more fixes

pyscal · Oct 24, 2024 · d4dab6c · d4dab6c
1 parent 8c1373c
commit d4dab6c
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Showing 11 changed files with 8,153 additions and 9,777 deletions.
diff --git a/atomrdf/graph.py b/atomrdf/graph.py
@@ -1500,10 +1500,11 @@ def _get_ancestor(self, prop, prov):
         propname = _name(prop)
 
         operation = [x[1] for x in self.triples((prop, ASMO.wasCalculatedBy, None))]
+
         if len(operation) > 0:
             parent = [x[2] for x in self.triples((prop, ASMO.wasCalculatedBy, None))]
             operation = operation[0]
-            parent = parent[0]        
+            parent = parent[0]      
             prov[propname]['operation'] = 'output_parameter'
             prov[propname]['inputs'] = {}
             prov[propname]['inputs']['0'] = _name(parent)
@@ -1583,7 +1584,7 @@ def _get_ancestor(self, prop, prov):
                 prov[propname]['inputs']['1'] = _name(dividend)
                 self._add_to_dict(divisor, prov)
                 self._add_to_dict(dividend, prov)
-
+        print(operation)
         prov[propname]['found'] = True
         return prov
 

diff --git a/atomrdf/structure.py b/atomrdf/structure.py
@@ -1480,7 +1480,8 @@ def add_interstitial_impurities(
 
         if copy_structure:
             #sys = self.duplicate()
-            sys = System(source=sys.add_atoms({"positions": randpos, "species": element}))        
+            sys = System(source=sys.add_atoms({"positions": randpos, "species": element}))
+            sys.graph = self.graph        
             sys.to_graph()
             sys.copy_defects(self.sample)
         else:

diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py
@@ -395,7 +395,7 @@ def _add_outputs(self, job_dict, activity):
             for out in job_dict["outputs"]:
                 #here we add the classes by property
                 #call func here
-                prop = self._select_base_property(out, main_id, ASMO.CalculatedProperty)
+                prop = self._select_base_property(out, main_id, CMSO.CalculatedProperty)
                 self.kg.add((prop, UNSAFEASMO.wasCalculatedBy, activity))
 
                 if out["associate_to_sample"]:

diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb
diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
diff --git a/examples/03_point_defects.ipynb b/examples/03_point_defects.ipynb
diff --git a/examples/09_structure_modification.ipynb b/examples/09_structure_modification.ipynb
diff --git a/examples/workflow_examples/01_lammps_pyiron.ipynb b/examples/workflow_examples/01_lammps_pyiron.ipynb
diff --git a/examples/workflow_examples/02_vasp.ipynb b/examples/workflow_examples/02_vasp.ipynb
diff --git a/examples/workflow_examples/03_murnaghan_pyiron.ipynb b/examples/workflow_examples/03_murnaghan_pyiron.ipynb
diff --git a/examples/workflow_examples/04_vacancy_formation_lammps.ipynb b/examples/workflow_examples/04_vacancy_formation_lammps.ipynb