JuliaMolSim / Molly.jl

Molecular simulation in Julia
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Add `LennardJonesSoftCore` and `CoulombSoftCore` #89

Closed JaydevSR closed 1 year ago

JaydevSR commented 1 year ago

This PR adds soft core version of the Lennard jones and Coulomb pairwise interactions following the expressions in Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529−539.

codecov[bot] commented 1 year ago

Codecov Report

Merging #89 (48cc4a3) into master (5c72eef) will decrease coverage by 0.17%. The diff coverage is 62.61%.

@@            Coverage Diff             @@
##           master      #89      +/-   ##
==========================================
- Coverage   83.89%   83.71%   -0.18%     
==========================================
  Files          31       31              
  Lines        3489     3678     +189     
==========================================
+ Hits         2927     3079     +152     
- Misses        562      599      +37     
Impacted Files Coverage Δ
src/interactions/lennard_jones.jl 81.19% <62.06%> (-18.81%) :arrow_down:
src/interactions/coulomb.jl 70.21% <63.26%> (-7.57%) :arrow_down:
src/neighbors.jl 89.87% <0.00%> (-2.08%) :arrow_down:
src/energy.jl 94.93% <0.00%> (-0.84%) :arrow_down:
src/simulators.jl 95.95% <0.00%> (-0.65%) :arrow_down:
src/types.jl 74.58% <0.00%> (-0.42%) :arrow_down:
src/gradients.jl 71.73% <0.00%> (-0.14%) :arrow_down:
src/makie.jl 0.00% <0.00%> (ø)
src/spatial.jl 75.36% <0.00%> (ø)
src/setup.jl 93.27% <0.00%> (+0.08%) :arrow_up:
... and 5 more

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JaydevSR commented 1 year ago

In the added tests, the values which are being tested against were explicitly calculated for the particular case of $\alpha=1$, $\lambda=0.5$ and $p=2$ using the formula by me. So I think this address all the comments.

jgreener64 commented 1 year ago

:tada: