From ba88d156854346ebdcfce02cfddfcb0cd38800ba Mon Sep 17 00:00:00 2001
From: Rashid Rafeek <rashidrafeek@gmail.com>
Date: Sat, 7 Dec 2024 13:16:39 +0530
Subject: [PATCH] Add system level property definitions removed in AtomsBase
 0.5

---
 src/AtomsToolbox.jl | 10 ++++++++--
 src/getters.jl      | 11 -----------
 src/piracy.jl       | 15 +++++++++++++++
 3 files changed, 23 insertions(+), 13 deletions(-)
 create mode 100644 src/piracy.jl

diff --git a/src/AtomsToolbox.jl b/src/AtomsToolbox.jl
index 2db9d1f..62945ea 100644
--- a/src/AtomsToolbox.jl
+++ b/src/AtomsToolbox.jl
@@ -2,7 +2,8 @@ module AtomsToolbox
 
 using Distances: Distances, pairwise, euclidean, peuclidean,
                  Euclidean, PeriodicEuclidean
-using AtomsBase: AbstractSystem,
+using AtomsBase: AtomsBase,
+                 AbstractSystem,
                  FastSystem,
                  FlexibleSystem,
                  Atom,
@@ -12,13 +13,18 @@ using AtomsBase: AbstractSystem,
                  atomic_symbol,
                  atomic_mass,
                  cell_vectors,
-                 periodicity
+                 periodicity,
+                 species
 using Unitful: Unitful, ustrip, @u_str, unit
 import Graphs
 using LinearAlgebra: LinearAlgebra, ⋅, det, norm, lu, ×
 using StaticArrays: StaticMatrix, Size
 import Base: angle, sort # To extend for AbstractSystem 
 
+# Some type piracy to deal with other packages
+# Should be upstreamed or removed eventually
+include("piracy.jl")
+
 # Constants
 include("constants.jl")
 
diff --git a/src/getters.jl b/src/getters.jl
index 47eddef..6b190b5 100644
--- a/src/getters.jl
+++ b/src/getters.jl
@@ -1,14 +1,3 @@
-# Workaround for Unitful StaticMatrix not working.
-# See: https://github.com/PainterQubits/Unitful.jl/issues/538
-function Base.inv(x::StaticMatrix{N,M,T}) where {N,M,T <: Unitful.AbstractQuantity}
-    m = inv(ustrip.(x))
-    iq = eltype(m)
-    reinterpret(
-        Unitful.Quantity{iq, inv(Unitful.dimension(T)), typeof(inv(unit(T)))}, 
-        m
-    )
-end 
-
 # Functions to find shortest distance accounting for PBC, from pymatgen.
 include("pbc_utils.jl")
 
diff --git a/src/piracy.jl b/src/piracy.jl
new file mode 100644
index 0000000..d004a0d
--- /dev/null
+++ b/src/piracy.jl
@@ -0,0 +1,15 @@
+# Workaround for Unitful StaticMatrix not working.
+# See: https://github.com/PainterQubits/Unitful.jl/issues/538
+function Base.inv(x::StaticMatrix{N,M,T}) where {N,M,T <: Unitful.AbstractQuantity}
+    m = inv(ustrip.(x))
+    iq = eltype(m)
+    reinterpret(
+        Unitful.Quantity{iq, inv(Unitful.dimension(T)), typeof(inv(unit(T)))}, 
+        m
+    )
+end 
+
+# These were removed in the AtomsBase 0.4 update
+Base.position(sys::AbstractSystem) = position.(sys, :)
+AtomsBase.atomic_symbol(sys::AbstractSystem) = atomic_symbol.(species(sys, :))
+AtomsBase.atomic_number(sys::AbstractSystem) = atomic_number.(species(sys, :))