From db0ea0f103e4d8013a4e39e119881271350322a1 Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Wed, 7 Feb 2024 14:53:32 +0000
Subject: [PATCH 1/4] Made ASE interface aware of FixAtoms constraints

---
 Project.toml                |  8 +++++++-
 ext/AdvancedASEFunctions.jl | 14 ++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 ext/AdvancedASEFunctions.jl

diff --git a/Project.toml b/Project.toml
index 9a89b5d..c157d8d 100644
--- a/Project.toml
+++ b/Project.toml
@@ -19,6 +19,12 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
+[weakdeps]
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+
+[extensions]
+AdvancedASEFunctions = "PyCall"
+
 [compat]
 FastGaussQuadrature = "0.4, 0.5, 1"
 ForwardDiff = "0.10"
@@ -30,7 +36,7 @@ Requires = "1"
 StaticArrays = "1"
 Unitful = "1"
 UnitfulAtomic = "1"
-julia = "1.7"
+julia = "≥1.9"
 
 [extras]
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
diff --git a/ext/AdvancedASEFunctions.jl b/ext/AdvancedASEFunctions.jl
new file mode 100644
index 0000000..2518446
--- /dev/null
+++ b/ext/AdvancedASEFunctions.jl
@@ -0,0 +1,14 @@
+module AdvancedASEFunctions
+using NQCModels, PyCall
+
+"""
+This module contains methods related to the NQCModels ASE interface that need access to Python types. (e.g. constraint checking) 
+"""
+
+function NQCModels.mobileatoms(model::NQCModels.AdiabaticModels.AdiabaticASEModel, n::Int)
+	ase=pyimport("ase")
+	constraints_FixAtoms=isa.(model.atoms.constraints, typeof(ase.constraints.FixAtoms))
+	return symdiff(1:length(model.atoms), [constraint.get_indices() .+ 1 for constraint in model.atoms.constraints[constraints_FixAtoms]]...)
+end
+
+end
\ No newline at end of file

From 391f0380afe2758966fe47a7e522fbb94cc5860f Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 10:22:57 +0100
Subject: [PATCH 2/4] Update constraint logic if no constraints found.

---
 ext/AdvancedASEFunctions.jl | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/ext/AdvancedASEFunctions.jl b/ext/AdvancedASEFunctions.jl
index 2518446..3ef5427 100644
--- a/ext/AdvancedASEFunctions.jl
+++ b/ext/AdvancedASEFunctions.jl
@@ -1,14 +1,24 @@
 module AdvancedASEFunctions
 using NQCModels, PyCall
 
+const ase = PyNULL()
+
+function __init__()
+    copy!(ase, pyimport("ase"))
+end
+
 """
-This module contains methods related to the NQCModels ASE interface that need access to Python types. (e.g. constraint checking) 
+This module contains methods related to the NQCModels ASE interface that need access to Python types. (e.g. constraint checking)
 """
 
 function NQCModels.mobileatoms(model::NQCModels.AdiabaticModels.AdiabaticASEModel, n::Int)
-	ase=pyimport("ase")
 	constraints_FixAtoms=isa.(model.atoms.constraints, typeof(ase.constraints.FixAtoms))
-	return symdiff(1:length(model.atoms), [constraint.get_indices() .+ 1 for constraint in model.atoms.constraints[constraints_FixAtoms]]...)
+	ase_constraints = [constraint for constraint in model.atoms.constraints[constraints_FixAtoms]]
+	if length(ase_constraints) == 0
+        return 1:length(model.atoms)
+	else
+        return symdiff(1:length(model.atoms), [constraint.get_indices() .+ 1 for constraint in constraints]...)
+    end
 end
 
-end
\ No newline at end of file
+end

From bedb74857de04a29fe783ce9545d35979904a0bd Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Mon, 29 Apr 2024 10:37:43 +0100
Subject: [PATCH 3/4] Can't type check FixAtoms constraints so will have to
 take all constraints in good faith

---
 ext/AdvancedASEFunctions.jl | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/ext/AdvancedASEFunctions.jl b/ext/AdvancedASEFunctions.jl
index 3ef5427..339ccdd 100644
--- a/ext/AdvancedASEFunctions.jl
+++ b/ext/AdvancedASEFunctions.jl
@@ -1,19 +1,13 @@
 module AdvancedASEFunctions
 using NQCModels, PyCall
 
-const ase = PyNULL()
-
-function __init__()
-    copy!(ase, pyimport("ase"))
-end
 
 """
 This module contains methods related to the NQCModels ASE interface that need access to Python types. (e.g. constraint checking)
 """
 
 function NQCModels.mobileatoms(model::NQCModels.AdiabaticModels.AdiabaticASEModel, n::Int)
-	constraints_FixAtoms=isa.(model.atoms.constraints, typeof(ase.constraints.FixAtoms))
-	ase_constraints = [constraint for constraint in model.atoms.constraints[constraints_FixAtoms]]
+	ase_constraints = [constraint for constraint in model.atoms.constraints]
 	if length(ase_constraints) == 0
         return 1:length(model.atoms)
 	else

From 9a1657c06276b3104cded9f1e0620d8fe66fb1ee Mon Sep 17 00:00:00 2001
From: Alexander Spears <alexander.spears@warwick.ac.uk>
Date: Mon, 13 May 2024 15:43:03 +0100
Subject: [PATCH 4/4] Fixed distribution generation from Simulation

---
 ext/AdvancedASEFunctions.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/AdvancedASEFunctions.jl b/ext/AdvancedASEFunctions.jl
index 339ccdd..d20cd8b 100644
--- a/ext/AdvancedASEFunctions.jl
+++ b/ext/AdvancedASEFunctions.jl
@@ -11,7 +11,7 @@ function NQCModels.mobileatoms(model::NQCModels.AdiabaticModels.AdiabaticASEMode
 	if length(ase_constraints) == 0
         return 1:length(model.atoms)
 	else
-        return symdiff(1:length(model.atoms), [constraint.get_indices() .+ 1 for constraint in constraints]...)
+        return symdiff(1:length(model.atoms), [constraint.get_indices() .+ 1 for constraint in ase_constraints]...)
     end
 end