Update src/MD/Recipes.jl

src/MD/Recipes.jl

@@ -0,0 +1,117 @@
+module Recipes
+
+using Configurations: from_dict
+using EasyJobsBase: Job, ConditionalJob, ArgDependentJob, →
+using ExpressBase: IonDynamics, VariableCellMolecularDynamics, think
+using ExpressBase.Files: load
+using ExpressBase.Recipes: Recipe
+using SimpleWorkflows: Workflow, run!
+
+using ..Config: StaticConfig, expand
+
+struct IonDynamicsRecipe <: Recipe
+    config
+end
+struct VariableCellMolecularDynamicsRecipe <: 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 .→ writeinputs .→ runcmds
+    return steps = (;
+        download=download,
+        makeinputs=makeinputs,
+        writeinputs=writeinputs,
+        runcmds=runcmds,
+        # extractdata=extractdata,
+        # gatherdata=gatherdata,
+        # savedata=savedata,
+    )
+end
+function stage(::VariableCellMolecularDynamics, r::VariableCellMolecularDynamicsRecipe)
+    conf = expand(r.config, VariableCellMolecularDynamics())
+    steps = map((
+        DownloadPotentials(VariableCellMolecularDynamics()),
+        CreateInput(VariableCellMolecularDynamics()),
+        WriteInput(VariableCellMolecularDynamics()),
+        RunCmd(VariableCellMolecularDynamics()),
+        # ExtractData(VariableCellMolecularDynamics()),
+        # GatherData(VariableCellMolecularDynamics()),
+        # SaveData(VariableCellMolecularDynamics()),
+    )) 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 .→ writeinputs .→ runcmds
+    return steps = (;
+        download=download,
+        makeinputs=makeinputs,
+        writeinputs=writeinputs,
+        runcmds=runcmds,
+        # extractdata=extractdata,
+        # gatherdata=gatherdata,
+        # savedata=savedata,
+    )
+end
+
+function build(::Type{Workflow}, r::IonDynamicsRecipe)
+    stages = [stage(IonDynamics(), r)]
+    return Workflow(stages[1].download)
+end
+function build(::Type{Workflow}, file)
+    dict = load(file)
+    recipe = dict["recipe"]
+    config = from_dict(StaticConfig, dict)
+    if recipe == "md"
+        return build(Workflow, IonDynamicsRecipe(config))
+    elseif recipe == "vc-md"
+        return build(Workflow, VariableCellMolecularDynamicsRecipe(config))
+    else
+        error("unsupported recipe $recipe.")
+    end
+end
+
+end