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Quantum Workflows in Python (QWiP) is a framework for running experiments with superconducting qubit devices. To get started using this library follow the installation instructions below, and then check out the User Guide.(https://qnl-internal.berkeley.edu/QWiP/user-guide/)
Project Overview and Goal: Create a Python Toolkit for UQ (PyTUQ) to facilitate the interoperability of FASTMath UQ tools (Dakota, UQTk, KLPC), as well as other ASCR funded capabilities for UQ workflows.
Orchestrating the execution of ensembles of processes lies at the core of scientific workflow engines on large scale parallel platforms. This is usually handled using platform-specific command line tools, with limited process management control and potential strain on system resources. The PMIx standard provides a uniform interface to system resources. The low level C implementation of PMIx has hampered its use in workflow engines, leading to the development of Python binding that has yet to gain traction. In this paper, we present our work to harden the PMIx Python client, demonstrating its usability using a prototype Python driver to orchestrate the execution of an ensemble of processes. We present experimental results using the prototype on the Summit supercomputer at Oak Ridge National Laboratory. This work lays the foundation for wider adoption of PMIx for workflow engines, and encourages wider support of more PMIx functionality in vendor provided system software stacks.
Analysis of advanced controls and novel system types is often not directly feasible in building energy simulation tools. Various techniques extend building energy simulation tool capabilities to allow the use of user-defined scripts and programs, but these approaches have limitations. The EnergyPlus Python plugin offers users new flexibility to use EnergyPlus to call an external Python module at specific points in the simulation, as well as to use Python to call EnergyPlus functionality through an application programming interface (API). This paper presents four case studies leveraging the EnergyPlus Python plugin to facilitate analysis of advanced controls and system types. The use of the Python plugin offers greater modularity and flexibility relative to previous approaches, is less error prone, and is simpler for users to adopt. The Python plugin allows EnergyPlus to be used in a more flexible manner and to accommodate the expanding realm of energy modeling applications.
This dataset supports hydrologic modeling and stream network expansion–contraction analysis for the East Fork Poplar Creek (EFPC) Watershed in Tennessee. It includes a Jupyter notebook for model setup, model configuration files, simulation outputs, and derived products used to evaluate model performance and investigate stream dynamics under varying hydrologic conditions. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations using a stream-aligned mesh. Outputs include high-resolution time series of streamflow, active network length, water table depth, and related hydrologic variables. Also included are spatially explicit stream persistency indices and classifications of reaches as perennial or non-perennial. These data facilitate reproducibility and support further research on stream intermittency and variability in network extent.The model data archive is organized in following directories:1) model_setup_inputsContains the Watershed Workflow Jupyter notebooks (accessed through any open source code editor), selected input datasets, and resulting ATS input files, including XML files (access through any open source code editor), computational mesh (.exo files can be viewed using Paraview), and meteorological forcing files (.h5 files can be accessed through h5py python package and HDFView open source software). 2) model_outputsIncludes ATS simulation outputs relevant to this study. Time series of spatially integrated or averaged variables (e.g., streamflow, water table depth) are provided as CSV files. Select spatial fields (e.g., ponded depth and water table depth) are saved as pickled Python objects to reduce file size, and can be accessed through pickle package in Python. Key geometry objects from Watershed Workflow—such as the surface mesh and river tree—are also included to support analysis of streamflow persistency and expansion–contraction dynamics. These files can also be accessed through Watershed Workflow Python package.3) model_evaluationProvides observed streamflow time series and field survey-based flow regime classifications used to evaluate model performance. Jupyter notebooks for processing ATS outputs and comparing model predictions with observations to build confidence in the model prior to scientific analysis are also included.4) Q_L_relationshipsContains workflows for generating time series of discharge, active network length, and related hydrologic variables used in the stream network expansion–contraction analysis. Includes routines for delineating baseflow-dominated periods. For each catchment, notebooks and processed data (as pickled DataFrames accessed through Pandas Python package) are provided. 5) figure_scriptsProvides the Jupyter notebooks used to generate the figures presented in the paper.
Abstract We develop an open-source python workflow package, py GWBSE to perform automated first-principles calculations within the GW-BSE (Bethe-Salpeter) framework. GW-BSE is a many body perturbation theory based approach to explore the quasiparticle (QP) and excitonic properties of materials. GW approximation accurately predicts bandgaps of materials by overcoming the bandgap underestimation issue of the more widely used density functional theory (DFT). BSE formalism produces absorption spectra directly comparable with experimental observations. py GWBSE package achieves complete automation of the entire multi-step GW-BSE computation, including the convergence tests of several parameters that are crucial for the accuracy of these calculations. py GWBSE is integrated with Wannier90 , to generate QP bandstructures, interpolated using the maximally-localized wannier functions. py GWBSE also enables the automated creation of databases of metadata and data, including QP and excitonic properties, which can be extremely useful for future material discovery studies in the field of ultra-wide bandgap semiconductors, electronics, photovoltaics, and photocatalysis.
The Neighborhood Adaptive Tissues for Urban Resilience Futures tool (NATURF) is a Python workflow that generates les readable by the Weather Research and Forecasting (WRF) model. The NATURF Python modules use shapefiles containing building footprint and height data as input to calculate 132 building parameters at any resolution and converts the parameters into a binary file format.
This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.
ML-AMD is a Python workflow framework designed to accelerate the discovery and design of functional materials.
This dataset supports infrastructure-aware hydrologic modeling and flood scenario analysis for the Alligator Bayou Watershed, a highly managed urban watershed in Southeast Texas. It includes Jupyter notebooks for figure reproduction, model configuration files, simulation outputs, and derived products used to quantify the influence of engineered stormwater infrastructure on flood behavior across multiple spatial scales. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations on a channel-aligned mesh with explicit representations of pump stations, gate structures, detention basins, and impervious surfaces. Outputs include time series of gate and pump flows, stage observations, and water balance components, as well as spatially explicit fields of peak ponded depth and flood duration across multiple infrastructure scenarios spanning a single-location detention basin expansion, distributed drainage limitations, and compound coastal flooding. These data facilitate full reproducibility of the manuscript figures and support further research on urban flood dynamics and the role of stormwater infrastructure in shaping watershed-scale flood response.
The Neighborhood Adaptive Tissues for Urban Resilience Futures tool (NATURF) is a Python workflow that generates files readable by the Weather Research and Forecasting (WRF) model. NATURF uses geopandas and hamilton to calculate 132 building parameters from shapefiles with building footprint and height information. These parameters can be collected and used in many formats, and the primary output is a binary file configured for input to WRF. This workflow is a flexible adaptation of the National/World Urban Database and Access Portal Tool (NUDAPT/WUDAPT) that can be used with any study area at any spatial resolution. The climate modeling community and urban planners can identify the effects of building/neighborhood morphology on the microclimate using the urban parameters and WRF-readable files produced by NATURF. More information on the urban parameters calculated can be found in the documentation.
Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.
Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.
Cosmic Microwave Background (CMB) experiments study faint radiation left over from the early universe. The CMB was created when the universe became cool enough for light to travel freely through space, and today it gives scientists one of the earliest images of the universe. One important goal of modern CMB experiments is to measure this radiation with higher precision in order to search for evidence that supports the theory of cosmic inflation. To do this, scientists use extremely sensitive detectors that must be calibrated accurately. The Frequency Selectable Laser Source, or FLS, is a new calibration tool that can send selected frequencies to detectors and help measure their response. During my internship, I worked on the FLS after it returned to Fermilab from Chile, where it had been used to characterize detectors at the Simons Observatory. The system came back in parts, so the first part of my project was helping rebuild the optical and mechanical setup. After the system was rebuilt, we performed alignments to maximize the receiver photocurrent. We then collected calibration measurements over different frequency ranges, including 543 GHz to 568 GHz, 740 GHz to 766 GHz, and 60 GHz to 500 GHz. These measurements were used to check waterline calibration and reflectivity features and compare new data with previous data. Another major part of my project was learning Python so I could understand previous analysis code, modify it for new files, and write my own code to compare the mean response between datasets. The results showed that the new data was close to previous measurements and that waterline features near 556 GHz and 752 GHz were found within less than 1.5 GHz of the expected values. I also completed the reflectivity analysis for five prisms in two polarization orientations. In the original orientation, the results were consistent between the five prisms and close to values measured on a different system at the University of Chicago. I then collected a second set of measurements on my own with the polarization of the laser rotated by 90 degrees and compared them with the original data using the same Python workflow. The measured reflectivity increased for all five prisms in the new orientation, showing that the prism reflectivity depends on polarization. Future work will focus on using the FLS to characterize real CMB detectors.
AlabOS is a workflow orchestration framework designed to address the increased complexity in autonomous laboratories, featuring a reconfigurable experiment workflow model and a resource reservation mechanism.
This repository contains analysis workflows, associated python packages, and documentation of the Whole Energy Homes study. A reproducible Snakemake workflow for data processing, feature extraction, and modeling using the weh python package. Built with Copier from the able-workflow-copier template.
Academic quantum computing platforms often face unique challenges in executing quantum workloads due to fragmented software environments and limited engineering support. Unlike commercial ecosystems, academic devices typically evolve without full-stack integration in mind, making it difficult to run complex applications—such as variational quantum algorithms (VQA)—reliably and efficiently. Issues such as incompatible software layers and lack of automated job management significantly increase the overhead of theory-experiment collaboration. To address these challenges, we develop a modular, end-to-end workflow that decouples application-layer code from low-level hardware control, automates circuit submission and result collection, and supports fine-grained circuit-level job scheduling and recovery. The architecture employs a dual-end application programming interface (API) design, enabling robust operation across unstable or resource-constrained hardware backends. For practical use, the framework is lightweight and user-friendly, allowing rapid prototyping of full-stack workflows using basic Python tools. We validate this workflow on a high-fidelity trapped-ion quantum computer by demonstrating a variational quantum eigensolver (VQE) experiment with a classically bootstrapped ansatz initialization technique. The system successfully executed over 60,000 circuits across multiple molecular test cases with minimal human intervention, highlighting the framework’s effectiveness in enabling reproducible, resilient quantum experimentation in academic settings.
Abstract. Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales.