tkemmer / cunessie.jl

CUDA-accelerated Nonlocal Electrostatics in Structured Solvents

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

This package version requires Julia 1.8 or above. In the Julia shell, switch to the Pkg shell by pressing ] and enter the following command:

pkg> add https://github.com/tkemmer/NESSie.jl
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:

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:

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.