The Pencil Code, a modular MPI code for partial differential equations and particles

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained - Published in JOSS (2021)

https://github.com/pencil-code/pencil-code

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • Academic publication links
  • Committers with academic emails
    74 of 284 committers (26.1%) from academic institutions
  • Institutional organization owner
  • JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Mathematics Computer Science - 63% confidence
Last synced: 6 months ago · JSON representation

Repository

A high-order finite-difference code for compressible hydrodynamic flows with magnetic fields and particles

Basic Info
Statistics
  • Stars: 211
  • Watchers: 93
  • Forks: 103
  • Open Issues: 0
  • Releases: 5
Created almost 11 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

The Pencil Code

The Pencil Code is a high-order finite-difference code for compressible hydrodynamic flows with magnetic fields and particles. It is highly modular and can easily be adapted to different types of problems. The code runs efficiently under MPI on massively parallel shared- or distributed-memory computers.

The Pencil Code is available from pencil-code.org and is mirrored to GitHub. It was previously hosted at Google Code.

In order to checkout the code with read-write premissions Subversion, use the command sh svn checkout https://pencil-code.org/svn/trunk pencil-code --username=<your-username> where <your-username> is your GitHub username that you should use identically to register on account.pencil-code.org for write access to the code repository.

For read-only access via SVN, a username is not required: sh svn checkout https://pencil-code.org/svn/trunk pencil-code

To get started, run one of the samples: sh unix> cd pencil-code unix> source sourceme.sh unix> cd samples/conv-slab unix> mkdir data To set up the symbolic links and compile the code: sh unix> pc_setupsrc unix> pc_build [ -f /path/to/config/file.conf ] To create the initial condition and run the code: sh unix> pc_start [ -f /path/to/config/file.conf ] unix> pc_run [ -f /path/to/config/file.conf ]

See pencil-code/config/hosts/*/*.conf for sample config files. For more details, see the manual in the doc/ directory (also available here).


If you are using bash and you do not want to "source sourceme.sh" on each session, you can insert the following into your .bashrc and/or .bashprofile: ```sh export PENCILHOME=$HOME/pencil-code [or wherever you have the code] sourcemequiet=1; . $PENCILHOME/sourceme.sh; unset _sourcemequiet ```

Documentation

List of Contributors

  • Around 100 people have contributed to various extent during the nearly 20 years of Pencil Code history.
  • The current list of contributors shows the temporal check-in activity of the those who stayed connected with the code over the various host changes (Nordita 2001-2007, Google Code 2007-2015, and Github since 2015). Some additional contributors are also listed in the manual.

How to contribute to the Pencil Code

  • For all changes to the code, make sure the auto-test still runs

  • If you have write access: check in your changes and make sure you can fix possible problems emerging on travis-ci.com as well as the minutely, hourly, and daily auto-tests.

  • If you have only read access: fork this repository and use pull requests to contribute.

Code of Conduct

License

Owner

  • Name: Pencil Code
  • Login: pencil-code
  • Kind: organization

JOSS Publication

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained
Published
February 21, 2021
Volume 6, Issue 58, Page 2807
Authors
The Pencil Code Collaboration
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Axel Brandenburg ORCID
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden, Department of Astronomy, Stockholm University, Sweden, McWilliams Center for Cosmology & Department of Physics, Carnegie Mellon University, PA, USA
Anders Johansen ORCID
GLOBE Institute, University of Copenhagen, Denmark
Philippe A. Bourdin ORCID
Space Research Institute, Graz, Austria, Institute of Physics, University of Graz, Graz, Austria
Wolfgang Dobler
Bruker, Potsdam, Germany
Wladimir Lyra ORCID
New Mexico State University, Department of Astronomy, Las Cruces, NM, USA
Matthias Rheinhardt
Astroinformatics, Department of Computer Science, Aalto University, Finland
Sven Bingert ORCID
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen, Germany
Nils Erland L. Haugen ORCID
SINTEF Energy Research, Trondheim, Norway, Norwegian University of Science and Technology, Norway, Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Antony Mee
Bank of America Merrill Lynch, London, UK
Frederick Gent ORCID
Astroinformatics, Department of Computer Science, Aalto University, Finland, School of Mathematics, Statistics and Physics, Newcastle University, UK
Natalia Babkovskaia
No current affiliation
Chao-Chin Yang ORCID
University of Nevada, Las Vegas, USA
Tobias Heinemann ORCID
Niels Bohr International Academy, Denmark
Boris Dintrans
CINES, Montpellier, France
Dhrubaditya Mitra ORCID
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Simon Candelaresi ORCID
School of Mathematics and Statistics, University of Glasgow, UK
Jörn Warnecke ORCID
Max Planck Institute for Solar System Research, Germany
Petri J. Käpylä ORCID
Institute for Astrophysics, University of Göttinge, Germany
Andreas Schreiber
No current affiliation
Piyali Chatterjee ORCID
Indian Institute of Astrophysics, Bengaluru, India
Maarit J. Käpylä ORCID
Astroinformatics, Department of Computer Science, Aalto University, Finland, Max Planck Institute for Solar System Research, Germany
Xiang-Yu Li ORCID
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Jonas Krüger ORCID
SINTEF Energy Research, Trondheim, Norway, Norwegian University of Science and Technology, Norway
Jørgen R. Aarnes ORCID
Norwegian University of Science and Technology, Norway
Graeme R. Sarson ORCID
School of Mathematics, Statistics and Physics, Newcastle University, UK
Jeffrey S. Oishi ORCID
Department of Physics & Astronomy, Bates College, ME, USA
Jennifer Schober ORCID
Laboratoire d'Astrophysique, EPFL, Sauverny, Switzerland
Raphaël Plasson ORCID
Avignon Université, France
Christer Sandin ORCID
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Ewa Karchniwy ORCID
Norwegian University of Science and Technology, Norway, Institute of Thermal Technology, Silesian University of Technology, Poland
Luiz Felippe S. Rodrigues ORCID
School of Mathematics, Statistics and Physics, Newcastle University, UK, Radboud University, Netherlands
Alexander Hubbard
Department of Astrophysics, American Museum of Natural History, NY, USA
Gustavo Guerrero ORCID
Physics Department, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
Andrew Snodin
School of Mathematics, Statistics and Physics, Newcastle University, UK
Illa R. Losada ORCID
Nordita, KTH Royal Institute of Technology and Stockholm University, Sweden
Johannes Pekkilä ORCID
Astroinformatics, Department of Computer Science, Aalto University, Finland
Chengeng Qian ORCID
State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, China
Editor
Arfon Smith ORCID
Tags
Fortran90 fluid dynamics magnetohydrodynamics IDL astrophysics radiation inertial particles combustion

GitHub Events

Total
  • Create event: 4
  • Commit comment event: 23
  • Issues event: 5
  • Watch event: 22
  • Delete event: 5
  • Issue comment event: 13
  • Push event: 1,041
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 3
  • Fork event: 6
Last Year
  • Create event: 4
  • Commit comment event: 23
  • Issues event: 5
  • Watch event: 22
  • Delete event: 5
  • Issue comment event: 13
  • Push event: 1,043
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 3
  • Fork event: 6

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 39,937
  • Total Committers: 284
  • Avg Commits per committer: 140.623
  • Development Distribution Score (DDS): 0.854
Past Year
  • Commits: 1,921
  • Committers: 50
  • Avg Commits per committer: 38.42
  • Development Distribution Score (DDS): 0.797
Top Committers
Name Email Commits
Axel Brandenburg b****b@n****g 5,842
Philippe Bourdin g****t@B****h 4,133
mrheinhardt m****t@n****g 3,705
Anders Johansen a****s@a****e 3,654
Wolfgang Dobler w****r@g****m 2,901
Wladimir Lyra w****a@g****m 2,665
Sven Bingert s****t@g****e 1,991
Chao-Chin Yang c****g@a****e 1,546
Frederick Gent f****l@g****m 1,467
Antony J. Mee e****a@g****m 846
Natalia Babkovskaia n****a@g****m 813
Kishore Gopalakrishnan k****6@g****m 796
Nils Erland L. Haugen n****u@n****o 787
Tobias Heinemann t****n@g****m 778
Boris Dintrans b****s@i****u 678
Iomsn i****1@g****m 622
Dhrubaditya Mitra d****a@g****m 563
Jörn Warnecke j****e@g****m 480
Nils Erland L. Haugen n****n@g****m 376
Hongzhe Zhou z****2@g****m 374
Matthias Rheinhardt m****t@a****i 363
ToxPuro t****o@a****i 328
Petri Käpylä p****a@a****i 313
andreas-schreiber a****8@g****m 240
Xiangyu LI x****y@g****m 206
Piyali Chatterjee m****i@g****m 199
Jonas Krueger j****r@g****m 169
Jørgen R. Aarnes j****s@n****o 167
alexrichert a****7@p****u 129
Petri Käpylä p****l@u****e 125
and 254 more...
Committer Domains (Top 20 + Academic)
aalto.fi: 8 mycompany.com: 7 helsinki.fi: 5 puhti-login1.bullx: 5 nordita.org: 4 puhti-login11.bullx: 3 puhti-login2.bullx: 3 ncl.ac.uk: 3 astro.lu.se: 3 service1.vilje.hpc.ntnu.no: 3 uni-graz.at: 2 helios2.mps.mpg.de: 2 andrew.cmu.edu: 2 astro.columbia.edu: 2 service0.vilje.hpc.ntnu.no: 2 mahti-login11.mahti.csc.fi: 2 nordita.dk: 2 aip.de: 2 login3.stampede2.tacc.utexas.edu: 2 mahti-login15.mahti.csc.fi: 2 draco03.mpcdf.mpg.de: 2 newcastle.ac.uk: 2 mps.mpg.de: 2 ntnu.no: 2 uni-goettingen.de: 1 qmul.ac.uk: 1 mail.uni-oldenburg.de: 1 impact1.csl.illinois.edu: 1 isaac2.bc.rzg.mpg.de: 1 psu.edu: 1 login2.polaris.leeds.ac.uk: 1 sisu-login5.csc.fi: 1 kth.se: 1 yale.edu: 1 pas.rochester.edu: 1 isaac1.bc.rzg.mpg.de: 1 my.csun.edu: 1 hs.uni-hamburg.de: 1 stud.ntnu.no: 1 glasgow.ac.uk: 1 zju.edu.cn: 1 physics.ucla.edu: 1 colorado.edu: 1 univ-avignon.fr: 1 unige.ch: 1 nmsu.edu: 1 durham.ac.uk: 1 login1.hsn.dardel.pdc.kth.se: 1 m005.opa.vera.psc.edu: 1 login03.jncasr.ac.in: 1 draco04.mpcdf.mpg.de: 1 manchester.ac.uk: 1 login1.stampede.tacc.utexas.edu: 1 comet-ln3.sdsc.edu: 1 hs.uni-harmburg.de: 1 n135-p66.eduroam.kth.se: 1 draco01.mpcdf.mpg.de: 1 iis.u-tokyo.ac.jp: 1 sisu-login3.csc.fi: 1 iiap.ac.in: 1 epfl.ch: 1 n176-p186.eduroam.kth.se: 1 n181-p239.eduroam.kth.se: 1 warnecke-tme7.pc.linmpi.mpg.de: 1 gate.tiara.sinica.edu.tw: 1 draco02.mpcdf.mpg.de: 1 beskow-login2.pdc.kth.se: 1 login4.stampede3.tacc.utexas.edu: 1 astro.uni-bonn.de: 1 login1.stampede2.tacc.utexas.edu: 1 nasa.gov: 1 jpl.nasa.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 35
  • Total pull requests: 17
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 10 months
  • Total issue authors: 23
  • Total pull request authors: 12
  • Average comments per issue: 4.37
  • Average comments per pull request: 2.59
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 3
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 4 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 7.0
  • Average comments per pull request: 7.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • WangYijun2022 (4)
  • himakarganti (4)
  • zingale (4)
  • andreas-schreiber (2)
  • nishkpph (2)
  • kedarbhide (2)
  • migueldvb (1)
  • alexrichert (1)
  • iomsn (1)
  • WenyinWei (1)
  • augustfly (1)
  • HarryMichal (1)
  • alvin-garcia (1)
  • toddmmendenhall (1)
  • mppiyali (1)
Pull Request Authors
  • tobson (3)
  • betsyhern (3)
  • hosseinahmd1995 (2)
  • Kishore96in (2)
  • ssriv98 (2)
  • IvanYashchuk (2)
  • yangdns (1)
  • luoyh15 (1)
  • ToxPuro (1)
  • mviviani (1)
  • luizfelippesr (1)
  • WenyinWei (1)
Top Labels
Issue Labels
help wanted (1)
Pull Request Labels

Dependencies

doc/readthedocs/requirements.txt pypi
  • Cython >=0.29.23
  • GitPython *
  • astropy >=4.0
  • dill >=0.3.3
  • eqtools >=1.3.1
  • h5py >=2.10.0
  • matplotlib >=3.1.2
  • numpy >=1.17.4
  • pexpect >=4.8.0
  • plotly >=4.4.1
  • retrying >=1.3.3
  • scipy >=1.3.3
  • sphinx-fortran *
  • sphinxcontrib.images *
  • tqdm >=4.60.0
  • vtk >=9.0.1
python/docs/requirements.txt pypi
  • Cython ==0.29.23
  • astropy ==4.0
  • dill ==0.3.3
  • eqtools ==1.3.1
  • h5py ==2.10.0
  • matplotlib ==3.1.2
  • numpy ==1.17.4
  • pexpect ==4.8.0
  • plotly ==4.4.1
  • retrying ==1.3.3
  • scipy ==1.3.3
  • tqdm ==4.60.0
  • vtk ==9.0.1
python/pencil/requirements.txt pypi
  • Cython ==0.29.23
  • astropy ==4.0
  • dill ==0.3.3
  • eqtools ==1.3.1
  • h5py ==2.10.0
  • matplotlib ==3.1.2
  • mpi4py ==3.0.3
  • numpy ==1.17.4
  • pen ==0.1.0a4
  • pencil ==0.7
  • pexpect ==4.8.0
  • plotly ==4.4.1
  • retrying ==1.3.3
  • scipy ==1.3.3
  • tqdm ==4.60.0
  • vtk ==9.0.1