Add PythonCall.jl support (#11)

* Add PythonCall.jl support by duplicating Python ase interface

* Version bump

Project.toml

@@ -1,7 +1,7 @@
 name = "NQCBase"
 uuid = "78c76ebc-5665-4934-b512-82d81b5cbfb7"
 authors = ["James Gardner <[email protected]> and contributors"]
-version = "0.2.1"
+version = "0.2.9"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"

src/NQCBase.jl

@@ -10,7 +10,8 @@ include("cells.jl")
 include("io/extxyz.jl")
 
 function __init__()
-    @require PyCall="438e738f-606a-5dbb-bf0a-cddfbfd45ab0" @eval include("io/ase.jl")
+    @require PyCall="438e738f-606a-5dbb-bf0a-cddfbfd45ab0" @eval include("io/PyCall-ase.jl")
+    @require PythonCall="6099a3de-0909-46bc-b1f4-468b9a2dfc0d" @eval include("io/PythonCall-ase.jl")
 end
 
 include("atoms_base.jl")

src/io/PythonCall-ase.jl

@@ -0,0 +1,41 @@
+
+using .PythonCall
+using Unitful, UnitfulAtomic
+
+export convert_from_ase_atoms
+export convert_to_ase_atoms
+
+const ase = pyimport("ase")
+
+convert_to_ase_atoms(atoms::Atoms, R::Matrix) =
+    ase.Atoms(positions=ustrip.(u"Å", R'u"bohr"), symbols=string.(atoms.types))
+
+convert_to_ase_atoms(atoms::Atoms, R::Matrix, ::InfiniteCell) =
+    convert_to_ase_atoms(atoms, R)
+
+function convert_to_ase_atoms(atoms::Atoms, R::Matrix, cell::PeriodicCell)
+    ase.Atoms(
+        positions=ustrip.(u"Å", R'u"bohr"),
+        cell=ustrip.(u"Å", cell.vectors'u"bohr"),
+        symbols=string.(atoms.types),
+        pbc=cell.periodicity)
+end
+
+function convert_to_ase_atoms(atoms::Atoms, R::Vector{<:Matrix}, cell::AbstractCell)
+    convert_to_ase_atoms.(Ref(atoms), R, Ref(cell))
+end
+
+convert_from_ase_atoms(ase_atoms::Py) =
+    Atoms(ase_atoms), positions(ase_atoms), Cell(ase_atoms)
+
+Atoms(ase_atoms::Py) = Atoms{Float64}(Symbol.(PyList(ase_atoms.get_chemical_symbols())))
+
+positions(ase_atoms::Py) = austrip.(PyArray(ase_atoms.get_positions())'u"Å")
+
+function Cell(ase_atoms::Py)
+    if all(PyArray(ase_atoms.cell.array) .== 0)
+        return InfiniteCell()
+    else
+        return PeriodicCell{Float64}(austrip.(PyArray(ase_atoms.cell.array)'u"Å"), [Bool(x) for x in ase_atoms.pbc])
+    end
+end