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Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number…
We present PySCo, a fast and user-friendly Python library designed to run cosmological $N$-body simulations across various cosmological models, such as $\Lambda$CDM and $w_0w_a$CDM, and alternative theories of gravity, including $f(R)$,…
A fast multigrid solver is presented for high-order accurate Stokes problems discretised by local discontinuous Galerkin (LDG) methods. The multigrid algorithm consists of a simple V-cycle, using an element-wise block Gauss-Seidel smoother.…
pyGDM is a python toolkit for electro-dynamical simulations in nano-optics based on the Green Dyadic Method (GDM). In contrast to most other coupled-dipole codes, pyGDM uses a generalized propagator, which allows to cost-efficiently solve…
Surrogate models are necessary to optimize meaningful quantities in physical dynamics as their recursive numerical resolutions are often prohibitively expensive. It is mainly the case for fluid dynamics and the resolution of Navier-Stokes…
Gaussian Processes (GPs) are flexible, nonparametric Bayesian models widely used for regression and classification because of their ability to capture complex data patterns and quantify predictive uncertainty. However, the O(n^3)…
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
We present diffSPH, a novel open-source differentiable Smoothed Particle Hydrodynamics (SPH) framework developed entirely in PyTorch with GPU acceleration. diffSPH is designed centrally around differentiation to facilitate optimization and…
High-order numerical methods for unstructured grids combine the superior accuracy of high-order spectral or finite difference methods with the geometric flexibility of low-order finite volume or finite element schemes. The Flux…
Strain localization and resulting plasticity and failure play an important role in the evolution of the lithosphere. These phenomena are commonly modeled by Stokes flows with viscoplastic rheologies. The nonlinearities of these rheologies…
Three-dimensional topology optimization (TO) is a powerful technique in engineering design, but readily usable, open-source implementations remain limited within the popular Python scientific environment. This paper introduces PyTopo3D, a…
We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it…
Advancement in recent years in the field of experimental gravitation has allowed to test the equivalence principle in regimes that were previously unexplored, allowing for unprecedented verifications of general relativity and also enabling…
Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density…
GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…
Stokesian Dynamics (SD) is a powerful computational framework for simulating the motion of particles in a viscous Newtonian fluid under Stokes-flow conditions. Traditional SD implementations can be computationally expensive as they rely on…
We develop a linearly-scaling variant of the Force Coupling Method [K. Yeo and M. R. Maxey, J. Fluid Mech. 649, 205-231 (2010)] for computing hydrodynamic interactions among particles confined to a doubly-periodic geometry with either a…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier--Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of…
All major weather and climate applications are currently developed using languages such as Fortran or C++. This is typical in the domain of high performance computing (HPC), where efficient execution is an important concern. Unfortunately,…