Search · four archives
Search · four archives
28 papers · ranked by Valyu relevance
Uwe Schmitt, Beatrice Moser, Christiane S. Lorenz, Alexandre Réfrégier
'Alexandre Réfrégier'] Computer algebra systems play an important role in science as they facilitate the development of new theoretical models. The resulting symbolic equations are often implemented in a compiled programming language in order to provide fast and portable codes for practical applications. We describe…
Amina Kammoun, Rim Slama, Hedi Tabia, Tarek Ouni + 1 more
Python has become the de facto language for scientific computing. Programming in Python is highly productive, mainly due to its rich science-oriented software ecosystem built around the NumPy module. As a result, the demand for Python support in High Performance Computing (HPC) has skyrocketed. However, the Python…
Idil Ismail, Shayantan Chaudhuri, Dylan B. Morgan, Christopher D. Woodgate + 4 more
'Christopher D. Woodgate' 'Ziad Fakhoury' 'James M. Targett' 'Charlie Pilgrim' 'Carlo Maino'] This article is intended as a guide for new graduate students in the field of computational science. With the increasing influx of students from diverse backgrounds joining the ever-popular field, this short guide aims to help…
Chansup Byun, William Arcand, David Bestor, Bill Bergeron + 17 more
'Vijay Gadepally' 'Michael E. Houle' 'Matthew Hubbell' 'Hayden Jananthan' 'Michael Jones' 'Kurt Keville' 'Anna Klein' 'Peter Michaleas' 'Lauren Milechin' 'Guillermo Morales' 'Julie Mullen' 'Andrew Prout' 'Albert Reuther' 'Antonio De Rosa' 'Siddharth Samsi' 'Charles Yee' 'Jeremy Kepner'] Abstract—pPython seeks to…
Zeyi Zhang, Carlos Mora Perez, Patrick Kwon, Martin Head‐Gordon + 1 more
PARSEC.py is a Python-based real-space Kohn-Sham density functional theory (real-space KS-DFT) framework designed to provide a user- and developer-friendly platform for first-principles electronic-structure simulations. Discretization on real-space grids eliminates basis-set approximations, while enabling systematic…
Maria Babiuc-Hamilton
This chapter narrates the journey of developing and integrating computing into the physics curriculum through three consecutive courses, each tailored to the learners' level. It starts with the entry-level "Physics Playground in Python" for high school and freshman students with no programming experience, designed in…
Simon Perkins, Jonathan S. Kenyon, Lexy A. L. Andati, Hertzog L. Bester + 2 more
with Dask-MS and Codex Africanus Authors: ['Simon Perkins' 'Jonathan S. Kenyon' 'Lexy A. L. Andati' 'Hertzog L. Bester' 'O. Smirnov' 'B. Hugo'] The physical configuration of new radio interferometers such as MeerKAT, SKA, ngVLA and DSA-2000 informs the development of software in two important areas. Firstly, tractably…
Tuteja, Keshvi, Olenik, Gregor + 12 more
Sparse linear algebra is a cornerstone of many scientific computing and machine learning applications. Python has become a popular choice for these applications due to its simplicity and ease of use. Yet high-performance sparse kernels in Python remain limited in functionality, especially on modern CPU and GPU…
Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk + 1 more
Coupled-Cluster Implementations: A Comparison Between CPUs and GPUs Authors: Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk, Katharina Boguslawski In this work, we benchmark several Python routines for time and memory requirements to identify the optimal choice of the tensor contraction…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Gregor Mönke, Tim Schäfer, Mohsen Parto-Dezfouli, Diljit Singh Kajal + 3 more
We introduce an open-source Python package for the analysis of large-scale electrophysiological data called SyNCoPy, for Systems Neuroscience Computing in Python. The package includes signal processing analyses across time (e.g. time-lock analysis), frequency (e.g. power spectrum), and connectivity (e.g. coherence)…
Gregor Mönke, Tim Schäfer, Mohsen Parto-Dezfouli, Diljit Singh Kajal + 3 more
'Stefan Fürtinger' 'Joscha Tapani Schmiedt' 'Pascal Fries'] We introduce an open-source Python package for the analysis of large-scale electrophysiological data, named SyNCoPy, which stands for Systems Neuroscience Computing in Python. The package includes signal processing analyses across time (e.g., time-lock…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Kacper Derlatka, Maciej Manna, Oleksii Bulenok, David Zwicker + 1 more
'Sylwester Arabas'] The numba-mpi package offers access to the Message Passing Interface (MPI) routines from Python code that uses the Numba just-in-time (JIT) compiler. As a result, high-performance and multi-threaded Python code may utilize MPI communication facilities without leaving the JIT-compiled code blocks…
Chaoming Wang, Sichao He, Shouwei Luo, Yuxiang Huan + 1 more
Artificial intelligence (AI) is revolutionizing scientific research across various disciplines. The foundation of scientific research lies in rigorous scientific computing based on standardized physical units. However, current mainstream high-performance numerical computing libraries for AI generally lack native…
Chaoming Wang, Tianqiu Zhang, Xiaoyu Chen, Sichao He + 4 more
'Si Wu' 'Marcel Stimberg' 'Panayiota Poirazi'] Elucidating the intricate neural mechanisms underlying brain functions requires integrative brain dynamics modeling. To facilitate this process, it is crucial to develop a general-purpose programming framework that allows users to freely define neural models across…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Authors not listed
The field of chemical reaction dynamics has evolved considerably since its inception, driven by advances in computational power and theoretical methodologies. While ab initio molecular dynamics (AIMD) simulations offer high accuracy by computing forces directly from electronic structure theory, its high computational…
Miranda Mundt, William E. Hart, Emma S. Johnson, Bethany Nicholson + 1 more
'John D. Siirola'] Title: Summary Pyomo is an open-source optimization modeling software that has undergone significant evolution since its inception in 2008. Pyomo has evolved to enhance flexibility, solver integration, and community engagement. Modern collaborative tools for open-source software have facilitated the…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
James B. Aimone, Omar Awile, Markus Diesmann, James C. Knight + 2 more
At the turn of the millennium the computational neuroscience community realized that neuroscience was in a software crisis: software development was no longer progressing as expected and reproducibility declined. The International Neuroinformatics Coordinating Facility (INCF) was inaugurated in 2007 as an initiative to…
Jeremy Li, Alex Rubinsteyn, Sergey Feldman, Timothy O’Donnell + 18 more
Scientific computing has become a central component of modern scientific discovery. Yet many computational tools are developed by small, specialized teams under incentives that encourage the release of rapidly prototyped tooling without commensurate attention to engineering concerns, including performance and…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…