Merge pull request #130 from pyscal/add_disl_triples

Add disl triples

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.16
+current_version = 0.9.0
 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: 0.8.16
+version: 0.9.0

atomrdf/namespace.py

@@ -79,6 +79,7 @@ def __init__(self, infile, delimiter="/"):
 file_location = os.path.dirname(__file__)
 
 CMSO = Namespace(os.path.join(file_location, "data/cmso.owl"))
+LDO = Namespace(os.path.join(file_location, "data/ldo.owl"))
 PLDO = Namespace(os.path.join(file_location, "data/pldo.owl"))
 PODO = Namespace(os.path.join(file_location, "data/podo.owl"))
 ASMO = Namespace(os.path.join(file_location, "data/asmo.owl"))

atomrdf/network/ontology.py

@@ -38,9 +38,10 @@ def read_ontology():
     pldo = OntologyNetwork(os.path.join(file_location, "data/pldo.owl")) #d15d27712e3f64b405d75c70ad970c9d54ff0b51
     podo = OntologyNetwork(os.path.join(file_location, "data/podo.owl")) #6a74d511c5b78042e1cb7a6e76e948fa56de598e
     asmo = OntologyNetwork(os.path.join(file_location, "data/asmo.owl")) #c7e2da99b9126844f19f225c6a10cdb01aeb55e6
+    ldo = OntologyNetwork(os.path.join(file_location, "data/ldo.owl")) #52fc756d2e2f9baedfce478e7f8b790365648cea
 
     # combine them
-    combo = cmso + pldo + podo + asmo
+    combo = cmso + pldo + podo + asmo + ldo
 
     # add namespaces
     combo.add_namespace("prov", "http://www.w3.org/ns/prov#")
@@ -95,7 +96,12 @@ def read_ontology():
     combo.add_path(("podo:InterstitialImpurity", "rdfs:label", "string"))
     combo.add_path(("cmso:AtomicScaleSample", "podo:hasNumberOfImpurityAtoms", "int"))
     combo.add_path(("cmso:AtomicScaleSample", "podo:hasImpurityConcentration", "float"))
-
+
+    #CMSO -> LDO DISL paths
+    combo.add_path(("cmso:Material", "cmso:hasDefect", "ldo:LineDefect"))
+    combo.add_path(("cmso:Material", "cmso:hasDefect", "ldo:Dislocation"))
+
+
     combo.add_path(
         ("cmso:ComputationalSample", "prov:wasDerivedFrom", "cmso:ComputationalSample")
     )

atomrdf/structure.py

@@ -32,7 +32,7 @@
 import atomrdf.properties as prp
 
 from rdflib import Graph, Namespace, XSD, RDF, RDFS, BNode, URIRef
-from atomrdf.namespace import CMSO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV, Literal
+from atomrdf.namespace import CMSO, LDO, PLDO, PODO, UNSAFEASMO, UNSAFECMSO, PROV, Literal
 
 from atomman.defect.Dislocation import Dislocation
 import atomman as am
@@ -175,10 +175,10 @@ def _make_general_lattice(
 
 
 def _make_dislocation(
-    burgers_vector,
-    slip_vector,
+    slip_system,
     dislocation_line,
     elastic_constant_dict,
+    burgers_vector=None,
     dislocation_type="monopole",
     structure=None,
     element=None,
@@ -190,20 +190,27 @@ def _make_dislocation(
     graph=None,
     names=False,
     label=None,
+    return_atomman_dislocation=False,
 ):
     """
     Generate a dislocation structure. Wraps the atomman.defect.Dislocation class.
 
     Parameters
     ----------
-    burgers_vector : numpy array of length 3
-        The Burgers vector of the dislocation.
-    slip_vector : numpy array of length 3
-        The slip vector of the dislocation.
+    slip_system : list of lists, shape (2 x 3)
+        the slip system for the given system. The input should of type [[u, v, w], [h, k, l]].
+        [u, v, w] is the slip direction and [h, k, l] is the slip plane.
     dislocation_line : numpy array of length 3
         The dislocation line direction.
+        This determines the type of dislocation to generate, screw, edge or mixed.
+    burgers_vector : scalar or numpy array of length 3, optional
+        if a scalar value (b) is provided, the burgers vector is assumed to be b*[u, v, w].
+        if a numpy array is provided, the burgers vector is set to this value.
+        Default is equal to slip direction [u, v, w] from slip_system.
     elastic_constant_dict : dict
-        Dictionary of elastic constants.
+        Dictionary of elastic constants. The keys should be in Voigt notation.
+    burgers_vector : numpy array of length 3
+        The Burgers vector of the dislocation.
     dislocation_type : str, optional
         The type of dislocation to generate. Default is "monopole".
     structure : crystal lattice to be used
@@ -247,6 +254,15 @@ def _make_dislocation(
     will be generated. If set to "periodicarray", a periodic array of dislocations will be generated.
 
     """
+    slip_direction = slip_system[0]
+    slip_plane = slip_system[1]
+    if burgers_vector is None:
+        burgers_vector = slip_direction
+    elif np.isscalar(burgers_vector):
+        burgers_vector = burgers_vector * np.array(slip_direction)
+    elif len(burgers_vector) != 3:
+        raise ValueError('burgers vector should be None, scalar, or of length 3')
+
 
     if structure is not None:
         # create a structure with the info
@@ -298,7 +314,7 @@ def _make_dislocation(
         C,
         burgers_vector,
         dislocation_line,
-        slip_vector,
+        slip_plane,
     )
     if dislocation_type == "monopole":
         disl_system = disc.monopole()
@@ -318,6 +334,20 @@ def _make_dislocation(
     positions = np.column_stack(
         (atom_df["pos[0]"].values, atom_df["pos[1]"].values, atom_df["pos[2]"].values)
     )
+
+    #find dislocation character
+    angle = np.dot(dislocation_line, burgers_vector)/(np.linalg.norm(dislocation_line)*np.linalg.norm(burgers_vector))
+    angle_rad = np.arccos(angle)
+    angle_deg = np.degrees(angle_rad)
+
+    disl_dict = {
+        'BurgersVector': burgers_vector,
+        'SlipPlane': slip_plane,
+        'SlipDirection': slip_direction,
+        'DislocationLine': dislocation_line,
+        'DislocationCharacter': angle_deg,
+    }
+
     atom_dict = {"positions": positions, "types": types, "species": species}
     atom_obj = Atoms()
     atom_obj.from_dict(atom_dict)
@@ -326,7 +356,12 @@ def _make_dislocation(
     output_structure.atoms = atom_obj
     output_structure = output_structure.modify.remap_to_box()
     output_structure.label = label
+    output_structure.graph = graph
+    output_structure.to_graph()
+    output_structure.add_dislocation(disl_dict)
 
+    if return_atomman_dislocation:
+        return output_structure, disc
     return output_structure
 
 
@@ -1930,6 +1965,52 @@ def _add_atoms(self):
         #    force_identifier = uuid.uuid4()
         #    self.add((force, CMSO.hasIdentifier, Literal(force_identifier, datatype=XSD.string)))
 
+    def add_dislocation(self, disl_dict):
+        if self.graph is None:
+            return
+
+        #find what kind of disl is present
+        angle_deg = disl_dict['DislocationCharacter']
+        if (np.abs(angle_deg-0) < 1E-3) or (np.abs(angle_deg-180) < 1E-3) or (np.abs(angle_deg-360) < 1E-3):
+            disl_type = LDO.ScrewDislocation
+        elif (np.abs(angle_deg-90) < 1E-3) or (np.abs(angle_deg-270) < 1E-3):
+            disl_type = LDO.EdgeDislocation
+        else:
+            disl_type = LDO.MixedDislocation
+
+        line_defect = self.graph.create_node(f"{self._name}_Dislocation", disl_type)
+        self.graph.add((self.material, CMSO.hasDefect, line_defect))
+
+        line_direction = self.graph.create_node(f"{self._name}_DislocationLineDirection", LDO.LineDirection)
+        self.graph.add((line_direction, CMSO.hasComponent_x, Literal(disl_dict['DislocationLine'][0], datatype=XSD.float)))
+        self.graph.add((line_direction, CMSO.hasComponent_y, Literal(disl_dict['DislocationLine'][1], datatype=XSD.float)))
+        self.graph.add((line_direction, CMSO.hasComponent_z, Literal(disl_dict['DislocationLine'][2], datatype=XSD.float)))
+        self.graph.add((line_defect, LDO.hasLineDirection, line_direction))                
+
+        burgers_vector = self.graph.create_node(f"{self._name}_DislocationBurgersVector", LDO.BurgersVector)
+        self.graph.add((burgers_vector, CMSO.hasComponent_x, Literal(disl_dict['BurgersVector'][0], datatype=XSD.float)))
+        self.graph.add((burgers_vector, CMSO.hasComponent_y, Literal(disl_dict['BurgersVector'][1], datatype=XSD.float)))
+        self.graph.add((burgers_vector, CMSO.hasComponent_z, Literal(disl_dict['BurgersVector'][2], datatype=XSD.float)))
+        self.graph.add((line_defect, LDO.hasBurgersVector, burgers_vector))
+
+        slip_direction = self.graph.create_node(f"{self._name}_DislocationSlipDirection", LDO.SlipDirection)
+        self.graph.add((slip_direction, CMSO.hasComponent_x, Literal(disl_dict['SlipDirection'][0], datatype=XSD.float)))
+        self.graph.add((slip_direction, CMSO.hasComponent_y, Literal(disl_dict['SlipDirection'][1], datatype=XSD.float)))
+        self.graph.add((slip_direction, CMSO.hasComponent_z, Literal(disl_dict['SlipDirection'][2], datatype=XSD.float)))
+
+        slip_plane = self.graph.create_node(f"{self._name}_DislocationSlipPlane", LDO.SlipPlane)
+        normal_vector = self.graph.create_node(f"{self._name}_DislocationNormalVector", LDO.NormalVector)
+        self.graph.add((normal_vector, CMSO.hasComponent_x, Literal(disl_dict['SlipPlane'][0], datatype=XSD.float)))
+        self.graph.add((normal_vector, CMSO.hasComponent_y, Literal(disl_dict['SlipPlane'][1], datatype=XSD.float)))
+        self.graph.add((normal_vector, CMSO.hasComponent_z, Literal(disl_dict['SlipPlane'][2], datatype=XSD.float)))
+        self.graph.add((slip_plane, LDO.hasNormalVector, normal_vector))
+
+        slip_system = self.graph.create_node(f"{self._name}_DislocationSlipSystem", LDO.SlipSystem)
+        self.graph.add((slip_direction, LDO.belongsToSystem, slip_system))
+        self.graph.add((slip_plane, LDO.belongsToSystem, slip_system))
+        self.graph.add((line_defect, LDO.movesOn, slip_system))
+
+
     def add_gb(self, gb_dict):
         """
         Add GB details which will be annotated using PLDO