Query results can be returned in a pandas dataframe for further processing

I am retrieving system object using get_system_from_sample, I expected system.graph to return a ref to the Knowledge graph. However it returns None.

Code to reproduce

from atomrdf import System, KnowledgeGraph
# Create data file
kg = KnowledgeGraph()
struct_Mg =  System.create.element.Mg(graph=kg, repetitions=(10,10,10))

kg.write("Mg.ttl", format="ttl")


# Read file
kg_2 = KnowledgeGraph(graph_file="Mg.ttl")
system = kg_2.get_system_from_sample(kg_2.samples[0])

print(system.graph)

Versions
atomrdf: 0.4.4
pyscal3: 3.1.12

When creating an l12 structure, it gives the following error:

TypeError: System.init() got an unexpected keyword argument 'species'

The versions of pyscal and pyscal_rdf in conda are:

pyscal-rdf 0.1.5
pyscal3 3.1.1

Features

• Add substitutional defects (#78 )
• Add interstitial defects (#79 )
• Wrapper for dislocations using atomman
• Reach test coverage
• Add ASE bulk as a direct option for structure creation
• Add API docs
• Add type hinting
• lint with black
• Add example notebooks

When deleting atoms, and inserting substitutions and interstitials, atomRDF currently sets the predicate as hasSymbol. It should be hasChemicalSymbol instead.

• Ontology network module sometimes has owl#Thing as domain. This is currently ignored. Instead, this should be assigned to all classes.
• superproperties do not inherit domains from their subproperties. This is probably what is expected; nevertheless we should discuss if it makes sense for implementation purposes.

Currently creating HCP lattice using primitive=False, leads to lattice angle 90,90,90. On discussion with @aazocar we think that lattice angle should still be 90,90,120. The cell angle however will still be 90,90,90 which is currently done correctly.

Code to reproduce:

kg = KnowledgeGraph()

struct_Mg = System.create.element.Mg(graph=kg,  repetitions=(10,10,10))
kg.write("test_mg.ttl", format="ttl")

Versions
pyscal_rdf : 0.3.2

• DC3 variety of structures at different temperatures
• Carbon dataset ML potential fitting
• Copper dataset ML potential fitting
• Magnesium dataset ML potential fitting
• GB dataset GB, surface data for a variety of elements
• Si Va dataset
• Fe-H
• Al-Li

Hi,

I am trying to delete an atom in the lattice and writing it to a turtle file. The final hasNumberOfAtoms recorded in the turtle file is incorrect.

Steps to reproduce

from pyscal_rdf import KnowledgeGraph, System
kg = KnowledgeGraph()

# Create Al lattice
struct_Al = System.create.element.Al(graph=kg)

# Write initial data to ttl file
kg.write("initial.ttl", format="ttl")

# Delete one atom
struct_Al.delete(indices=[0])

# Write final data to file
kg.write("final.ttl", format="ttl")

Version

pyscal3: 3.1.7
pyscal-rdf: 0.2.3

Issue

The hasNumberOfAtoms field in initial.ttl is 4, which is correct. However, the hasNumberOfAtoms field in final.ttl is 2, which seems incorrect.

Can you kindly look into this?

Thanks

when calling the query_sample() on the getting_started and grain_boundaries notebooks, one gets the following error:

---

UnboundLocalError Traceback (most recent call last)
Cell In[11], line 1
----> 1 res = g.query_sample(g.ontology.terms.cmso.hasAltName,
2 condition=(g.ontology.terms.cmso.hasAltName=='bcc'))
3 res

File ~/miniconda3/envs/rdf/lib/python3.11/site-packages/pyscal_rdf/graph.py:930, in RDFGraph.query_sample(self, destination, condition, return_query, enforce_types)
929 def query_sample(self, destination, condition=None, return_query=False, enforce_types=True):
--> 930 return self.auto_query(self.ontology.terms.cmso.AtomicScaleSample, destination,
931 condition=condition, return_query=return_query, enforce_types=enforce_types)

File ~/miniconda3/envs/rdf/lib/python3.11/site-packages/pyscal_rdf/graph.py:919, in RDFGraph.auto_query(self, source, destination, condition, return_query, enforce_types)
916 return res
917 else:
918 query = self.ontology.create_query(source, destination,
--> 919 condition=condition, enforce_types=val)
920 if return_query:
921 return query

UnboundLocalError: cannot access local variable 'val' where it is not associated with a value

Creating a HCP Mg lattice with primitive=True and no repetitions shows a volume of "2993.63" (hasVolume field in turtle file). This is higher than expected as the cell lengths are (3.21,3.21,5.25).

Code to reproduce error:

kg = KnowledgeGraph()

struct_Mg = System.create.element.Mg(graph=kg, primitive=True)
kg.write("test_mg.ttl", format="ttl")

Versions
pyscal_rdf: 0.3.2

process_structure in RDFGraph allows giving a filename instead of a system object for the calculations. However, there is possibility to specify the format. These method should be ideally removed.

species should be known for StructureGraph methods. In case of create_structure, this is currently optional. For read_structure, when the format itself does not specify species information, for example lammps-dump, this will throw an error.