Merge pull request #149 from MineralsCloud:parser

Replace `parse_electrons_energies` & `parsefinal` with `eachconvergedenergy` & `eachcellparameterscard` or `eachatomicpositionscard`
MineralsCloud · Oct 30, 2023 · 66abca6 · 66abca6
2 parents 3fa6d98 + ccaf234
commit 66abca6
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Showing 3 changed files with 23 additions and 28 deletions.
diff --git a/src/ConvergenceTestWorkflow/actions.jl b/src/ConvergenceTestWorkflow/actions.jl
@@ -2,7 +2,7 @@ using AbInitioSoftwareBase: Setter
 using CrystallographyBase: MonkhorstPackGrid
 using Dates: format, now
 using QuantumESPRESSO.PWscf:
-    PWInput, KMeshCard, PWInput, VerbositySetter, Preamble, parse_electrons_energies
+    PWInput, KMeshCard, PWInput, VerbositySetter, Preamble, eachconvergedenergy
 using Setfield: @set!
 using UnifiedPseudopotentialFormat  # To work with `download_potential`
 using Unitful: ustrip, @u_str
@@ -17,12 +17,9 @@ end
 function (::ExtractData)(file)
     str = read(file, String)
     preamble = tryparse(Preamble, str)
-    e = try
-        parse_electrons_energies(str, :converged)
-    catch
-    end
-    if preamble !== nothing && !isempty(e)
-        return preamble.ecutwfc * u"Ry" => e.ε[end] * u"Ry"  # volume, energy
+    energies = collect(eachconvergedenergy(str))
+    if !isnothing(preamble) && !isempty(energies)
+        return preamble.ecutwfc * u"Ry" => last(energies) * u"Ry"  # volume, energy
     else
         throw(DataExtractionFailed("no data found in file $file."))
     end

diff --git a/src/EquationOfStateWorkflow/EquationOfStateWorkflow.jl b/src/EquationOfStateWorkflow/EquationOfStateWorkflow.jl
@@ -4,13 +4,7 @@ using AtomsIO: Atom, periodic_system, save_system
 using CrystallographyBase: Lattice, Cell, basisvectors, cellvolume, eachatom
 using ExpressBase: Calculation
 using QuantumESPRESSO.PWscf:
-    CellParametersCard,
-    AtomicPositionsCard,
-    Preamble,
-    parse_electrons_energies,
-    parsefinal,
-    isjobdone,
-    tryparsefinal
+    Preamble, isjobdone, isoptimized, eachcellparameterscard, eachconvergedenergy
 using Unitful: @u_str
 using UnitfulAtomic
 
@@ -27,12 +21,9 @@ end
 function (::ExtractData{SelfConsistentField})(file)
     str = read(file, String)
     preamble = tryparse(Preamble, str)
-    e = try
-        parse_electrons_energies(str, :converged)
-    catch
-    end
-    if preamble !== nothing && !isempty(e)
-        return preamble.omega * u"bohr^3" => e.ε[end] * u"Ry"  # volume, energy
+    energies = collect(eachconvergedenergy(str))
+    if !isnothing(preamble) && !isempty(energies)
+        return preamble.omega * u"bohr^3" => last(energies) * u"Ry"  # volume, energy
     else
         throw(DataExtractionFailed("no data found in file $file."))
     end
@@ -42,19 +33,23 @@ function (::ExtractData{VariableCellOptimization})(file)
     if !isjobdone(str)
         @warn "Job is not finished!"
     end
-    x = tryparsefinal(CellParametersCard, str)
-    if x !== nothing
-        return cellvolume(parsefinal(CellParametersCard, str)) * u"bohr^3" =>
-            parse_electrons_energies(str, :converged).ε[end] * u"Ry"  # volume, energy
+    if !isoptimized(str)
+        @warn "Cell is not completely optimized!"
+    end
+    cards, energies = collect(eachcellparameterscard(str)),
+    collect(eachconvergedenergy(str))
+    if !isempty(cards) && !isempty(energies)
+        lastcell, lastenergy = last(cards), last(energies)
+        return cellvolume(lastcell) * u"bohr^3" => lastenergy * u"Ry"  # volume, energy
     else
         throw(DataExtractionFailed("no data found in file $file."))
     end
 end
 
 function (::ExtractCell)(file)
     str = read(file, String)
-    cell_parameters = parsefinal(CellParametersCard, str)
-    atomic_positions = parsefinal(AtomicPositionsCard, str)
+    cell_parameters = last(collect(eachcellparameterscard(str)))
+    atomic_positions = last(collect(eachatomicpositionscard(str)))
     return Cell(cell_parameters, atomic_positions)
 end
 

diff --git a/src/PhononWorkflow/actions.jl b/src/PhononWorkflow/actions.jl
@@ -13,15 +13,18 @@ using QuantumESPRESSO.PWscf:
     AtomicPositionsCard,
     CellParametersCardSetter,
     AtomicPositionsCardSetter,
-    tryparsefinal
+    eachatomicpositionscard,
+    eachcellparameterscard
 using QuantumESPRESSO.PHonon: PhInput, Q2rInput, MatdynInput, VerbositySetter, relayinfo
 using Setfield: @set!
 using UnifiedPseudopotentialFormat  # To work with `download_potential`
 
 import Express.PhononWorkflow: CreateInput, RunCmd, parsecell
 
 function parsecell(str)
-    return tryparsefinal(AtomicPositionsCard, str), tryparsefinal(CellParametersCard, str)
+    cell_parameters = last(collect(eachcellparameterscard(str)))
+    atomic_positions = last(collect(eachatomicpositionscard(str)))
+    return atomic_positions, cell_parameters
 end
 
 (::CreateInput{SelfConsistentField})(file::AbstractString) =