SpiDy.jl
SpiDy.jl: open-source Julia package for the study of non-Markovian stochastic dynamics - Published in JOSS (2024)
Science Score: 93.0%
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Published in Journal of Open Source Software
Keywords
Repository
:spider: Non-Markovian stochastic SPIn (and harmonic oscillator) DYnamics.
Basic Info
Statistics
- Stars: 14
- Watchers: 2
- Forks: 2
- Open Issues: 2
- Releases: 8
Topics
Metadata Files
README.md
SpiDy.jl
(It is pronounced "spee-dee" 😊)
SpiDy.jl is a Julia package that solves the non-Markovian stochastic dynamics of interacting classical spin vectors and harmonic oscillator networks in contact with a dissipative environment. The methods implemented allow the user to include arbitrary memory effects and colored quantum noise spectra. In this way, SpiDy.jl provides key tools for the simulation of classical and quantum open systems including non-Markovian effects and arbitrarily strong coupling to the environment. Among the wide range of applications, some examples range from atomistic spin dynamics to ultrafast magnetism and the study of anisotropic materials. We provide the user with Julia notebooks to guide them through the various mathematical methods and help them quickly set up complex simulations.
Reference paper
This is the reference paper for a quick overview. You might also want to cite it in case it is useful!
JOSS publication -> https://joss.theoj.org/papers/10.21105/joss.06263
arXiv preprint -> https://arxiv.org/abs/2310.03008
Bibtex citation
```tex @article{Scali2024, doi = {10.21105/joss.06263}, url = {https://doi.org/10.21105/joss.06263}, year = {2024}, publisher = {The Open Journal}, volume = {9}, number = {97}, pages = {6263}, author = {Stefano Scali and Simon Horsley and Janet Anders and Federico Cerisola}, title = {SpiDy.jl: open-source Julia package for the study of non-Markovian stochastic dynamics}, journal = {Journal of Open Source Software} } ```Online documentation
Check the online documentation at this link.
Install Julia
If you are new to Julia, here is how to install it.
If you are a Windows/Mac user, download Julia here and run the installer. On Mac, drag-and-drop the app to the Applications.
If you are a Linux user, just open a terminal and use your package manager, e.g. on Debian-based distros run "sudo apt-get install julia", on RedHat-based distros run "sudo dnf install julia".
Install SpiDy
Start Julia and enter in Pkg REPL mode by pressing ] then run the following,
Julia
add SpiDy
NB: the entire installation of SpiDy and its dependencies takes about 5 minutes on a bare-bones Julia environment.
Run SpiDy
To run the code, * save rundynamics.jl and <a href=https://raw.githubusercontent.com/quantum-exeter/SpiDy.jl/main/runs/runsteadystate.jl>runsteadystate.jl in your preferred location (open the link -> right click on the page -> save as... should work to save the file) * open the terminal or command line * run the following command, ```Julia julia "path-to-your-file"/rundynamics.jl ``` where "path-to-your-file" is the one where you saved your file. Replace run_dynamics.jl with run_steadystate.jl to run the one of your choice.
This last command will run the code and save plots/datafile of the chosen run. CONGRATS, you have just run SpiDy for the first time!
NB: the code can exploit parallel computation. To do this, run your files as
Julia
julia -t 6 "path-to-your-file"/run_dynamics.jl
where you want to replace "6" with the number of threads that you wish to use. As a general idea, you do not want to use more than 80% of the number of threads you have available in your machine, e.g. if you have a 4-core CPU, you are likely to have 8 threads and you may want to run the parallelization as indicated above.
Repo structure
- .github/workflows: contains the yml file to build the documentation and commit on the gh-pages branch
- docs: contains the logos, make.jl and index.md for the generation of documentation
- runs: contains run_*.jl files which can be used as a template to run the code
- src: contains the source code
- starthere: contains an ipynb notebook written in Julia which walks you through bits and pieces of the code with explanatory plots (the notebook is evolving over time but always ready to use)
Owner
- Name: Quantum Exeter
- Login: quantum-exeter
- Kind: organization
- Location: United Kingdom
- Website: http://www.quantum-exeter.co.uk
- Repositories: 2
- Profile: https://github.com/quantum-exeter
Quantum Non-equilibrium group at the University of Exeter
JOSS Publication
SpiDy.jl: open-source Julia package for the study of non-Markovian stochastic dynamics
Authors
Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom
Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom
Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom, Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom, Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
Editor
Matthew Feickert
Tags
spin-boson model harmonic oscillator stochastic field non-Markovian memory colored noise anisotropic coupling magnetismGitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stefano Scali | s****o@g****m | 209 |
| Federico Cerisola | f****o@c****t | 99 |
| CompatHelper Julia | c****y@j****g | 10 |
| Hogg | c****g@m****m | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 10
- Total pull requests: 19
- Average time to close issues: 18 days
- Average time to close pull requests: about 6 hours
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 1.7
- Average comments per pull request: 0.05
- Merged pull requests: 19
- Bot issues: 0
- Bot pull requests: 10
Past Year
- Issues: 0
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 0.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- cerisola (4)
- matthewfeickert (2)
- mekise (1)
- mdavezac (1)
- github-actions[bot] (1)
- JuliaTagBot (1)
Pull Request Authors
- github-actions[bot] (10)
- quantum-charlie (7)
- cerisola (6)
- mekise (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
juliahub.com: SpiDy
:spider: Non-Markovian stochastic SPIn (and harmonic oscillator) DYnamics.
- Documentation: https://docs.juliahub.com/General/SpiDy/stable/
- License: GPL-3.0
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Latest release: 1.3.0
published over 1 year ago
Rankings
Dependencies
- actions/checkout v2 composite
- julia-actions/setup-julia v1 composite