improved wannier projections regex and standardize_cell! added

Author: louisponet

Project.toml

@@ -2,7 +2,7 @@ name = "DFControl"
 uuid = "1e31e15d-4957-550d-a244-318eced754ae"
 authors = ["Louis Ponet <[email protected]>"]
 repo = "https://github.com/louisponet/DFControl.jl.git"
-version = "0.5.26"
+version = "0.5.27"
 
 [deps]
 ANSIColoredPrinters = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"

src/Display/printing.jl

@@ -1,5 +1,5 @@
-show_type(io::IO, ::MIME"text/plain", ::Type{T}) where {T} = println(io, crayon"red", "$T:", crayon"reset")
-show_type(io::IO, ::MIME"text/plain", x) = show_type(io, typeof(x))
+show_type(io::IO, ::Type{T}) where {T} = println(io, crayon"red", "$T:", crayon"reset")
+show_type(io::IO, x) = show_type(io, typeof(x))
 
 function Base.show(io::IO, ::MIME"text/plain", block::InputData)
     s = """Block name: $(block.name)

src/FileIO/wannier.jl

@@ -114,9 +114,9 @@ function wan_parse_calculation(file)
                     if occursin("random", line)
                         proj_block = InputData(:projections, :random, nothing)
                     else
-                        split_line  = strip_split(line, ':')
-                        atom        = Symbol(split_line[1])
-                        projections = [proj for proj in strip_split(split_line[2], ';')]
+                        m = match(r"\b([\w\d]+):", line)
+                        atom        = Symbol(m.captures[1])
+                        projections = map(x->x.captures[1], eachmatch(r"[\s,;]([\w\d]+)", line))
                         push!(proj_dict, (atom, projections))
                     end
                     i += 1

src/Structures/structure.jl

@@ -414,6 +414,37 @@ function find_primitive(s::Structure; kwargs...)
     return Structure(new_cell, newats)
 end
 
+function standardize_cell!(s::SPGStructure; tolerance = DEFAULT_TOLERANCE, to_primitive=false, no_idealize=false)
+    nat = length(s.species_indices)
+    if !to_primitive
+        t_positions = [s.positions  zeros(Float64, 3, 3*nat)]
+        t_species_indices = [s.species_indices;  zeros(Int, 3*nat)]
+    else
+        t_positions       = s.positions
+        t_species_indices = s.species_indices
+    end
+    # @show t_species_indices
+    numat = ccall((:spg_standardize_cell, SPGLIB), Cint,
+                   (Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cint}, Cint, Cint, Cint, Cdouble),
+                   s.lattice, t_positions, t_species_indices, nat, to_primitive, no_idealize, tolerance)
+    numat == 0 && error("Could not find the standardized cell of the supplied structure.")
+    return SPGStructure(s.lattice, t_positions[:, 1:numat], t_species_indices[1:numat])
+end
+
+function standardize_cell(s::Structure; kwargs...)
+    uats = unique(s.atoms)
+    spg = standardize_cell!(SPGStructure(s); kwargs...)
+    new_cell = Mat3{Float64}(spg.lattice') * unit(eltype(s.cell))
+    newats = eltype(uats)[]
+    for i in 1:length(spg.species_indices)
+        tat = deepcopy(uats[spg.species_indices[i]])
+        set_position!(tat, Point3(spg.positions[:, i]), new_cell)
+        push!(newats, tat)
+    end
+
+    return Structure(new_cell, newats)
+end
+
 """
     cell_parameters(cell::Mat3)
     cell_parameters(str::Structure)