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Introducing GPU Acceleration into the Python-Based Simulations of Chemistry Framework
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.
AlabOS: a Python-based reconfigurable workflow management framework for autonomous laboratories
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.
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.
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.
python package for dark matter scattering in dielectric targets
Not Available
reciprocalspaceship: a Python library for crystallographic data analysis
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PyPhase – a Python package for X-ray phase imaging
X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).
Strym: A Python Package for Real-time CAN Data Logging, Analysis and Visualization to Work with USB-CAN Interface
In this report, we describe a data analysis tool developed for decoding and analyzing vehicle data obtained from a passenger vehicle’s onboard controller area network (CAN) bus. The tool developed in this paper provides a timeseries framework to perform domain-specific analysis at scale when interpreting data from a vehicle or a collection of vehicles in light of how to design intelligent vehicle applications. The tool, called Strym, exploits the CAN bus mechanism of modern vehicles to capture data using commercially available CAN-to-USB hardware Comma.ai Panda devices, managed through open-source software Libpanda. Strym permits the decoding of vendor-specific CAN messages in a vehicle-agnostic manner. Through this, a researcher can characterize data throughput, assess data quality, and perform analyses. Such analyses are useful in a number of research such as studying human driving behavior in mixed-autonomy, new driver models, rare-event detection, traffic flow estimation, and custom control of vehicles.
Panel Segmentation: A Python Package for Automated Solar Array Metadata Extraction Using Satellite Imagery
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Bridging Python to Silicon: The SODA Toolchain
Systems performing scientific computing, data analysis, and machine learning tasks have a growing demand for application-specific accelerators that can provide high computational performance while meeting strict size and power requirements. However, the algorithms and applications that need to be accelerated are evolving at a rate that is incompatible with manual design processes based on hardware description languages. Agile hardware design tools based on compiler techniques can help by quickly producing an application-specific integrated circuit (ASIC) accelerator starting from a high-level algorithmic description. Here, we present the software-defined accelerator (SODA) synthesizer, a modular and open-source hardware compiler that provides automated end-to-end synthesis from high-level software frameworks to ASIC implementation, relying on multilevel representations to progressively lower and optimize the input code. Our approach does not require the application developer to write any register-transfer level code, and it is able to reach up to 364 giga floating point operations per second (GFLOPS)/W efficiency (32-bit precision) on typical convolutional neural network operators.
Practical implementations of speckle-based phase-retrieval methods in Python and GPU for tomography
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Time Domain Moment Tensor Inversion in Python
MTtime is a software tool developed for time domain inversion of complete seismic waveform data to obtain the seismic moment tensor. It supports both deviatoric and full moment tensor inversions as well as 1-D and 3-D basis Green's functions.
HyPerPy (Hydrogen Extraction and Parabolic Trough Plant Performance Models using Python) [SWR-21-53]
The HyPerPy package consists of three scripts: 1) Model for Hydrogen Tracking in Parabolic Trough Power Plants, 2) Model for Receiver Performance, and 3) Model for Hydrogen Extraction Process. The power plant model (1) tracks hydrogen generation and transport within the circulating heat transfer fluid (HTF) of the power plant. This script is a transient, initial value simulation, in which the hydrogen concentration in the circulating HTF is 0 moles per cubic meter everywhere at time 0 seconds. Hydrogen concentration is calculated at discrete locations within the circulating HTF with 4-second time resolution. During each time step, the change in hydrogen concentration due to hydrogen generation and permeation is calculated for each location according to the local HTF temperature, vessel or piping properties, hydrogen concentration and partial pressure. This model predicts hourly hydrogen concentrations for typical operating days in the spring, summer, fall, and winter seasons. Data is used to create hourly mappings of hydrogen concentrations for a typical operating year. The receiver model (2) uses a 1-hour time step to estimate getter loading and annulus pressure. For each time step, the model uses HTF and ambient temperature data to estimate absorber tube, bellows, and getter temperatures for the time step. In addition, the model uses hourly HTF hydrogen concentrations that are generated by the power plant model (1), and annulus hydrogen pressure from the previous time step. With these data, the model calculates the moles of hydrogen permeating across the absorber tube and bellows during the time step. The net change in moles hydrogen is added or subtracted from the getter loading for the previous time step, and the hydrogen pressure is re-calculated based on getter loading and temperature. The model uses this algorithm to simulate hydrogen permeation and loading 24 hours per day, 365 days per year using seasonal temperature data. The model repeats these calculations for 25 years to create a mapping of receiver getter loading and annulus hydrogen pressure for four seasons of each year. The model for hydrogen extraction (3) estimates hydrogen extraction rates for a specific separation module configuration. The rate depends primarily on membrane area, vacuum pump performance, headspace gas flowrate to the membrane, and headspace gas hydrogen partial pressure. This model has two versions. The steady-state version predicts hydrogen extraction rates when the module is operating in separation mode. The dynamic version predicts hydrogen transfer through the membrane when the module is operating in sensor mode. The steady-state version is used with the plant model (1) to predict hydrogen partial pressures in the power plant when the extraction process is operating.
PyChargeModel (Oriented Programming Based Electric Vehicle and Electric Vehicle Supply Equipment Charging Model in Python) [SWR-22-39]
The PyChargeModel creates two classes called "ElectricVehicles" and "evse_class", which can be used to create multiple instances of electric vehicles (EVs) and electric vehicle supply equipment (EVSE or charging ports) and simulate charging behavior. These objects can be instantiated with several properties such as battery chemistries, battery pack sizes, cell sizes, charging port power, dc or ac chargers etc. The objects can communicate with each other by calling different methods built within the classes. Through these methods, each EV object can be assigned to an EVSE, charged either using a default protocol or using setpoint values communicated from a site controller via the EVSE object.
SDynPy: A Structural Dynamics Python Library
SAND2023-11957O SDynPy software can be used in digital signal processing, modal analysis, and geometry algorithms that are available in open literature, specifically the Synthesize Modes and Correlate and polynomial-based multiple reference modal fitters. This software can be used to perform structural dynamic testing and analysis. 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.
pytank (Python Thermal Tank Model) [SWR-22-76]
Thermal tank model that accounts for phase change of the tank medium.