Fix CI and rename Temperature to TemperatureSetting

docs/src/NQCModels/combining_models.md

@@ -19,7 +19,7 @@ For example, in order to run [Molecular Dynamics with Electronic friction](@ref
 However, most models for potential energy surfaces only provide `potential` and `derivative`, whereas `friction!` is provided by an `ElectronicFrictionProvider`. 
 
 To combine different models together for a system, we can use [`Subsystem`](@ref)s to define which atoms in the system a given model should be applied to, and a [`CompositeModel`](@ref) to combine the different models into one. 
-If different [`Subsystem`](@ref)s should experience different effective temperatures, a [`Thermostat`](@ref) can be provided when initialising a [`Simulation`](@ref). 
+If different [`Subsystem`](@ref)s should experience different effective temperatures, a [`TemperatureSetting`](@ref) can be provided when initialising a [`Simulation`](@ref). 
 
 ![An overview of the different components used to combine models in NQCModels.jl](../assets/compositemodels/struct-explainer.svg)
 

docs/src/dynamicssimulations/dynamicssimulations.md

@@ -49,7 +49,7 @@ For time-dependent temperatures, the temperature can be set to a function. This
 
 **Different temperatures per atom**
 
-If different parts of the simulated system should be affected by different effective temperatures, a `Vector` of [`Temperature`](@ref)s can be passed as the temperature argument. 
+If different parts of the simulated system should be affected by different effective temperatures, a `Vector` of [`TemperatureSetting`](@ref)s can be passed as the temperature argument. 
 However, only one temperature should be applied to each atom in the system. 
 
 ### DynamicsVariables

docs/src/examples/mdef_multithermostat.md

@@ -181,11 +181,11 @@ combined_model = CompositeModel(
 	phononic_friction
 )
 
-# Create Temperature objects to apply T_el to adsorbates, T_ph to surface
+# Create TemperatureSetting objects to apply T_el to adsorbates, T_ph to surface
 # Manually specified indices
-electron_thermostat = Temperature(T_el_function, indices = [55,56]) 
+electron_thermostat = TemperatureSetting(T_el_function, indices = [55,56]) 
 # Inherit indices from a Subsystem
-phonon_thermostat = Temperature(T_ph_function, phononic_friction) 
+phonon_thermostat = TemperatureSetting(T_ph_function, phononic_friction) 
 
 sim_T_el_only = Simulation{MDEF}(
 	atoms, 

src/NQCDynamics.jl

@@ -18,7 +18,7 @@ export Simulation,
        RingPolymerSimulation,
        natoms,
        masses,
-       Thermostat,
+       TemperatureSetting,
        get_temperature
 
 @reexport using NQCDistributions

src/simulations.jl

@@ -28,12 +28,12 @@ function Simulation(atoms::Atoms{T}, model::Model, method::M;
         temperature=0u"K", cell::AbstractCell=InfiniteCell()) where {M,T}
     calc = Calculator(model, length(atoms), T)
     # If a thermostat is provided, check it covers the whole system. 
-    isa(temperature, Thermostat{Vector{Int}}) ? throw(DomainError(temperature, "Thermostat must apply to all atoms.")) : nothing
-    # If multiple Thermostats are provided, check that each atom only has one thermostat applied to it.
-    if isa(temperature, Vector{<:Thermostat})
+    isa(temperature, TemperatureSetting{Vector{Int}}) ? throw(DomainError(temperature, "TemperatureSetting must apply to all atoms.")) : nothing
+    # If multiple TemperatureSettings are provided, check that each atom only has one thermostat applied to it.
+    if isa(temperature, Vector{<:TemperatureSetting})
         indices = vcat([thermostat.indices for thermostat in temperature]...)
         if length(unique(indices)) != length(atoms.masses)
-            throw(DomainError(temperature, "Every atom must have a Thermostat applied to it."))
+            throw(DomainError(temperature, "Every atom must have a TemperatureSetting applied to it."))
         end
         if length(indices) != length(unique(indices))
             throw(DomainError(temperature, "Atoms can only have one thermostat applied to them."))
@@ -113,7 +113,7 @@ function Base.show(io::IO, sim::RingPolymerSimulation{M}) where {M}
 end
 
 """
-A Temperature contains both temperature information and the atom indices within a Simulation that it is applied to. 
+A TemperatureSetting contains both temperature information and the atom indices within a Simulation that it is applied to. 
 
 **If you don't need to apply different temperatures to different parts of your Simulation, assign the `temperature` keyword argument of your simulation to a number or function.**
 
@@ -124,46 +124,46 @@ A Temperature contains both temperature information and the atom indices within
 `indices`: Indices of the atoms to which this thermostat is applied. Can be a range of indices, a single `Int`, or a `Vector{Int}`.
 
 """
-struct Temperature{I}
+struct TemperatureSetting{I}
     value::Function
     indices::I
 end
 
-function Base.show(io::IO, temperature::Temperature)
-    print(io, "Temperature:\n\tT(t=0) = $(get_temperature(temperature, 0u"fs"))\n\tApplies to atoms: $(temperature.indices)\n")
+function Base.show(io::IO, temperature::TemperatureSetting)
+    print(io, "TemperatureSetting:\n\tT(t=0) = $(get_temperature(temperature, 0u"fs"))\n\tApplies to atoms: $(temperature.indices)\n")
 end
 
-function Temperature(value, indices=:)
+function TemperatureSetting(value, indices=:)
     if isa(indices, UnitRange)
         indices=collect(indices)
     elseif isa(indices, Int)
         indices=[indices]
     end
     if !isa(value, Function)
         temperature_function(t)=value
-        return Temperature(temperature_function, indices)
+        return TemperatureSetting(temperature_function, indices)
     else
-        return Temperature(value, indices)
+        return TemperatureSetting(value, indices)
     end
 end
 
 """
-    Temperature(temperature, subsystem::NQCModels.Subsystem)
+    TemperatureSetting(temperature, subsystem::NQCModels.Subsystem)
 
-Apply a `Temperature` to all atoms in a `Subsystem`. 
+Apply a `TemperatureSetting` to all atoms in a `Subsystem`. 
 """
-function Temperature(temperature, subsystem::NQCModels.Subsystem)
-    Temperature(temperature, subsystem.indices)
+function TemperatureSetting(temperature, subsystem::NQCModels.Subsystem)
+    TemperatureSetting(temperature, subsystem.indices)
 end
 
-get_temperature(thermostat::Temperature{<:Any}, t=0u"fs") = austrip(thermostat.value(t))
+get_temperature(thermostat::TemperatureSetting{<:Any}, t=0u"fs") = austrip(thermostat.value(t))
 
 """
-    get_temperature(thermostats::Vector{<:Temperature}, t=0u"fs")
+    get_temperature(thermostats::Vector{<:TemperatureSetting}, t=0u"fs")
 
-Gets the temperature from multiple `Temperature`s and returns a vector of the temperature applied to each atom. 
+Gets the temperature from multiple `TemperatureSetting`s and returns a vector of the temperature applied to each atom. 
 """
-function get_temperature(thermostats::Vector{<:Temperature}, t=0u"fs")
+function get_temperature(thermostats::Vector{<:TemperatureSetting}, t=0u"fs")
     indices=vcat([thermostat.indices for thermostat in thermostats]...)
     temperature_vector=zeros(Number, length(indices))
     for thermostat in thermostats

test/Core/simulations.jl

@@ -24,17 +24,17 @@ model = NQCModels.Free()
 
 @testset "Thermostats" begin
     # Init thermostat with Unitful quantity
-    thermostat1=Thermostat(10u"K", [1,2])
+    thermostat1=TemperatureSetting(10u"K", [1,2])
     @test NQCDynamics.get_temperature(thermostat1, 0) == NQCDynamics.get_temperature(thermostat1, 100)
     # Init thermostat with function
-    thermostat2=Thermostat(x->(10+x*u"fs^-1")*u"K", [2,3])
+    thermostat2=TemperatureSetting(x->(10+x*u"fs^-1")*u"K", [2,3])
     @test NQCDynamics.get_temperature(thermostat2) == austrip(10u"K")
     @test NQCDynamics.get_temperature(thermostat2, 10u"fs") == austrip(20u"K")
     # Test that thermostats with overlapping indices throw an error
     @test_throws DomainError Simulation(atoms, model; temperature=[thermostat1, thermostat2])
     # Test system size / total thermostat size mismatch
     @test_throws DomainError Simulation(Atoms([:N, :H, :H, :H,]), model; temperature=thermostat1)
-    thermostat3=thermostat2=Thermostat(x->(10+x*u"fs^-1")*u"K", [3,4])
+    thermostat3=thermostat2=TemperatureSetting(x->(10+x*u"fs^-1")*u"K", [3,4])
     # Combined temperature evaluation
     sim = Simulation(Atoms([:N, :H, :H, :H,]), model; temperature=[thermostat1, thermostat3])
     @test NQCDynamics.get_temperature(sim, austrip(1u"fs")) == austrip.([10u"K", 10u"K", 11u"K", 11u"K"])