AtomsBase compat

Project.toml

@@ -46,7 +46,7 @@ MollyPythonCallExt = "PythonCall"
 
 [compat]
 Atomix = "0.1"
-AtomsBase = "0.4"
+AtomsBase = "0.5"
 AtomsCalculators = "0.2"
 BioStructures = "4"
 CUDA = "4.2, 5"
@@ -69,7 +69,7 @@ PeriodicTable = "1.1"
 PythonCall = "0.9"
 Random = "1.9"
 Reexport = "1"
-SimpleCrystals = "0.3"
+SimpleCrystals = "0.4"
 SparseArrays = "1.9"
 StaticArrays = "1.8.2"
 Statistics = "1.9"

docs/src/examples.md

@@ -791,7 +791,7 @@ using AtomsCalculators
 
 ab_sys = AtomsBase.AbstractSystem(
     make_test_system().system; 
-    bounding_box = [[1.54732, 0.0      , 0.0      ],
+    cell_vectors = [[1.54732, 0.0      , 0.0      ],
                     [0.0    , 1.4654985, 0.0      ],
                     [0.0    , 0.0      , 1.7928950]]u"Å",
 )

src/spatial.jl

@@ -208,7 +208,7 @@ Unitful.ustrip(u::Unitful.Units, b::CubicBoundary) = CubicBoundary(ustrip.(u, b.
 Unitful.ustrip(b::RectangularBoundary) = RectangularBoundary(ustrip.(b.side_lengths))
 Unitful.ustrip(u::Unitful.Units, b::RectangularBoundary) = RectangularBoundary(ustrip.(u, b.side_lengths))
 
-function AtomsBase.bounding_box(b::CubicBoundary)
+function AtomsBase.cell_vectors(b::CubicBoundary)
     z = zero(b[1])
     bb = (
         SVector(b[1], z   , z   ),
@@ -218,7 +218,7 @@ function AtomsBase.bounding_box(b::CubicBoundary)
     return unit(z) == NoUnits ? (bb .* u"nm") : bb # Assume nm without other information
 end
 
-function AtomsBase.bounding_box(b::RectangularBoundary)
+function AtomsBase.cell_vectors(b::RectangularBoundary)
     z = zero(b[1])
     bb = (
         SVector(b[1], z   ),
@@ -227,7 +227,7 @@ function AtomsBase.bounding_box(b::RectangularBoundary)
     return unit(z) == NoUnits ? (bb .* u"nm") : bb
 end
 
-function AtomsBase.bounding_box(b::TriclinicBoundary)
+function AtomsBase.cell_vectors(b::TriclinicBoundary)
     bb = (b.basis_vectors[1], b.basis_vectors[2], b.basis_vectors[3])
     return unit(b[1][1]) == NoUnits ? (bb .* u"nm") : bb
 end

src/types.jl

@@ -677,7 +677,7 @@ function System(crystal::Crystal{D};
     coords = [SVector{D}(AtomsBase.position(crystal, i)) for i in 1:length(crystal)]
 
     # Build bounding box
-    side_lengths = norm.(AtomsBase.bounding_box(crystal))
+    side_lengths = norm.(AtomsBase.cell_vectors(crystal))
     if any(typeof(crystal.lattice.crystal_family) .<: [CubicLattice, OrthorhombicLattice, TetragonalLattice])
         boundary = CubicBoundary(side_lengths...)
     elseif any(typeof(crystal.lattice.crystal_family) .<: [SquareLattice, RectangularLattice])
@@ -1162,12 +1162,12 @@ function AtomsBase.atomic_number(s::Union{System, ReplicaSystem}, i::Integer)
     end
 end
 
-AtomsBase.bounding_box(s::System) = AtomsBase.bounding_box(s.boundary)
-AtomsBase.bounding_box(s::ReplicaSystem) = AtomsBase.bounding_box(s.replicas[1])
+AtomsBase.cell_vectors(s::System) = AtomsBase.cell_vectors(s.boundary)
+AtomsBase.cell_vectors(s::ReplicaSystem) = AtomsBase.cell_vectors(s.replicas[1])
 
 function AtomsBase.cell(sys::System{D}) where D
     return AtomsBase.PeriodicCell(
-        AtomsBase.bounding_box(sys),
+        AtomsBase.cell_vectors(sys),
         has_infinite_boundary(sys) ? ntuple(i -> !isinf(sys.boundary.side_lengths[i]), D) :
                                      ntuple(i -> true, D),
     )
@@ -1199,7 +1199,7 @@ convenience constructor `System(sys::System)`.
 function System(sys::AtomsBase.AbstractSystem{D};
                 force_units=u"kJ * mol^-1 * nm^-1",
                 energy_units=u"kJ * mol^-1") where D
-    bb = AtomsBase.bounding_box(sys)
+    bb = AtomsBase.cell_vectors(sys)
     is_cubic = true
     for (i, bv) in enumerate(bb)
         for j in 1:(i - 1)

test/basic.jl

@@ -91,7 +91,7 @@
     @test TriclinicBoundary(b.basis_vectors) == b
     @test TriclinicBoundary([b.basis_vectors[1], b.basis_vectors[2], b.basis_vectors[3]]) == b
 
-    @test AtomsBase.bounding_box(b) == (b.basis_vectors[1], b.basis_vectors[2], b.basis_vectors[3])
+    @test AtomsBase.cell_vectors(b) == (b.basis_vectors[1], b.basis_vectors[2], b.basis_vectors[3])
     @test volume(b) ≈ 3.89937463181886u"nm^3"
     @test isapprox(box_center(b), SVector(2.28944, 1.1359815, 0.5116602)u"nm"; atol=1e-6u"nm")
     sb = scale_boundary(b, 1.2)
@@ -476,7 +476,7 @@ end
     # Update values to be something that works with Molly
     ab_sys_2 = AtomsBase.AbstractSystem(
         ab_sys_1;
-        bounding_box = [[1.54732, 0.0      , 0.0],
+        cell_vectors = [[1.54732, 0.0      , 0.0],
                         [0.0    , 1.4654985, 0.0],
                         [0.0    , 0.0      , Inf]]u"Å",
     )
@@ -487,7 +487,7 @@ end
 @testset "AtomsCalculators" begin
     ab_sys = AtomsBase.AbstractSystem(
         make_test_system().system;
-        bounding_box = [[1.54732, 0.0      , 0.0      ],
+        cell_vectors = [[1.54732, 0.0      , 0.0      ],
                         [0.0    , 1.4654985, 0.0      ],
                         [0.0    , 0.0      , 1.7928950]]u"Å",
     )

test/simulation.jl

@@ -27,7 +27,7 @@
     random_velocities!(s, temp)
 
     @test masses(s) == fill(10.0u"g/mol", n_atoms)
-    @test AtomsBase.bounding_box(s) == (
+    @test AtomsBase.cell_vectors(s) == (
         SVector(2.0, 0.0)u"nm",
         SVector(0.0, 2.0)u"nm",
     )
@@ -109,7 +109,7 @@ end
         @test AtomsBase.mass(s, 5) == atom_mass
         @test AtomsBase.atomic_symbol(s) == fill(:Ar, n_atoms)
         @test AtomsBase.atomic_symbol(s, 5) == :Ar
-        @test AtomsBase.bounding_box(s) == (
+        @test AtomsBase.cell_vectors(s) == (
             SVector(2.0, 0.0, 0.0)u"nm",
             SVector(0.0, 2.0, 0.0)u"nm",
             SVector(0.0, 0.0, 2.0)u"nm",
@@ -671,7 +671,7 @@ end
     @test eachindex(repsys) == Base.OneTo(n_atoms)
     @test AtomsBase.mass(repsys, :) == fill(atom_mass, n_atoms)
     @test AtomsBase.mass(repsys, 5) == atom_mass
-    @test AtomsBase.bounding_box(repsys) == (
+    @test AtomsBase.cell_vectors(repsys) == (
         SVector(2.0, 0.0, 0.0)u"nm",
         SVector(0.0, 2.0, 0.0)u"nm",
         SVector(0.0, 0.0, 2.0)u"nm",