populus adopts a building-level modeling approach. This shift is an operational decision aimed at aligning LandScan HD outputs with confidence measures, which are computed and validated at the building level (confidence measures are not included in this version of terra-populus, aside from those associated with the occupancy rates). Additional advancements to the LandScan HD modeling, as implemented by terra-populus, include a minimum population value parameter and an auto assignment of building floor counts. The population minimum value was implemented to prevent buildings and subsequent LandScan HD pixels that contained small values that may not rasterize in production. An 'auto' value has been included as a method for dealing with buildings lacking floor count information, where it is the average floor count of all other buildings with a residential building use type tag. The logic behind this is to remain consistent with the current logic employed for dealing with building use type null instances, where a null use type is defaulted to residential since it is the most common building type. The auto logic is intended to apply the most common building floor count of the most common type of buildings. The tools provided in terra-populus represent a significant step forward in improving the efficiency, reproducibility, and transparency of the LandScan HD modeling process. As the library evolves, it will continue to serve as a foundational resource for high-resolution population modeling.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION