Dispatch materialize

Manifest.toml

@@ -2,7 +2,7 @@
 
 [[AbInitioSoftwareBase]]
 deps = ["Configurations", "IsURL", "JSON", "Pkg", "YAML"]
-git-tree-sha1 = "7ae139ee9c89fe6e6ec81b28c8692c9e55499293"
+git-tree-sha1 = "3a3ac0ec81aaf25f97be132438d03ac293cbc0ab"
 repo-rev = "master"
 repo-url = "[email protected]:MineralsCloud/AbInitioSoftwareBase.jl.git"
 uuid = "df5135bc-470e-46c6-b451-292e27ca5b84"
@@ -191,17 +191,17 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "5a9a742ae30f13d6172c7ea245988d932134e25b"
+git-tree-sha1 = "0fc424e725eaec6ea3e9fa8df773bee18a1ab503"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.24.13"
+version = "0.24.14"
 
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[EquationsOfStateOfSolids]]
 deps = ["AutoHashEquals", "Compat", "Configurations", "ConstructionBase", "InteractiveUtils", "LsqFit", "PolynomialRoots", "Polynomials", "Roots", "Serialization", "UnPack", "Unitful"]
-git-tree-sha1 = "52caa9a6a8ad896ba8f590c88e69c0f10ba06736"
+git-tree-sha1 = "6cdb7e3b7800750321a0fcd16e523ef1e1c2e9be"
 repo-rev = "master"
 repo-url = "[email protected]:MineralsCloud/EquationsOfStateOfSolids.jl.git"
 uuid = "1eaa2786-f833-4167-8397-974edad0881e"
@@ -214,7 +214,7 @@ version = "0.1.3"
 
 [[Express]]
 deps = ["AbInitioSoftwareBase", "Compat", "Configurations", "Crystallography", "Distributed", "EquationsOfStateOfSolids", "Mustache", "PyQHA", "Serialization", "Setfield", "SimpleWorkflow", "Unitful", "UnitfulAtomic", "UrlDownload"]
-git-tree-sha1 = "c46bfa614a53235a776460b62e82d65eba2c2c5d"
+git-tree-sha1 = "2db6b7526fe5ce4d3973acfd9eedac98ae300a0b"
 repo-rev = "master"
 repo-url = "[email protected]:MineralsCloud/Express.jl.git"
 uuid = "b12df14e-adf7-11e9-0606-d5813a258349"
@@ -228,9 +228,9 @@ version = "1.1.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "bed538ad14d132aa8240bb2e8ab82fcd2fd2f548"
+git-tree-sha1 = "4705cc4e212c3c978c60b1b18118ec49b4d731fd"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.11.3"
+version = "0.11.5"
 
 [[FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"]
@@ -457,9 +457,9 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
-git-tree-sha1 = "76622f08645764e040b4d7e86d0ff471fd126ae4"
+git-tree-sha1 = "986e7c0a0ef1863be969d191957ac32cb17d0d79"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.5.3"
+version = "1.6.0"
 
 [[OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -789,9 +789,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[Unitful]]
 deps = ["ConstructionBase", "LinearAlgebra", "Random"]
-git-tree-sha1 = "2b643523d52fc9fb4fe0729e6561d066055d58d8"
+git-tree-sha1 = "fdfbea79b5b9a305bf226eb4730321f603281290"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.5.0"
+version = "1.6.0"
 
 [[UnitfulAtomic]]
 deps = ["Unitful"]

src/EosFitting/Config.jl

@@ -1,18 +1,14 @@
 module Config
 
 using Configurations: from_dict, @option
-using Express.EosFitting.Config:
-    Pressures,
-    EosFittingConfig,
-    materialize_eos,
-    materialize_press,
-    materialize_vol,
-    materialize_dir
-import Express.EosFitting.Config: materialize
+using Crystallography: cellvolume
+using Express.EosFitting.Config: Pressures, Volumes, EosFittingConfig
 using QuantumESPRESSO.Cli: QuantumESPRESSOCliConfig
 using QuantumESPRESSO.Inputs.PWscf:
     CellParametersCard, PWInput, VerbositySetter, VolumeSetter, PressureSetter
 
+import Express.EosFitting.Config: materialize
+
 function _materialize_tmpl(config, fixed)
     arr = map(config.paths) do file
         str = read(expanduser(file), String)
@@ -25,24 +21,25 @@ function _materialize_tmpl(config, fixed)
     end
 end
 
-function materialize(config)
+function materialize(config::AbstractDict)
     config = from_dict(EosFittingConfig{QuantumESPRESSOCliConfig}, config)
 
     templates = _materialize_tmpl(config.templates, config.fixed)
 
-    fixed = if config.fixed isa Pressures
-        materialize_press(config.fixed)
+    fixed = if config.fixed === nothing
+        # If no volume or pressure is provided, use templates cell volumes
+        Volumes(map(cellvolume, config.templates))
     else
-        materialize_vol(config)
-    end
+        config.fixed
+    end |> materialize
 
     return (
         templates = templates,
         fixed = fixed,
-        trial_eos = materialize_eos(config.trial_eos),
-        workdir = config.outdirs.root,
-        dirs = materialize_dir(config),
-        num_inv = config.num_inv,
+        trial_eos = materialize(config.trial_eos),
+        workdir = config.dirs.root,
+        dirs = materialize(config.dirs, config.fixed),
+        inv_opt = config.inv_opt,
         cli = config.cli,
     )
 end

src/EosFitting/EosFitting.jl

@@ -1,13 +1,11 @@
 module EosFitting
 
-using AbInitioSoftwareBase.Cli: MpiexecOptions
 using Crystallography: cellvolume
 using QuantumESPRESSOCli: PwxConfig, makecmd
 using QuantumESPRESSO.Inputs.PWscf: CellParametersCard
 using QuantumESPRESSO.Outputs.PWscf:
     Preamble, parse_electrons_energies, parsefinal, isjobdone, tryparsefinal
 using Setfield: @set!
-using SimpleWorkflow: ExternalAtomicJob, parallel
 using Unitful: Pressure, Volume, @u_str
 import Unitful
 using UnitfulAtomic
@@ -16,92 +14,41 @@ using ..QuantumESPRESSOExpress: QE
 
 using Express: loadconfig
 using Express.EosFitting: SelfConsistentField, StOptim, VcOptim, ScfOrOptim, iofiles
-import Express.Shell: MakeCmd, distprocs
-import Express.EosFitting: shortname, buildjob
+import Express.EosFitting: shortname
 import Express.EosFitting.DefaultActions: parseoutput
 
 include("Config.jl")
 
 module DefaultActions
 
+using AbInitioSoftwareBase.Cli: MpiexecOptions
 using AbInitioSoftwareBase.Inputs: Setter
 using Dates: format, now
 using EquationsOfStateOfSolids: EquationOfStateOfSolids, PressureEquation, Parameters
 using EquationsOfStateOfSolids.Inverse: NumericalInversionOptions, inverse
 using QuantumESPRESSOCli: PwxConfig, makecmd
 using QuantumESPRESSO.Inputs.PWscf: PWInput, VerbositySetter, VolumeSetter, PressureSetter
 using Setfield: @set!
+using SimpleWorkflow: ExternalAtomicJob, parallel
 using Unitful: Pressure, Volume, @u_str
 import Unitful
 using UnitfulAtomic
 
 using Express.EosFitting:
     SelfConsistentField, Optimization, StOptim, VcOptim, ScfOrOptim, iofiles, loadconfig
-import Express.EosFitting.DefaultActions: MakeInput, FitEos
+import Express.EosFitting: buildjob
+import Express.EosFitting.DefaultActions: MakeInput, FitEos, MakeCmd
+import Express.Shell: distprocs
 
 include("MakeInput.jl")
+include("MakeCmd.jl")
 
 end
 
 shortname(::Type{SelfConsistentField}) = "scf"
 shortname(::Type{StOptim}) = "relax"
 shortname(::Type{VcOptim}) = "vc-relax"
 
-function (::MakeCmd)(
-    input;
-    output = tempname(; cleanup = false),
-    error = "",
-    mpi = MpiexecOptions(),
-    options = PwxConfig(),
-)
-    mkpath(dirname(input))
-    @set! options.script_dest = mktemp(dirname(input); cleanup = false)[1]
-    return makecmd(input; output = output, error = error, mpi = mpi, options = options)
-end
-function (x::MakeCmd)(
-    inputs::AbstractArray;
-    outputs,
-    errors = outputs,
-    mpi,
-    options = PwxConfig(),
-)
-    if !isempty(outputs)
-        if size(inputs) != size(outputs)
-            throw(DimensionMismatch("size of inputs and outputs are different!"))
-        end
-    end
-    if !isempty(errors)
-        if size(inputs) != size(errors)
-            throw(DimensionMismatch("size of inputs and outputs are different!"))
-        end
-    end
-    @set! mpi.np = distprocs(mpi.np, length(inputs))
-    distkeys = []
-    for (key, value) in mpi.options
-        if value isa AbstractArray
-            push!(distkeys, key)
-        end
-    end
-    return map(enumerate(inputs)) do (i, input)
-        tempmpi = mpi
-        for key in distkeys
-            @set! tempmpi.options[key] = mpi.options[key][i]
-        end
-        x(input; output = outputs[i], error = errors[i], mpi = tempmpi, options = options)
-    end
-end
-
-function buildjob(x::MakeCmd{T}, cfgfile) where {T}
-    config = loadconfig(cfgfile)
-    io = iofiles(T(), cfgfile)
-    infiles, outfiles = first.(io), last.(io)
-    jobs = map(
-        ExternalAtomicJob,
-        x(infiles; outputs = outfiles, mpi = config.cli.mpi, options = config.cli.pw),
-    )
-    return parallel(jobs...)
-end
-
 function parseoutput(::SelfConsistentField)
     function (file)
         str = read(file, String)

src/EosFitting/MakeCmd.jl

@@ -0,0 +1,54 @@
+function (::MakeCmd)(
+    input;
+    output = tempname(; cleanup = false),
+    error = "",
+    mpi = MpiexecOptions(),
+    options = PwxConfig(),
+)
+    mkpath(dirname(input))
+    @set! options.script_dest = mktemp(dirname(input); cleanup = false)[1]
+    return makecmd(input; output = output, error = error, mpi = mpi, options = options)
+end
+function (x::MakeCmd)(
+    inputs::AbstractArray;
+    outputs,
+    errors = outputs,
+    mpi,
+    options = PwxConfig(),
+)
+    if !isempty(outputs)
+        if size(inputs) != size(outputs)
+            throw(DimensionMismatch("size of inputs and outputs are different!"))
+        end
+    end
+    if !isempty(errors)
+        if size(inputs) != size(errors)
+            throw(DimensionMismatch("size of inputs and outputs are different!"))
+        end
+    end
+    @set! mpi.np = distprocs(mpi.np, length(inputs))
+    distkeys = []
+    for (key, value) in mpi.options
+        if value isa AbstractArray
+            push!(distkeys, key)
+        end
+    end
+    return map(enumerate(inputs)) do (i, input)
+        tempmpi = mpi
+        for key in distkeys
+            @set! tempmpi.options[key] = mpi.options[key][i]
+        end
+        x(input; output = outputs[i], error = errors[i], mpi = tempmpi, options = options)
+    end
+end
+
+function buildjob(x::MakeCmd{T}, cfgfile) where {T}
+    config = loadconfig(cfgfile)
+    io = iofiles(T(), cfgfile)
+    infiles, outfiles = first.(io), last.(io)
+    jobs = map(
+        ExternalAtomicJob,
+        x(infiles; outputs = outfiles, mpi = config.cli.mpi, options = config.cli.pw),
+    )
+    return parallel(jobs...)
+end

src/EosFitting/MakeInput.jl

@@ -23,7 +23,7 @@ function (x::MakeInput{T})(cfgfile) where {T}
             fill(config.trial_eos, length(infiles)),
             config.fixed,
             fill("Y-m-d_H:M:S", length(infiles)),
-            fill(config.num_inv, length(infiles)),
+            fill(config.inv_opt, length(infiles)),
         )
     end
 end
@@ -75,9 +75,9 @@ function Customizer(
     eos::EquationOfStateOfSolids,
     pressure::Pressure,
     timefmt,
-    num_inv = NumericalInversionOptions(),
+    inv_opt = NumericalInversionOptions(),
 )
-    volume = inverse(eos)(pressure, num_inv)
+    volume = inverse(eos)(pressure, inv_opt)
     return Customizer(volume, pressure, timefmt)
 end
 Customizer(params::Parameters, pressure::Pressure, args...) =

src/Phonon/Config.jl

@@ -8,8 +8,7 @@ using QuantumESPRESSO.Inputs.PWscf: PWInput
 using QuantumESPRESSO.Inputs.PHonon: PhInput, Q2rInput, MatdynInput
 using Unitful: ustrip
 
-using Express.Phonon.Config:
-    Pressures, Volumes, PhononConfig, DfptTemplate, materialize_press_vol, materialize_dir
+using Express.Phonon.Config: Pressures, Volumes, PhononConfig, DfptTemplate
 import Express.Phonon.Config: materialize
 
 function _materialize_tmpl(
@@ -33,16 +32,16 @@ function _materialize_tmpl(
     end
 end
 
-function materialize(config)
+function materialize(config::AbstractDict)
     config = from_dict(PhononConfig{QuantumESPRESSOCliConfig}, config)
 
     templates = _materialize_tmpl(config.templates, config.fixed)
 
     return (
         templates = templates,
-        fixed = materialize_press_vol(config.fixed),
-        workdir = config.outdirs.root,
-        dirs = materialize_dir(config),
+        fixed = materialize(config.fixed),
+        workdir = config.dirs.root,
+        dirs = materialize(config.dirs, config.fixed),
         cli = config.cli,
     )
 end

src/Phonon/Phonon.jl

@@ -37,8 +37,8 @@ using SimpleWorkflow: ExternalAtomicJob, parallel
 using ...QuantumESPRESSOExpress: QE
 
 import Express.Phonon: shortname, buildjob
-import Express.Phonon.DefaultActions: MakeInput, parsecell, inputtype
-import Express.Shell: MakeCmd, distprocs
+import Express.Phonon.DefaultActions: MakeInput, MakeCmd, parsecell, inputtype
+import Express.Shell: distprocs
 
 include("MakeInput.jl")
 include("MakeCmd.jl")