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View Code? Open in Web Editor NEWXCrySDen XSF read/write support for Julia
License: MIT License
XCrySDen XSF read/write support for Julia
License: MIT License
TIL that the XSF format also allows for specifying atoms by their symbols instead of the atomic number. Quoting the spec (http://www.xcrysden.org/doc/XSF.html):
An entry for an atom looks like:
AtNum X Y Z
where AtNum stands for atomic number (or symbol)
I noticed this trying to parse this file using AtomsIO: https://github.com/aiidateam/acwf-verification-scripts/blob/main/0-preliminary-do-not-run/oxides/xsfs-oxides-verification-PBE-v1/Li-XO.xsf
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.
It looks like the current implementation does not handle the case of atomic symbols. For comparison, here is the corresponding line in ASE https://wiki.fysik.dtu.dk/ase/_modules/ase/io/xsf.html:
tokens = positionline.split()
symbol = tokens[0]
if symbol.isdigit():
numbers.append(int(symbol))
else:
numbers.append(atomic_numbers[symbol.capitalize()])
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I'm currently working on Electrum.jl, which has some support for reading XSF files. There's support for some functionality that isn't implemented in this package (primarily reading/writing of data grids), and some that I'd like to implement (animated XSFs/band grids).
I do think it's good for a package to exist independently of Electrum that provides support for XSF file I/O; I just want to make sure that we can benefit from each other and not have to reinvent the wheel too many times. Feel free to just pull code straight from Electrum and adapt it as needed.
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