Merge pull request #123 from MineralsCloud:fix-input

Fix regex `CELL_PARAMETERS` to work both in input & output

src/PWscf/input.jl

@@ -20,7 +20,7 @@ using QuantumESPRESSOBase.PWscf:
     CellParametersCard,
     PWInput
 
-# This regular expression is taken from https://github.com/aiidateam/qe-tools/blob/aedee19/qe_tools/parsers/_input_base.py
+# This regular expression is taken from https://github.com/aiidateam/qe-tools/blob/aedee19/qe_tools/parsers/_input_base.py#L374-L413.
 const ATOMIC_POSITIONS_BLOCK = r"""
 ^ \s* ATOMIC_POSITIONS \s*                      # Atomic positions start with that string
 [{(]? \s* (?P<units>\S+?)? \s* [)}]? \s* $\R    # The units are after the string in optional brackets
@@ -62,29 +62,29 @@ const ATOMIC_POSITIONS_BLOCK = r"""
     )+                                          # A positions block should be one or more lines
 )
 """imx
-# This regular expression is referenced from https://github.com/aiidateam/qe-tools/blob/aedee19/qe_tools/parsers/_input_base.py.
+# This regular expression is referenced from https://github.com/aiidateam/qe-tools/blob/aedee19/qe_tools/parsers/_input_base.py#L548-L593.
 const CELL_PARAMETERS_BLOCK = r"""
-^ [ \t]*
+^[ \t]*
 CELL_PARAMETERS [ \t]*
-[{(]? \s* (?P<option>[a-z]*) \s* [)}]? \h* (?:[\#!].*)? \v  # Match option, do not match comment
+[{(]? [ \t]* (?P<option>[a-zA-Z]*) [ \t]* =? [ \t]* ([-+]?[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)? [)}]? [ \t]* (?:[\#!].*)? \R  # Match option, do not match comment
 (?P<data>
-(?:
-    \s*              # White space in front of the element spec is ok
     (?:
-        [-+]?(?:[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)(?:[ED][-+]?[0-9]+)?  # First number
+        \s*              # White space in front of the element spec is ok
         (?:
-        \s+          # White space between numbers
-        [-+]?(?:[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)(?:[ED][-+]?[0-9]+)?
-        ){2}         # I expect 3 numbers
-        |
-        \#           # If a line is commented out, that is also ok
-        |
-        !            # If a line is commented out, that is also ok
-    )
-    .*               # I do not care what is after the comment or the vector
-    |                # Or
-    ^\s*$            # A line only containing white space
-){3}                 # I need exactly 3 vectors
+            [-+]?(?:[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)(?:[ED][-+]?[0-9]+)?  # First number
+            \s+          # White space between numbers
+            [-+]?(?:[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)(?:[ED][-+]?[0-9]+)?
+            \s+
+            [-+]?(?:[0-9]*\.[0-9]+|[0-9]+\.?[0-9]*)(?:[ED][-+]?[0-9]+)?
+            |
+            \#           # If a line is commented out, that is also ok
+            |
+            !            # If a line is commented out, that is also ok
+        )
+        .*               # I do not care what is after the comment or the vector
+        |                # Or
+        ^\s*$            # A line only containing white space
+    ){3}                 # I need exactly 3 vectors
 )
 """imx
 # This regular expression is referenced from https://github.com/aiidateam/qe-tools/blob/aedee19/qe_tools/parsers/_input_base.py#L683-L691
@@ -239,14 +239,6 @@ function Base.tryparse(::Type{SpecialPointsCard}, str::AbstractString)
         )
     end
 end
-function Base.tryparse(::Type{KPointsCard}, str::AbstractString)
-    for T in (GammaPointCard, KMeshCard, SpecialPointsCard)
-        x = tryparse(T, str)
-        if x !== nothing
-            return x
-        end
-    end
-end
 function Base.tryparse(::Type{CellParametersCard}, str::AbstractString)
     m = match(CELL_PARAMETERS_BLOCK, str)
     # Function `match` only searches for the first match of the regular expression, so it could be a `nothing`
@@ -271,13 +263,29 @@ function Base.tryparse(::Type{CellParametersCard}, str::AbstractString)
     end
 end
 
-function Base.parse(::Type{T}, str::AbstractString) where {T<:Card}
-    x = tryparse(T, str)
-    if x === nothing
-        throw(Meta.ParseError("cannot find card `$(groupname(T))`!"))
-    else
-        return x
-    end
+function Base.parse(::Type{AtomicSpeciesCard}, str::AbstractString)
+    obj = tryparse(AtomicSpeciesCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
+end
+function Base.parse(::Type{AtomicPositionsCard}, str::AbstractString)
+    obj = tryparse(AtomicPositionsCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
+end
+function Base.parse(::Type{CellParametersCard}, str::AbstractString)
+    obj = tryparse(CellParametersCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
+end
+function Base.parse(::Type{GammaPointCard}, str::AbstractString)
+    obj = tryparse(GammaPointCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
+end
+function Base.parse(::Type{KMeshCard}, str::AbstractString)
+    obj = tryparse(KMeshCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
+end
+function Base.parse(::Type{SpecialPointsCard}, str::AbstractString)
+    obj = tryparse(SpecialPointsCard, str)
+    isnothing(obj) ? throw(ParseError("no matched string found!")) : return obj
 end
 function Base.parse(::Type{PWInput}, str::AbstractString)
     args = []
@@ -288,12 +296,17 @@ function Base.parse(::Type{PWInput}, str::AbstractString)
         nml = tryparse(T, str)
         push!(args, f => (nml === nothing ? T() : nml))
     end
-    for (f, T) in zip(
-        (:atomic_species, :atomic_positions, :k_points),
-        (AtomicSpeciesCard, AtomicPositionsCard, KPointsCard),
-    )  # Must-have cards, or else error
+    for (f, T) in
+        zip((:atomic_species, :atomic_positions), (AtomicSpeciesCard, AtomicPositionsCard))  # Must-have cards, or else error
         push!(args, f => parse(T, str))
     end
+    for (T) in (GammaPointCard, KMeshCard, SpecialPointsCard)
+        card = tryparse(T, str)
+        if !isnothing(card)
+            push!(args, :k_points => card)
+            break
+        end
+    end
     for (f, T) in zip((:cell_parameters,), (CellParametersCard,))
         card = tryparse(T, str)  # Optional cards
         push!(args, f => card)

src/PWscf/output/each.jl

@@ -6,6 +6,8 @@ export eachstep,
     eachunconvergedenergy,
     eachconvergedenergy,
     each_energy_by_step,
+    eachcellparameterscard,
+    eachatomicpositionscard,
     eachtimeditem
 
 abstract type Each end
@@ -281,6 +283,12 @@ eachconvergedenergy(str::AbstractString) =
 
 function each_energy_by_step end
 
+eachcellparameterscard(str::AbstractString) =
+    EachParsed{CellParametersCard}(CELL_PARAMETERS_BLOCK, str)
+
+eachatomicpositionscard(str::AbstractString) =
+    EachParsed{AtomicPositionsCard}(ATOMIC_POSITIONS_BLOCK, str)
+
 struct TimedItem <: PWOutputItem
     name::String
     cpu::Millisecond

src/PWscf/output/output.jl

@@ -12,7 +12,6 @@ abstract type PWOutputItem end
 include("regexes.jl")
 include("once.jl")
 include("each.jl")
-include("atomicstructure.jl")
 include("misc.jl")
 
 function parse_symmetries(str::AbstractString)