Merge pull request #43 from MineralsCloud/feature/docs

Finish docs

Manifest.toml

@@ -41,9 +41,9 @@ version = "0.2.0"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "84aa74986c5b9b898b0d1acaf3258741ee64754f"
+git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "2.1.0"
+version = "2.2.0"
 
 [[ConstructionBase]]
 git-tree-sha1 = "e3efe0a0f49dcd294c8c73e897b4fdf891f0fbd3"
@@ -179,10 +179,10 @@ deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUID
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Polynomials]]
-deps = ["LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "62142bd65d3f8aeb2226ec64dd8493349147df94"
+deps = ["LinearAlgebra", "RecipesBase"]
+git-tree-sha1 = "f7c0c07e82798aef542d60a6e6e85e39f4590750"
 uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
-version = "0.5.2"
+version = "0.5.3"
 
 [[Printf]]
 deps = ["Unicode"]
@@ -202,6 +202,11 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
+[[RecipesBase]]
+git-tree-sha1 = "7bdce29bc9b2f5660a6e5e64d64d91ec941f6aa2"
+uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+version = "0.7.0"
+
 [[Reexport]]
 deps = ["Pkg"]
 git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
@@ -302,6 +307,6 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 deps = ["LinearAlgebra", "Random"]
 git-tree-sha1 = "0e9ad8a9621a9e1ec48f7cb48a5d6ded9e2c68f3"
 repo-rev = "master"
-repo-url = "https://github.com/PainterQubits/Unitful.jl.git"
+repo-url = "https://github.com/PainterQubits/Unitful.jl"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
 version = "0.17.0"

docs/Manifest.toml

@@ -0,0 +1,104 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "88bb0edb352b16608036faadcc071adda068582a"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.8.1"
+
+[[Documenter]]
+deps = ["Base64", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "d45c163c7a3ae293c15361acc52882c0f853f97c"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "0.23.4"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.0"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Parsers]]
+deps = ["Dates", "Test"]
+git-tree-sha1 = "ef0af6c8601db18c282d092ccbd2f01f3f0cd70b"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "0.3.7"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[Unitful]]
+deps = ["LinearAlgebra", "Random"]
+git-tree-sha1 = "0e9ad8a9621a9e1ec48f7cb48a5d6ded9e2c68f3"
+repo-rev = "master"
+repo-url = "https://github.com/PainterQubits/Unitful.jl.git"
+uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
+version = "0.17.0"

docs/Project.toml

@@ -1,2 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"

docs/make.jl

@@ -1,13 +1,16 @@
 using Documenter, EquationsOfState
 
+DocMeta.setdocmeta!(EquationsOfState, :DocTestSetup, :(using EquationsOfState, EquationOfState.Collections, Unitful); recursive=true)
 makedocs(;
     modules=[EquationsOfState],
     format=Documenter.HTML(),
     pages=[
         "Home" => "index.md",
+        "Installation" => "Installation.md",
         "Manual" => [
             "Collections" => "Collections.md",
-            "Nonlinear fitting" => "NonlinearFitting.md"
+            "Nonlinear fitting" => "NonlinearFitting.md",
+            "Find volume" => "Find.md"
         ]
     ],
     repo="https://github.com/MineralsCloud/EquationsOfState.jl/blob/{commit}{path}#L{line}",

docs/src/Collections.md

@@ -18,94 +18,67 @@ EquationOfState
 │  ├─ PoirierTarantola3rd
 │  └─ PoirierTarantola4th
 ├─ Murnaghan
-├─ PolynomialEquationOfState
 └─ Vinet
 ```
 
-## Types
-
-```@docs
-EquationOfState
-FiniteStrainEquationOfState
-Murnaghan
-BirchMurnaghan2nd
-BirchMurnaghan3rd
-BirchMurnaghan4th
-PoirierTarantola2nd
-PoirierTarantola3rd
-PoirierTarantola4th
-Vinet
-```
-
 ## Usage
 
 ### Construct an `EquationOfState`
+
 We will use `BirchMurnaghan3rd` as an example.
 
-`BirchMurnaghan3rd` can be constructed from scratch:
+A `BirchMurnaghan3rd` can be constructed from scratch, as shown above. It can
+also be constructed from an existing `BirchMurnaghan3rd`, with
+[`Setfield.jl`](https://github.com/jw3126/Setfield.jl)
+[`@set!`](https://jw3126.github.io/Setfield.jl/stable/#Setfield.@set!-Tuple{Any})
+macro:
 
 ```julia
-julia> BirchMurnaghan3rd(1, 2, 3)
-4-element BirchMurnaghan3rd{Int64}:
- 1
- 2
- 3
- 0
-
-julia> BirchMurnaghan3rd(1, 2, 3, 4)
-4-element BirchMurnaghan3rd{Int64}:
- 1
- 2
- 3
- 4
-
-julia> BirchMurnaghan3rd(1, 2, 3, 4.0)
-4-element BirchMurnaghan3rd{Float64}:
- 1.0
- 2.0
- 3.0
- 4.0
+julia> using Setfield
+
+julia> eos = Murnaghan(1, 2, 3.0)
+Murnaghan{Float64}(1.0, 2.0, 3.0, 0.0)
+
+julia> @set! eos.v0 = 4
+Murnaghan{Float64}(4.0, 2.0, 3.0, 0.0)
+
+julia> eos
+Murnaghan{Float64}(4.0, 2.0, 3.0, 0.0)
 ```
 
-It can also be constructed from an existing `BirchMurnaghan3rd`:
+To modify multiple fields (say, `:v0`, `:bp0`, `:bpp0`, `:e0`) at a time, use
+[`@batchlens`](https://tkf.github.io/Kaleido.jl/stable/#Kaleido.@batchlens) from
+[`Kaleido.jl`](https://github.com/tkf/Kaleido.jl):
 
 ```julia
-julia> BirchMurnaghan3rd(BirchMurnaghan3rd(1, 2, 3, 4.0), b0=10, e0=5)
-4-element BirchMurnaghan3rd{Float64}:
-  1.0
- 10.0
-  3.0
-  5.0
+julia> using Setfield, Kaleido
 
-julia> BirchMurnaghan3rd(BirchMurnaghan3rd(1, 2, 3, 4.0), Dict(:b0=>10, :e0=>5))
-4-element BirchMurnaghan3rd{Float64}:
-  1.0
- 10.0
-  3.0
-  5.0
+julia> lens = @batchlens(begin
+           _.v0
+           _.bp0
+           _.bpp0
+           _.e0
+       end)
+IndexBatchLens(:v0, :bp0, :bpp0, :e0)
 
-julia> BirchMurnaghan3rd(BirchMurnaghan3rd(1, 2, 3, 4.0), (:b0, 10))
-4-element BirchMurnaghan3rd{Float64}:
-  1.0
- 10.0
-  3.0
-  4.0
+julia> eos = BirchMurnaghan4th(1, 2.0, 3, 4)
+BirchMurnaghan4th{Float64}(1.0, 2.0, 3.0, 4.0, 0.0)
+
+julia> set(eos, lens, (5, 6, 7, 8))
+BirchMurnaghan4th{Float64}(5.0, 2.0, 6.0, 7.0, 8.0)
 ```
 
-Users can access `BirchMurnaghan3rd`'s element by either "dot notation" or indexing:
+Users can access `BirchMurnaghan3rd`'s elements by "dot notation":
 
 ```julia
-julia> b = BirchMurnaghan3rd(1, 2, 3, 4.0)
+julia> eos = BirchMurnaghan3rd(1, 2, 3, 4.0)
 4-element BirchMurnaghan3rd{Float64}:
  1.0
  2.0
  3.0
  4.0
 
-julia> b.v0
-1.0
-
-julia> b[1]
+julia> eos.v0
 1.0
 ```
 
@@ -114,6 +87,7 @@ julia> b[1]
 The $E(V)$ relation of equations of state are listed as below:
 
 1. `Murnaghan`:
+
    ```math
    E(V) = E_{0}+K_{0} V_{0}\left[\frac{1}{K_{0}^{\prime}\left(K_{0}^{\prime}-1\right)}\left(\frac{V}{V_{0}}\right)^{1-K_{0}^{\prime}}+\frac{1}{K_{0}^{\prime}} \frac{V}{V_{0}}-\frac{1}{K_{0}^{\prime}-1}\right].
    ```
@@ -130,7 +104,8 @@ The $E(V)$ relation of equations of state are listed as below:
    E(V) = E_{0}+\frac{9}{16} V_{0} B_{0} \frac{\left(x^{2 / 3}-1\right)^{2}}{x^{7 / 3}}\left\{x^{1 / 3}\left(B_{0}^{\prime}-4\right)-x\left(B_{0}^{\prime}-6\right)\right\}.
    ```
 
-   where ``x = V / V_0``, and ``f = \frac{ 1 }{ 2 } \bigg[ \bigg( \frac{ V_0 }{ V } \bigg)^{2/3} - 1 \bigg]``.
+   where ``x = V / V_0``, and
+   ``f = \frac{ 1 }{ 2 } \bigg[ \bigg( \frac{ V_0 }{ V } \bigg)^{2/3} - 1 \bigg]``.
 
 4. `BirchMurnaghan4th`:
 
@@ -157,6 +132,7 @@ The $E(V)$ relation of equations of state are listed as below:
    ```math
    E(V) = E_{0}+\frac{1}{24} B_{0} V_{0} \ln ^{2} x\left\{\left(H+3 B_{0}^{\prime}+3\right) \ln ^{2} x\right. \left.+4\left(B_{0}^{\prime}+2\right) \ln x+12\right\}.
    ```
+
    where ``H = B_0 B_0'' + (B_0')^2``.
 
 8. `Vinet`:
@@ -242,7 +218,7 @@ The $B(V)$ relation of equations of state are listed as below:
 2. `BirchMurnaghan3rd`:
 
    ```math
-   B(V) = \frac{B_{0}}{8 \chi^{10 / 3}}\left\{x^{5 / 3}\left(15 B_{0}^{\prime}-80\right)-x\left(42 B_{0}^{\prime}-196\right)\right.\left.+27 x^{1 / 3}\left(B_{0}^{\prime}-4\right)\right\}.
+   B(V) = \frac{B_{0}}{8 x^{10 / 3}}\left\{x^{5 / 3}\left(15 B_{0}^{\prime}-80\right)-x\left(42 B_{0}^{\prime}-196\right)\right.\left.+27 x^{1 / 3}\left(B_{0}^{\prime}-4\right)\right\}.
    ```
 
 3. `BirchMurnaghan4th`:
@@ -281,38 +257,26 @@ 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
+
+```@docs
+EquationOfState
+FiniteStrainEquationOfState
+Murnaghan
+BirchMurnaghan2nd
+BirchMurnaghan3rd
+BirchMurnaghan4th
+PoirierTarantola2nd
+PoirierTarantola3rd
+PoirierTarantola4th
+Vinet
+```
 
 ## Public interfaces
 
 ```@docs
 apply(::EnergyForm, eos::EquationOfState)
-apply(::EnergyForm, eos::Murnaghan, v::Real)
-apply(::EnergyForm, eos::BirchMurnaghan2nd, v::Real)
-apply(::EnergyForm, eos::BirchMurnaghan3rd, v::Real)
-apply(::EnergyForm, eos::BirchMurnaghan4th, v::Real)
-apply(::EnergyForm, eos::PoirierTarantola2nd, v::Real)
-apply(::EnergyForm, eos::PoirierTarantola3rd, v::Real)
-apply(::EnergyForm, eos::PoirierTarantola4th, v::Real)
-apply(::EnergyForm, eos::Vinet, v::Real)
-apply(::EnergyForm, eos::AntonSchmidt, v::Real)
-apply(::PressureForm, eos::EquationOfState)
-apply(::PressureForm, eos::Murnaghan, v::Real)
-apply(::PressureForm, eos::BirchMurnaghan2nd, v::Real)
-apply(::PressureForm, eos::BirchMurnaghan3rd, v::Real)
-apply(::PressureForm, eos::BirchMurnaghan4th, v::Real)
-apply(::PressureForm, eos::PoirierTarantola2nd, v::Real)
-apply(::PressureForm, eos::PoirierTarantola3rd, v::Real)
-apply(::PressureForm, eos::PoirierTarantola4th, v::Real)
-apply(::PressureForm, eos::Vinet, v::Real)
-apply(::PressureForm, eos::AntonSchmidt, v::Real)
-apply(::PressureForm, eos::BreenanStacey, v::Real)
-apply(::BulkModulusForm, eos::EquationOfState)
-apply(::BulkModulusForm, eos::BirchMurnaghan2nd, v::Real)
-apply(::BulkModulusForm, eos::BirchMurnaghan3rd, v::Real)
-apply(::BulkModulusForm, eos::BirchMurnaghan4th, v::Real)
-apply(::BulkModulusForm, eos::PoirierTarantola2nd, v::Real)
-apply(::BulkModulusForm, eos::PoirierTarantola3rd, v::Real)
-apply(::BulkModulusForm, eos::PoirierTarantola4th, v::Real)
-apply(::BulkModulusForm, eos::Vinet, v::Real)
-apply(::BulkModulusForm, eos::AntonSchmidt, v::Real)
+apply(::EnergyForm, eos::Murnaghan, v)
+apply(::PressureForm, eos::Murnaghan, v)
+apply(::BulkModulusForm, eos::BirchMurnaghan2nd, v)
 ```