Add all files

src/MolecularDynamics/Config.jl

@@ -0,0 +1,70 @@
+module Config
+
+using Configurations: from_dict, @option
+using EasyConfig: Config as Conf
+using ExpressBase: Calculation
+using ExpressBase.Config: AbstractConfig, SoftwareConfig, SamplingPoints, IO, list_io
+using Unitful: FreeUnits
+
+@option "pressures" struct Pressures <: SamplingPoints
+    numbers::Vector{Float64}
+    unit::FreeUnits
+    Pressures(numbers, unit="GPa") = new(numbers, unit)
+end
+
+@option "volumes" struct Volumes <: SamplingPoints
+    numbers::Vector{Float64}
+    unit::FreeUnits
+    Volumes(numbers, unit="bohr^3") = new(numbers, unit)
+end
+
+@option struct Data <: AbstractConfig
+    static::String = "energies.json"
+end
+
+@option struct StaticConfig <: AbstractConfig
+    recipe::String
+    templates::Vector{String}
+    at::Union{Pressures,Volumes}
+    io::IO = IO()
+    data::Data = Data()
+    cli::SoftwareConfig
+    function StaticConfig(recipe, templates, at, io, data, cli)
+        @assert recipe in ("md", "vc-md")
+        for template in templates
+            if !isfile(template)
+                @warn "I cannot find template file `$template`!"
+            end
+        end
+        return new(recipe, templates, at, io, data, cli)
+    end
+end
+
+function _update!(conf::Conf, at::Union{Pressures,Volumes})
+    conf.at = collect(number for number in at)
+    return conf
+end
+function _update!(conf::Conf, io::IO, at::Union{Pressures,Volumes})
+    conf.io = collect(
+        list_io(io, number, string(nameof(typeof(conf.calculation)))) for
+        number in at.numbers
+    )
+    return conf
+end
+function _update!(conf::Conf, data::Data)
+    conf.data.static = abspath(expanduser(data.static))
+    return conf
+end
+
+function expand(config::StaticConfig, calculation::Calculation)
+    conf = Conf()
+    conf.cli = config.cli
+    conf.calculation = calculation
+    _update!(conf, config.templates)
+    _update!(conf, config.at)
+    _update!(conf, config.io, config.at)
+    _update!(conf, config.data)
+    return conf
+end
+
+end

src/MolecularDynamics/MolecularDynamics.jl

@@ -1,5 +1,8 @@
 module MolecularDynamics
 
-
+include("Config.jl")
+include("actions.jl")
+include("think.jl")
+include("Recipes.jl")
 
 end

src/MolecularDynamics/Recipes.jl

@@ -0,0 +1,51 @@
+module Recipes
+
+struct IonDynamicsRecipe <: Recipe
+    config
+end
+struct VDOSRecipe <: Recipe
+    config
+end
+
+function stage(::IonDynamics, r::IonDynamicsRecipe)
+    conf = expand(r.config, IonDynamics())
+    steps = map((
+        DownloadPotentials(IonDynamics()),
+        CreateInput(IonDynamics()),
+        WriteInput(IonDynamics()),
+        RunCmd(IonDynamics()),
+        # ExtractData(IonDynamics()),
+        # GatherData(IonDynamics()),
+        # SaveData(IonDynamics()),
+    )) do action
+        think(action, conf)
+    end
+    steps = Iterators.Stateful(steps)
+    download = Job(first(iterate(steps)); name="download potentials")
+    makeinputs = map(thunk -> Job(thunk; name="update input in MD"), first(iterate(steps)))
+    writeinputs = map(
+        thunk -> ArgDependentJob(thunk; name="write input in MD"), first(iterate(steps))
+    )
+    runcmds = map(
+        thunk -> ConditionalJob(thunk; name="run ab initio software in MD"),
+        first(iterate(steps)),
+    )
+    # extractdata = map(
+    #     thunk -> ConditionalJob(thunk; name="extract E(V) data in MD"),
+    #     first(iterate(steps)),
+    # )
+    # gatherdata = ArgDependentJob(first(iterate(steps)); name="gather E(V) data in MD")
+    # savedata = ArgDependentJob(first(iterate(steps)); name="save E(V) data in MD")
+    download .→ makeinputs .→ runcmds
+    return steps = (;
+        download=download,
+        makeinputs=makeinputs,
+        writeinputs=writeinputs,
+        runcmds=runcmds,
+        # extractdata=extractdata,
+        # gatherdata=gatherdata,
+        # savedata=savedata,
+    )
+end
+
+end

src/MolecularDynamics/actions.jl

@@ -0,0 +1,34 @@
+using AbInitioSoftwareBase: Input
+using EasyJobsBase: Job
+using ExpressBase:
+    IonDynamics,
+    VariableCellMolecularDynamics,
+    Action,
+    DownloadPotentials,
+    RunCmd,
+    WriteInput
+using ExpressBase.Files: save
+
+struct CreateInput{T} <: Action{T}
+    calculation::T
+end
+(action::CreateInput)(template::Input) = Base.Fix1(action, template)
+
+struct ExtractTrajectory{T} <: Action{T}
+    calculation::T
+end
+
+struct GatherTrajectories{T} <: Action{T}
+    calculation::T
+end
+(::GatherTrajectories)(iter) = collect(iter)
+
+struct SaveTrajectory{T} <: Action{T}
+    calculation::T
+end
+function (action::SaveTrajectory)(path, raw)
+    raw = collect(raw)  # In case the data is not sorted
+    data = Dict("volume" => (string ∘ first).(raw), "energy" => (string ∘ last).(raw))
+    return save(path, data)
+end
+(action::SaveTrajectory)(path) = Base.Fix1(action, path)