azadoks / xcrysdenstructureformat.jl Goto Github PK

julia> using AtomsIO

julia> system = load_system("data/Li-XO.xsf")
ERROR: ArgumentError: invalid base 10 digit 'L' in "Li"
Stacktrace:
  [1] tryparse_internal(::Type{Int64}, s::SubString{String}, startpos::Int64, endpos::Int64, base_::Int64, raise::Bool)
    @ Base ./parse.jl:143
  [2] parse(::Type{Int64}, s::SubString{String}; base::Nothing)
    @ Base ./parse.jl:254
  [3] parse
    @ ./parse.jl:253 [inlined]
  [4] parse_coord_line(T::Type{Float64}, line::String)
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:84
  [5] (::XCrySDenStructureFormat.var"#3#4"{DataType, Base.EachLine{IOStream}})(::Int64)
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:101
  [6] iterate
    @ ./generator.jl:47 [inlined]
  [7] _collect(c::UnitRange{…}, itr::Base.Generator{…}, ::Base.EltypeUnknown, isz::Base.HasShape{…})
    @ Base ./array.jl:854
  [8] collect_similar
    @ ./array.jl:763 [inlined]
  [9] map
    @ ./abstractarray.jl:3285 [inlined]
 [10] parse_coord_block(T::Type{Float64}, lines::Base.EachLine{IOStream})
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:100
 [11] parse_xsf_block(T::Type{Float64}, keyword::SubString{String}, lines::Base.EachLine{IOStream})
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:112
 [12] parse_periodic_frame(T::Type{Float64}, lines::Base.EachLine{IOStream}, bcs::Vector{Periodic}, previous_frame::Nothing)
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:140
 [13] load_xsf(T::Type{Float64}, file::String)
    @ XCrySDenStructureFormat ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:202
 [14] load_xsf
    @ ~/.julia/packages/XCrySDenStructureFormat/1Yzsb/src/fileio.jl:208 [inlined]
 [15] load_system
    @ ~/.julia/packages/AtomsIO/NAVEQ/src/xsf.jl:19 [inlined]
 [16] load_system(file::String, index::Nothing; kwargs::@Kwargs{})
    @ AtomsIO ~/.julia/packages/AtomsIO/NAVEQ/src/saveload.jl:45
 [17] load_system
    @ ~/.julia/packages/AtomsIO/NAVEQ/src/saveload.jl:44 [inlined]
 [18] load_system(file::String)
    @ AtomsIO ~/.julia/packages/AtomsIO/NAVEQ/src/saveload.jl:44
 [19] top-level scope
    @ REPL[2]:1
Some type information was truncated. Use `show(err)` to see complete types.

tokens = positionline.split()
symbol = tokens[0]
if symbol.isdigit():
    numbers.append(int(symbol))
else:
    numbers.append(atomic_numbers[symbol.capitalize()])