Merge pull request #143 from MineralsCloud:PhononWorkflow

Fix `PhononWorkflow`
MineralsCloud · Oct 15, 2023 · f107bf5 · f107bf5
2 parents 7aa6de3 + 22a7247
commit f107bf5
Show file tree

Hide file tree

Showing 6 changed files with 223 additions and 320 deletions.
diff --git a/src/ConvergenceTestWorkflow/Config.jl b/src/ConvergenceTestWorkflow/Config.jl
@@ -1,9 +1,11 @@
 module Config
 
-using Configurations: OptionField, @option
+using Configurations: OptionField
 using ExpressBase.Config: SoftwareConfig
 using QuantumESPRESSO.PWscf: PWInput
 
+using ...QuantumESPRESSOExpress: QuantumESPRESSOConfig, MpiexecConfig, PwxConfig
+
 import Configurations: from_dict
 import Express.ConvergenceTestWorkflow.Config: StaticConfig, _update!
 
@@ -13,132 +15,6 @@ function _update!(conf, template::AbstractString)
     return conf
 end
 
-@option struct MpiexecOptions <: SoftwareConfig
-    path::String = "mpiexec"
-    f::String = ""
-    hosts::Vector{String} = String[]
-    wdir::String = ""
-    configfile::String = ""
-    env::Union{Dict,Vector} = Dict(ENV)
-    np::UInt = 1
-end
-
-const MpiexecConfig = MpiexecOptions
-
-"""
-    ParallelizationFlags(; nimage=0, npool=0, ntg=0, nyfft=0, nband=0, ndiag=0)
-
-Construct parallelization flags of QuantumESPRESSO commands.
-"""
-@option mutable struct ParallelizationFlags
-    nimage::UInt = 0
-    npool::UInt = 0
-    ntg::UInt = 0
-    nyfft::UInt = 0
-    nband::UInt = 0
-    ndiag::UInt = 0
-end
-
-"""
-    PwxConfig(; path, chdir, options)
-
-Create configurations for `pw.x`.
-
-# Arguments
-- `path::String="pw.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `pw.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `pw.x`.
-"""
-@option mutable struct PwxConfig <: SoftwareConfig
-    path::String = "pw.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    PhxConfig(; path, chdir, options)
-
-Create configurations for `ph.x`.
-
-# Arguments
-- `path::String="ph.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `ph.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `ph.x`.
-"""
-@option mutable struct PhxConfig <: SoftwareConfig
-    path::String = "ph.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    Q2rxConfig(; path, chdir, options)
-
-Create configurations for `q2r.x`.
-
-# Arguments
-- `path::String="q2r.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `q2r.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `q2r.x`.
-"""
-@option mutable struct Q2rxConfig <: SoftwareConfig
-    path::String = "q2r.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    MatdynxConfig(; path, chdir, options)
-
-Create configurations for `matdyn.x`.
-
-# Arguments
-- `path::String="matdyn.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `matdyn.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `matdyn.x`.
-"""
-@option mutable struct MatdynxConfig <: SoftwareConfig
-    path::String = "matdyn.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    DynmatxConfig(; path, chdir, options)
-
-Create configurations for `dynmat.x`.
-
-# Arguments
-- `path::String="dynmat.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `dynmat.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `dynmat.x`.
-"""
-@option mutable struct DynmatxConfig <: SoftwareConfig
-    path::String = "dynmat.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-
-@option mutable struct QuantumESPRESSOConfig <: SoftwareConfig
-    mpi::MpiexecConfig = MpiexecConfig()
-    pw::PwxConfig = PwxConfig()
-    ph::PhxConfig = PhxConfig()
-    q2r::Q2rxConfig = Q2rxConfig()
-    matdyn::MatdynxConfig = MatdynxConfig()
-    dynmat::DynmatxConfig = DynmatxConfig()
-end
-
 function from_dict(
     ::Type{<:StaticConfig}, ::OptionField{:cli}, ::Type{SoftwareConfig}, dict
 )

diff --git a/src/EquationOfStateWorkflow/Config.jl b/src/EquationOfStateWorkflow/Config.jl
@@ -1,9 +1,11 @@
 module Config
 
-using Configurations: OptionField, @option
+using Configurations: OptionField
 using ExpressBase.Config: SoftwareConfig
 using QuantumESPRESSO.PWscf: PWInput
 
+using ...QuantumESPRESSOExpress: QuantumESPRESSOConfig, MpiexecConfig, PwxConfig
+
 import Configurations: from_dict
 import Express.EquationOfStateWorkflow.Config: StaticConfig, _update!
 
@@ -13,132 +15,6 @@ function _update!(conf, template::AbstractString)
     return conf
 end
 
-@option struct MpiexecOptions <: SoftwareConfig
-    path::String = "mpiexec"
-    f::String = ""
-    hosts::Vector{String} = String[]
-    wdir::String = ""
-    configfile::String = ""
-    env::Union{Dict,Vector} = Dict(ENV)
-    np::UInt = 1
-end
-
-const MpiexecConfig = MpiexecOptions
-
-"""
-    ParallelizationFlags(; nimage=0, npool=0, ntg=0, nyfft=0, nband=0, ndiag=0)
-
-Construct parallelization flags of QuantumESPRESSO commands.
-"""
-@option mutable struct ParallelizationFlags
-    nimage::UInt = 0
-    npool::UInt = 0
-    ntg::UInt = 0
-    nyfft::UInt = 0
-    nband::UInt = 0
-    ndiag::UInt = 0
-end
-
-"""
-    PwxConfig(; path, chdir, options)
-
-Create configurations for `pw.x`.
-
-# Arguments
-- `path::String="pw.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `pw.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `pw.x`.
-"""
-@option mutable struct PwxConfig <: SoftwareConfig
-    path::String = "pw.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    PhxConfig(; path, chdir, options)
-
-Create configurations for `ph.x`.
-
-# Arguments
-- `path::String="ph.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `ph.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `ph.x`.
-"""
-@option mutable struct PhxConfig <: SoftwareConfig
-    path::String = "ph.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    Q2rxConfig(; path, chdir, options)
-
-Create configurations for `q2r.x`.
-
-# Arguments
-- `path::String="q2r.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `q2r.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `q2r.x`.
-"""
-@option mutable struct Q2rxConfig <: SoftwareConfig
-    path::String = "q2r.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    MatdynxConfig(; path, chdir, options)
-
-Create configurations for `matdyn.x`.
-
-# Arguments
-- `path::String="matdyn.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `matdyn.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `matdyn.x`.
-"""
-@option mutable struct MatdynxConfig <: SoftwareConfig
-    path::String = "matdyn.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-"""
-    DynmatxConfig(; path, chdir, options)
-
-Create configurations for `dynmat.x`.
-
-# Arguments
-- `path::String="dynmat.x"`: the path to the executable.
-- `chdir::Bool=true`: whether to change directory to where the input file is
-  stored when running `dynmat.x`. If `false`, stay in the current directory.
-- `options::ParallelizationFlags=ParallelizationFlags()`: the parallelization
-  flags of `dynmat.x`.
-"""
-@option mutable struct DynmatxConfig <: SoftwareConfig
-    path::String = "dynmat.x"
-    chdir::Bool = true
-    options::ParallelizationFlags = ParallelizationFlags()
-    env::Union{Dict,Vector} = Dict(ENV)
-end
-
-@option mutable struct QuantumESPRESSOConfig <: SoftwareConfig
-    mpi::MpiexecConfig = MpiexecConfig()
-    pw::PwxConfig = PwxConfig()
-    ph::PhxConfig = PhxConfig()
-    q2r::Q2rxConfig = Q2rxConfig()
-    matdyn::MatdynxConfig = MatdynxConfig()
-    dynmat::DynmatxConfig = DynmatxConfig()
-end
-
 function from_dict(
     ::Type{<:StaticConfig}, ::OptionField{:cli}, ::Type{SoftwareConfig}, dict
 )

diff --git a/src/PhononWorkflow/Config.jl b/src/PhononWorkflow/Config.jl
@@ -1,34 +1,44 @@
 module Config
 
-using AbInitioSoftwareBase.Commands: MpiexecConfig
 using Configurations: OptionField
-using Express.PhononWorkflow.Config: StaticConfig, Template
+using Express.PhononWorkflow.Config: StaticConfig
+using ExpressBase:
+    SelfConsistentField,
+    DensityFunctionalPerturbationTheory,
+    RealSpaceForceConstants,
+    PhononDispersion,
+    PhononDensityOfStates
 using ExpressBase.Config: SoftwareConfig
-using QuantumESPRESSO.Commands:
-    QuantumESPRESSOConfig, PwxConfig, PhxConfig, Q2rxConfig, MatdynxConfig
 using QuantumESPRESSO.PWscf: PWInput
 using QuantumESPRESSO.PHonon: PhInput, Q2rInput, MatdynInput
 
+using ...QuantumESPRESSOExpress:
+    MpiexecConfig, QuantumESPRESSOConfig, PwxConfig, PhxConfig, Q2rxConfig, MatdynxConfig
+
 import Configurations: from_dict
-import Express.PhononWorkflow.Config: ExpandConfig
+import Express.PhononWorkflow.Config: StaticConfig, _update!
 
-function (::ExpandConfig)(template::Template)
-    inputs = map(
-        (:scf, :dfpt, :q2r, :disp), (PWInput, PhInput, Q2rInput, MatdynInput)
-    ) do field, T
-        str = read(getproperty(template, field), String)
-        parse(T, str)
+function _update!(conf, templates::Vector{String})
+    stage, T = if conf.calculation isa SelfConsistentField
+        1, PWInput
+    elseif conf.calculation isa DensityFunctionalPerturbationTheory
+        2, PhInput
+    elseif conf.calculation isa RealSpaceForceConstants
+        3, Q2rInput
+    elseif conf.calculation isa PhononDispersion
+        4, MatdynInput
+    elseif conf.calculation isa PhononDensityOfStates
+        4, MatdynInput
+    else
+        4, DynmatInput
     end
-    return (; zip((:scf, :dfpt, :q2r, :disp), inputs)...)
+    str = read(templates[stage], String)
+    conf.template = parse(T, str)
+    return conf
 end
 
 function from_dict(
-    ::Type{<:StaticConfig}, ::OptionField{:cli}, ::Type{<:SoftwareConfig}, dict
-)
-    return from_dict(StaticConfig, OptionField{:cli}(), QuantumESPRESSOConfig, dict)
-end
-function from_dict(
-    ::Type{<:StaticConfig}, ::OptionField{:cli}, ::Type{QuantumESPRESSOConfig}, dict
+    ::Type{<:StaticConfig}, ::OptionField{:cli}, ::Type{SoftwareConfig}, dict
 )
     return QuantumESPRESSOConfig(;
         mpi=get(dict, "mpi", MpiexecConfig()),