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Add missing λ-factor in force and potential for LennardJonesSoftCoreBeutler #232

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Merged
jgreener64 merged 4 commits into from
Nov 29, 2025
Merged

Add missing λ-factor in force and potential for LennardJonesSoftCoreBeutler #232

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bc60d0c
added missing λ factor in force and potential for SoftCoreBeutler
Immi000 Nov 26, 2025
51bd1f9
missing λ factor for Coulomb Beutler, updated docstrings
Immi000 Nov 26, 2025
4666161
Adjusted test for CoulombSoftCoreBeutler
Immi000 Nov 26, 2025
3ea323b
lambda for gapsys
Immi000 Nov 29, 2025
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34 changes: 17 additions & 17 deletions src/interactions/coulomb.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -118,15 +118,15 @@ the appearing and disappearing of atoms.
See [Beutler et al. 1994](https://doi.org/10.1016/0009-2614(94)00397-1).
The potential energy is defined as
```math
V(r_{ij}) = \frac{1}{4\pi\epsilon_0} \frac{q_iq_j}{r_Q^{1/6}}
V(r_{ij}) = \lambda\frac{1}{4\pi\epsilon_0} \frac{q_iq_j}{r_Q^{1/6}}
```
and the force on each atom by
```math
\vec{F}_i = \frac{1}{4\pi\epsilon_0} \frac{q_iq_jr_{ij}^5}{r_Q^{7/6}}\frac{\vec{r_{ij}}}{r_{ij}}
\vec{F}_i = \lambda\frac{1}{4\pi\epsilon_0} \frac{q_iq_jr_{ij}^5}{r_Q^{7/6}}\frac{\vec{r_{ij}}}{r_{ij}}
```
where
```math
r_{Q} = (\frac{\alpha(1-\lambda)C^{(12)}}{C^{(6)}})+r_{ij}^6)
r_{Q} = \left(\frac{\alpha(1-\lambda)C^{(12)}}{C^{(6)}}\right)+r_{ij}^6
```
and
```math
Expand Down Expand Up @@ -194,7 +194,7 @@ end
σ6 = inter.σ_mixing(atom_i, atom_j)^6
ϵ = inter.ϵ_mixing(atom_i, atom_j)
C6 = 4 * ϵ * σ6
params = (ke, qi, qj, C6 * σ6, C6, inter.σ6_fac)
params = (ke, qi, qj, C6 * σ6, C6, inter.σ6_fac, inter.λ)

f = force_cutoff(cutoff, inter, r, params)
fdr = (f / r) * dr
Expand All @@ -205,10 +205,10 @@ end
end
end

function pairwise_force(::CoulombSoftCoreBeutler, r, (ke, qi, qj, C12, C6, σ6_fac))
function pairwise_force(::CoulombSoftCoreBeutler, r, (ke, qi, qj, C12, C6, σ6_fac, λ))
r3 = r^3
R = ((σ6_fac*(C12/C6))+(r3*r3))*sqrt(cbrt(((σ6_fac*(C12/C6))+(r3*r3))))
return ke * ((qi*qj)/R) * (r3*r*r)
return λ * ke * ((qi*qj)/R) * (r3*r*r)
end

@inline function potential_energy(inter::CoulombSoftCoreBeutler,
Expand All @@ -225,7 +225,7 @@ end
σ6 = inter.σ_mixing(atom_i, atom_j)^6
ϵ = inter.ϵ_mixing(atom_i, atom_j)
C6 = 4 * ϵ * σ6
params = (ke, qi, qj, C6 *σ6, C6, inter.σ6_fac)
params = (ke, qi, qj, C6 *σ6, C6, inter.σ6_fac, inter.λ)

pe = pe_cutoff(cutoff, inter, r, params)
if special
Expand All @@ -235,9 +235,9 @@ end
end
end

function pairwise_pe(::CoulombSoftCoreBeutler, r, (ke, qi, qj, C12, C6, σ6_fac))
function pairwise_pe(::CoulombSoftCoreBeutler, r, (ke, qi, qj, C12, C6, σ6_fac, λ))
R = sqrt(cbrt((σ6_fac*(C12/C6))+r^6))
return ke * ((qi * qj)/R)
return λ * ke * ((qi * qj)/R)
end

@doc raw"""
Expand Down Expand Up @@ -321,7 +321,7 @@ end
cutoff = inter.cutoff
ke = inter.coulomb_const
qi, qj = atom_i.charge, atom_j.charge
params = (ke, qi, qj, inter.σQ, inter.σ6_fac)
params = (ke, qi, qj, inter.σQ, inter.σ6_fac, inter.λ)

f = force_cutoff(cutoff, inter, r, params)
fdr = (f / r) * dr
Expand All @@ -332,13 +332,13 @@ end
end
end

function pairwise_force(::CoulombSoftCoreGapsys, r, (ke, qi, qj, σQ, σ6_fac))
function pairwise_force(::CoulombSoftCoreGapsys, r, (ke, qi, qj, σQ, σ6_fac, λ))
qij = qi * qj
R = σ6_fac*(oneunit(r)+(σQ*abs(qij)))
if r >= R
return ke * (qij/(r^2))
return λ * ke * (qij/(r^2))
elseif r < R
return ke * (-(((2*qij)/(R^3)) * r) + ((3*qij)/(R^2)))
return λ * ke * (-(((2*qij)/(R^3)) * r) + ((3*qij)/(R^2)))
end
end

Expand All @@ -353,7 +353,7 @@ end
cutoff = inter.cutoff
ke = inter.coulomb_const
qi, qj = atom_i.charge, atom_j.charge
params = (ke, qi, qj, inter.σQ, inter.σ6_fac)
params = (ke, qi, qj, inter.σQ, inter.σ6_fac, inter.λ)

pe = pe_cutoff(cutoff, inter, r, params)
if special
Expand All @@ -363,13 +363,13 @@ end
end
end

function pairwise_pe(::CoulombSoftCoreGapsys, r, (ke, qi, qj, σQ, σ6_fac))
function pairwise_pe(::CoulombSoftCoreGapsys, r, (ke, qi, qj, σQ, σ6_fac, λ))
qij = qi * qj
R = σ6_fac*(oneunit(r)+(σQ*abs(qij)))
if r >= R
return ke * (qij/r)
return λ * ke * (qij/r)
elseif r < R
return ke * (((qij/(R^3))*(r^2))-(((3*qij)/(R^2))*r)+((3*qij)/R))
return λ * ke * (((qij/(R^3))*(r^2))-(((3*qij)/(R^2))*r)+((3*qij)/R))
end
end

Expand Down
34 changes: 17 additions & 17 deletions src/interactions/lennard_jones.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -149,15 +149,15 @@ the appearing and disappearing of atoms.
See [Beutler et al. 1994](https://doi.org/10.1016/0009-2614(94)00397-1).
The potential energy is defined as
```math
V(r_{ij}) = \frac{C^{(12)}}{r_{LJ}^{12}} - \frac{C^{(6)}}{r_{LJ}^{6}}
V(r_{ij}) = \lambda\left(\frac{C^{(12)}}{r_{LJ}^{12}} - \frac{C^{(6)}}{r_{LJ}^{6}}\right
```
and the force on each atom by
```math
\vec{F}_i = ((\frac{12C^{(12)}}{r_{LJ}^{13}} - \frac{6C^{(6)}}{r_{LJ}^7})(\frac{r_{ij}}{r_{LJ}})^5) \frac{\vec{r_{ij}}}{r_{ij}}
\vec{F}_i = \lambda\left(\left(\frac{12C^{(12)}}{r_{LJ}^{13}} - \frac{6C^{(6)}}{r_{LJ}^7}\right)\left(\frac{r_{ij}}{r_{LJ}}\right)^5\right) \frac{\vec{r_{ij}}}{r_{ij}}
```
where
```math
r_{LJ} = (\frac{\alpha(1-\lambda)C^{(12)}}{C^{(6)}}+r^6)^{1/6}
r_{LJ} = \left(\frac{\alpha(1-\lambda)C^{(12)}}{C^{(6)}}+r^6\right)^{1/6}
```
and
```math
Expand Down Expand Up @@ -228,7 +228,7 @@ end
cutoff = inter.cutoff
r = norm(dr)
C6 = 4 * ϵ * σ6
params = (C6 * σ6, C6, inter.σ6_fac)
params = (C6 * σ6, C6, inter.σ6_fac, inter.λ)

f = force_cutoff(cutoff, inter, r, params)
fdr = (f / r) * dr
Expand All @@ -239,10 +239,10 @@ end
end
end

function pairwise_force(::LennardJonesSoftCoreBeutler, r, (C12, C6, σ6_fac))
function pairwise_force(::LennardJonesSoftCoreBeutler, r, (C12, C6, σ6_fac, λ))
R = sqrt(cbrt((σ6_fac*(C12/C6))+r^6))
R6 = R^6
return (((12*C12)/(R6*R6*R)) - ((6*C6)/(R6*R)))*((r/R)^5)
return λ*(((12*C12)/(R6*R6*R)) - ((6*C6)/(R6*R)))*((r/R)^5)
end

@inline function potential_energy(inter::LennardJonesSoftCoreBeutler,
Expand All @@ -261,7 +261,7 @@ end
cutoff = inter.cutoff
r = norm(dr)
C6 = 4 * ϵ * σ6
params = (C6 * σ6, C6, inter.σ6_fac)
params = (C6 * σ6, C6, inter.σ6_fac, inter.λ)

pe = pe_cutoff(cutoff, inter, r, params)
if special
Expand All @@ -271,9 +271,9 @@ end
end
end

function pairwise_pe(::LennardJonesSoftCoreBeutler, r, (C12, C6, σ6_fac))
function pairwise_pe(::LennardJonesSoftCoreBeutler, r, (C12, C6, σ6_fac, λ))
R6 = (σ6_fac*(C12/C6))+r^6
return ((C12/(R6*R6)) - (C6/(R6)))
return λ*((C12/(R6*R6)) - (C6/(R6)))
end

@doc raw"""
Expand Down Expand Up @@ -368,7 +368,7 @@ end
cutoff = inter.cutoff
r = norm(dr)
C6 = 4 * ϵ * σ6
params = (C6 * σ6, C6)
params = (C6 * σ6, C6, inter.λ)

f = force_cutoff(cutoff, inter, r, params)
fdr = (f / r) * dr
Expand All @@ -379,16 +379,16 @@ end
end
end

function pairwise_force(inter::LennardJonesSoftCoreGapsys, r, (C12, C6))
function pairwise_force(inter::LennardJonesSoftCoreGapsys, r, (C12, C6, λ))
R = inter.α*sqrt(cbrt((26*(C12/C6)*(1-inter.λ)/7)))
r6 = r^6
invR = inv(R)
invR2 = invR^2
invR6 = invR^6
if r >= R
return (((12*C12)/(r6*r6*r))-((6*C6)/(r6*r)))
return λ * (((12*C12)/(r6*r6*r))-((6*C6)/(r6*r)))
elseif r < R
return (((-156*C12*(invR6*invR6*invR2)) + (42*C6*(invR2*invR6)))*r +
return λ * (((-156*C12*(invR6*invR6*invR2)) + (42*C6*(invR2*invR6)))*r +
(168*C12*(invR6*invR6*invR)) - (48*C6*(invR6*invR)))
end
end
Expand All @@ -409,7 +409,7 @@ end
cutoff = inter.cutoff
r = norm(dr)
C6 = 4 * ϵ * σ6
params = (C6 * σ6, C6)
params = (C6 * σ6, C6, inter.λ)

pe = pe_cutoff(cutoff, inter, r, params)
if special
Expand All @@ -419,16 +419,16 @@ end
end
end

function pairwise_pe(inter::LennardJonesSoftCoreGapsys, r, (C12, C6))
function pairwise_pe(inter::LennardJonesSoftCoreGapsys, r, (C12, C6, λ))
R = inter.α*sqrt(cbrt((26*(C12/C6)*(1-inter.λ)/7)))
r6 = r^6
invR = inv(R)
invR2 = invR^2
invR6 = invR^6
if r >= R
return (C12/(r6*r6))-(C6/(r6))
return λ * (C12/(r6*r6))-(C6/(r6))
elseif r < R
return ((78*C12*(invR6*invR6*invR2)) - (21*C6*(invR2*invR6)))*(r^2) -
return λ * ((78*C12*(invR6*invR6*invR2)) - (21*C6*(invR2*invR6)))*(r^2) -
((168*C12*(invR6*invR6*invR)) - (48*C6*(invR6*invR)))*r +
(91*C12*(invR6*invR6)) - (28*C6*(invR6))
end
Expand Down
32 changes: 16 additions & 16 deletions test/interactions.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,44 +47,44 @@
inter = LennardJonesSoftCoreBeutler(α=0.3, λ=0.5)
@test isapprox(
force(inter, dr14, a1, a1),
SVector(35.093676538737824, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(17.546838269368916, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-9u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
force(inter, dr13, a1, a1),
SVector(-1.3236594727846438, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(-0.6618297363923222, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-9u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
potential_energy(inter, dr14, a1, a1),
29.629058917654785u"kJ * mol^-1";
14.814529458827394u"kJ * mol^-1";
atol=1e-9u"kJ * mol^-1",
)
@test isapprox(
potential_energy(inter, dr13, a1, a1),
-0.11464014233084913u"kJ * mol^-1";
-0.05732007116542457u"kJ * mol^-1";
atol=1e-9u"kJ * mol^-1",
)

inter = LennardJonesSoftCoreGapsys(α=0.85, λ=0.5)
@test isapprox(
force(inter, dr14, a1, a1),
SVector(516.8457758610879, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(258.42288793054365, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-9u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
force(inter, dr13, a1, a1),
SVector(-1.37550973892212, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(-0.68775486946106, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-9u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
potential_energy(inter, dr14, a1, a1),
51.814929518108826u"kJ * mol^-1";
45.35853723577515u"kJ * mol^-1";
atol=1e-9u"kJ * mol^-1",
)
@test isapprox(
potential_energy(inter, dr13, a1, a1),
-0.1170417308807374u"kJ * mol^-1";
-0.12971227169036878u"kJ * mol^-1";
atol=1e-9u"kJ * mol^-1",
)

Expand Down Expand Up @@ -231,44 +231,44 @@
inter = CoulombSoftCoreBeutler(α=0.3, λ=0.5)
@test isapprox(
force(inter, dr13, a1, a1),
SVector(842.06163558501, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(421.030817792505, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-5u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
force(inter, dr14, a1, a1),
SVector(57.48819886473348, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(28.74409943236674, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-5u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
potential_energy(inter, dr13, a1, a1),
345.81678703197457u"kJ * mol^-1";
172.90839351598729u"kJ * mol^-1";
atol=1e-5u"kJ * mol^-1",
)
@test isapprox(
potential_energy(inter, dr14, a1, a1),
634.3822744723304u"kJ * mol^-1";
317.1911372361652u"kJ * mol^-1";
atol=1e-5u"kJ * mol^-1",
)

inter = CoulombSoftCoreGapsys(α=0.3, λ=0.5, σQ=1u"nm")
@test isapprox(
force(inter, dr13, a1, a1),
SVector(731.0108657043696, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(365.5054328521848, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-5u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
force(inter, dr14, a1, a1),
SVector(1276.8008892849266, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
SVector(638.4004446424633, 0.0, 0.0)u"kJ * mol^-1 * nm^-1";
atol=1e-5u"kJ * mol^-1 * nm^-1",
)
@test isapprox(
potential_energy(inter, dr13, a1, a1),
341.80053925707637u"kJ * mol^-1";
170.90026962853818u"kJ * mol^-1";
atol=1e-5u"kJ * mol^-1",
)
@test isapprox(
potential_energy(inter, dr14, a1, a1),
642.9723025054708u"kJ * mol^-1";
321.4861512527354u"kJ * mol^-1";
atol=1e-5u"kJ * mol^-1",
)

Expand Down
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