Add qha model

atomrdf/graph.py

@@ -18,7 +18,7 @@
 """
 
 
-from rdflib import Graph, Literal, XSD, RDF, RDFS, BNode, URIRef
+from rdflib import Graph, XSD, RDF, RDFS, BNode, URIRef
 
 import os
 import numpy as np
@@ -50,7 +50,7 @@
 from atomrdf.sample import Sample
 import atomrdf.mp as amp 
 
-from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO, PROV, MATH, UNSAFECMSO, UNSAFEASMO
+from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO, PROV, MATH, UNSAFECMSO, UNSAFEASMO, Literal
 
 # read element data file
 file_location = os.path.dirname(__file__).split("/")

atomrdf/namespace.py

@@ -10,13 +10,25 @@
 """
 
 import os
-from rdflib import Literal, URIRef
+import json
+import numpy as np
+from rdflib import URIRef
 from rdflib import Namespace as RDFLibNamespace
+from rdflib import Literal as RDFLibLiteral
 from pyscal3.atoms import AttrSetter
 
 from atomrdf.network.network import OntologyNetwork
 
-
+def Literal(value, datatype=None):
+    if datatype is not None:
+        return RDFLibLiteral(value, datatype=datatype)
+    elif isinstance(value, list):
+        return RDFLibLiteral(json.dumps(value))
+    elif isinstance(value, np.ndarray):
+        return RDFLibLiteral(json.dumps(value.tolist()))
+    else:
+        return RDFLibLiteral(value)
+
 class Namespace(AttrSetter, RDFLibNamespace):
     """A class representing a namespace in the AtomRDF library.
 

atomrdf/network/ontology.py

@@ -11,8 +11,8 @@
 - StructureOperation: 
     - RotationOperation and associated vectors, see structure.py
     - TranslationOperation - no triples yet, see structure.py
-
-- PROV activities
+    - ADD SHEAR OPERATION
+- PointDefectCreation
     - DeleteAtom - to create vacancy - Now Just added as label to PROV activities
     - AddAtom - to create impurity
     - SubstituteAtom - to create impurity

atomrdf/sample.py

@@ -4,10 +4,12 @@
 In this module a new Sample class is defined.
 """
 from pyscal3.atoms import AttrSetter
-from atomrdf.namespace import CMSO, PLDO, PODO, ASMO, PROV
-from rdflib import RDFS, Namespace, RDF, URIRef, Literal
+from atomrdf.namespace import CMSO, PLDO, PODO, ASMO, PROV, Literal
+from rdflib import RDFS, Namespace, RDF, URIRef
 import numpy as np
 import uuid
+import re
+import json
 
 MATH = Namespace("http://purls.helmholtz-metadaten.de/asmo/")
 
@@ -115,12 +117,18 @@ def _output_properties(self):
 
 class Property:
     def __init__(self, value, unit=None, graph=None, parent=None):
-        self._value = value
+        self._value = self._clean_value(value)
         self._unit = unit
         self._graph = graph
         self._parent = parent
         self._label = None
 
+    def _clean_value(self, value):
+        if isinstance(value, str):
+            if (value[0] == '[') and (value[-1] == ']'):
+                value = np.array(json.loads(value))
+        return value
+
     def __repr__(self):
         if self._unit is not None:
             return f"{self._value} {self._unit}"

atomrdf/stores.py

@@ -1,6 +1,7 @@
 from rdflib.store import NO_STORE, VALID_STORE
 from rdflib import plugin
-from rdflib import Graph, Literal
+from rdflib import Graph
+from atomrdf.namespace import Literal
 
 import os
 

atomrdf/structure.py

@@ -31,8 +31,8 @@
 import atomrdf.json_io as json_io
 import atomrdf.properties as prp
 
-from rdflib import Graph, Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef
-from atomrdf.namespace import CMSO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV
+from rdflib import Graph, Namespace, XSD, RDF, RDFS, BNode, URIRef
+from atomrdf.namespace import CMSO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV, Literal
 
 from atomman.defect.Dislocation import Dislocation
 import atomman as am

atomrdf/visualize.py

@@ -1,6 +1,6 @@
 import graphviz
 import os
-from rdflib import BNode, URIRef, Literal, Namespace
+from rdflib import BNode, URIRef, Namespace, Literal
 import uuid
 import json
 

atomrdf/workflow/pyiron/pyiron.py

@@ -10,6 +10,7 @@
 import atomrdf.workflow.pyiron.lammps as lammps
 import atomrdf.workflow.pyiron.vasp as vasp
 import atomrdf.workflow.pyiron.murnaghan as murnaghan
+import atomrdf.workflow.pyiron.quasiharmonic as qha
 
 def process_job(job):
     """
@@ -32,6 +33,8 @@ def process_job(job):
         return vasp.process_job(job)    
     elif type(job).__name__ == 'Murnaghan':
         return murnaghan.process_job(job)
+    elif type(job).__name__ == 'QuasiHarmonicJob':
+        return qha.process_job(job)
     else:
         raise TypeError("These type of pyiron Job is not currently supported")
 

atomrdf/workflow/pyiron/quasiharmonic.py

@@ -0,0 +1,47 @@
+import os
+import numpy as np
+import ast
+from atomrdf.structure import System
+import atomrdf.workflow.pyiron.lammps as lammps
+
+def process_job(job):
+    #murnaghan job processing; add individual lammps jobs first
+    job_dicts = []
+
+    #create an additional jobdict with the murnaghan job
+    quasi_dict = {}
+    lammps.get_structures(job, quasi_dict)
+    quasi_dict['intermediate'] = False
+    lammps.get_simulation_folder(job, quasi_dict)
+
+    #add the murnaghan method
+    quasi_dict['method'] = "QuasiHarmonicModel"
+    outputs = []
+    outputs.append(
+        {
+            "label": "QuasiHarmonicFreeEnergy",
+            "value": np.round(job['output/free_energy'].T, decimals=4),
+            "unit": "EV",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "QuasiHarmonicVolume",
+            "value": np.round(job['output/volumes'].T, decimals=4),
+            "unit": "ANGSTROM3",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "QuasiHarmonicTemperature",
+            "value": np.round(job['output/temperatures'][0], decimals=2),
+            "unit": "K",
+            "associate_to_sample": True,
+        }
+    )
+    quasi_dict['outputs'] = outputs
+    lammps.add_software(quasi_dict)
+    job_dicts.append(quasi_dict)
+    return job_dicts

atomrdf/workflow/workflow.py

@@ -14,7 +14,7 @@
 See atomrdf.workflow.pyiron for more details
 """
 
-from rdflib import Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef
+from rdflib import Namespace, XSD, RDF, RDFS, BNode, URIRef
 
 import warnings
 import numpy as np
@@ -28,7 +28,7 @@
 from atomrdf.structure import System
 
 # Move imports to another file
-from atomrdf.namespace import PROV, CMSO, PODO, ASMO, MDO
+from atomrdf.namespace import PROV, CMSO, PODO, ASMO, MDO, Literal
 
 class Workflow:
     def __init__(self, kg):
@@ -303,7 +303,10 @@ def _add_method(
         elif job_dict["method"] == "EquationOfState":            
             #special type of EOS should be initialised!
             self.kg.add((activity, RDF.type, Namespace("http://purls.helmholtz-metadaten.de/asmo/").EquationOfStateFit))
-
+
+        elif job_dict["method"] == "QuasiHarmonicModel":            
+            self.kg.add((activity, RDF.type, Namespace("http://purls.helmholtz-metadaten.de/asmo/").QuasiHarmonicModel))
+
         # add that structure was generated
         self.kg.add((activity, ASMO.hasComputationalMethod, method))
         self.kg.add((job_dict['sample']['final'], PROV.wasGeneratedBy, activity))

examples/04_substitution.ipynb

@@ -1342,7 +1342,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.1.-1"
   }
  },
  "nbformat": 4,