Added the force fields necessary for Calvados2 #189
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Signed-off-by: ywitzky <[email protected]>
Codecov ReportAttention: Patch coverage is
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## master #189 +/- ##
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+ Coverage 74.20% 74.49% +0.28%
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Files 36 36
Lines 4943 5038 +95
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+ Hits 3668 3753 +85
- Misses 1275 1285 +10 ☔ View full report in Codecov by Sentry. |
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Looks great. I just merged a major change to master, would you mind rebasing/merging on top of that? It will involve changes to the mixing functions and zero shortcuts, hopefully you can use the changes to |
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I should have done the changes you mentioned. Let me know if i forgot something. |
test/interactions.jl
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| 0.0253410816u"kJ * mol^-1"; | |||
| atol=1e-9u"kJ * mol^-1", | |||
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test/interactions.jl
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| atol=1e-9u"kJ * mol^-1 * nm^-1", | ||
| ) | ||
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| c2 = SVector(1.28, 1.0, 1.0)u"nm" |
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Use c4 and dr14 here to avoid confusion if more tests are added.
src/interactions/lennard_jones.jl
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| @doc raw""" | ||
| AshbaughHatch(; cutoff, α, λ, p, use_neighbors, lorentz_mixing, weight_special, |
src/interactions/lennard_jones.jl
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| σ::S =0.0u"nm" | ||
| ϵ::E =0.0u"kJ * mol^-1" | ||
| λ::L=1.0 | ||
| solute::Bool = false |
| ``` | ||
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| ```math | ||
| V_{\text{AH}}(r_{ij}) = |
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As it stands I think we don't apply the VLJ(rc) term by default? So either remove it in the docstring or add it to the code, in which case probably remove the cutoff option and don't use the cutoff path.
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I removed it to make the implementation more general.
src/interactions/coulomb.jl
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| @doc raw""" | ||
| Yukawa(; cutoff, use_neighbors, weight_special, coulomb_const, force_units, energy_units) |
src/interactions/coulomb.jl
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| use_neighbors::Bool= false | ||
| weight_special::W =1 | ||
| coulomb_const::T = coulomb_const | ||
| kappa::D = kappa=1.0*u"nm^-1" |
src/interactions/coulomb.jl
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| function force_divr(::Yukawa, r2, invr2, (coulomb_const, qi, qj, kappa)) | ||
| r = sqrt(r2) | ||
| return (coulomb_const * qi * qj) / r^3 *exp(-kappa*r) * (kappa*r+1.0) |
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+1 rather than +1.0 to avoid promoting Float32 to Float64.
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I added the remarks in the code and added some tests for the options "special" and "shortcut". |
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Great, thanks. |
Calvados2 is a strongly coarse grained model for intrinsically disordered proteins (IDP) which requires a yukawa potential, an harmonic potential and a modified Lennard Jones potential.