Fix bug in parse_as_chemfile, types need to be reversed (#19)

* Fix bug in `parse_as_chemfile`, `types` need to be reversed * Add Non-CIF tests and fix an UndefVarError in error string
coudertlab · Nov 21, 2023 · 6fb53b3 · 6fb53b3
1 parent bcdd0aa
commit 6fb53b3
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Showing 3 changed files with 49 additions and 1 deletion.
diff --git a/src/input.jl b/src/input.jl
@@ -730,7 +730,8 @@ function sanitize_removeatoms!(graph::PeriodicGraph3D, pos, types, mat, options)
                     typu = types[u.v]
                     if typu === :C
                         u.v ∈ toremove && continue
-                        Float64(norm(mat * (pos[u.v] .+ u.ofs .- pos[i]))) > 1.45 && continue
+                        bondlength = Float64(norm(mat * (pos[u.v] .+ u.ofs .- pos[i])))
+                        bondlength > 1.45 && continue
                         @ifwarn if isempty(toremove)
                             @warn lazy"C suspiciously close to a metal (bond length: $bondlength) will be removed."
                         end
@@ -1110,6 +1111,7 @@ function parse_as_chemfile(frame::Chemfiles.Frame, options::Options, name::Strin
             push!(types, typ)
         end
     end
+    reverse!(types)
 
     _pos = collect(eachcol(Chemfiles.positions(frame)))
     cell = cell_with_warning(SMatrix{3,3,BigFloat,9}(Chemfiles.matrix(Chemfiles.UnitCell(frame)))')

diff --git a/test/Moganite.xyz b/test/Moganite.xyz
@@ -0,0 +1,38 @@
+36
+Lattice="8.7371 0.0 0.0 0.0 4.8692 0.0 -0.036115822218046476 0.0 10.721639172131542" Properties=species:S:1:pos:R:3 pbc="T T T"
+Si       2.18427500       4.73578392       0.00000000
+Si       6.53476709       2.30118392       5.36081959
+Si       6.55282500       0.13341608       0.00000000
+Si       2.16621709       2.56801608       5.36081959
+Si       0.08391745       1.21048312       1.80337971
+Si       4.43440954       3.64508312       7.16419929
+Si       4.24851673       1.21048312       8.91825946
+Si       8.63512464       3.64508312       3.55743988
+Si       4.45246745       3.65871688       1.80337971
+Si       0.06585954       1.22411688       7.16419929
+Si       8.61706673       3.65871688       8.91825946
+Si       4.26657464       1.22411688       3.55743988
+O        8.53536338       0.31357648       3.08568775
+O        4.14875547       2.74817648       8.44650734
+O        4.53417080       0.31357648       7.63595142
+O        0.18367871       2.74817648       2.27513183
+O        4.16681338       4.55562352       3.08568775
+O        8.51730547       2.12102352       8.44650734
+O        0.16562080       4.55562352       7.63595142
+O        4.55222871       2.12102352       2.27513183
+O        1.46246657       0.83165936       1.07430825
+O        5.81295866       3.26625936       6.43512783
+O        2.86996760       0.83165936       9.64733093
+O        7.25657551       3.26625936       4.28651134
+O        5.83101657       4.03754064       1.07430825
+O        1.44440866       1.60294064       6.43512783
+O        7.23851760       4.03754064       9.64733093
+O        2.88802551       1.60294064       4.28651134
+O        7.60146031       1.11796832       0.72371064
+O        3.21485240       3.55256832       6.08453023
+O        5.46807387       1.11796832       9.99792853
+O        1.11758178       3.55256832       4.63710894
+O        3.23291031       3.75123168       0.72371064
+O        7.58340240       1.31663168       6.08453023
+O        1.09952387       3.75123168       9.99792853
+O        5.48613178       1.31663168       4.63710894
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -409,3 +409,11 @@ end
     Test.get_testset().n_passed += length(unstabletry) - failures
     @test failures == 0
 end
+
+@testset "Non-CIF Files" begin
+    testcase = joinpath(last(_finddirs()), "test", "Moganite.xyz")
+    mogtopo = extract1(determine_topology(testcase))
+    @test string(mogtopo) == "mog"
+    # Test ordering of species is correct while parsing with chemfiles
+    @test parse_chemfile(testcase).types == [repeat([:Si], 12); repeat([:O], 24)]
+end