From fb3a6ae27e05ab57949b4f6e4949c4f4509560b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Teemu=20J=C3=A4rvinen?= <teemu.j.jarvinen@gmail.com>
Date: Tue, 10 Sep 2024 19:18:35 -0700
Subject: [PATCH] AtomsBase v0.4 support

---
 Project.toml           |  4 ++--
 src/atoms.jl           | 13 +++++--------
 test/test_atomsbase.jl |  4 ++--
 3 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/Project.toml b/Project.toml
index 828c60f..43a9419 100644
--- a/Project.toml
+++ b/Project.toml
@@ -34,11 +34,11 @@ ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 [compat]
 ACEbase = "0.4"
 AlgebraicMultigrid = "0.5, 0.6"
-AtomsBase = "0.3"
+AtomsBase = "0.4"
 Calculus = "0.5"
 CommonSubexpressions = "0.2, 0.3"
 DataDeps = "0.7"
-ExtXYZ = "0.1"
+ExtXYZ = "0.2"
 ForwardDiff = "0.10"
 FunctionWrappers = "1"
 Interpolations = "0.13, 0.14, 0.15"
diff --git a/src/atoms.jl b/src/atoms.jl
index bb30409..ff955bf 100644
--- a/src/atoms.jl
+++ b/src/atoms.jl
@@ -96,11 +96,11 @@ function Atoms(sys::AtomsBase.AbstractSystem)
    M = [ ustrip(u"u", AtomsBase.atomic_mass(sys,i) ) for i in 1:length(sys) ]
    Z = [ (AtomicNumber ∘ AtomsBase.atomic_number)(sys,i) for i in 1:length(sys) ]
    cell = map( x -> ustrip.(u"Å", x), sys[:bounding_box])
-   pbc = map( x -> x == AtomsBase.Periodic ? true : false , AtomsBase.boundary_conditions(sys))
+   pbc = JVec(AtomsBase.periodicity(sys))
    data = Dict{Any,JData{eltype(M)}}( String(key)=>JData(sys[key]) for key in keys(sys) 
-      if !( key in (:bounding_box, :boundary_conditions) )
+      if !( key in (:bounding_box, :periodicity) )
    )
-   return JuLIP.Atoms(X, M .* V, M, Z, hcat(cell...)', pbc; data=data)
+   return JuLIP.Atoms(X, M .* V, M, Z, hcat(cell...)', pbc, nothing; data=data)
 end
 
 
@@ -112,14 +112,11 @@ function AtomsBase.FlexibleSystem(sys::Atoms)
        v = (sys.P[i] ./ sys.M[i]) * sqrt(u"eV/u")
        AtomsBase.Atom(s, r, v; atomic_mass=m)
    end
-   pbc = map( sys.pbc ) do a
-       a ? AtomsBase.Periodic() : AtomsBase.DirichletZero()
-   end
-   cell = [ c * u"Å" for c in eachrow(sys.cell) ]
+   cell = Tuple( c * u"Å" for c in eachrow(sys.cell) )
    data = Dict(
       Symbol(key)=>val.data  for (key,val) in sys.data 
    )
-   return AtomsBase.FlexibleSystem(atoms, cell, pbc; data...)
+   return AtomsBase.FlexibleSystem(atoms, cell, sys.pbc; data...)
 end
 
 Base.convert(::Type{Atoms}, a::AtomsBase.AbstractSystem) = Atoms(a)
diff --git a/test/test_atomsbase.jl b/test/test_atomsbase.jl
index 8600479..7ba1ba0 100644
--- a/test/test_atomsbase.jl
+++ b/test/test_atomsbase.jl
@@ -50,8 +50,8 @@ hh = FlexibleSystem(a)
 
 a1 = AtomsBase.Atom( :Ti, [1.4175416,1.3076719,2.0027419]u"Å" )
 a2 = AtomsBase.Atom( :Al, [-0.0784151, -0.17961, -0.0164296]u"Å" )
-cell = [ [2.65283,  0.0,      0.0]u"Å", [0.0,      2.65283,  0.0273594]u"Å", [0.0,      0.0,      3.82503]u"Å" ]
-pbc = [Periodic(), Periodic(), Periodic()]
+cell = ( [2.65283,  0.0,      0.0]u"Å", [0.0,      2.65283,  0.0273594]u"Å", [0.0,      0.0,      3.82503]u"Å" )
+pbc = (true, true, true)
 
 ab = FlexibleSystem([a1,a2], cell, pbc)