Properly integrate XSF

docs/src/file_formats.md

@@ -46,6 +46,7 @@ The following list all currently available parsers, in the order they are tried
 
 ```@docs
 AtomsIO.ExtxyzParser
+AtomsIO.XcrysdenstructureformatParser
 AtomsIO.ChemfilesParser
 AtomsIOPython.AseParser
 ```

docs/src/index.md

@@ -6,6 +6,7 @@ AtomsIO currently integrates with
 
   - [Chemfiles](https://github.com/chemfiles/Chemfiles.jl)
   - [ExtXYZ](https://github.com/libAtoms/ExtXYZ.jl)
+  - [XCrySDenStructureFormat](https://github.com/azadoks/XCrySDenStructureFormat.jl)
   - [ASEconvert](https://github.com/mfherbst/ASEconvert.jl)
     (respectively [ASE](https://wiki.fysik.dtu.dk/ase/))
 
@@ -16,6 +17,7 @@ and supports all file formats any of these packages support
   - [Quantum Espresso](https://www.quantum-espresso.org/Doc/INPUT_PW.html) / [ABINIT](https://docs.abinit.org/variables/) / [VASP](https://www.vasp.at/wiki/) input files
   - ASE / [Gromacs](http://manual.gromacs.org/archive/5.0.7/online/trj.html) / [LAMMPS](https://lammps.sandia.gov/doc/dump.html) / [Amber](http://ambermd.org/netcdf/nctraj.xhtml) trajectory files
   - [XYZ](https://openbabel.org/wiki/XYZ) and [extxyz](https://github.com/libAtoms/extxyz#extended-xyz-specification-and-parsing-tools) files
+  - [XSF](http://www.xcrysden.org/doc/XSF.html) (XCrySDen) atomic structure files.
 
 For more details see [Saving and loading files](@ref) and [File Formats](@ref).
 

src/AtomsIO.jl

@@ -6,8 +6,10 @@ import PeriodicTable
 include("parser.jl")
 include("chemfiles.jl")
 include("extxyz.jl")
+include("xsf.jl")
 include("saveload.jl")
 
 export load_system, save_system, load_trajectory, save_trajectory
-export AbstractParser, ChemfilesParser, ExtxyzParser
+export AbstractParser
+export ChemfilesParser, ExtxyzParser, XcrysdenstructureformatParser
 end

src/saveload.jl

@@ -4,7 +4,9 @@
 # *breaking change* (as it alters the behaviour of AtomsIO.load_system).
 # Moreover since not all users will want to rely on Python dependencies, it is
 # crucial that the python packages are only *appended* to this list.
-const DEFAULT_PARSER_ORDER = AbstractParser[ExtxyzParser(), ChemfilesParser()]
+const DEFAULT_PARSER_ORDER = AbstractParser[
+    ExtxyzParser(), XcrysdenstructureformatParser(), ChemfilesParser(),
+]
 
 function determine_parser(file; save=false, trajectory=false)
     idx_parser = findfirst(DEFAULT_PARSER_ORDER) do parser

src/xsf.jl

@@ -1,43 +1,55 @@
 import XCrySDenStructureFormat as XSF
 
 """
-Parse or write file using [XSF](https://github.com/azadoks/XCrySDenStructureFormat.jl)
+Parse or write file using [XCrySDenStructureFormat](https://github.com/azadoks/XCrySDenStructureFormat.jl).
 
 Supported formats:
-  - [XSF](http://www.xcrysden.org/doc/XSF.html)
+  - [XSF](http://www.xcrysden.org/doc/XSF.html) and [AXSF](XCrySDenStructureFormat)
+    atomic structure files. These are the files typically used by the
+    [XCrySDen](http://www.xcrysden.org/) visualisation program.
 """
-struct XsfParser <: AbstractParser end
+struct XcrysdenstructureformatParser <: AbstractParser end
 
-function supports_parsing(::XsfParser, file; save, trajectory)
+function supports_parsing(::XcrysdenstructureformatParser, file; save, trajectory)
     _, ext = splitext(file)
     ext in (".xsf", ".axsf")
 end
 
-function load_system(::XsfParser, file::AbstractString, index=nothing)
-    if isnothing(index)
-        frames = XSF.load_xsf(file)
+function load_system(::XcrysdenstructureformatParser, file::AbstractString, index=nothing)
+    if !isnothing(index)
+        return XSF.load_xsf(file)[index]
+    end
+
+
+    frames = XSF.load_xsf(file)
+    if !(frames isa AbstractVector)
+        # load_xsf Returns plain structure in case only a single structure in the file
+        return frames
+    else
         isempty(frames) && error(
             "XSF returned no frames. Check the passed file is a valid (a)xsf file."
         )
         return last(frames)
-    else
-        return XSF.load_xsf(file)[index]
     end
 end
 
-function save_system(::XsfParser, file::AbstractString, system::AbstractSystem)
+function save_system(::XcrysdenstructureformatParser,
+                     file::AbstractString, system::AbstractSystem)
     XSF.save_xsf(file, system)
 end
 
-function load_trajectory(::XsfParser, file::AbstractString)
-    XSF.load_xsf(file)
-end
-
-function save_system(::XsfParser, file::AbstractString, system::AbstractSystem)
-    XSF.save_xsf(file, system)
+function load_trajectory(::XcrysdenstructureformatParser, file::AbstractString)
+    # load_xsf Returns plain structure in case only a single structure in the file,
+    # so we need to re-wrap to keep a consistent interface.
+    ret = XSF.load_xsf(file)
+    if !(ret isa AbstractVector)
+        return [ret]
+    else
+        return ret
+    end
 end
 
-function save_trajectory(::XsfParser, file::AbstractString,
+function save_trajectory(::XcrysdenstructureformatParser, file::AbstractString,
                          systems::AbstractVector{<:AbstractSystem})
     XSF.save_xsf(file, systems)
 end

test/failed_files.jl

@@ -5,6 +5,14 @@ using LinearAlgebra
 
 # Tests parsing files, where previously users reported problems
 @testset "Failed files" begin
+@testset "Empty XYZ" begin
+    @test_throws "ExtXYZ returned no frames." load_system("files/empty.xyz")
+end
+
+@testset "XYZ from Lammps" begin
+    @test_throws "ExtXYZ returned no frames." load_system("files/lammps.xyz")
+end
+
 @testset "CIF Graphene P6/mmm" begin
     parsed = load_system("files/graphene.cif")
     reduced = reduce(hcat, bounding_box(parsed))
@@ -15,7 +23,5 @@ using LinearAlgebra
     @test atomic_symbol(parsed) == [:C1, :C2, :C3, :C4]
     @test atomic_number(parsed) == [6, 6, 6, 6]
     @test parsed[:name] == "Graphene"
-
-
 end
 end

test/files/empty.xyz

@@ -0,0 +1,4 @@
+
+
+
+

test/files/lammps.xyz

@@ -0,0 +1,3 @@
+1
+Atoms. Timestep: 1000000
+Ar    1.4102613692638457    0.9647607662828660    1.3209769521273491

test/runtests.jl

@@ -8,6 +8,7 @@ if GROUP == "Core"
     @testset "AtomsIO.jl" begin
         include("chemfiles.jl")
         include("extxyz.jl")
+        include("xsf.jl")
         include("failed_files.jl")
         # For the comparison tests (also between Chemfiles and ExtXYZ and other
         # non-python libraries) see the AtomsIOPython subproject

test/xsf.jl

@@ -3,6 +3,8 @@ using Test
 using AtomsBaseTesting
 
 @testset "XSF system write / read" begin
+    XsfParser = AtomsIO.XcrysdenstructureformatParser
+
     system = make_test_system().system
     mktempdir() do d
         outfile = joinpath(d, "output.xsf")
@@ -13,6 +15,8 @@ using AtomsBaseTesting
 end
 
 @testset "XSF trajectory write/read" begin
+    XsfParser = AtomsIO.XcrysdenstructureformatParser
+
     systems = [make_test_system().system for _ in 1:3]
     mktempdir() do d
         outfile = joinpath(d, "output.axsf")
@@ -28,6 +32,8 @@ end
 
 @testset "ExtXYZ supports_parsing" begin
     import AtomsIO: supports_parsing
+    XsfParser = AtomsIO.XcrysdenstructureformatParser
+
     prefix = "test"
     save = trajectory = true
     @test  supports_parsing(XsfParser(), prefix * ".xsf";    save, trajectory)