Merge pull request #177 from pyscal/Sf_fixes_3

Sf fixes 3

Author: srmnitc

atomrdf/graph.py

@@ -639,7 +639,65 @@ def _initialize_graph(self):
             (CMSO.Vector, CMSO.hasUnit, URIRef("http://qudt.org/vocab/unit/ANGSTROM"))
         )
 
-    def add_calculated_quantity(self, sample, propertyname, value, unit=None):
+    def add_output_of_simulation(self, simulation_term,
+                                value,
+                                property_label,
+                                base_quantity=None,
+                                unit=None,
+                                has_simulation_algorithm=None,
+                                has_computational_method=None):
+        """
+        Create a new output of simulation in the graph. The types of different terms are defined in the ontology.
+        Those should be access by kg.terms.ontolog.ontology_term.
+
+        Parameters
+        ----------
+        simulation_term : OntoTerm
+            The term representing the simulation.
+        
+        value : float
+            The value of the output.
+        
+        property_label : str
+            The label of the property.
+        
+        base_quantity : OntoTerm, optional
+            The base quantity of the output. Default is None.
+        
+        unit : OntoTerm, optional
+            The unit of the output. Default is None.
+        
+        
+        has_simulation_algorithm : OntoTerm, optional
+            The simulation algorithm used. Default is None.
+        
+        has_computational_method : OntoTerm, optional
+            The computational method used. Default is None.
+        
+        Returns
+        -------
+        URIRef
+            The newly created output of simulation.
+
+        """
+        main_id = str(uuid.uuid4())
+        simulation_node = self.create_node(f"simulation:{main_id}", simulation_term)
+        if has_simulation_algorithm is not None:
+            self.add((simulation_node, ASMO.usesSimulationAlgorithm, has_simulation_algorithm))
+        if has_computational_method is not None:
+            self.add((simulation_node, ASMO.hasComputationalMethod, has_computational_method))
+        if base_quantity is None:
+            base_quantity = ASMO.CalculatedProperty
+        prop = self.create_node(f"simulation:{main_id}_{property_label}", base_quantity)
+        self.add((prop, ASMO.wasCalculatedBy, simulation_node))
+        self.add((prop, RDFS.label, Literal(property_label)))
+        self.add((prop, ASMO.hasValue, Literal(value)))
+        if unit is not None:
+            self.add((prop, ASMO.hasUnit, unit))
+        return prop
+
+
+    def add_calculated_quantity(self, sample, propertyname, value, base_quantity=None, unit=None):
         """
         Add a calculated quantity to a sample.
 
@@ -669,8 +727,10 @@ def add_calculated_quantity(self, sample, propertyname, value, unit=None):
         >>> sample = graph.create_node("Sample1", CMSO.Sample)
         >>> graph.add_calculated_quantity(sample, "energy", "10.5", "eV")
         """
+        if base_quantity is None:
+            base_quantity = ASMO.CalculatedProperty
 
-        prop = self.create_node(f"{sample}_{propertyname}", CMSO.CalculatedProperty)
+        prop = self.create_node(f"{sample}_{propertyname}", base_quantity)
         self.add((sample, CMSO.hasCalculatedProperty, prop))
         self.add((prop, RDFS.label, Literal(propertyname)))
         self.add((prop, ASMO.hasValue, Literal(value)))

atomrdf/sample.py

@@ -213,17 +213,32 @@ def __init__(self, value, unit=None, graph=None, parent=None, sample_parent=None
         self._label = None
         self._sample_parent = sample_parent
 
+    def __getitem__(self, index):
+        if isinstance(self._value, (list, np.ndarray)):
+            if isinstance(index, slice):
+                value = self._value[index.start:index.stop:index.step]
+            else:
+                value = self._value[index]
+            return Property(value, unit=self._unit, graph=self._graph, parent=self._parent, sample_parent=self._sample_parent)
+            
+        else:
+            raise TypeError('This property is not a list or array, therefore not subscriptable.')
+    
+
     def _clean_value(self, value):
         if isinstance(value, str):
             if (value[0] == '[') and (value[-1] == ']'):
                 value = np.array(json.loads(value))
+        if isinstance(value, (list, np.ndarray)):
+            value = np.array(value)
         return value
 
     def __repr__(self):
         if self._unit is not None:
             return f"{self._value} {self._unit}"
         return f"{self._value}"
 
+    #
     @property
     def value(self):
         return self._value
@@ -275,6 +290,13 @@ def _create_node(self, res):
             self._graph.add((parent, ASMO.hasUnit, URIRef(f"http://qudt.org/vocab/unit/{self._unit}")))
         return parent
 
+    def update_physical_quantity(self, ontoterm):
+        if self._graph is not None:
+            if self._parent is not None:
+                self._graph.remove((self._parent, RDF.type, None))
+            #remove the old type
+            self._graph.add((self._parent, RDF.type, ontoterm.URIRef))
+
     #overloaded operations
     def __add__(self, value):
         res = self._value + self._declass(value)

atomrdf/structure.py

@@ -1976,13 +1976,13 @@ def _add_simulation_cell(self):
         )
         self.graph.add((self.sample, CMSO.hasSimulationCell, simulation_cell))
         volume = self.graph.create_node(
-            f"{self._name}_Volume", UNSAFEASMO.Volume, label="SimulationCellVolume"
+            f"{self._name}_Volume", ASMO.Volume, label="SimulationCellVolume"
         )
-        self.graph.add((simulation_cell, UNSAFECMSO.hasVolume, volume))
+        self.graph.add((simulation_cell, CMSO.hasVolume, volume))
         self.graph.add(
             (
                 volume,
-                UNSAFEASMO.hasValue,
+                ASMO.hasValue,
                 Literal(
                     np.round(self.schema.simulation_cell.volume(), decimals=2),
                     datatype=XSD.float,
@@ -1992,7 +1992,7 @@ def _add_simulation_cell(self):
         self.graph.add(
             (
                 volume,
-                UNSAFEASMO.hasUnit,
+                ASMO.hasUnit,
                 URIRef(f"http://qudt.org/vocab/unit/ANGSTROM3"),
             )
         )

atomrdf/workflow/jobdict.yml

@@ -5,7 +5,7 @@ structure:
   initial: System obj
   final: System obj 
 intermediate: False
-method: MolecularStatics/MolecularDynamics/DensityFunctionalTheory/EquationOfState/QuasiHarmonicModel
+method: MolecularStatics/MolecularDynamics/DensityFunctionalTheory/EquationOfState/QuasiHarmonicModel/ThermodynamicIntegration
 path: job path folder
 dof:
   - AtomicPositionRelaxation

atomrdf/workflow/pyiron/murnaghan.py

@@ -42,6 +42,24 @@ def process_job(job):
             "base": "Volume",
         }
     )
+    outputs.append(
+        {
+            "label": "TotalEnergy",
+            "value": np.round(job['output/energy'], decimals=4),
+            "unit": "EV",
+            "associate_to_sample": True,
+            "base": "TotalEnergy",
+        }
+    )
+    outputs.append(
+        {
+            "label": "Volume",
+            "value": np.round(job['output/volume'], decimals=4),
+            "unit": "ANGSTROM3",
+            "associate_to_sample": True,
+            "base": "Volume",
+        }
+    )
     outputs.append(
         {
             "label": "BulkModulus",

atomrdf/workflow/workflow.py

@@ -415,7 +415,7 @@ def _add_outputs(self, job_dict, activity):
                 #here we add the classes by property
                 #call func here
                 prop = self._select_base_property(out, main_id, CMSO.CalculatedProperty)
-                self.kg.add((prop, ASMO.wasCalculatedBy, activity))
+                self.kg.add((prop, UNSAFEASMO.wasCalculatedBy, activity))
 
                 if out["associate_to_sample"]:
                     self.kg.add((job_dict['sample']['final'], CMSO.hasCalculatedProperty, prop))