more AtomsBase compatibility (#151)

* more AtomsBase compatibility

* change `chemical_formula` to `empirical_formula`

Project.toml

@@ -1,7 +1,7 @@
 name = "Xtals"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 authors = ["SimonEnsemble <cory.simon@oregonstate.edu>"]
-version = "0.3.13"
+version = "0.4.0"
 
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

docs/src/crystal.md

@@ -71,7 +71,7 @@ xtal.atoms.n, super_xtal.atoms.n
 ```julia
 rho = crystal_density(xtal)         # Crystal density of the crystal in kg/m^2
 mw = molecular_weight(xtal)         # The molecular weight of the unit cell in amu
-formula = chemical_formula(xtal)    # The irreducible chemical formula of the crystal
+formula = empirical_formula(xtal)    # The irreducible chemical formula of the crystal
 ```
 
 ## Assigning new charges
@@ -95,7 +95,7 @@ Bravais unit cell of a crystal.
 
 	# atoms = 424
 	# charges = 424
-	chemical formula: Dict(:Zn => 4, :H => 12, :O => 13, :C => 24)
+	chemical formula: C₁₉₂H₉₆O₁₀₄Zn₃₂
 	space Group: P1
 	symmetry Operations:
 		'x, y, z'
@@ -125,7 +125,7 @@ write_xyz(xtal, "my_new_xyz_file.xyz")      # stored in the current directory
     replicate
     molecular_weight
     crystal_density
-    chemical_formula
+    empirical_formula
     assign_charges
     write_cif
     write_xyz

src/Xtals.jl

@@ -50,7 +50,7 @@ export
     read_xyz, write_xyz, read_mol, write_mol2, assert_P1_symmetry, set_paths, view_crystal,
 
     # crystal.jl
-    Crystal, strip_numbers_from_atom_labels!, assign_charges, chemical_formula, molecular_weight, 
+    Crystal, strip_numbers_from_atom_labels!, assign_charges, empirical_formula, molecular_weight, 
     crystal_density, write_cif, has_charges, apply_symmetry_operations, write_cssr, rename,
     # AtomsBase things also from crystal
     position, velocity, bounding_box, boundary_conditions,

src/crystal.jl

@@ -627,7 +627,7 @@ end
 vtk_filename(crystal::Crystal) = replace(replace(crystal.name, ".cif" => ""), ".cssr" => "") * ".vtk"
 
 """
-    formula = chemical_formula(crystal, verbose=false)
+    formula = empirical_formula(crystal, verbose=false)
 
 Find the irreducible chemical formula of a crystal structure.
 
@@ -638,7 +638,7 @@ Find the irreducible chemical formula of a crystal structure.
 # Returns
 - `formula::Dict{Symbol, Int}`: A dictionary with the irreducible chemical formula of a crystal structure
 """
-function chemical_formula(crystal::Crystal; verbose::Bool=false)
+function empirical_formula(crystal::Crystal; verbose::Bool=false)
     unique_atoms = unique(crystal.atoms.species)
     # use dictionary to count atom types
     atom_counts = Dict{Symbol, Int}([a => 0 for a in unique_atoms])
@@ -1110,11 +1110,19 @@ function Base.:+(crystals::Crystal...; check_overlap::Bool=true, name::String="a
     return crystal
 end
 
-# AtomsBase interface things...NB that the indexing/iteration aspects aren't included because they would conflict with how slicing is defined in this package
+# AtomsBase interface things
 import Base.position
 import AtomsBase.velocity
 import AtomsBase.bounding_box
 import AtomsBase.boundary_conditions
+import Base.length, Base.getindex
+import AtomsBase.atomic_symbol
+
+length(xtal::Crystal) = xtal.atoms.n
+
+getindex(xtal::Crystal, index::Int) = xtal.atoms[index]
+
+atomic_symbol(atom::Atoms) = atom.species[1]
 
 function position(crystal::Crystal)
     pos = Cart(crystal.atoms.coords, crystal.box).x
@@ -1124,4 +1132,5 @@ end
 velocity(::Crystal) = missing
 
 bounding_box(crystal::Crystal) = SVector{3}([SVector{3}(crystal.box.f_to_c[:,i]u"Å") for i in 1:3])
+
 boundary_conditions(::Crystal) = SVector{3,BoundaryCondition}([Periodic(), Periodic(), Periodic()])

test/crystal.jl

@@ -62,7 +62,7 @@ irmof1 = Crystal("IRMOF-1.cif")
     @test isapprox(xtal2.charges, Charges([-2.0, 2.0], Frac([0.2 0.6; 0.5 0.3; 0.7 0.1])))
     @test ! neutral(assign_charges(xtal, Dict(:Ca => 2.0, :O => 2.0), 100.0)) # not charge neutral
     @test_throws ErrorException assign_charges(xtal, Dict(:Ca => 2.0, :O => 2.0)) # not charge neutral
-    @test chemical_formula(xtal) == Dict(:Ca => 1, :O => 1)
+    @test empirical_formula(xtal) == Dict(:Ca => 1, :O => 1)
     @test molecular_weight(xtal) ≈ 15.9994 + 40.078
     xtal3 = assign_charges(xtal2, Dict(:Ca => -2.0, :O => 2.0))
     @test isapprox(xtal2.charges, xtal3.charges)
@@ -78,7 +78,7 @@ irmof1 = Crystal("IRMOF-1.cif")
 
     @test isapprox(xtal.atoms, Atoms([:Ca, :Ca, :O, :C], f))
     @test isapprox(net_charge(xtal), 2.0)
-    @test chemical_formula(xtal) == Dict(:Ca => 2, :O => 1, :C => 1)
+    @test empirical_formula(xtal) == Dict(:Ca => 2, :O => 1, :C => 1)
     infer_bonds!(xtal, true)
     @test_throws ErrorException Xtals.remove_duplicate_atoms_and_charges(xtal)
 
@@ -225,7 +225,7 @@ irmof1 = Crystal("IRMOF-1.cif")
     @test Xtals.replication_factors(replicated_sbmof.box, 14.0) == (1, 1, 1)
     @test isapprox(sbmof.atoms.coords.xf[:, 1] ./ repfactors, replicated_sbmof.atoms.coords.xf[:, 1])
     @test isapprox(replicated_sbmof.box.reciprocal_lattice, 2 * π * inv(replicated_sbmof.box.f_to_c))
-    @test chemical_formula(sbmof) == chemical_formula(replicated_sbmof)
+    @test empirical_formula(sbmof) == empirical_formula(replicated_sbmof)
     @test isapprox(crystal_density(sbmof), crystal_density(replicated_sbmof), atol=1e-7)
 
     xtal = deepcopy(sbmof1)
@@ -355,8 +355,8 @@ irmof1 = Crystal("IRMOF-1.cif")
     infer_bonds!(xtal1, true)
     @test_throws ErrorException replicate(xtal1, (1,1,1))
 
-    # test verbose printing in chemical_formula
-    Xtals.chemical_formula(xtal1, verbose=true)
+    # test verbose printing in empirical_formula
+    empirical_formula(xtal1, verbose=true)
     @test true
 
     @test xtal1 == apply_symmetry_operations(xtal1)