Added soft-core potentials (Beutler et al. & Gapsys et al.) #222
Conversation
…xamples.md, test/interactions.jl
…MD, reversed lambda scaling in function
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #222 +/- ##
==========================================
+ Coverage 58.43% 58.84% +0.41%
==========================================
Files 42 42
Lines 8223 8296 +73
==========================================
+ Hits 4805 4882 +77
+ Misses 3418 3414 -4 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
src/interactions/lennard_jones.jl
Outdated
| R = inter.α*sqrt(cbrt(((26/7)*(C12/C6)*(1-inter.λ)))) | ||
| invR = 1/R | ||
| if r >= R | ||
| return (((12*C12)/r^13)-((6*C6)/r^7)) |
There was a problem hiding this comment.
To save computation you can set r6 = r^6 then use r6 * r and r6 * r6 * r as appropriate. This also applies elsewhere.
src/types.jl
Outdated
| end | ||
|
|
||
| """ | ||
| Atom_L(; <keyword arguments>) |
There was a problem hiding this comment.
For now don't add this to Molly, as we may decide to have lambda in the main atom type.
src/cutoffs.jl
Outdated
| ShiftedForceCutoff, | ||
| CubicSplineCutoff | ||
| CubicSplineCutoff, | ||
| force_cutoff |
There was a problem hiding this comment.
Don't export, you can access with Molly.force_cutoff or using Molly: force_cutoff.
src/interactions/coulomb.jl
Outdated
| CoulombSoftCoreBeutler(; cutoff, α, λ, use_neighbors, σ_mixing, weight_special, coulomb_const) | ||
| The Coulomb electrostatic interaction between two atoms with a soft core. | ||
| The Coulomb electrostatic interaction between two atoms with a soft core, used for appearing and disappearing of atoms based on the potential described in Beutler et al. 1994 (Chem. Phys. Lett.). |
There was a problem hiding this comment.
Link to the DOI of the paper, like in src/simulators.jl line 358. Also link where it is mentioned in the docs.
2 participants
I have added four functions of which two replace the previous soft-core potentials (LennardJonesSoftCore and CoulombSoftCore).
Important note: These interactions are for appearing and disappearing atoms only, not for transformations between different atoms (e.g. a alchemical transformation from carbon to hydrogen atom).