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The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained

A. Brandenburg, A. Johansen, P. A. Bourdin, W. Dobler, W. Lyra, M. Rheinhardt, S. Bingert, N. E. L. Haugen, A. Mee, F. Gent, N. Babkovskaia, C. -C. Yang, T. Heinemann, B. Dintrans, D. Mitra, S. Candelaresi, J. Warnecke, P. J. Käpylä, A. Schreiber, P. Chatterjee, M. J. Käpylä, X. -Y. Li, J. Krüger, J. R. Aarnes, G. R. Sarson, J. S. Oishi, J. Schober, R. Plasson, C. Sandin, E. Karchniwy, L. F. S. Rodrigues, A. Hubbard, G. Guerrero, A. Snodin, I. R. Losada, J. Pekkilä, C. Qian

arXiv:2009.08231v1astro-ph.IMastro-ph.COastro-ph.SRphysics.flu-dyn

TL;DR

The paper concerns adapting simulation software to standard MHD and other equations. It presents the Pencil Code as an adaptable tool with runtime diagnostics and post-processing libraries, and reports 564 acknowledging papers by July 2020.

Abstract

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The Pencil Code is a highly modular physics-oriented simulation code that can be adapted to a wide range of applications. It is primarily designed to solve partial differential equations (PDEs) of compressible hydrodynamics and has lots of add-ons ranging from astrophysical magnetohydrodynamics (MHD) to meteorological cloud microphysics and engineering applications in combustion. Nevertheless, the framework is general and can also be applied to situations not related to hydrodynamics or even PDEs, for example when just the message passing interface or input/output strategies of the code are to be used. The code can also evolve Lagrangian (inertial and noninertial) particles, their coagulation and condensation, as well as their interaction with the fluid.

High-level functionality

The code’s high-level functionality spans many application areas, with examples ranging from cloud microphysics and radiative transfer to combustion and dust-gas dynamics.

High-level functionality

  • Examples include coagulation and condensation, radiative transfer, chiral magnetic effects, gravitational waves, and models of homochirality and photochemical systems.Source: High-level functionality · p. 2
  • The code is also used for gaseous combustion, burning particles, flows around immersed objects, and dust-gas dynamics with mutual drag.Source: High-level functionality · p. 2
  • Other listed applications include turbulent MHD transport, mean-field MHD, spherical-shell dynamos and convection, coronal physics, thermal instability, and temperature solving.Source: High-level functionality · p. 2

Statement of need and purpose of software

The Pencil Code is presented as an adaptable tool for standard MHD and other equations, supported by diagnostics and post-processing libraries. Its development includes automated testing and community structures for user and developer interaction.

Statement of need and purpose of software

  • The code is an easily adaptable tool for standard MHD equations and others, including test-field equations.It provides runtime diagnostics and Python and IDL libraries for post-processing.Source: Statement of need and purpose of… · p. 2
  • Users can access the latest development version and ask to join the developers by contacting one of 18 owners among 83 developers with check-in permission.34 developers have made more than 34 commits.Source: Statement of need and purpose of… · p. 2
  • Every GitHub revision is verified on 9 tests, while the current version is also tested on 59 hourly and 79 daily tests.Source: Statement of need and purpose of… · p. 3
  • Annual user meetings have been promoted since 2004, and newsletters since 2020; since 2016, a steering committee of five elected owners reviews progress and can take decisions of general concern.Source: Statement of need and purpose of… · p. 3

Ongoing research using the Pencil Code

Pencil Code use spans research from stellar physics and the early universe to meteorology and engineering. By July 2020, 564 papers had acknowledged using the code.

Ongoing research using the Pencil Code

Key references

The cited work highlights the Pencil Code’s flexibility and modularity alongside its open, distributed development model. Its applications are illustrated through examples spanning astrophysics, fluid turbulence, particles, and engineering.

Key references

  • The Pencil Code is described as distinctive for its flexibility and modularity, as well as open-source development with distributed ownership.Source: Key references · p. 3
  • Related software includes Athena, CO5BOLD, ENZO, MuRAM, NIRVANA, Stagger, and ZEUS; S3D is identified as a non-open-source engineering DNS code.Source: Key references · p. 3
  • Cited applications include immersed-object flows, particle clustering, cloud microphysics, planet formation, debris disks, and supernova-driven turbulence.Source: Key references · p. 3
  • Further examples include spherical-shell dynamo waves, convection with Kramers opacity, MHD turbulence and cascades, and test-field turbulent-diffusivity studies.Source: Key references · p. 4
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