https://github.com/unixjunkie/vdw_grid_bench

Van der Waals 3D grid initialization benchmark
https://github.com/unixjunkie/vdw_grid_bench

computational-chemistry high-performance-computing molecular-mechanics ocaml-program van-der-waals

Last synced: about 1 month ago
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Van der Waals 3D grid initialization benchmark

• Host: GitHub
• URL: https://github.com/unixjunkie/vdw_grid_bench
• Owner: UnixJunkie
• License: bsd-3-clause
• Created: 2024-02-22T00:34:55.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-02-26T05:27:17.000Z (9 months ago)
• Last Synced: 2024-02-27T05:35:09.232Z (9 months ago)
• Topics: computational-chemistry, high-performance-computing, molecular-mechanics, ocaml-program, van-der-waals
• Language: OCaml
• Homepage:
• Size: 36.1 KB
• Stars: 4
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# vdW_grid_bench

Van der Waals 3D grid initialization benchmark

# problem statement

We want to know the interaction energy between one

atom [l_a] located at any grid point [i,j,k] and a fixed set of atoms [A].

We use the Van der Waals non-bonded interaction energy and

Universal Force Field (UFF) parameters.

# standard OCaml; before loop modification

time ./grid_init -dx 0.1 -l data/lig.pqrs -p data/prot.pqrs 

real    1m19.899s

# w/ dune's --profile=release

real    1m10.603s

# w/ V3 @@inline annotations plus dist2 optims

real    0m57.384s

# w/ optims in vdW_grid

real    0m49.096s

# w/ pow3 and V3.dist2 instead of pow6 and V3.dist in vdW_grid

real    0m41.282s