AtomsBase v0.4 support (#74)

Author: tjjarvinen

Project.toml

@@ -35,7 +35,7 @@ ACE1 = "0.12.1"
 ACE1x = "0.1.8"
 ACEbase = "0.4.3"
 ACEfit = "0.1.4, 0.2.0"
-AtomsBase = "0.3"
+AtomsBase = "0.3, 0.4"
 AtomsCalculators = "0.2"
 ChunkSplitters = "2"
 Folds = "0.2"

src/utils.jl

@@ -68,17 +68,7 @@ end
 
 
 function neighborlist(ab, cutoff; length_unit=default_length, kwargs...)
-    cell = ustrip.(length_unit, hcat( bounding_box(ab)... )' )
-    pbc = map( boundary_conditions(ab) ) do x
-        x == Periodic()
-    end
-    r = map( 1:length(ab)) do i
-        # Need to have SVector here for PairList to work
-        # if position does not give SVector
-        SVector( ustrip.(length_unit, position(ab,i))...)
-    end
-    nlist = PairList(r, ustrip(length_unit, cutoff), cell, pbc; int_type=Int)
-    return nlist
+    return PairList(ab, cutoff)
 end
 
 

test/runtests.jl

@@ -61,7 +61,7 @@ end
 @testset "AtomsBase" begin
     pot = load_ace_model(fname_ace)
     julip_data = read_extxyz(fname_xyz)[end]
-    ab_data = FastSystem(ExtXYZ.Atoms(read_frame(fname_xyz)))
+    ab_data = ExtXYZ.Atoms(read_frame(fname_xyz))
 
     @test ace_energy(pot, julip_data) ≈ ace_energy(pot, ab_data)
     @test all( ace_forces(pot, julip_data) .≈ ace_forces(pot, ab_data) )
@@ -104,7 +104,7 @@ end
 
 @testset "Units" begin
     pot = load_ace_model(fname_ace; energy_unit=u"eV", length_unit=u"pm")
-    data = FastSystem(ExtXYZ.Atoms(read_frame(fname_xyz)))
+    data = ExtXYZ.Atoms(read_frame(fname_xyz))
 
     @test unit( ace_energy(pot, data) ) == u"eV"
     @test unit( ace_forces(pot, data)[1][1] ) == u"eV" / u"pm"
@@ -128,7 +128,7 @@ end
 
 @testset "Combination interface" begin
     pot = load_ace_model(fname_ace)
-    data = FastSystem(ExtXYZ.Atoms(read_frame(fname_xyz)))
+    data = ExtXYZ.Atoms(read_frame(fname_xyz))
 
     E = ace_energy(pot, data)
     F = ace_forces(pot, data)