cunessie.jl
CUDA-accelerated Nonlocal Electrostatics in Structured Solvents
Science Score: 57.0%
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CUDA-accelerated Nonlocal Electrostatics in Structured Solvents
Basic Info
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- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 3
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Metadata Files
README.md
CUDA-accelerated Nonlocal Electrostatics
CuNESSie.jl is an extension to the NESSie.jl package, providing CUDA-accelerated drop-in replacements for the package's numerical solvers and post-processors.
Installation
In the Julia shell, switch to the
Pkg shell by pressing ] and enter the following command:
sh
pkg> add https://github.com/tkemmer/CuNESSie.jl
Usage example
The basic usage of this package is the same as for NESSie.jl. Just replace the NESSie.BEM module by CuNESSie in your code and you're ready to go:
```julia using NESSie using CuNESSie # before: NESSie.BEM using NESSie.Format: readoff, readpqr
I. Create model
model = readoff("data/born/na.off") model.charges = readpqr("data/born/na.pqr") model.params.εΩ = 1 # dielectric constant for vacuum model model.params.εΣ = 78 # dielectric constant for water
II. Apply nonlocal solver
bem = solve(NonlocalES, model) # <-- CUDA-accelerated solver
III. Apply postprocessor
val = rfenergy(bem) # <-- CUDA-accelerated post-processor println("Reaction field energy: $val kJ/mol") ```
CuNESSie.jl reuses the system models and solver results from NESSie.jl, so the local and nonlocal BEM solvers as well as the corresponding post-processors from both packages can be interchanged freely.
Testing
CuNESSie.jl provides tests for most of its functions. You can run the test suite with the
following command in the Pkg shell:
sh
pkg> test CuNESSie
Citing
If you use CuNESSie.jl in your research, please cite the following publications:
T. Kemmer, S. Hack, B. Schmidt, A. Hildebrandt. CUDA-accelerated protein electrostatics in linear space. Journal of Computational Science 70 (2023) 102022. https://doi.org/10.1016/j.jocs.2023.102022
T. Kemmer. Space-efficient and exact system representations for the nonlocal protein electrostatics problem. Ph. D. thesis (2021), Johannes Gutenberg University Mainz. Mainz, Germany. https://doi.org/10.25358/openscience-5689
Citation items for BibTeX can be found in CITATION.bib.
Owner
- Name: Thomas Kemmer
- Login: tkemmer
- Kind: user
- Location: Germany
- Company: University of Mainz
- Repositories: 5
- Profile: https://github.com/tkemmer
Computer scientist and Gentoo Linux enthusiast
Citation (CITATION.bib)
@article{cunessie-2023,
author = {Thomas Kemmer and Sebastian Hack and Bertil Schmidt and Andreas Hildebrandt},
title = {CUDA-accelerated protein electrostatics in linear space},
year = {2023},
journal = {Journal of Computational Science},
volume = {70},
pages = {102022},
doi = {https://doi.org/10.1016/j.jocs.2023.102022}
}
@phdthesis{cunessie-2021,
author = {Kemmer, Thomas},
title = {{Space-efficient and exact system representations for the nonlocal protein electrostatics problem}},
year = {2021},
school = {Johannes Gutenberg University Mainz},
address = {Mainz, Germany},
doi = {10.25358/openscience-5689}
}
GitHub Events
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- Delete event: 9
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Last Year
- Delete event: 9
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- Create event: 12
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Thomas Kemmer | t****s@b****e | 180 |
| CompatHelper Julia | c****y@j****g | 4 |
Committer Domains (Top 20 + Academic)
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Last synced: 6 months ago
All Time
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Top Authors
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- github-actions[bot] (4)
- dependabot[bot] (2)
- tkemmer (2)