Merge pull request #143 from pyscal/track_lattice_constant

Track lattice constant

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.4
+current_version = 0.9.5
 commit = True
 tag = False
 

CITATION.cff

@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.4
+version: 0.9.5

atomrdf/network/ontology.py

@@ -82,6 +82,7 @@ def read_ontology():
 
     # General fixes
     combo.add_path(("cmso:CrystalStructure", "cmso:hasAltName", "string"))
+    combo.add_path(("cmso:LatticeParameter", "asmo:wasCalculatedBy", "prov:Activity"))
 
     # interontology paths
     #CMSO -> PODO VACANCY

atomrdf/sample.py

@@ -69,7 +69,7 @@ def _volume(self):
             self._graph.add((parent, ASMO.hasUnit, URIRef(f"http://qudt.org/vocab/unit/ANGSTROM3")))
         else:
             parent = inps[labels.index("Volume")]
-        return Property(volume.toPython(), graph=self._graph, parent=parent, unit='ANGSTROM3')
+        return Property(volume.toPython(), graph=self._graph, parent=parent, unit='ANGSTROM3', sample_parent=self._sample_id)
 
     @property
     def _no_of_atoms(self):
@@ -83,7 +83,7 @@ def _no_of_atoms(self):
             self._graph.add((self._sample_id, CMSO.hasCalculatedProperty, parent))
         else:
             parent = inps[labels.index("NumberOfAtoms")]
-        return Property(no_atoms.toPython(), graph=self._graph, parent=parent)
+        return Property(no_atoms.toPython(), graph=self._graph, parent=parent, sample_parent=self._sample_id)
 
 
     @property
@@ -98,7 +98,7 @@ def _input_properties(self):
             units = [unit if unit is None else unit.toPython().split('/')[-1] for unit in units]
             props = []
             for count, value in enumerate(values):
-                props.append(Property(value.toPython(), unit=units[count], graph=self._graph, parent=inps[count]))
+                props.append(Property(value.toPython(), unit=units[count], graph=self._graph, parent=inps[count], sample_parent=self._sample_id))
             return labels, props
         return [], []
 
@@ -112,16 +112,17 @@ def _output_properties(self):
         units = [unit if unit is None else unit.toPython().split('/')[-1] for unit in units]
         props = []
         for count, value in enumerate(values):
-            props.append(Property(value.toPython(), unit=units[count], graph=self._graph, parent=inps[count]))
+            props.append(Property(value.toPython(), unit=units[count], graph=self._graph, parent=inps[count], sample_parent=self._sample_id))
         return labels, props
 
 class Property:
-    def __init__(self, value, unit=None, graph=None, parent=None):
+    def __init__(self, value, unit=None, graph=None, parent=None, sample_parent=None):
         self._value = self._clean_value(value)
         self._unit = unit
         self._graph = graph
         self._parent = parent
         self._label = None
+        self._sample_parent = sample_parent
 
     def _clean_value(self, value):
         if isinstance(value, str):
@@ -191,51 +192,63 @@ def __add__(self, value):
         parent = self._create_node(res)
         res_prop = Property(res, unit=self._unit, graph=self._graph, parent=parent) 
         res_prop.label = self._create_label(self, value, '+')
+        res_prop._sample_parent = self._sample_parent
         if self._graph is not None:
             operation = URIRef(f'operation:{uuid.uuid4()}')
             self._graph.add((operation, RDF.type, MATH.Addition))
+            self._graph.add((operation, RDF.type, PROV.Activity))
             self._graph.add((operation, MATH.hasAddend, self._wrap(value)))
             self._graph.add((operation, MATH.hasAddend, self._wrap(self)))
             self._graph.add((operation, MATH.hasSum, self._wrap(res_prop)))
+            self._graph.add((parent, MATH.wasCalculatedBy, operation))
         return res_prop
 
     def __sub__(self, value):
         res = self._value - self._declass(value)
         parent = self._create_node(res)
         res_prop = Property(res, unit=self._unit, graph=self._graph, parent=parent)
         res_prop.label = self._create_label(self, value, '-') 
+        res_prop._sample_parent = self._sample_parent
         if self._graph is not None:
             operation = URIRef(f'operation:{uuid.uuid4()}')
             self._graph.add((operation, RDF.type, MATH.Subtraction))
+            self._graph.add((operation, RDF.type, PROV.Activity))
             self._graph.add((operation, MATH.hasMinuend, self._wrap(self)))
             self._graph.add((operation, MATH.hasSubtrahend, self._wrap(value)))
             self._graph.add((operation, MATH.hasDifference, self._wrap(res_prop)))
+            self._graph.add((parent, MATH.wasCalculatedBy, operation))
         return res_prop    
 
     def __mul__(self, value):
         res = self._value * self._declass(value)
         parent = self._create_node(res)
         res_prop = Property(res, unit=self._unit, graph=self._graph, parent=parent)
         res_prop.label = self._create_label(self, value, '*') 
+        res_prop._sample_parent = self._sample_parent
         if self._graph is not None:
             operation = URIRef(f'operation:{uuid.uuid4()}')
             self._graph.add((operation, RDF.type, MATH.Multiplication))
+            self._graph.add((operation, RDF.type, PROV.Activity))
             self._graph.add((operation, MATH.hasFactor, self._wrap(self)))
             self._graph.add((operation, MATH.hasFactor, self._wrap(value)))
             self._graph.add((operation, MATH.hasProduct, self._wrap(res_prop)))
+            self._graph.add((parent, MATH.wasCalculatedBy, operation))
         return res_prop
 
     def __truediv__(self, value):
         res = self._value / self._declass(value)
         parent = self._create_node(res)
         res_prop = Property(res, unit=self._unit, graph=self._graph, parent=parent)
         res_prop.label = self._create_label(self, value, '/') 
+        res_prop._sample_parent = self._sample_parent
         if self._graph is not None:
             operation = URIRef(f'operation:{uuid.uuid4()}')
             self._graph.add((operation, RDF.type, MATH.Division))
+            self._graph.add((operation, RDF.type, PROV.Activity))
             self._graph.add((operation, MATH.hasDivisor, self._wrap(self)))
             self._graph.add((operation, MATH.hasDividend, self._wrap(value)))
             self._graph.add((operation, MATH.hasQuotient, self._wrap(res_prop)))
+            self._graph.add((parent, MATH.wasCalculatedBy, operation))
         return res_prop
 
 

atomrdf/structure.py

@@ -30,9 +30,10 @@
 
 import atomrdf.json_io as json_io
 import atomrdf.properties as prp
+from atomrdf.sample import Property
 
 from rdflib import Graph, Namespace, XSD, RDF, RDFS, BNode, URIRef
-from atomrdf.namespace import CMSO, LDO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV, Literal
+from atomrdf.namespace import CMSO, LDO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV, Literal, ASMO
 
 # read element data file
 file_location = os.path.dirname(__file__).split("/")
@@ -41,6 +42,13 @@
 with open(file_location, "r") as fin:
     element_indetifiers = yaml.safe_load(fin)
 
+#declassing special variables
+def _declass(item):
+    if isinstance(item, Property):
+        return item.value
+    else:
+        return item
+
 def _make_crystal(
     structure,
     lattice_constant=1.00,
@@ -85,9 +93,9 @@ def _make_crystal(
     """
     atoms, box, sdict = pcs.make_crystal(
         structure,
-        lattice_constant=lattice_constant,
+        lattice_constant = _declass(lattice_constant),
         repetitions=repetitions,
-        ca_ratio=ca_ratio,
+        ca_ratio = _declass(ca_ratio),
         noise=noise,
         element=element,
         return_structure_dict=True,
@@ -98,10 +106,12 @@ def _make_crystal(
     s.box = box
     s.atoms = atoms
     s.atoms._lattice = structure
-    s.atoms._lattice_constant = lattice_constant
+    s.atoms._lattice_constant = _declass(lattice_constant)
     s._structure_dict = sdict
     s.label = label
     s.to_graph()
+    s.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+    s.add_property_mappings(ca_ratio, mapping_quantity='lattice_constant')    
     return s
 
 
@@ -152,7 +162,7 @@ def _make_general_lattice(
         positions,
         types,
         box,
-        lattice_constant=lattice_constant,
+        lattice_constant=_declass(lattice_constant),
         repetitions=repetitions,
         noise=noise,
         element=element,
@@ -162,11 +172,12 @@ def _make_general_lattice(
     s.box = box
     s.atoms = atoms
     s.atoms._lattice = "custom"
-    s.atoms._lattice_constant = lattice_constant
+    s.atoms._lattice_constant = _declass(lattice_constant)
     s._structure_dict = sdict
     s.label = label
     s.to_graph()
-
+    s.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+
     return s
 
 
@@ -273,9 +284,9 @@ def _make_dislocation(
         # create a structure with the info
         input_structure = _make_crystal(
             structure,
-            lattice_constant=lattice_constant,
+            lattice_constant=_declass(lattice_constant),
             repetitions=repetitions,
-            ca_ratio=ca_ratio,
+            ca_ratio=_declass(ca_ratio),
             noise=noise,
             element=element,
             primitive=primitive,
@@ -288,9 +299,9 @@ def _make_dislocation(
             raise ValueError("Please provide structure")
         input_structure = _make_crystal(
             structure,
-            lattice_constant=lattice_constant,
+            lattice_constant=_declass(lattice_constant),
             repetitions=repetitions,
-            ca_ratio=ca_ratio,
+            ca_ratio=_declass(ca_ratio),
             noise=noise,
             element=element,
             primitive=primitive,
@@ -364,6 +375,8 @@ def _make_dislocation(
     output_structure.graph = graph
     output_structure.to_graph()
     output_structure.add_dislocation(disl_dict)
+    output_structure.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+    output_structure.add_property_mappings(ca_ratio, mapping_quantity='lattice_constant')
 
     if return_atomman_dislocation:
         return output_structure, disc
@@ -423,7 +436,7 @@ def _make_grain_boundary(
         atoms, box, sdict = gb.populate_grain_boundary(
             structure,
             repetitions=repetitions,
-            lattice_parameter=lattice_constant,
+            lattice_parameter=_declass(lattice_constant),
             overlap=overlap,
         )
     elif element is not None:
@@ -434,10 +447,12 @@ def _make_grain_boundary(
     s.box = box
     s.atoms = atoms
     s.atoms._lattice = structure
-    s.atoms._lattice_constant = lattice_constant
+    s.atoms._lattice_constant = _declass(lattice_constant)
     s._structure_dict = sdict
     s.label = label
     s.to_graph()
+    s.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+
     gb_dict = {
         "GBPlane": " ".join(np.array(gb_plane).astype(str)),
         "RotationAxis": axis,
@@ -506,7 +521,7 @@ def _read_structure(
             datadict = structure_dict[lattice]["conventional"]
         datadict["lattice"] = lattice
     if lattice_constant is not None:
-        datadict["lattice_constant"] = lattice_constant
+        datadict["lattice_constant"] = _declass(lattice_constant)
     if basis_box is not None:
         datadict["box"] = basis_box
     if basis_positions is not None:
@@ -523,6 +538,7 @@ def _read_structure(
     s.lattice_properties = datadict
     s.label = label
     s.to_graph()
+    s.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
     return s
 
 
@@ -840,6 +856,35 @@ def delete(self, ids=None, indices=None, condition=None, selection=False, copy_s
 
         return sys
 
+
+    def add_property_mappings(self, output_property, mapping_quantity=None):
+        if self.graph is None:
+            return
+        if not isinstance(output_property, Property):
+            return
+
+        #if the property is a directly calculated value
+        parent_samples = list([x[0] for x in self.graph.triples((None, CMSO.hasCalculatedProperty, output_property._parent))])
+        if len(parent_samples)>0:
+            for parent_sample in parent_samples:
+                self.graph.add((self.sample, PROV.wasDerivedFrom, parent_sample))
+        else:
+            #this is quantity that is derived -> for example volume/3 -> it has only sample parent, but no direct connection
+            if output_property._sample_parent is not None:
+                self.graph.add((self.sample, PROV.wasDerivedFrom, output_property._sample_parent))
+
+        if mapping_quantity=='lattice_constant':
+            #add lattice constant mapping
+            material = self.graph.value(self.sample, CMSO.hasMaterial)
+            crystal_structure = self.graph.value(material, CMSO.hasStructure)
+            unit_cell = self.graph.value(crystal_structure, CMSO.hasUnitCell)
+            lattice_parameter = self.graph.value(unit_cell, CMSO.hasLatticeParameter)
+
+            #also get activity
+            activity = self.graph.value(output_property._parent, ASMO.wasCalculatedBy)
+            self.graph.add((lattice_parameter, UNSAFEASMO.wasCalculatedBy, activity))
+
+
     def add_vacancy(self, concentration, number=None):
         """
         Add Vacancy details which will be annotated by PODO

atomrdf/workflow/pyiron/lammps.py

@@ -162,4 +162,34 @@ def extract_calculated_quantities(job, method_dict):
             "associate_to_sample": True,
         }
     )
+
+    structure = job.get_structure(frame=-1)
+    lx = np.linalg.norm(structure.cell[0])
+    ly = np.linalg.norm(structure.cell[1])
+    lz = np.linalg.norm(structure.cell[2])
+
+    outputs.append(
+        {
+            "label": "SimulationCellLength_x",
+            "value": np.round(lx, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "SimulationCellLength_y",
+            "value": np.round(ly, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "SimulationCellLength_z",
+            "value": np.round(lz, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )    
     method_dict['outputs'] =  outputs

atomrdf/workflow/pyiron/murnaghan.py

@@ -48,6 +48,37 @@ def process_job(job):
             "associate_to_sample": True,
         }
     )
+
+    structure = job.get_structure(frame=-1)
+    lx = np.linalg.norm(structure.cell[0])
+    ly = np.linalg.norm(structure.cell[1])
+    lz = np.linalg.norm(structure.cell[2])
+
+    outputs.append(
+        {
+            "label": "SimulationCellLength_x",
+            "value": np.round(lx, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "SimulationCellLength_y",
+            "value": np.round(ly, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "SimulationCellLength_z",
+            "value": np.round(lz, decimals=4),
+            "unit": "ANGSTROM",
+            "associate_to_sample": True,
+        }
+    )   
+
     murnaghan_dict['outputs'] = outputs
     lammps.add_software(murnaghan_dict)
     job_dicts.append(murnaghan_dict)