diff --git a/src/bodies/spheres.jl b/src/bodies/spheres.jl index e0e57a2..4ad2ce0 100644 --- a/src/bodies/spheres.jl +++ b/src/bodies/spheres.jl @@ -3,7 +3,7 @@ export HyperSphere, contact, is_encounter # dispatch hides call to Point HyperSphere(center::SVector{D}, radius::Real) where D = HyperSphere(Point(Float64.(center)), Float64(radius)) -@inline position(a::HyperSphere{D}) where D = SVector{D}(a.center) +@inline Base.position(a::HyperSphere{D}) where D = SVector{D}(a.center) #@inline radius(a::AbstractMicrobe) = a.radius @inline radius(a::HyperSphere) = a.r @inline contact(a,b,model) = distance(a,b,model) ≤ radius(a) + radius(b) diff --git a/src/chemotaxis/brumley.jl b/src/chemotaxis/brumley.jl index 98c94f7..09310b0 100644 --- a/src/chemotaxis/brumley.jl +++ b/src/chemotaxis/brumley.jl @@ -7,7 +7,7 @@ The model is optimized for simulation of marine bacteria and accounts for the presence of (gaussian) sensing noise in the chemotactic pathway. Default parameters: -- `motility = RunReverseFlick(speed_forward = [46.5])` +- `motility = RunReverseFlick(speed = [46.5])` - `turn_rate = 2.22` Hz → '1/τ₀' - `state = 0.0` → 'S' - `rotational_diffusivity = 0.035` rad²/s @@ -19,7 +19,7 @@ Default parameters: """ @agent struct Brumley{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D} speed::Float64 - motility = RunReverseFlick(speed_forward = [46.5]) + motility = RunReverseFlick(speed = [46.5]) turn_rate::Float64 = 1 / 0.45 rotational_diffusivity::Float64 = 0.035 radius::Float64 = 0.5 diff --git a/src/chemotaxis/xie.jl b/src/chemotaxis/xie.jl index b79bdbd..7e817ea 100644 --- a/src/chemotaxis/xie.jl +++ b/src/chemotaxis/xie.jl @@ -14,7 +14,7 @@ tuned through a `chemotactic_precision` factor inspired by 'Brumley et al. (2019) PNAS' (defaults to 0, i.e. no noise). Default parameters: -- `motility = RunReverseFlick(speed_forward = [46.5])` +- `motility = RunReverseFlick(speed = [46.5])` - `turn_rate_forward = 2.3` Hz - `turn_rate_backward = 1.9` Hz - `state = 0.0` s