From 19826537c05a8af132b6ca6a415de471d52d65b7 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Tue, 16 Jul 2024 13:44:46 +0200
Subject: [PATCH 1/9] add aimsgb

---
 environment.yml | 1 +
 setup.py        | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index d248c6f..0401680 100644
--- a/environment.yml
+++ b/environment.yml
@@ -18,5 +18,6 @@ dependencies:
   #- atomman
   - mp-api
   - sqlalchemy
+  - aimsgb
   - pip:
     - "git+https://github.com/RDFLib/rdflib-sqlalchemy.git@develop"
diff --git a/setup.py b/setup.py
index ddf1700..a21d9a7 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@
     install_requires=['numpy', 'ase', 'rdflib', 
     'pyyaml', 'graphviz', 'networkx', 
     'pyscal3', 'spglib', 'pandas', 'owlready2',
-    'atomman', 'mp-api'],
+    'atomman', 'mp-api', 'aimsgb'],
     classifiers=[
         'Programming Language :: Python :: 3'
     ],

From ca983fa96d60135ed70a882432b062377fabb5c8 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Tue, 16 Jul 2024 13:49:51 +0200
Subject: [PATCH 2/9] add pymatgen

---
 environment.yml | 1 +
 setup.py        | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 0401680..8ef40d9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -19,5 +19,6 @@ dependencies:
   - mp-api
   - sqlalchemy
   - aimsgb
+  - pymatgen
   - pip:
     - "git+https://github.com/RDFLib/rdflib-sqlalchemy.git@develop"
diff --git a/setup.py b/setup.py
index a21d9a7..8a5b520 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@
     install_requires=['numpy', 'ase', 'rdflib', 
     'pyyaml', 'graphviz', 'networkx', 
     'pyscal3', 'spglib', 'pandas', 'owlready2',
-    'atomman', 'mp-api', 'aimsgb'],
+    'atomman', 'mp-api', 'aimsgb', 'pymatgen'],
     classifiers=[
         'Programming Language :: Python :: 3'
     ],

From 4d197d43519ed1113a59aa0cc9d33e9ab97ae074 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:16:42 +0200
Subject: [PATCH 3/9] add aimsgb based gb creation

---
 atomrdf/structure.py | 140 ++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 139 insertions(+), 1 deletion(-)

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index 2fa0a86..4f49ee0 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -382,8 +382,146 @@ def _make_dislocation(
         return output_structure, disc
     return output_structure
 
-
 def _make_grain_boundary(
+    axis,
+    sigma,
+    gb_plane,
+    structure=None,
+    element=None,
+    lattice_constant=1,
+    ca_ratio=1.633,
+    repetitions=(1, 1, 1),
+    overlap=0.0,
+    vacuum=0.0,
+    delete_layer="0b0t0b0t",
+    tolerance=  0.25,
+    primitive=False,
+    uc_a=1,
+    uc_b=1,
+    graph=None,
+    names=False,
+    label=None,
+    backend='aimsgb'         
+):
+    if backend == 'aimsgb':
+        return _make_grain_boundary_aimsgb(
+            axis,
+            sigma,
+            gb_plane,
+            structure=structure,
+            element=element,
+            lattice_constant=lattice_constant,
+            ca_ratio=ca_ratio,
+            repetitions=repetitions,
+            overlap=overlap,
+            vacuum=vacuum,
+            delete_layer=delete_layer,
+            tolerance=  tolerance,
+            primitive=primitive,
+            uc_a=uc_a,
+            uc_b=uc_b,
+            graph=graph,
+            names=names,
+            label=label,             
+        )
+    else:
+        return _make_grain_boundary_inbuilt(
+            axis,
+            sigma,
+            gb_plane,
+            structure=structure,
+            element=element,
+            lattice_constant=lattice_constant,
+            repetitions=repetitions,
+            overlap=overlap,
+            graph=graph,
+            names=names,
+            label=label,
+        )
+
+def _make_grain_boundary_aimsgb(
+    axis,
+    sigma,
+    gb_plane,
+    structure=None,
+    element=None,
+    lattice_constant=1,
+    ca_ratio=1.633,
+    repetitions=(1, 1, 1),
+    overlap=0.0,
+    vacuum=0.0,
+    delete_layer="0b0t0b0t",
+    tolerance=  0.25,
+    primitive=False,
+    uc_a=1,
+    uc_b=1,
+    graph=None,
+    names=False,
+    label=None,  
+):  
+    try:
+        from pymatgen.io.ase import AseAtomsAdaptor
+        from aimsgb import GrainBoundary, Grain
+    except ImportError:
+        raise ImportError("This function requires the aimsgb and pymatgen packages to be installed")
+    
+
+    init_sys = _make_crystal(
+        structure,
+        lattice_constant=_declass(lattice_constant),
+        repetitions=repetitions,
+        ca_ratio=_declass(ca_ratio),
+        noise=0,
+        element=element,
+        primitive=False,
+    )
+
+    sdict = copy.deepcopy(init_sys._structure_dict)
+
+    asesys = init_sys.write.ase()
+    pmsys = AseAtomsAdaptor().get_structure(atoms=asesys)
+    grain = Grain(pmsys.lattice, pmsys.species, pmsys.frac_coords)
+    gb = GrainBoundary(axis=axis, sigma=sigma, 
+                    plane=gb_plane, 
+                    initial_struct=grain, 
+                    uc_a=uc_a, 
+                    uc_b=uc_b)
+    gb_struct = Grain.stack_grains(
+                grain_a = gb.grain_a,
+                grain_b = gb.grain_b,
+                vacuum = vacuum,
+                gap=overlap,
+                direction = gb.direction,
+                delete_layer=delete_layer,
+                tol=tolerance,
+                to_primitive=primitive,
+            )
+    asestruct = AseAtomsAdaptor().get_atoms(structure=gb_struct)
+    sys = System.read.ase(asestruct, graph=graph, names=names, label=label)
+    sys.atoms._lattice = structure
+    sys.atoms._lattice_constant = _declass(lattice_constant)
+    sys._structure_dict = sdict
+    sys.label = label
+    sys.to_graph()
+    sys.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+    sys.add_property_mappings(ca_ratio, mapping_quantity='lattice_constant')
+
+    gb_inb = GrainBoundary()
+    gb_inb.create_grain_boundary(axis=axis, sigma=sigma, gb_plane=gb_plane)
+
+    gb_dict = {
+        "GBPlane": " ".join(np.array(gb_plane).astype(str)),
+        "RotationAxis": axis,
+        "MisorientationAngle": gb.theta[0],
+        "GBType": gb_inb.find_gb_character(),
+        "sigma": gb.sigma,
+    }
+    sys.add_gb(gb_dict)
+    return sys
+
+
+
+def _make_grain_boundary_inbuilt(
     axis,
     sigma,
     gb_plane,

From a66e17b86a644fc12e3ddb7bcf255a32c1be187a Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:22:41 +0200
Subject: [PATCH 4/9] fix structure in aimsgb

---
 atomrdf/structure.py         | 37 +++++++++++++++++++++++++++---------
 tests/test_structuregraph.py | 10 +++++++++-
 2 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index 4f49ee0..5c39fc1 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -466,15 +466,34 @@ def _make_grain_boundary_aimsgb(
         raise ImportError("This function requires the aimsgb and pymatgen packages to be installed")
     
 
-    init_sys = _make_crystal(
-        structure,
-        lattice_constant=_declass(lattice_constant),
-        repetitions=repetitions,
-        ca_ratio=_declass(ca_ratio),
-        noise=0,
-        element=element,
-        primitive=False,
-    )
+    if structure is not None:
+        # create a structure with the info
+        init_sys = _make_crystal(
+            structure,
+            lattice_constant=_declass(lattice_constant),
+            repetitions=repetitions,
+            ca_ratio=_declass(ca_ratio),
+            noise=0,
+            element=element,
+            primitive=primitive,
+        )
+    elif element is not None:
+        if element in element_dict.keys():
+            structure = element_dict[element]["structure"]
+            lattice_constant = element_dict[element]["lattice_constant"]
+        else:
+            raise ValueError("Please provide structure")
+        init_sys = _make_crystal(
+            structure,
+            lattice_constant=_declass(lattice_constant),
+            repetitions=repetitions,
+            ca_ratio=_declass(ca_ratio),
+            noise=0,
+            element=element,
+            primitive=primitive,
+        )
+    else:
+        raise ValueError("Provide either structure or element")
 
     sdict = copy.deepcopy(init_sys._structure_dict)
 
diff --git a/tests/test_structuregraph.py b/tests/test_structuregraph.py
index d9ffe30..77fd81d 100644
--- a/tests/test_structuregraph.py
+++ b/tests/test_structuregraph.py
@@ -16,10 +16,18 @@ def test_structuregraph():
                         sigma=5, 
                         gb_plane=[3, -1, 0],
                         element='Fe',
-                        graph=s)
+                        graph=s,
+						backend='inbuilt')
 
 	assert(sys.sample != None)
 
+	sys = System.create.defect.grain_boundary(axis=[0,0,1], 
+                        sigma=5, 
+                        gb_plane=[3, -1, 0],
+                        element='Fe',
+                        graph=s,
+						backend='aimsgb')
 
+	assert(sys.sample != None)
 
 

From f6c37cfa775ea7c5848a65aa8ed231bc92a4cb61 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:24:55 +0200
Subject: [PATCH 5/9] fix conflicting imports

---
 atomrdf/structure.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index 5c39fc1..5be0b10 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -461,7 +461,8 @@ def _make_grain_boundary_aimsgb(
 ):  
     try:
         from pymatgen.io.ase import AseAtomsAdaptor
-        from aimsgb import GrainBoundary, Grain
+        from aimsgb import GrainBoundary as AIMSGrainBoundary
+        from aimsgb import Grain as AIMSGrain
     except ImportError:
         raise ImportError("This function requires the aimsgb and pymatgen packages to be installed")
     
@@ -499,13 +500,13 @@ def _make_grain_boundary_aimsgb(
 
     asesys = init_sys.write.ase()
     pmsys = AseAtomsAdaptor().get_structure(atoms=asesys)
-    grain = Grain(pmsys.lattice, pmsys.species, pmsys.frac_coords)
-    gb = GrainBoundary(axis=axis, sigma=sigma, 
+    grain = AIMSGrain(pmsys.lattice, pmsys.species, pmsys.frac_coords)
+    gb = AIMSGrainBoundary(axis=axis, sigma=sigma, 
                     plane=gb_plane, 
                     initial_struct=grain, 
                     uc_a=uc_a, 
                     uc_b=uc_b)
-    gb_struct = Grain.stack_grains(
+    gb_struct = AIMSGrain.stack_grains(
                 grain_a = gb.grain_a,
                 grain_b = gb.grain_b,
                 vacuum = vacuum,

From ceabd2d87a875e016c7c418fb2abb474d661eeb8 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:35:51 +0200
Subject: [PATCH 6/9] make gb type optional

---
 atomrdf/structure.py               |  10 +-
 examples/02_grain_boundaries.ipynb | 412 ++++++++++++++---------------
 2 files changed, 208 insertions(+), 214 deletions(-)

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index 5be0b10..7af7bbe 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -526,14 +526,18 @@ def _make_grain_boundary_aimsgb(
     sys.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
     sys.add_property_mappings(ca_ratio, mapping_quantity='lattice_constant')
 
-    gb_inb = GrainBoundary()
-    gb_inb.create_grain_boundary(axis=axis, sigma=sigma, gb_plane=gb_plane)
+    try:
+        gb_inb = GrainBoundary()
+        gb_inb.create_grain_boundary(axis=axis, sigma=sigma, gb_plane=gb_plane)
+        gb_type = gb_inb.find_gb_character()
+    except:
+        gb_type = None
 
     gb_dict = {
         "GBPlane": " ".join(np.array(gb_plane).astype(str)),
         "RotationAxis": axis,
         "MisorientationAngle": gb.theta[0],
-        "GBType": gb_inb.find_gb_character(),
+        "GBType": gb_type,
         "sigma": gb.sigma,
     }
     sys.add_gb(gb_dict)
diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
index 14622db..76635ea 100644
--- a/examples/02_grain_boundaries.ipynb
+++ b/examples/02_grain_boundaries.ipynb
@@ -21,20 +21,7 @@
    "execution_count": 1,
    "id": "f88eacd6-1bdc-4321-9e80-3d2720d318a1",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c4f616c028b447b58dfe55c7d388eeee",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from atomrdf import KnowledgeGraph, System"
    ]
@@ -134,23 +121,23 @@
          "type": "scatter3d",
          "x": [
           0,
-          18.15147376,
-          18.15147376,
-          0,
+          18.151473769366497,
+          18.151473769366497,
+          -5.557286062865456e-16,
           0
          ],
          "y": [
           0,
           0,
-          2.87,
-          2.87,
+          9.075736884683248,
+          9.075736884683248,
           0
          ],
          "z": [
           0,
-          0,
-          0,
-          0,
+          1.1114572125730911e-15,
+          1.6671858188596366e-15,
+          5.557286062865456e-16,
           0
          ]
         },
@@ -165,24 +152,24 @@
          "type": "scatter3d",
          "x": [
           0,
-          18.15147376,
-          18.15147376,
-          0,
+          18.151473769366497,
+          18.151473769366497,
+          -5.557286062865456e-16,
           0
          ],
          "y": [
           0,
           0,
-          2.87,
-          2.87,
+          9.075736884683248,
+          9.075736884683248,
           0
          ],
          "z": [
-          9.07573688,
-          9.07573688,
-          9.07573688,
-          9.07573688,
-          9.07573688
+          2.8699999999999997,
+          2.870000000000001,
+          2.8700000000000014,
+          2.87,
+          2.8699999999999997
          ]
         },
         {
@@ -196,8 +183,8 @@
          "type": "scatter3d",
          "x": [
           0,
-          18.15147376,
-          18.15147376,
+          18.151473769366497,
+          18.151473769366497,
           0,
           0
          ],
@@ -210,9 +197,9 @@
          ],
          "z": [
           0,
-          0,
-          9.07573688,
-          9.07573688,
+          1.1114572125730911e-15,
+          2.870000000000001,
+          2.8699999999999997,
           0
          ]
         },
@@ -226,25 +213,25 @@
          "showlegend": false,
          "type": "scatter3d",
          "x": [
-          0,
-          18.15147376,
-          18.15147376,
-          0,
-          0
+          -5.557286062865456e-16,
+          18.151473769366497,
+          18.151473769366497,
+          -5.557286062865456e-16,
+          -5.557286062865456e-16
          ],
          "y": [
-          2.87,
-          2.87,
-          2.87,
-          2.87,
-          2.87
+          9.075736884683248,
+          9.075736884683248,
+          9.075736884683248,
+          9.075736884683248,
+          9.075736884683248
          ],
          "z": [
-          0,
-          0,
-          9.07573688,
-          9.07573688,
-          0
+          5.557286062865456e-16,
+          1.6671858188596366e-15,
+          2.8700000000000014,
+          2.87,
+          5.557286062865456e-16
          ]
         },
         {
@@ -258,23 +245,23 @@
          "type": "scatter3d",
          "x": [
           0,
-          0,
-          0,
+          -5.557286062865456e-16,
+          -5.557286062865456e-16,
           0,
           0
          ],
          "y": [
           0,
-          2.87,
-          2.87,
+          9.075736884683248,
+          9.075736884683248,
           0,
           0
          ],
          "z": [
           0,
-          0,
-          9.07573688,
-          9.07573688,
+          5.557286062865456e-16,
+          2.87,
+          2.8699999999999997,
           0
          ]
         },
@@ -288,25 +275,25 @@
          "showlegend": false,
          "type": "scatter3d",
          "x": [
-          18.15147376,
-          18.15147376,
-          18.15147376,
-          18.15147376,
-          18.15147376
+          18.151473769366497,
+          18.151473769366497,
+          18.151473769366497,
+          18.151473769366497,
+          18.151473769366497
          ],
          "y": [
           0,
-          2.87,
-          2.87,
+          9.075736884683248,
+          9.075736884683248,
           0,
           0
          ],
          "z": [
-          0,
-          0,
-          9.07573688,
-          9.07573688,
-          0
+          1.1114572125730911e-15,
+          1.6671858188596366e-15,
+          2.8700000000000014,
+          2.870000000000001,
+          1.1114572125730911e-15
          ]
         },
         {
@@ -325,130 +312,130 @@
          "opacity": 1,
          "type": "scatter3d",
          "x": [
-          9.983310568468324,
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        "                            \n",
-       "var gd = document.getElementById('65c649ba-863e-469d-bd98-3805739aa9c6');\n",
+       "var gd = document.getElementById('5e66beb6-7a38-4b8e-9a8c-bc03846f88a9');\n",
        "var x = new MutationObserver(function (mutations, observer) {{\n",
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@@ -1352,14 +1339,31 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
    "id": "27649a14-c9c9-415a-8bf2-c471a04101e7",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "IndexError",
+     "evalue": "list index out of range",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_gb_2 \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdefect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgrain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[43m                        \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      3\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m-\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m      4\u001b[0m \u001b[43m                        \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mFe\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      5\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      7\u001b[0m struct_gb_3 \u001b[38;5;241m=\u001b[39m System\u001b[38;5;241m.\u001b[39mcreate\u001b[38;5;241m.\u001b[39mdefect\u001b[38;5;241m.\u001b[39mgrain_boundary(axis\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m], \n\u001b[1;32m      8\u001b[0m                         sigma\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m19\u001b[39m, \n\u001b[1;32m      9\u001b[0m                         gb_plane\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m],\n\u001b[1;32m     10\u001b[0m                         element\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFe\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     11\u001b[0m                         graph\u001b[38;5;241m=\u001b[39mkg)\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:407\u001b[0m, in \u001b[0;36m_make_grain_boundary\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label, backend)\u001b[0m\n\u001b[1;32m    385\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_make_grain_boundary\u001b[39m(\n\u001b[1;32m    386\u001b[0m     axis,\n\u001b[1;32m    387\u001b[0m     sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    404\u001b[0m     backend\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m         \n\u001b[1;32m    405\u001b[0m ):\n\u001b[1;32m    406\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m backend \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m--> 407\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_make_grain_boundary_aimsgb\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    408\u001b[0m \u001b[43m            \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    409\u001b[0m \u001b[43m            \u001b[49m\u001b[43msigma\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    410\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    411\u001b[0m \u001b[43m            \u001b[49m\u001b[43mstructure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    412\u001b[0m \u001b[43m            \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43melement\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    413\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlattice_constant\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlattice_constant\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    414\u001b[0m \u001b[43m            \u001b[49m\u001b[43mca_ratio\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mca_ratio\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    415\u001b[0m \u001b[43m            \u001b[49m\u001b[43mrepetitions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrepetitions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    416\u001b[0m \u001b[43m            \u001b[49m\u001b[43moverlap\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moverlap\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    417\u001b[0m \u001b[43m            \u001b[49m\u001b[43mvacuum\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mvacuum\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    418\u001b[0m \u001b[43m            \u001b[49m\u001b[43mdelete_layer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdelete_layer\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    419\u001b[0m \u001b[43m            \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m  \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    420\u001b[0m \u001b[43m            \u001b[49m\u001b[43mprimitive\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprimitive\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    421\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_a\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_a\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    422\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_b\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_b\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    423\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    424\u001b[0m \u001b[43m            \u001b[49m\u001b[43mnames\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnames\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    425\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlabel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m             \u001b[49m\n\u001b[1;32m    426\u001b[0m \u001b[43m        \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    427\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    428\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m _make_grain_boundary_inbuilt(\n\u001b[1;32m    429\u001b[0m             axis,\n\u001b[1;32m    430\u001b[0m             sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    439\u001b[0m             label\u001b[38;5;241m=\u001b[39mlabel,\n\u001b[1;32m    440\u001b[0m         )\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:530\u001b[0m, in \u001b[0;36m_make_grain_boundary_aimsgb\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label)\u001b[0m\n\u001b[1;32m    527\u001b[0m sys\u001b[38;5;241m.\u001b[39madd_property_mappings(ca_ratio, mapping_quantity\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlattice_constant\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m    529\u001b[0m gb_inb \u001b[38;5;241m=\u001b[39m GrainBoundary()\n\u001b[0;32m--> 530\u001b[0m \u001b[43mgb_inb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_grain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msigma\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgb_plane\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    532\u001b[0m gb_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m    533\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBPlane\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(np\u001b[38;5;241m.\u001b[39marray(gb_plane)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;28mstr\u001b[39m)),\n\u001b[1;32m    534\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRotationAxis\u001b[39m\u001b[38;5;124m\"\u001b[39m: axis,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    537\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msigma\u001b[39m\u001b[38;5;124m\"\u001b[39m: gb\u001b[38;5;241m.\u001b[39msigma,\n\u001b[1;32m    538\u001b[0m }\n\u001b[1;32m    539\u001b[0m sys\u001b[38;5;241m.\u001b[39madd_gb(gb_dict)\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:93\u001b[0m, in \u001b[0;36mGrainBoundary.create_grain_boundary\u001b[0;34m(self, axis, sigma, gb_plane, limit, gb_index_limit)\u001b[0m\n\u001b[1;32m     91\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgb_plane \u001b[38;5;241m=\u001b[39m gb_plane\n\u001b[1;32m     92\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgb_index_limit \u001b[38;5;241m=\u001b[39m gb_index_limit\n\u001b[0;32m---> 93\u001b[0m valid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_if_gb_is_valid\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     94\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m valid:\n\u001b[1;32m     95\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGB cannot be created with the given input!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:65\u001b[0m, in \u001b[0;36mGrainBoundary.check_if_gb_is_valid\u001b[0;34m(self, gb_vector)\u001b[0m\n\u001b[1;32m     63\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcheck_if_gb_is_valid\u001b[39m(\u001b[38;5;28mself\u001b[39m, gb_vector):\n\u001b[1;32m     64\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_theta \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 65\u001b[0m         \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcalculate_theta\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     66\u001b[0m     validity, ortho_1, ortho_2 \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mfind_orthogonal_cell(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sigma, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_theta, \n\u001b[1;32m     67\u001b[0m                                                                \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_R, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_m, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_n, gb_vector,\n\u001b[1;32m     68\u001b[0m                                                                \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_M1, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_M2, tol \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0.001\u001b[39m)\n\u001b[1;32m     69\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ortho_1 \u001b[38;5;241m=\u001b[39m ortho_1\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:47\u001b[0m, in \u001b[0;36mGrainBoundary.calculate_theta\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     46\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcalculate_theta\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m---> 47\u001b[0m     theta, m, n \u001b[38;5;241m=\u001b[39m \u001b[43mcsl\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_theta_m_n_list\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_axis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sigma\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m     48\u001b[0m     R \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mrot(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, theta)\n\u001b[1;32m     49\u001b[0m     M1, M2 \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mcreate_minimal_cell_method_1(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sigma, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, R)\n",
+      "\u001b[0;31mIndexError\u001b[0m: list index out of range"
+     ]
+    }
+   ],
    "source": [
-    "struct_gb_2 = System.create.defect.grain_boundary(axis=[1,1,1], \n",
-    "                        sigma=19, \n",
-    "                        gb_plane=[-3, 2, 0],\n",
+    "struct_gb_2 = System.create.defect.grain_boundary(axis=[1,1,2], \n",
+    "                        sigma=3, \n",
+    "                        gb_plane=[1, -1, 0],\n",
     "                        element='Fe',\n",
     "                        graph=kg)\n",
     "\n",
@@ -1412,18 +1416,8 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>sample:fbb7c264-c89d-4694-b0d4-2c4719cd7e8a</td>\n",
-       "      <td>sample:fbb7c264-c89d-4694-b0d4-2c4719cd7e8a_Sy...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>sample:7cc8eed3-421f-41c2-8d46-64edf7c66d71</td>\n",
-       "      <td>sample:7cc8eed3-421f-41c2-8d46-64edf7c66d71_Mi...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>sample:d65ed919-688e-4161-b017-b67031138c47</td>\n",
-       "      <td>sample:d65ed919-688e-4161-b017-b67031138c47_Tw...</td>\n",
+       "      <td>sample:360dd33e-58a6-402b-add0-f45e9ebe0199</td>\n",
+       "      <td>sample:360dd33e-58a6-402b-add0-f45e9ebe0199_Sy...</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -1431,14 +1425,10 @@
       ],
       "text/plain": [
        "                             AtomicScaleSample  \\\n",
-       "0  sample:fbb7c264-c89d-4694-b0d4-2c4719cd7e8a   \n",
-       "1  sample:7cc8eed3-421f-41c2-8d46-64edf7c66d71   \n",
-       "2  sample:d65ed919-688e-4161-b017-b67031138c47   \n",
+       "0  sample:360dd33e-58a6-402b-add0-f45e9ebe0199   \n",
        "\n",
        "                        SymmetricalTiltGrainBoundary  \n",
-       "0  sample:fbb7c264-c89d-4694-b0d4-2c4719cd7e8a_Sy...  \n",
-       "1  sample:7cc8eed3-421f-41c2-8d46-64edf7c66d71_Mi...  \n",
-       "2  sample:d65ed919-688e-4161-b017-b67031138c47_Tw...  "
+       "0  sample:360dd33e-58a6-402b-add0-f45e9ebe0199_Sy...  "
       ]
      },
      "execution_count": 6,
@@ -1617,7 +1607,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

From 274f3acdc08b4e819e0597f82152cae085b63f4c Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:45:38 +0200
Subject: [PATCH 7/9] fix missing class

---
 atomrdf/structure.py               |  2 +-
 examples/02_grain_boundaries.ipynb | 22 ++++++++++------------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index 7af7bbe..b9a9e7d 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -2257,7 +2257,7 @@ def add_gb(self, gb_dict):
             return
 
         if gb_dict["GBType"] is None:
-            plane_defect = self.graph.create_node(f"{self._name}_GrainBoundary")
+            plane_defect = self.graph.create_node(f"{self._name}_GrainBoundary", PLDO.GrainBoundary)
 
         elif gb_dict["GBType"] == "Twist":
             plane_defect = self.graph.create_node(
diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
index 76635ea..e2c7e9b 100644
--- a/examples/02_grain_boundaries.ipynb
+++ b/examples/02_grain_boundaries.ipynb
@@ -1294,9 +1294,9 @@
        }
       },
       "text/html": [
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        "                            \n",
-       "var gd = document.getElementById('5e66beb6-7a38-4b8e-9a8c-bc03846f88a9');\n",
+       "var gd = document.getElementById('66e4b12a-d965-4f48-95eb-c663fd851cbb');\n",
        "var x = new MutationObserver(function (mutations, observer) {{\n",
        "        var display = window.getComputedStyle(gd).display;\n",
        "        if (!display || display === 'none') {{\n",
@@ -1339,24 +1339,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 5,
    "id": "27649a14-c9c9-415a-8bf2-c471a04101e7",
    "metadata": {},
    "outputs": [
     {
-     "ename": "IndexError",
-     "evalue": "list index out of range",
+     "ename": "TypeError",
+     "evalue": "KnowledgeGraph.create_node() missing 1 required positional argument: 'classtype'",
      "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_gb_2 \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdefect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgrain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[43m                        \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      3\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m-\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m      4\u001b[0m \u001b[43m                        \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mFe\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      5\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      7\u001b[0m struct_gb_3 \u001b[38;5;241m=\u001b[39m System\u001b[38;5;241m.\u001b[39mcreate\u001b[38;5;241m.\u001b[39mdefect\u001b[38;5;241m.\u001b[39mgrain_boundary(axis\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m], \n\u001b[1;32m      8\u001b[0m                         sigma\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m19\u001b[39m, \n\u001b[1;32m      9\u001b[0m                         gb_plane\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m],\n\u001b[1;32m     10\u001b[0m                         element\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFe\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     11\u001b[0m                         graph\u001b[38;5;241m=\u001b[39mkg)\n",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_gb_2 \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdefect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgrain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[43m                        \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      3\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m-\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m      4\u001b[0m \u001b[43m                        \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mFe\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      5\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      7\u001b[0m struct_gb_3 \u001b[38;5;241m=\u001b[39m System\u001b[38;5;241m.\u001b[39mcreate\u001b[38;5;241m.\u001b[39mdefect\u001b[38;5;241m.\u001b[39mgrain_boundary(axis\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m], \n\u001b[1;32m      8\u001b[0m                         sigma\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m19\u001b[39m, \n\u001b[1;32m      9\u001b[0m                         gb_plane\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m],\n\u001b[1;32m     10\u001b[0m                         element\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFe\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     11\u001b[0m                         graph\u001b[38;5;241m=\u001b[39mkg)\n",
       "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:407\u001b[0m, in \u001b[0;36m_make_grain_boundary\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label, backend)\u001b[0m\n\u001b[1;32m    385\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_make_grain_boundary\u001b[39m(\n\u001b[1;32m    386\u001b[0m     axis,\n\u001b[1;32m    387\u001b[0m     sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    404\u001b[0m     backend\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m         \n\u001b[1;32m    405\u001b[0m ):\n\u001b[1;32m    406\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m backend \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m--> 407\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_make_grain_boundary_aimsgb\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    408\u001b[0m \u001b[43m            \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    409\u001b[0m \u001b[43m            \u001b[49m\u001b[43msigma\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    410\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    411\u001b[0m \u001b[43m            \u001b[49m\u001b[43mstructure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    412\u001b[0m \u001b[43m            \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43melement\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    413\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlattice_constant\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlattice_constant\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    414\u001b[0m \u001b[43m            \u001b[49m\u001b[43mca_ratio\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mca_ratio\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    415\u001b[0m \u001b[43m            \u001b[49m\u001b[43mrepetitions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrepetitions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    416\u001b[0m \u001b[43m            \u001b[49m\u001b[43moverlap\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moverlap\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    417\u001b[0m \u001b[43m            \u001b[49m\u001b[43mvacuum\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mvacuum\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    418\u001b[0m \u001b[43m            \u001b[49m\u001b[43mdelete_layer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdelete_layer\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    419\u001b[0m \u001b[43m            \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m  \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    420\u001b[0m \u001b[43m            \u001b[49m\u001b[43mprimitive\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprimitive\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    421\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_a\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_a\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    422\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_b\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_b\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    423\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    424\u001b[0m \u001b[43m            \u001b[49m\u001b[43mnames\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnames\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    425\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlabel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m             \u001b[49m\n\u001b[1;32m    426\u001b[0m \u001b[43m        \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    427\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    428\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m _make_grain_boundary_inbuilt(\n\u001b[1;32m    429\u001b[0m             axis,\n\u001b[1;32m    430\u001b[0m             sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    439\u001b[0m             label\u001b[38;5;241m=\u001b[39mlabel,\n\u001b[1;32m    440\u001b[0m         )\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:530\u001b[0m, in \u001b[0;36m_make_grain_boundary_aimsgb\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label)\u001b[0m\n\u001b[1;32m    527\u001b[0m sys\u001b[38;5;241m.\u001b[39madd_property_mappings(ca_ratio, mapping_quantity\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlattice_constant\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m    529\u001b[0m gb_inb \u001b[38;5;241m=\u001b[39m GrainBoundary()\n\u001b[0;32m--> 530\u001b[0m \u001b[43mgb_inb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_grain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msigma\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgb_plane\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    532\u001b[0m gb_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m    533\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBPlane\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(np\u001b[38;5;241m.\u001b[39marray(gb_plane)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;28mstr\u001b[39m)),\n\u001b[1;32m    534\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRotationAxis\u001b[39m\u001b[38;5;124m\"\u001b[39m: axis,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    537\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msigma\u001b[39m\u001b[38;5;124m\"\u001b[39m: gb\u001b[38;5;241m.\u001b[39msigma,\n\u001b[1;32m    538\u001b[0m }\n\u001b[1;32m    539\u001b[0m sys\u001b[38;5;241m.\u001b[39madd_gb(gb_dict)\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:93\u001b[0m, in \u001b[0;36mGrainBoundary.create_grain_boundary\u001b[0;34m(self, axis, sigma, gb_plane, limit, gb_index_limit)\u001b[0m\n\u001b[1;32m     91\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgb_plane \u001b[38;5;241m=\u001b[39m gb_plane\n\u001b[1;32m     92\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgb_index_limit \u001b[38;5;241m=\u001b[39m gb_index_limit\n\u001b[0;32m---> 93\u001b[0m valid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_if_gb_is_valid\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     94\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m valid:\n\u001b[1;32m     95\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGB cannot be created with the given input!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:65\u001b[0m, in \u001b[0;36mGrainBoundary.check_if_gb_is_valid\u001b[0;34m(self, gb_vector)\u001b[0m\n\u001b[1;32m     63\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcheck_if_gb_is_valid\u001b[39m(\u001b[38;5;28mself\u001b[39m, gb_vector):\n\u001b[1;32m     64\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_theta \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 65\u001b[0m         \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcalculate_theta\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     66\u001b[0m     validity, ortho_1, ortho_2 \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mfind_orthogonal_cell(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sigma, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_theta, \n\u001b[1;32m     67\u001b[0m                                                                \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_R, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_m, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_n, gb_vector,\n\u001b[1;32m     68\u001b[0m                                                                \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_M1, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_M2, tol \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0.001\u001b[39m)\n\u001b[1;32m     69\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ortho_1 \u001b[38;5;241m=\u001b[39m ortho_1\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/pyscal3/grain_boundary.py:47\u001b[0m, in \u001b[0;36mGrainBoundary.calculate_theta\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     46\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcalculate_theta\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m---> 47\u001b[0m     theta, m, n \u001b[38;5;241m=\u001b[39m \u001b[43mcsl\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_theta_m_n_list\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_axis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sigma\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m     48\u001b[0m     R \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mrot(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, theta)\n\u001b[1;32m     49\u001b[0m     M1, M2 \u001b[38;5;241m=\u001b[39m csl\u001b[38;5;241m.\u001b[39mcreate_minimal_cell_method_1(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sigma, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_axis, R)\n",
-      "\u001b[0;31mIndexError\u001b[0m: list index out of range"
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:543\u001b[0m, in \u001b[0;36m_make_grain_boundary_aimsgb\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label)\u001b[0m\n\u001b[1;32m    534\u001b[0m     gb_type \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m    536\u001b[0m gb_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m    537\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBPlane\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(np\u001b[38;5;241m.\u001b[39marray(gb_plane)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;28mstr\u001b[39m)),\n\u001b[1;32m    538\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRotationAxis\u001b[39m\u001b[38;5;124m\"\u001b[39m: axis,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    541\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msigma\u001b[39m\u001b[38;5;124m\"\u001b[39m: gb\u001b[38;5;241m.\u001b[39msigma,\n\u001b[1;32m    542\u001b[0m }\n\u001b[0;32m--> 543\u001b[0m \u001b[43msys\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd_gb\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgb_dict\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    544\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m sys\n",
+      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:2260\u001b[0m, in \u001b[0;36mSystem.add_gb\u001b[0;34m(self, gb_dict)\u001b[0m\n\u001b[1;32m   2257\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m   2259\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m gb_dict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBType\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 2260\u001b[0m     plane_defect \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_name\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m_GrainBoundary\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m   2262\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m gb_dict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBType\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTwist\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m   2263\u001b[0m     plane_defect \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39mcreate_node(\n\u001b[1;32m   2264\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m_TwistGrainBoundary\u001b[39m\u001b[38;5;124m\"\u001b[39m, PLDO\u001b[38;5;241m.\u001b[39mTwistGrainBoundary\n\u001b[1;32m   2265\u001b[0m     )\n",
+      "\u001b[0;31mTypeError\u001b[0m: KnowledgeGraph.create_node() missing 1 required positional argument: 'classtype'"
      ]
     }
    ],

From 71acc5ad45f7f34c9fa0c34cb7218ddc3b2a358f Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:57:47 +0200
Subject: [PATCH 8/9] update example

---
 examples/02_grain_boundaries.ipynb | 105 ++++++++++++++++-------------
 1 file changed, 60 insertions(+), 45 deletions(-)

diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
index e2c7e9b..1604e85 100644
--- a/examples/02_grain_boundaries.ipynb
+++ b/examples/02_grain_boundaries.ipynb
@@ -1294,9 +1294,9 @@
        }
       },
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        "                            \n",
-       "var gd = document.getElementById('66e4b12a-d965-4f48-95eb-c663fd851cbb');\n",
+       "var gd = document.getElementById('91587d47-cabf-464f-ab50-d4106ac1b713');\n",
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        "        var display = window.getComputedStyle(gd).display;\n",
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@@ -1334,7 +1334,7 @@
    "id": "8146e662-d087-46a5-8ca3-dc3b3cd0342a",
    "metadata": {},
    "source": [
-    "Some other examples, $\\Sigma 19 (\\bar{3}20)$ and $\\Sigma 19 (111)$"
+    "Some other examples, $\\Sigma 3 (1\\bar{-1}0)$ and $\\Sigma 19 (111)$"
    ]
   },
   {
@@ -1342,22 +1342,7 @@
    "execution_count": 5,
    "id": "27649a14-c9c9-415a-8bf2-c471a04101e7",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "TypeError",
-     "evalue": "KnowledgeGraph.create_node() missing 1 required positional argument: 'classtype'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m struct_gb_2 \u001b[38;5;241m=\u001b[39m \u001b[43mSystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdefect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgrain_boundary\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[43m                        \u001b[49m\u001b[43msigma\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m      3\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m-\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m      4\u001b[0m \u001b[43m                        \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mFe\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      5\u001b[0m \u001b[43m                        \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkg\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      7\u001b[0m struct_gb_3 \u001b[38;5;241m=\u001b[39m System\u001b[38;5;241m.\u001b[39mcreate\u001b[38;5;241m.\u001b[39mdefect\u001b[38;5;241m.\u001b[39mgrain_boundary(axis\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m], \n\u001b[1;32m      8\u001b[0m                         sigma\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m19\u001b[39m, \n\u001b[1;32m      9\u001b[0m                         gb_plane\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m],\n\u001b[1;32m     10\u001b[0m                         element\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFe\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     11\u001b[0m                         graph\u001b[38;5;241m=\u001b[39mkg)\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:407\u001b[0m, in \u001b[0;36m_make_grain_boundary\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label, backend)\u001b[0m\n\u001b[1;32m    385\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_make_grain_boundary\u001b[39m(\n\u001b[1;32m    386\u001b[0m     axis,\n\u001b[1;32m    387\u001b[0m     sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    404\u001b[0m     backend\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m         \n\u001b[1;32m    405\u001b[0m ):\n\u001b[1;32m    406\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m backend \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124maimsgb\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m--> 407\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_make_grain_boundary_aimsgb\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    408\u001b[0m \u001b[43m            \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    409\u001b[0m \u001b[43m            \u001b[49m\u001b[43msigma\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    410\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgb_plane\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    411\u001b[0m \u001b[43m            \u001b[49m\u001b[43mstructure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    412\u001b[0m \u001b[43m            \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43melement\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    413\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlattice_constant\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlattice_constant\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    414\u001b[0m \u001b[43m            \u001b[49m\u001b[43mca_ratio\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mca_ratio\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    415\u001b[0m \u001b[43m            \u001b[49m\u001b[43mrepetitions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrepetitions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    416\u001b[0m \u001b[43m            \u001b[49m\u001b[43moverlap\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moverlap\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    417\u001b[0m \u001b[43m            \u001b[49m\u001b[43mvacuum\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mvacuum\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    418\u001b[0m \u001b[43m            \u001b[49m\u001b[43mdelete_layer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdelete_layer\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    419\u001b[0m \u001b[43m            \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m  \u001b[49m\u001b[43mtolerance\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    420\u001b[0m \u001b[43m            \u001b[49m\u001b[43mprimitive\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprimitive\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    421\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_a\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_a\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    422\u001b[0m \u001b[43m            \u001b[49m\u001b[43muc_b\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muc_b\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    423\u001b[0m \u001b[43m            \u001b[49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    424\u001b[0m \u001b[43m            \u001b[49m\u001b[43mnames\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnames\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    425\u001b[0m \u001b[43m            \u001b[49m\u001b[43mlabel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m             \u001b[49m\n\u001b[1;32m    426\u001b[0m \u001b[43m        \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    427\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    428\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m _make_grain_boundary_inbuilt(\n\u001b[1;32m    429\u001b[0m             axis,\n\u001b[1;32m    430\u001b[0m             sigma,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    439\u001b[0m             label\u001b[38;5;241m=\u001b[39mlabel,\n\u001b[1;32m    440\u001b[0m         )\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:543\u001b[0m, in \u001b[0;36m_make_grain_boundary_aimsgb\u001b[0;34m(axis, sigma, gb_plane, structure, element, lattice_constant, ca_ratio, repetitions, overlap, vacuum, delete_layer, tolerance, primitive, uc_a, uc_b, graph, names, label)\u001b[0m\n\u001b[1;32m    534\u001b[0m     gb_type \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m    536\u001b[0m gb_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m    537\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBPlane\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(np\u001b[38;5;241m.\u001b[39marray(gb_plane)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;28mstr\u001b[39m)),\n\u001b[1;32m    538\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRotationAxis\u001b[39m\u001b[38;5;124m\"\u001b[39m: axis,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    541\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msigma\u001b[39m\u001b[38;5;124m\"\u001b[39m: gb\u001b[38;5;241m.\u001b[39msigma,\n\u001b[1;32m    542\u001b[0m }\n\u001b[0;32m--> 543\u001b[0m \u001b[43msys\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd_gb\u001b[49m\u001b[43m(\u001b[49m\u001b[43mgb_dict\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    544\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m sys\n",
-      "File \u001b[0;32m~/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/structure.py:2260\u001b[0m, in \u001b[0;36mSystem.add_gb\u001b[0;34m(self, gb_dict)\u001b[0m\n\u001b[1;32m   2257\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m   2259\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m gb_dict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBType\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 2260\u001b[0m     plane_defect \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_node\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_name\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m_GrainBoundary\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m   2262\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m gb_dict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGBType\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTwist\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m   2263\u001b[0m     plane_defect \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgraph\u001b[38;5;241m.\u001b[39mcreate_node(\n\u001b[1;32m   2264\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m_TwistGrainBoundary\u001b[39m\u001b[38;5;124m\"\u001b[39m, PLDO\u001b[38;5;241m.\u001b[39mTwistGrainBoundary\n\u001b[1;32m   2265\u001b[0m     )\n",
-      "\u001b[0;31mTypeError\u001b[0m: KnowledgeGraph.create_node() missing 1 required positional argument: 'classtype'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "struct_gb_2 = System.create.defect.grain_boundary(axis=[1,1,2], \n",
     "                        sigma=3, \n",
@@ -1367,7 +1352,7 @@
     "\n",
     "struct_gb_3 = System.create.defect.grain_boundary(axis=[1,1,1], \n",
     "                        sigma=19, \n",
-    "                        gb_plane=[-1, -1, -1],\n",
+    "                        gb_plane=[1, 1, 1],\n",
     "                        element='Fe',\n",
     "                        graph=kg)"
    ]
@@ -1414,8 +1399,18 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>sample:360dd33e-58a6-402b-add0-f45e9ebe0199</td>\n",
-       "      <td>sample:360dd33e-58a6-402b-add0-f45e9ebe0199_Sy...</td>\n",
+       "      <td>sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb</td>\n",
+       "      <td>sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb_Sy...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6</td>\n",
+       "      <td>sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6_Gr...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>sample:0e1b3f66-d381-464f-8114-6e8ab8e91611</td>\n",
+       "      <td>sample:0e1b3f66-d381-464f-8114-6e8ab8e91611_Tw...</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -1423,10 +1418,14 @@
       ],
       "text/plain": [
        "                             AtomicScaleSample  \\\n",
-       "0  sample:360dd33e-58a6-402b-add0-f45e9ebe0199   \n",
+       "0  sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb   \n",
+       "1  sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6   \n",
+       "2  sample:0e1b3f66-d381-464f-8114-6e8ab8e91611   \n",
        "\n",
        "                        SymmetricalTiltGrainBoundary  \n",
-       "0  sample:360dd33e-58a6-402b-add0-f45e9ebe0199_Sy...  "
+       "0  sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb_Sy...  \n",
+       "1  sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6_Gr...  \n",
+       "2  sample:0e1b3f66-d381-464f-8114-6e8ab8e91611_Tw...  "
       ]
      },
      "execution_count": 6,
@@ -1484,20 +1483,36 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>sample:969bfa49-7ff8-4a49-97c8-ac97881505cc</td>\n",
-       "      <td>sample:969bfa49-7ff8-4a49-97c8-ac97881505cc_Sy...</td>\n",
+       "      <td>sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb</td>\n",
+       "      <td>sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb_Sy...</td>\n",
        "      <td>5</td>\n",
        "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6</td>\n",
+       "      <td>sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6_Gr...</td>\n",
+       "      <td>3</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>sample:0e1b3f66-d381-464f-8114-6e8ab8e91611</td>\n",
+       "      <td>sample:0e1b3f66-d381-464f-8114-6e8ab8e91611_Tw...</td>\n",
+       "      <td>19</td>\n",
+       "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
        "                             AtomicScaleSample  \\\n",
-       "0  sample:969bfa49-7ff8-4a49-97c8-ac97881505cc   \n",
+       "0  sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb   \n",
+       "1  sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6   \n",
+       "2  sample:0e1b3f66-d381-464f-8114-6e8ab8e91611   \n",
        "\n",
        "                        SymmetricalTiltGrainBoundary hasSigmaValuevalue  \n",
-       "0  sample:969bfa49-7ff8-4a49-97c8-ac97881505cc_Sy...                  5  "
+       "0  sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb_Sy...                  5  \n",
+       "1  sample:08b2ed7d-c51c-4da8-b608-0a946a8a4ad6_Gr...                  3  \n",
+       "2  sample:0e1b3f66-d381-464f-8114-6e8ab8e91611_Tw...                 19  "
       ]
      },
      "execution_count": 7,
@@ -1528,7 +1543,7 @@
     {
      "data": {
       "text/plain": [
-       "rdflib.term.URIRef('sample:969bfa49-7ff8-4a49-97c8-ac97881505cc')"
+       "rdflib.term.URIRef('sample:5a36022f-d8d3-43e8-9aaa-e9a451760fbb')"
       ]
      },
      "execution_count": 8,
@@ -1561,26 +1576,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Fe \n",
+      "Fe\n",
       " 1.0000000000000000\n",
-      "    18.1514737599999982    0.0000000000000000    0.0000000000000000\n",
-      "     0.0000000000000000    2.8700000000000001    0.0000000000000000\n",
-      "     0.0000000000000000    0.0000000000000000    9.0757368799999991\n",
+      "    18.1514737693664969   -0.0000000000000006    0.0000000000000000\n",
+      "     0.0000000000000000    9.0757368846832485    0.0000000000000000\n",
+      "     0.0000000000000011    0.0000000000000006    2.8699999999999997\n",
       " Fe \n",
       "  40\n",
       "Cartesian\n",
-      "  9.9833105684683243  1.4350000000000001  7.2605895077465998\n",
-      "  9.0757368799999991  1.4350000000000001  4.5378684423416242\n",
-      " 11.7984579454049729  0.0000000000000000  8.1681631962149233\n",
-      " 12.7060316338732981  1.4350000000000001  6.3530158192782746\n",
-      " 10.8908842569366495  0.0000000000000000  5.4454421308099494\n",
-      " 11.7984579454049729  1.4350000000000001  3.6302947538732999\n",
-      "  9.9833105684683243  0.0000000000000000  2.7227210654049747\n",
-      " 10.8908842569366495  1.4350000000000001  0.9075736884683248\n",
-      "  9.0757368799999991  0.0000000000000000  0.0000000000000000\n",
-      " 16.3363263877465990  1.4350000000000001  8.1681631962149233\n",
-      " 14.5211790108099486  0.0000000000000000  7.2605895077465998\n",
-      " 15.4287526992782738  1.4350000000000001  5.4454421308099494\n"
+      "  0.0000000000000000  0.0000000000000000  0.0000000000000000\n",
+      "  2.7227210654049743  0.9075736884683246  0.0000000000000002\n",
+      "  1.8151473769366497  3.6302947538732990  0.0000000000000003\n",
+      "  0.9075736884683242  6.3530158192782737  0.0000000000000004\n",
+      "  5.4454421308099485  1.8151473769366493  0.0000000000000004\n",
+      "  4.5378684423416242  4.5378684423416233  0.0000000000000006\n",
+      "  3.6302947538732995  7.2605895077465981  0.0000000000000007\n",
+      "  8.1681631962149215  2.7227210654049738  0.0000000000000007\n",
+      "  7.2605895077465972  5.4454421308099477  0.0000000000000008\n",
+      "  6.3530158192782693  8.1681631962149215  0.0000000000000009\n",
+      "  0.9075736884683249  1.8151473769366495  1.4350000000000001\n",
+      "  3.6302947538732990  2.7227210654049743  1.4350000000000003\n"
      ]
     }
    ],

From fb3943c8d7b76312284d7db9040fcee49b1a9724 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Wed, 17 Jul 2024 18:57:56 +0200
Subject: [PATCH 9/9] =?UTF-8?q?Bump=20version:=200.9.5=20=E2=86=92=200.9.6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg | 2 +-
 CITATION.cff     | 2 +-
 setup.py         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index b5f1cbb..5a55534 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.5
+current_version = 0.9.6
 commit = True
 tag = False
 
diff --git a/CITATION.cff b/CITATION.cff
index 987bab5..9d8b7f6 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.5
+version: 0.9.6
diff --git a/setup.py b/setup.py
index 8a5b520..e34169f 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.9.5',
+    version='0.9.6',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='sarath.menon@pyscal.org',
     description='Ontology based structural manipulation and quering',