Update to AtomsBase v0.5 (#10)

* Add scaled_position for `AtomView` * Replace bounding_box to cell_vectors, boundary_conditions to periodicity, remove AtomsBase 0.3 support * Remove julia 0.6 support, update CI to newer versions, update test * Update documentation CI julia version to 1.11
rashidrafeek · Dec 7, 2024 · 493696e · 493696e · rashidrafeek · Dec 7, 2024
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -18,8 +18,9 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.9'
           - '1.10'
+          - '1.11'
           - 'nightly'
         os:
           - ubuntu-latest

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -18,7 +18,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.6'
+          version: '1.11'
       - uses: julia-actions/cache@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "AtomsToolbox"
 uuid = "f386ec8f-7408-45ea-aa1c-e80969af901e"
 authors = ["Rashid Rafeek <rashidrafeek@gmail.com> and contributors"]
-version = "0.1.1"
+version = "0.1.2"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -13,13 +13,13 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
-AtomsBase = "0.3, 0.4"
+AtomsBase = "0.5"
 PeriodicTable = "1"
 StaticArrays = "1"
 Graphs = "1"
 Distances = "0.10"
 Unitful = "1"
-julia = "1.6"
+julia = "1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

diff --git a/src/AtomsToolbox.jl b/src/AtomsToolbox.jl
@@ -6,12 +6,12 @@ using AtomsBase: AbstractSystem,
                  FastSystem,
                  FlexibleSystem,
                  Atom,
+                 AtomView,
                  position,
                  atomic_number,
                  atomic_symbol,
                  atomic_mass,
-                 bounding_box,
-                 boundary_conditions,
+                 cell_vectors,
                  periodicity
 using Unitful: Unitful, ustrip, @u_str, unit
 import Graphs

diff --git a/src/atomsbase.jl b/src/atomsbase.jl
@@ -15,10 +15,10 @@
 # function Base.getindex(system::AbstractSystem, range::AbstractVector)
 #     particles = collect(system)
 #     return _getconstructor(system)(particles[range],
-#                                    bounding_box(system),
-#                                    boundary_conditions(system))
+#                                    cell_vectors(system),
+#                                    periodicity(system))
 #     # _getconstructor(system)(
-#     #     bounding_box(system), boundary_conditions(system), 
+#     #     cell_vectors(system), periodicity(system), 
 #     #     position(system)[range], atomic_symbol(system)[range],
 #     #     atomic_number(system)[range], atomic_mass(system)[range])
 # end
diff --git a/src/build.jl b/src/build.jl
@@ -8,13 +8,13 @@ function interpolate_systems(sys1::FastSystem, sys2::FastSystem, nimg::Int)
     particles2 = collect(sys2)
     pos1 = position(sys1)
     pos2 = position(sys2)
-    bcs = boundary_conditions(sys1)
-    box = bounding_box(sys1)
+    bcs = periodicity(sys1)
+    box = cell_vectors(sys1)
     syms, nums, masses = atomic_symbol.(particles1),
                          atomic_number.(particles1),
                          atomic_mass.(particles1)
 
-    if !(box == bounding_box(sys2))
+    if !(box == cell_vectors(sys2))
         error("Can't interpolate systems with different cells.")
     end
 

diff --git a/src/getters.jl b/src/getters.jl
@@ -17,15 +17,15 @@ include("pbc_utils.jl")
 
 Obtain the cell lengths as a Vector, [a,b,c].
 """
-cell_lengths(sys::AbstractSystem) = norm.(bounding_box(sys))
+cell_lengths(sys::AbstractSystem) = norm.(cell_vectors(sys))
 
 """
     cell_parameters(sys::AbstractSystem)
 
 Obtain the cell lengths and angles as a Vector, [a,b,c,α,β,γ].
 """
 function cell_parameters(sys::AbstractSystem)
-    av,bv,cv = bounding_box(sys)
+    av,bv,cv = cell_vectors(sys)
     a,b,c = norm.((av,bv,cv))
 
     α = acosd((bv⋅cv)/(b*c))u"°"
@@ -41,7 +41,7 @@ end
 Obtain the cell angles as a Vector, [α,β,γ].
 """
 function cell_angles(sys::AbstractSystem)
-    av,bv,cv = bounding_box(sys)
+    av,bv,cv = cell_vectors(sys)
     a,b,c = norm.((av,bv,cv))
 
     α = acosd((bv⋅cv)/(b*c))u"°"
@@ -83,9 +83,9 @@ number of atoms in the given `system`.
 """
 function distance_matrix(system::AbstractSystem; pbc=all(periodicity(system)))
     if pbc
-        dists = pbc_shortest_vectors(system, position(system), Val(true), Val(false))
+        dists = pbc_shortest_vectors(system, position(system, :), Val(true), Val(false))
     else
-        dists = pairwise(Euclidean(), position(system))
+        dists = pairwise(Euclidean(), position(system, :))
     end
 
     return dists
@@ -108,7 +108,7 @@ function angle(
         system::AbstractSystem, pos1::T, pos2::T, pos3::T; pbc=all(periodicity(system))
     ) where {T <: AbstractVector{<:Unitful.Length}}
     if pbc
-        cell = reduce(hcat, bounding_box(system))'
+        cell = reduce(hcat, cell_vectors(system))'
         icell = inv(cell)
         frpos1 = pos1' * icell
         frpos2 = pos2' * icell
@@ -149,7 +149,7 @@ function dihedral(
     # Source: Blondel and Karplus, J. Comp. Chem., Vol. 17, No. 9, 1
     #   132-1 141 (1 996).
     # if pbc
-    #     cell = reduce(hcat, bounding_box(system))'
+    #     cell = reduce(hcat, cell_vectors(system))'
     #     icell = inv(cell)
     #     frpos1 = pos1' * icell
     #     frpos2 = pos2' * icell
@@ -174,7 +174,7 @@ function dihedral(
 
     # Obtained from pymatgen
     if pbc
-        cell = reduce(hcat, bounding_box(system))'
+        cell = reduce(hcat, cell_vectors(system))'
         icell = inv(cell)
         frpos1 = pos1' * icell
         frpos2 = pos2' * icell
@@ -289,12 +289,12 @@ matrix for the given system or `atom`.
 """
 function scaled_position(sys::AbstractSystem)
     cellmat = cell_matrix(sys)
-    frpos = reduce(hcat, position(sys))' * inv(cellmat')
+    frpos = reduce(hcat, position(sys, :))' * inv(cellmat')
 
     Vector.(eachrow(frpos))
 end
 scaled_position(sys::AbstractSystem, index) = scaled_position(sys[index], cell_matrix(sys))
-function scaled_position(atom::Atom, cellmat)
+function scaled_position(atom::Union{Atom,AtomView}, cellmat)
     frpos = position(atom)' * inv(cellmat')
 
     frpos'
@@ -304,7 +304,7 @@ end
 # Cell utils
 # 
 
-@inline cell_matrix(sys::AbstractSystem) = reduce(hcat, bounding_box(sys))
+@inline cell_matrix(sys::AbstractSystem) = reduce(hcat, cell_vectors(sys))
 # lu is required as unitful matrices are erroring without it
 # when the cell matrix is diagonal
 """

diff --git a/src/pbc_utils.jl b/src/pbc_utils.jl
@@ -49,7 +49,7 @@ function pbc_shortest_vectors(
         system::AbstractSystem, pos1::T, pos2::U,
         return_dists::Val{RD}=Val(false), return_vects::Val{RV}=Val(true)
     ) where {T <: AbstractVector{<: Unitful.Length}, U <: AbstractVector{<: Unitful.Length}, RD, RV}
-    cell = reduce(hcat, bounding_box(system))'
+    cell = reduce(hcat, cell_vectors(system))'
     icell = inv(cell)
     frpos1 = pos1' * icell
     frpos2 = pos2' * icell
@@ -61,7 +61,7 @@ function pbc_shortest_vectors(
         return_dists::Val{RD}=Val(false), 
         return_vects::Val{RV}=Val(true)
     ) where {T <: Vector{<: AbstractVector{<: Unitful.Length}}, RD, RV}
-    cell = reduce(hcat, bounding_box(system))'
+    cell = reduce(hcat, cell_vectors(system))'
     pos = reduce(hcat, posvec)'
     frpos = pos * inv(cell)
 

diff --git a/src/transform.jl b/src/transform.jl
@@ -1,8 +1,8 @@
 function _getdefaultdata(system::AbstractSystem)
     particles = collect(system)
     positions = position(system)
-    box = bounding_box(system)
-    bc = boundary_conditions(system)
+    box = cell_vectors(system)
+    bc = periodicity(system)
 
     return particles, positions, box, bc
 end
@@ -15,9 +15,9 @@ system.
 """
 # function transformpositions(f::Function, system::AbstractSystem)
 #     positions = map(f, position(system))
-#     cell = bounding_box(system)
+#     cell = cell_vectors(system)
 #     at = species(system)
-#     bc = boundary_conditions(system)
+#     bc = periodicity(system)
 #     
 #     typeof(system)(cell, positions, at)
 # end
@@ -76,16 +76,16 @@ function supercell(system::AbstractSystem, supercellvec::Vector{Int}; sorted=fal
     end
 
     system_props = Dict{Symbol, Any}()
-    # All system properties except bounding_box is copied to the new system
+    # All system properties except cell_vectors is copied to the new system
     for (k,v) in pairs(system)
-        if k != :bounding_box
+        if k != :cell_vectors
             system_props[k] = v
         end
     end
 
     cellmat = cell_matrix(system)
     newcellmat = cellmat .* supercellvec'
-    system_props[:bounding_box] = collect(eachcol(newcellmat))
+    system_props[:cell_vectors] = collect(eachcol(newcellmat))
 
     particles = collect(system)
     newparticles = copy(particles)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -20,7 +20,7 @@ using AtomsIO
             @test distance(si_primitive, 1, 2) ≈ 2.35719227u"Å"
             @test distance(si_primitive, 1, 2; pbc=false) ≈ 7.07157681u"Å"
 
-            box = bounding_box(si_primitive)
+            box = cell_vectors(si_primitive)
             for i in 1:3
                 @test distance(si_primitive, zeros(3)u"Å", box[i]) ≈ 0.0u"Å" atol=1e-8u"Å"
             end