bug fixes in graph

pyscal · Jun 26, 2023 · ac86cd4 · ac86cd4
1 parent 5b8da11
commit ac86cd4
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Showing 2 changed files with 16 additions and 13 deletions.
diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
@@ -11,6 +11,7 @@
 import numpy as np
 import inspect
 from ase.io import write
+import copy
 
 from pyscal_rdf.visualize import visualize_graph
 from pyscal_rdf.network import OntologyNetwork
@@ -230,7 +231,9 @@ def add_structure_to_graph(self, structure, names=True, name_index=None, format=
         if name_index is None:
             name_index = self.n_samples + 1
         self.create_graph(names=names, name_index=name_index)
-
+        structure.sample = self.sample
+        structure._atom_ids = copy.copy(self._atom_ids)
+        structure.graph = self
 
     def create_graph(self, names=False, name_index="1"):
         """

diff --git a/pyscal_rdf/structure.py b/pyscal_rdf/structure.py
@@ -62,9 +62,9 @@ def create_element(self, element, repetitions=(1,1,1),
                         element = element))
             if add_to_graph:
                 self.add_structure_to_graph(sys, names=names)
-                sys.sample = self.sample
-                sys._atom_ids = copy.copy(self._atom_ids)
-                sys.graph = self
+                #sys.sample = self.sample
+                #sys._atom_ids = copy.copy(self._atom_ids)
+                #sys.graph = self
             return sys
 
     def create_structure(self, structure, 
@@ -116,9 +116,9 @@ def create_structure(self, structure,
                         ))
             if add_to_graph:
                 self.add_structure_to_graph(sys, names = names)
-                sys.sample = self.sample
-                sys._atom_ids = copy.copy(self._atom_ids)
-                sys.graph = self
+                #sys.sample = self.sample
+                #sys._atom_ids = copy.copy(self._atom_ids)
+                #sys.graph = self
             return sys
 
     def read_structure(self, filename, format="lammps-dump",
@@ -149,9 +149,9 @@ def read_structure(self, filename, format="lammps-dump",
         sys = System(filename, format=format)
         if add_to_graph:
             self.add_structure_to_graph(sys, names=names)
-            sys.sample = self.sample
-            sys._atom_ids = copy.copy(self._atom_ids)
-            sys.graph = self
+            #sys.sample = self.sample
+            #sys._atom_ids = copy.copy(self._atom_ids)
+            #sys.graph = self
         return sys
 
     def create_grain_boundary(self, axis, 
@@ -223,9 +223,9 @@ def create_grain_boundary(self, axis,
 
         #mapping of the system can be done
         self.add_structure_to_graph(sys, names=names)
-        sys.sample = self.sample
-        sys._atom_ids = copy.copy(self._atom_ids)
-        sys.graph = self
+        #sys.sample = self.sample
+        #sys._atom_ids = copy.copy(self._atom_ids)
+        #sys.graph = self
         gb_dict = {"GBPlane": " ".join(np.array(gb_plane).astype(str)),
                   "RotationAxis": axis,
                   "MisorientationAngle": gb.theta,