From 056697e8e255af46a2e29bf86eecc91636e5b576 Mon Sep 17 00:00:00 2001 From: Sarath Date: Wed, 26 Jun 2024 21:12:48 +0200 Subject: [PATCH 1/3] update ontology --- atomrdf/data/ldo.owl | 27 +++++++++++++++++++++++++++ atomrdf/network/ontology.py | 2 +- 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/atomrdf/data/ldo.owl b/atomrdf/data/ldo.owl index f071855..742d356 100644 --- a/atomrdf/data/ldo.owl +++ b/atomrdf/data/ldo.owl @@ -253,6 +253,15 @@ + + + + + + + + + @@ -308,6 +317,7 @@ + Angular Vector Frank Vector @@ -324,6 +334,14 @@ + + + + Character Angle + + + + @@ -467,6 +485,15 @@ + + + + An angle is a measure of the the space (usually in degrees) between two intersecting lines at the point where they meet or vertex. + Angle + + + + diff --git a/atomrdf/network/ontology.py b/atomrdf/network/ontology.py index ec24cc9..f96317f 100644 --- a/atomrdf/network/ontology.py +++ b/atomrdf/network/ontology.py @@ -38,7 +38,7 @@ 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 + ldo = OntologyNetwork(os.path.join(file_location, "data/ldo.owl")) #e23fa9930351787e701347878a3e1a0e3924d084 # combine them combo = cmso + pldo + podo + asmo + ldo From 3e7676e91f9ca392d52f4795c840b67245fb34e1 Mon Sep 17 00:00:00 2001 From: Sarath Date: Wed, 26 Jun 2024 21:19:13 +0200 Subject: [PATCH 2/3] add character angle --- atomrdf/structure.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index c135527..6d594e5 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -1973,10 +1973,13 @@ def add_dislocation(self, disl_dict): 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 + disl_name = "ScrewDislocation" elif (np.abs(angle_deg-90) < 1E-3) or (np.abs(angle_deg-270) < 1E-3): disl_type = LDO.EdgeDislocation + disl_name = "EdgeDislocation" else: disl_type = LDO.MixedDislocation + disl_name = "MixedDislocation" line_defect = self.graph.create_node(f"{self._name}_Dislocation", disl_type) self.graph.add((self.material, CMSO.hasDefect, line_defect)) @@ -1993,6 +1996,8 @@ def add_dislocation(self, disl_dict): 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)) + self.graph.add((line_defect, LDO.hasCharacterAngle, Literal(angle_deg, datatype=XSD.float))) + 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))) From 1c767ff71af916662c61f7fd89e740b6b17bf5c5 Mon Sep 17 00:00:00 2001 From: Sarath Date: Wed, 26 Jun 2024 21:20:49 +0200 Subject: [PATCH 3/3] =?UTF-8?q?Bump=20version:=200.9.0=20=E2=86=92=200.9.1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- CITATION.cff | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index e34834e..8ef8f7b 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.9.0 +current_version = 0.9.1 commit = True tag = False diff --git a/CITATION.cff b/CITATION.cff index 57f38cf..2a93fd2 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org' license: "MIT" repository-code: https://github.com/pyscal/atomRDF type: software -version: 0.9.0 +version: 0.9.1 diff --git a/setup.py b/setup.py index 41e5701..ccb0b9a 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='atomrdf', - version='0.9.0', + version='0.9.1', author='Abril Azocar Guzman, Sarath Menon', author_email='sarath.menon@pyscal.org', description='Ontology based structural manipulation and quering',