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Merge pull request #39 from MineralsCloud/feature/type
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Deprecate the multiple-type-parameter EOS
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@singularitti
singularitti authored Oct 10, 2019
2 parents add6dc6 + 6b8c53b commit 4752766
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182 changes: 110 additions & 72 deletions src/Collections.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@ julia>
module Collections

using InteractiveUtils
using Unitful: AbstractQuantity, @u_str, Dimension, Dimensions
using Unitful: AbstractQuantity, @u_str, Dimension, Dimensions, upreferred
import Unitful

using EquationsOfState
using EquationsOfState: EnergyForm, PressureForm, BulkModulusForm

export apply,
EquationOfState,
Expand All @@ -35,18 +35,18 @@ export apply,
# Types #
# ============================================================================ #
"""
EquationOfState
EquationOfState{T}
An abstraction of equations of state, where `T` specifies the elements' type.
"""
abstract type EquationOfState end
abstract type EquationOfState{T} end

"""
FiniteStrainEquationOfState <: EquationOfState
FiniteStrainEquationOfState{T} <: EquationOfState{T}
An abstraction of finite strain equations of state.
"""
abstract type FiniteStrainEquationOfState <: EquationOfState end
abstract type FiniteStrainEquationOfState{T} <: EquationOfState{T} end

"""
Murnaghan(v0, b0, bp0, e0=0)
Expand All @@ -59,15 +59,19 @@ Create a Murnaghan equation of state. The elements' type will be handled automat
- `bp0`: the first-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct Murnaghan{A,B,C,D} <: EquationOfState
v0::A
b0::B
bp0::C
e0::D
struct Murnaghan{T} <: EquationOfState{T}
v0::T
b0::T
bp0::T
e0::T
end
function Murnaghan(v0, b0, bp0, e0)
T = Base.promote_typeof(v0, b0, bp0, e0)
return Murnaghan{T}(convert.(T, [v0, b0, bp0, e0])...)
end
Murnaghan(v0::Real, b0::Real, bp0::Real) = Murnaghan(v0, b0, bp0, 0)
Murnaghan(v0::AbstractQuantity, b0::AbstractQuantity, bp0::AbstractQuantity) =
Murnaghan(v0, b0, bp0, 0 * u"eV")
Murnaghan(v0::AbstractQuantity, b0::AbstractQuantity, bp0) =
Murnaghan(v0, b0, bp0, 0 * upreferred(Unitful.J))

"""
BirchMurnaghan2nd(v0, b0, e0=0)
Expand All @@ -79,14 +83,18 @@ Create a Birch–Murnaghan 2nd order equation of state. The elements' type will
- `b0`: the bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct BirchMurnaghan2nd{A,B,C} <: FiniteStrainEquationOfState
v0::A
b0::B
e0::C
struct BirchMurnaghan2nd{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
e0::T
end
function BirchMurnaghan2nd(v0, b0, e0)
T = Base.promote_typeof(v0, b0, e0)
return BirchMurnaghan2nd{T}(convert.(T, [v0, b0, e0])...)
end
BirchMurnaghan2nd(v0::Real, b0::Real) = BirchMurnaghan2nd(v0, b0, 0)
BirchMurnaghan2nd(v0::AbstractQuantity, b0::AbstractQuantity) =
BirchMurnaghan2nd(v0, b0, 0 * u"eV")
BirchMurnaghan2nd(v0, b0, 0 * upreferred(Unitful.J))

"""
BirchMurnaghan3rd(v0, b0, bp0, e0=0)
Expand All @@ -99,15 +107,19 @@ Create a Birch–Murnaghan 3rd order equation of state. The elements' type will
- `bp0`: the first-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct BirchMurnaghan3rd{A,B,C,D} <: FiniteStrainEquationOfState
v0::A
b0::B
bp0::C
e0::D
struct BirchMurnaghan3rd{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
bp0::T
e0::T
end
function BirchMurnaghan3rd(v0, b0, bp0, e0)
T = Base.promote_typeof(v0, b0, bp0, e0)
return BirchMurnaghan3rd{T}(convert.(T, [v0, b0, bp0, e0])...)
end
BirchMurnaghan3rd(v0::Real, b0::Real, bp0::Real) = BirchMurnaghan3rd(v0, b0, bp0, 0)
BirchMurnaghan3rd(v0::AbstractQuantity, b0::AbstractQuantity, bp0::AbstractQuantity) =
BirchMurnaghan3rd(v0, b0, bp0, 0 * u"eV")
BirchMurnaghan3rd(v0::AbstractQuantity, b0::AbstractQuantity, bp0) =
BirchMurnaghan3rd(v0, b0, bp0, 0 * upreferred(Unitful.J))

"""
BirchMurnaghan4th(v0, b0, bp0, bpp0, e0=0)
Expand All @@ -121,21 +133,25 @@ Create a Birch–Murnaghan 4th order equation of state. The elements' type will
- `bpp0`: the second-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct BirchMurnaghan4th{A,B,C,D,E} <: FiniteStrainEquationOfState
v0::A
b0::B
bp0::C
bpp0::D
e0::E
struct BirchMurnaghan4th{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
bp0::T
bpp0::T
e0::T
end
function BirchMurnaghan4th(v0, b0, bp0, bpp0, e0)
T = Base.promote_typeof(v0, b0, bp0, bpp0, e0)
return BirchMurnaghan4th{T}(convert.(T, [v0, b0, bp0, bpp0, e0])...)
end
BirchMurnaghan4th(v0::Real, b0::Real, bp0::Real, bpp0::Real) =
BirchMurnaghan4th(v0, b0, bp0, bpp0, 0)
BirchMurnaghan4th(
v0::AbstractQuantity,
b0::AbstractQuantity,
bp0::AbstractQuantity,
bp0,
bpp0::AbstractQuantity,
) = BirchMurnaghan4th(v0, b0, bp0, bpp0, 0 * u"eV")
) = BirchMurnaghan4th(v0, b0, bp0, bpp0, 0 * upreferred(Unitful.J))

"""
PoirierTarantola2nd(v0, b0, e0=0)
Expand All @@ -147,14 +163,18 @@ Create a Poirier–Tarantola order equation of state. The elements' type will be
- `b0`: the bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct PoirierTarantola2nd{A,B,C} <: FiniteStrainEquationOfState
v0::A
b0::B
e0::C
struct PoirierTarantola2nd{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
e0::T
end
function PoirierTarantola2nd(v0, b0, e0)
T = Base.promote_typeof(v0, b0, e0)
return PoirierTarantola2nd{T}(convert.(T, [v0, b0, e0])...)
end
PoirierTarantola2nd(v0::Real, b0::Real) = PoirierTarantola2nd(v0, b0, 0)
PoirierTarantola2nd(v0::AbstractQuantity, b0::AbstractQuantity) =
PoirierTarantola2nd(v0, b0, 0 * u"eV")
PoirierTarantola2nd(v0, b0, 0 * upreferred(Unitful.J))

"""
PoirierTarantola3rd(v0, b0, bp0, e0=0)
Expand All @@ -167,15 +187,19 @@ Create a Poirier–Tarantola 3rd order equation of state. The elements' type wil
- `bp0`: the first-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct PoirierTarantola3rd{A,B,C,D} <: FiniteStrainEquationOfState
v0::A
b0::B
bp0::C
e0::D
struct PoirierTarantola3rd{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
bp0::T
e0::T
end
function PoirierTarantola3rd(v0, b0, bp0, e0)
T = Base.promote_typeof(v0, b0, bp0, e0)
return PoirierTarantola3rd{T}(convert.(T, [v0, b0, bp0, e0])...)
end
PoirierTarantola3rd(v0::Real, b0::Real, bp0::Real) = PoirierTarantola3rd(v0, b0, bp0, 0)
PoirierTarantola3rd(v0::AbstractQuantity, b0::AbstractQuantity, bp0::AbstractQuantity) =
PoirierTarantola3rd(v0, b0, bp0, 0 * u"eV")
PoirierTarantola3rd(v0::AbstractQuantity, b0::AbstractQuantity, bp0) =
PoirierTarantola3rd(v0, b0, bp0, 0 * upreferred(Unitful.J))

"""
PoirierTarantola4th(v0, b0, bp0, bpp0, e0=0)
Expand All @@ -189,21 +213,25 @@ Create a Birch–Murnaghan 4th order equation of state. The elements' type will
- `bpp0`: the second-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct PoirierTarantola4th{A,B,C,D,E} <: FiniteStrainEquationOfState
v0::A
b0::B
bp0::C
bpp0::D
e0::E
struct PoirierTarantola4th{T} <: FiniteStrainEquationOfState{T}
v0::T
b0::T
bp0::T
bpp0::T
e0::T
end
function PoirierTarantola4th(v0, b0, bp0, bpp0, e0)
T = Base.promote_typeof(v0, b0, bp0, bpp0, e0)
return PoirierTarantola4th{T}(convert.(T, [v0, b0, bp0, bpp0, e0])...)
end
PoirierTarantola4th(v0::Real, b0::Real, bp0::Real, bpp0::Real) =
PoirierTarantola4th(v0, b0, bp0, bpp0, 0)
PoirierTarantola4th(
v0::AbstractQuantity,
b0::AbstractQuantity,
bp0::AbstractQuantity,
bp0,
bpp0::AbstractQuantity,
) = PoirierTarantola4th(v0, b0, bp0, bpp0, 0 * u"eV")
) = PoirierTarantola4th(v0, b0, bp0, bpp0, 0 * upreferred(Unitful.J))

"""
Vinet(v0, b0, bp0, e0=0)
Expand All @@ -216,29 +244,41 @@ Create a Vinet equation of state. The elements' type will be handled automatical
- `bp0`: the first-order pressure-derivative bulk modulus of solid at zero pressure.
- `e0=0`: the energy of solid at zero pressure. By default is `0`.
"""
struct Vinet{A,B,C,D} <: EquationOfState
v0::A
b0::B
bp0::C
e0::D
struct Vinet{T} <: EquationOfState{T}
v0::T
b0::T
bp0::T
e0::T
end
function Vinet(v0, b0, bp0, e0)
T = Base.promote_typeof(v0, b0, bp0, e0)
return Vinet{T}(convert.(T, [v0, b0, bp0, e0])...)
end
Vinet(v0::Real, b0::Real, bp0::Real) = Vinet(v0, b0, bp0, 0)
Vinet(v0::AbstractQuantity, b0::AbstractQuantity, bp0::AbstractQuantity) =
Vinet(v0, b0, bp0, 0 * u"eV")
Vinet(v0::AbstractQuantity, b0::AbstractQuantity, bp0) =
Vinet(v0, b0, bp0, 0 * upreferred(Unitful.J))

struct AntonSchmidt{A,B,C,D} <: EquationOfState
v0::A
β::B
n::C
e∞::D
struct AntonSchmidt{T} <: EquationOfState{T}
v0::T
β::T
n::T
e∞::T
end
function AntonSchmidt(v0, β, n, e∞)
T = Base.promote_typeof(v0, β, n, e∞)
return AntonSchmidt{T}(convert.(T, [v0, β, n, e∞])...)
end
AntonSchmidt(v0::Real, β::Real, n::Real) = AntonSchmidt(v0, β, n, 0)

struct BreenanStacey{A,B,C,D} <: EquationOfState
v0::A
b0::B
γ0::C
e0::D
struct BreenanStacey{T} <: EquationOfState{T}
v0::T
b0::T
γ0::T
e0::T
end
function BreenanStacey(v0, b0, γ0, e0)
T = Base.promote_typeof(v0, b0, γ0, e0)
return BreenanStacey{T}(convert.(T, [v0, b0, γ0, e0])...)
end
BreenanStacey(v0::Real, b0::Real, γ0::Real) = BreenanStacey(v0, b0, γ0, 0)
# =================================== Types ================================== #
Expand Down Expand Up @@ -662,8 +702,6 @@ end
# This is a helper function and should not be exported.
fieldvalues(eos::EquationOfState) = [getfield(eos, i) for i in 1:nfields(eos)]

Base.eltype(T::Type{<:EquationOfState}) = promote_type(T.types...)

Unitful.upreferred(::Dimensions{(
Dimension{:Length}(2 // 1),
Dimension{:Mass}(1 // 1),
Expand Down
36 changes: 8 additions & 28 deletions src/NonlinearFitting.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,14 +20,6 @@ using ..Collections

export lsqfit

# This idea is borrowed from [SimpleTraits.jl](https://github.com/mauro3/SimpleTraits.jl/blob/master/src/SimpleTraits.jl).
abstract type Trait end
abstract type Not{T<:Trait} <: Trait end
struct HasUnit <: Trait end

_unit_trait(T::Type{<:Real}) = Not{HasUnit}
_unit_trait(T::Type{<:AbstractQuantity}) = HasUnit

"""
lsqfit(form, eos, xdata, ydata; debug = false, kwargs...)
Expand All @@ -43,24 +35,13 @@ Fit an equation of state using least-squares fitting method (with the Levenberg-
"""
function lsqfit(
form::EquationForm,
eos::EquationOfState,
xdata::AbstractVector,
ydata::AbstractVector;
kwargs...,
)
T = promote_type(eltype(eos), eltype(xdata), eltype(ydata))
return lsqfit(_unit_trait(T), form, eos, xdata, ydata, kwargs...)
end # function lsqfit
function lsqfit(
::Type{Not{HasUnit}},
form::EquationForm,
eos::EquationOfState,
xdata::AbstractVector,
ydata::AbstractVector;
eos::EquationOfState{<:Real},
xdata::AbstractVector{<:Real},
ydata::AbstractVector{<:Real};
debug = false,
kwargs...,
)
T = promote_type(eltype(eos), eltype(xdata), eltype(ydata), Float64)
T = promote_type(eltype(xdata), eltype(ydata), Float64)
E = constructorof(typeof(eos))
model = (x, p) -> map(apply(form, E(p...)), x)
fitted = curve_fit(
Expand All @@ -73,18 +54,17 @@ function lsqfit(
return debug ? fitted : E(fitted.param...)
end # function lsqfit
function lsqfit(
::Type{HasUnit},
form::EquationForm,
eos::EquationOfState,
xdata::AbstractVector,
ydata::AbstractVector;
eos::EquationOfState{<:AbstractQuantity},
xdata::AbstractVector{<:AbstractQuantity},
ydata::AbstractVector{<:AbstractQuantity};
kwargs...,
)
E = constructorof(typeof(eos))
values = Collections.fieldvalues(eos)
original_units = map(unit, values)
trial_params, xdata, ydata = [map(ustrip ∘ upreferred, x) for x in (values, xdata, ydata)]
result = lsqfit(form, E(trial_params...), xdata, ydata, kwargs...)
result = lsqfit(form, E(trial_params...), xdata, ydata; kwargs...)
if result isa EquationOfState
data = Collections.fieldvalues(result)
return E(
Expand Down
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