Merge pull request #57 from tjjarvinen/ABv0.5_update

update to AtomsBase v0.5

Project.toml

@@ -12,7 +12,7 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 extxyz_jll = "6ecdc6fc-93a8-5528-aee3-ac7ae1c60be7"
 
 [compat]
-AtomsBase = "0.4.1"
+AtomsBase = "0.5"
 PeriodicTable = "1"
 StaticArrays = "1.5"
 Unitful = "1"

src/atoms.jl

@@ -72,13 +72,13 @@ function Atoms(system::AbstractSystem{D})
     end
 
     system_data = Dict{Symbol,Any}(
-        :bounding_box => bounding_box(system),
+        :cell_vectors => cell_vectors(system),
         :periodicity => periodicity(system) 
     )
 
     # Extract extra system properties
     for (k, v) in pairs(system)
-        atoms_base_keys = (:charge, :multiplicity, :periodicity, :bounding_box)
+        atoms_base_keys = (:charge, :multiplicity, :periodicity, :cell_vectors)
         if k in atoms_base_keys || v isa ExtxyzType || v isa AbstractArray{<: ExtxyzType}
             # These are either Unitful quantities, which are uniformly supported
             # across all of AtomsBase or the value has a type that Extxyz can write
@@ -149,7 +149,7 @@ function Atoms(dict::Dict{String, Any})
 
     system_data = Dict{Symbol, Any}()
     if haskey(dict, "cell")
-        system_data[:bounding_box] = collect(eachrow(dict["cell"]))u"Å"
+        system_data[:cell_vectors] = collect(eachrow(dict["cell"]))u"Å"
         if haskey(dict, "pbc")
             system_data[:periodicity] = tuple(dict["pbc"]...)
         else
@@ -159,7 +159,7 @@ function Atoms(dict::Dict{String, Any})
     else  # Infinite system
         haskey(dict, "pbc") && @warn "'pbc' ignored since no 'cell' entry found in dict."
         system_data[:periodicity] = (false, false, false) 
-        system_data[:bounding_box] = ( SVector(Inf, 0.0, 0.0) * u"Å", 
+        system_data[:cell_vectors] = ( SVector(Inf, 0.0, 0.0) * u"Å", 
                                        SVector(0.0, Inf, 0.0) * u"Å", 
                                        SVector(0.0, 0.0, Inf) * u"Å" )
     end
@@ -217,14 +217,14 @@ function write_dict(atoms::Atoms)
 
     pbc = atoms.system_data.periodicity
     cell = zeros(D, D)
-    for (i, bvector) in enumerate(atoms.system_data.bounding_box)
+    for (i, bvector) in enumerate(atoms.system_data.cell_vectors)
         cell[i, :] = ustrip.(u"Å", bvector)
     end
 
     # Deal with other system keys
     info = Dict{String,Any}()
     for (k, v) in pairs(atoms.system_data)
-        k in (:periodicity, :bounding_box) && continue # Already dealt with
+        k in (:periodicity, :cell_vectors) && continue # Already dealt with
         if k in (:charge, )
             info[string(k)] = ustrip(u"e_au", atoms.system_data[k])
         elseif v isa ExtxyzType
@@ -253,14 +253,14 @@ write_dict(system::AbstractSystem{D}) = write_dict(Atoms(system))
 
 Base.length(sys::Atoms) = length(sys.atom_data.position)
 Base.size(sys::Atoms)   = (length(sys), )
-AtomsBase.bounding_box(sys::Atoms) = sys.system_data.bounding_box
+AtomsBase.cell_vectors(sys::Atoms) = sys.system_data.cell_vectors
 AtomsBase.periodicity(sys::Atoms) = sys.system_data.periodicity
 
 # AtomsBase now requires a cell object to be returned instead of bounding_box 
 # and boundary conditions. But this can just be constructed on the fly. 
 AtomsBase.cell(sys::Atoms) = AtomsBase.PeriodicCell(; 
-                cell_vectors = sys.system_data.bounding_box, 
-                 periodicity = sys.system_data.periodicity )
+                cell_vectors = cell_vectors(sys), 
+                 periodicity = periodicity(sys) )
 
 Base.getindex(sys::Atoms, x::Symbol) = getindex(sys.system_data, x)
 Base.haskey(sys::Atoms, x::Symbol)   = haskey(sys.system_data, x)

test/Project.toml

@@ -1,5 +1,5 @@
 [compat]
-AtomsBaseTesting = "0.2"
+AtomsBaseTesting = "0.4"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"

test/atomsbase.jl

@@ -15,7 +15,7 @@ function simple_test_approx_eq(sys1, sys2; test_cell = true)
     @test atomic_number(sys1, :) == atomic_number(sys2, :)
     @test atomic_symbol(sys1, :) == atomic_symbol(sys2, :)
     @test periodicity(sys1) == periodicity(sys2)
-    @test all(bounding_box(sys1) .≈ bounding_box(sys2))
+    @test all(cell_vectors(sys1) .≈ cell_vectors(sys2))
     if test_cell 
         @test cell(sys1) == cell(sys2)
     end
@@ -27,7 +27,13 @@ end
 end
 
 @testset "Conversion AtomsBase -> dict (velocity)" begin
-    system, atoms, atprop, sysprop, box, bcs = make_test_system()
+    tmp = make_test_system()
+    system = tmp.system
+    atoms  = tmp.atoms
+    atprop = tmp.atprop
+    sysprop = tmp.sysprop
+    box = tmp.cell.cell_vectors
+    bcs = tmp.cell.periodicity
     atoms = ExtXYZ.write_dict(Atoms(system))
 
     c3ll = zeros(3, 3)
@@ -47,16 +53,16 @@ end
     @test info["multiplicity"] == sysprop.multiplicity
 
     arrays = atoms["arrays"]
-    @test arrays["Z"]          == AtomsBase.atomic_number.(atprop.atomic_symbol)
-    @test arrays["species"]    == string.(atprop.atomic_symbol)
+    @test arrays["Z"]          == AtomsBase.atomic_number.(atprop.species)
+    @test arrays["species"]    == string.(atprop.species)
     # mass is not written to the dict because the mass == mass(element)
     # @test arrays["mass"]       == ustrip.(u"u",  atprop.atomic_mass)
     @test arrays["pos"]        ≈  ustrip.(u"Å",  hcat(atprop.position...)) atol=1e-10
     @test arrays["velocities"] ≈  ustrip.(sqrt(u"eV"/u"u"),
                                           hcat(atprop.velocity...)) atol=1e-10
 
     expected_atkeys = ["Z", "species", "charge", "covalent_radius", 
-                       "magnetic_moment", "pos", "vdw_radius", "velocities"]
+                       "magnetic_moment", "mass", "pos", "vdw_radius", "velocities"]
     @test sort(collect(keys(arrays))) == sort(expected_atkeys)
     @test arrays["magnetic_moment"] == atprop.magnetic_moment
     @test arrays["vdw_radius"]      == ustrip.(u"Å", atprop.vdw_radius)
@@ -89,7 +95,6 @@ end
     atoms = @test_logs((:warn, r"Unitful quantity massdata is not yet"),
                        (:warn, r"Writing quantities of type Symbol"),
                        (:warn, r"Unitful quantity md is not yet"),
-                       (:warn, r"Mismatch between atomic numbers and atomic symbols"),
                        match_mode=:any, ExtXYZ.write_dict(Atoms(system)))
 
     @test atoms["arrays"]["species"] == ["H", "H", "C", "N", "He"]
@@ -156,7 +161,7 @@ end
         end
 
         atoms = ExtXYZ.load(fname)
-        box = bounding_box(atoms)
+        box = cell_vectors(atoms)
         @test [box[dim][dim] for dim=1:3] == [Inf * u"bohr" for dim=1:3]
     finally
         isfile(fname) && rm(fname)