MineralsCloud · singularitti · Apr 13, 2020 · Apr 12, 2020 · Apr 13, 2020 · Apr 13, 2020
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,7 +1,6 @@
 using EquationsOfState
 using Documenter
 
-DocMeta.setdocmeta!(EquationsOfState, :DocTestSetup, :(using EquationsOfState, EquationOfState.Collections, Unitful); recursive=true)
 makedocs(;
     modules=[EquationsOfState],
     authors="Qi Zhang <[email protected]>",

diff --git a/docs/src/Collections.md b/docs/src/Collections.md
@@ -2,6 +2,11 @@
 
 ```@meta
 CurrentModule = EquationsOfState.Collections
+DocTestSetup  = quote
+   using EquationsOfState.Collections
+   using Unitful
+   using UnitfulAtomic
+end
 ```
 
 The current `EquationOfState`s contain
@@ -257,9 +262,12 @@ The $B(V)$ relation of equations of state are listed as below:
    B(V) = \beta\left(\frac{V}{V_{0}}\right)^{n}\left[1+n \ln \frac{V}{V_{0}}\right].
    ```
 
-## Types
+## Public interfaces
 
 ```@docs
+Energy
+Pressure
+BulkModulus
 EquationOfState
 FiniteStrainEquationOfState
 Murnaghan
@@ -271,12 +279,3 @@ PoirierTarantola3rd
 PoirierTarantola4th
 Vinet
 ```
-
-## Public interfaces
-
-```@docs
-(eos::EquationOfState)(eq::EquationForm)
-(f::EquationOfStateOnVolume{<:Murnaghan,EnergyForm})(v)
-(f::EquationOfStateOnVolume{<:Murnaghan,PressureForm})(v)
-(f::EquationOfStateOnVolume{<:BirchMurnaghan2nd,BulkModulusForm})(v)
-```
diff --git a/docs/src/Find.md b/docs/src/Find.md
@@ -9,7 +9,7 @@ approximate volume at a given pressure, energy, or bulk modulus based on an
 equation of state. A result is not always guaranteed, especially when the
 equation of state is not a monotonic function of volume. However, according to
 experience, `P(V)` relation is usually a monotonic function. So we suggest using
-`PressureForm` to find the corresponding volume.
+`Pressure` to find the corresponding volume.
 
 ## Usage
 
@@ -21,7 +21,7 @@ julia> pressures = collect(0:20:200) .* u"GPa";
 julia> eos = BirchMurnaghan3rd(167u"angstrom^3", 2600u"kbar", 4.0);
 
 julia> volumes = map(
-           p -> findvolume(PressureForm(), eos, p, (eps() * u"bohr^3", eos.v0 * 1.3)),
+           p -> findvolume(Pressure(), eos, p, (eps() * u"bohr^3", eos.v0 * 1.3)),
            pressures
        )
 [ Info: Using method "Roots.Bisection"...
@@ -58,8 +58,9 @@ A figure is plotted below to verify our results, and it fits very well.
 
 ## Public interfaces
 
-```@docs
-findvolume(form::EquationForm, eos::EquationOfState, y, x0, method)
+```@autodocs
+Modules = [Find]
+Order   = [:type, :function]
 ```
 
 All available `method`s are the leaves of the tree below (Remember to add a `Roots.` prefix):

diff --git a/docs/src/NonlinearFitting.md b/docs/src/NonlinearFitting.md
@@ -94,25 +94,26 @@ energies = [
     -9.73155247952,
 ];
 
-julia> lsqfit(EnergyForm(), BirchMurnaghan3rd(40, 0.5, 4, 0), volumes, energies)
+julia> lsqfit(Energy(), BirchMurnaghan3rd(40, 0.5, 4, 0), volumes, energies)
 BirchMurnaghan3rd{Float64}(40.989265727925826, 0.5369258245608038, 4.1786442319302015, -10.842803908298968)
 
-julia> lsqfit(EnergyForm(), Murnaghan(41, 0.5, 4, 0), volumes, energies)
+julia> lsqfit(Energy(), Murnaghan(41, 0.5, 4, 0), volumes, energies)
 Murnaghan{Float64}(41.13757924894751, 0.5144967655882123, 3.912386317519504, -10.836794511015869)
 
-julia> lsqfit(EnergyForm(), PoirierTarantola3rd(41, 0.5, 4, 0), volumes, energies)
+julia> lsqfit(Energy(), PoirierTarantola3rd(41, 0.5, 4, 0), volumes, energies)
 PoirierTarantola3rd{Float64}(40.86770643567383, 0.5667729960008705, 4.331688934942696, -10.851486685029547)
 
-julia> lsqfit(EnergyForm(), Vinet(41, 0.5, 4, 0), volumes, energies)
+julia> lsqfit(Energy(), Vinet(41, 0.5, 4, 0), volumes, energies)
 Vinet{Float64}(40.91687567368755, 0.5493839427734198, 4.30519294991197, -10.846160810968053)
 ```
 
 Then 4 different equations of state will be fitted.
 
 ## Public interfaces
 
-```@docs
-lsqfit(form::EquationForm, eos::EquationOfState{<:Real}, xdata::AbstractVector{<:Real}, ydata::AbstractVector{<:Real}; debug::Bool, kwargs...)
+```@autodocs
+Modules = [NonlinearFitting]
+Order   = [:type, :function]
 ```
 
 ## References

diff --git a/docs/src/Python.md b/docs/src/Python.md
@@ -25,33 +25,31 @@ writing too much code. Luckily, Julia provides such a feature.
    ```python
    In [1]: from julia import Unitful
 
-   In [2]: from julia.EquationsOfState import *
+   In [2]: from julia.EquationsOfState.Collections import *
 
-   In [3]: from julia.EquationsOfState.Collections import *
+   In [3]: from julia.EquationsOfState import *
 
-   In [4]: from julia.EquationsOfState import *
+   In [4]: Murnaghan(1, 2, 3.0, 4)
+   Out[4]: <PyCall.jlwrap EquationsOfState.Collections.Murnaghan{Float64}(1.0, 2.0, 3.0, 4.0)>
 
-   In [5]: Murnaghan(1, 2, 3.0, 4)
-   Out[5]: <PyCall.jlwrap EquationsOfState.Collections.Murnaghan{Float64}(1.0, 2.0, 3.0, 4.0)>
-
-   In [6]: result = lsqfit(
-      ...:     PressureForm(),
+   In [5]: result = lsqfit(
+      ...:     Pressure(),
       ...:     BirchMurnaghan3rd(1, 2, 3.0, 0),
       ...:     [1, 2, 3, 4, 5],
       ...:     [5, 6, 9, 8, 7],
       ...: )
 
-   In [7]: result.v0, result.b0, result.bp0
-   Out[7]: (1.1024687826913997, 29.308616965851673, 12.689089874230556)
+   In [6]: result.v0, result.b0, result.bp0
+   Out[6]: (1.1024687826913997, 29.308616965851673, 12.689089874230556)
 
-   In [8]: from julia import Main
+   In [7]: from julia import Main
 
-   In [9]: volumes = Main.eval("data[:, 1] .* UnitfulAtomic.bohr^3")
+   In [8]: volumes = Main.eval("data[:, 1] .* UnitfulAtomic.bohr^3")
 
-   In [10]: energies = Main.eval("data[:, 2] .* UnitfulAtomic.Ry")
+   In [9]: energies = Main.eval("data[:, 2] .* UnitfulAtomic.Ry")
 
-   In [11]: Main.eval("EquationsOfState.NonlinearFitting.lsqfit(EquationsOfState.EnergyForm(), EquationsOfState.Collections.Murnaghan(224.445371 * UnitfulAtomic.bohr^3, 9.164446 * Unitful.GPa, 3.752432, -161.708856 * UnitfulAtomic.hartree), volumes, energies)")
-   Out[11]: <PyCall.jlwrap EquationsOfState.Collections.Murnaghan{Unitful.Quantity{Float64,D,U} where U where D}(224.5018173532159 a₀^3, 8.896845579229117 GPa, 3.7238388137735674, -161.70884303138902 Eₕ)>
+   In [10]: Main.eval("EquationsOfState.NonlinearFitting.lsqfit(EquationsOfState.Energy(), EquationsOfState.Collections.Murnaghan(224.445371 * UnitfulAtomic.bohr^3, 9.164446 * Unitful.GPa, 3.752432, -161.708856 * UnitfulAtomic.hartree), volumes, energies)")
+   Out[10]: <PyCall.jlwrap EquationsOfState.Collections.Murnaghan{Unitful.Quantity{Float64,D,U} where U where D}(224.5018173532159 a₀^3, 8.896845579229117 GPa, 3.7238388137735674, -161.70884303138902 Eₕ)>
    ```
 
    where `data` is copied from Julia:

diff --git a/scripts/findvolume.jl b/scripts/findvolume.jl
@@ -6,14 +6,13 @@ plotlyjs()
 
 pressures = collect(0:20:200) .* u"GPa"
 eos = BirchMurnaghan3rd(167 * u"angstrom^3", 2600 * u"kbar", 4.0)
-volumes = map(
-    p -> findvolume(PressureForm(), eos, p, (eps() * u"bohr^3", eos.v0 * 1.3)),
-    pressures,
-)
+volumes = map(pressures) do p
+    findvolume(eos(Pressure()), p, (eps(1.0 * u"bohr^3"), eos.v0 * 1.3))
+end
 plot(ustrip.(volumes), ustrip.(pressures), label = "pressures")
 scatter!(
     ustrip.(volumes),
-    ustrip.(u"GPa", eos(PressureForm()).(volumes)),
+    ustrip.(u"GPa", eos(Pressure()).(volumes)),
     label = "P(V)",
     dpi = 400,
 )