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fix nodes
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@srmnitc
srmnitc committed Apr 16, 2024
1 parent 2b53e03 commit 7ac4ddd
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Showing 2 changed files with 2,301 additions and 2,301 deletions.
36 changes: 18 additions & 18 deletions atomrdf/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -276,12 +276,12 @@ def delete(self, ids=None, indices=None, condition=None, selection=False):
break

if valid:
chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
self.graph.add((self.sample, CMSO.hasSpecies, chemical_species))

for e, r in composition.items():
if e in element_indetifiers.keys():
element = self.graph.add_node(element_indetifiers[e], CMSO.ChemicalElement)
element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement)
self.graph.add((chemical_species, CMSO.hasElement, element))
self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string)))
self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float)))
Expand Down Expand Up @@ -339,12 +339,12 @@ def substitute_atoms(self, substitution_element, ids=None, indices=None, conditi
break

if valid:
chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
self.graph.add((self.sample, CMSO.hasSpecies, chemical_species))

for e, r in composition.items():
if e in element_indetifiers.keys():
element = self.graph.add_node(element_indetifiers[e], CMSO.ChemicalElement)
element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement)
self.graph.add((chemical_species, CMSO.hasElement, element))
self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string)))
self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float)))
Expand Down Expand Up @@ -466,12 +466,12 @@ def add_interstitial_impurities(self, element, void_type='tetrahedral', lattice_
break

if valid:
chemical_species = self.graph.add_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
chemical_species = self.graph.create_node(f'{self._name}_ChemicalSpecies', CMSO.ChemicalSpecies)
self.graph.add((self.sample, CMSO.hasSpecies, chemical_species))

for e, r in composition.items():
if e in element_indetifiers.keys():
element = self.graph.add_node(element_indetifiers[e], CMSO.ChemicalElement)
element = self.graph.create_node(element_indetifiers[e], CMSO.ChemicalElement)
self.graph.add((chemical_species, CMSO.hasElement, element))
self.graph.add((element, CMSO.hasSymbol, Literal(e, datatype=XSD.string)))
self.graph.add((element, CMSO.hasElementRatio, Literal(r, datatype=XSD.float)))
Expand Down Expand Up @@ -671,7 +671,7 @@ def _add_crystal_structure(self, targets=None):
valid = self.graph._is_valid(targets)

if valid:
crystal_structure = self.graph.add_node(f'{self._name}_CrystalStructure', CMSO.CrystalStructure)
crystal_structure = self.graph.create_node(f'{self._name}_CrystalStructure', CMSO.CrystalStructure)
self.graph.add((self.material, CMSO.hasStructure, crystal_structure))
self.graph.add((crystal_structure, CMSO.hasAltName,
Literal(targets[0],
Expand Down Expand Up @@ -725,7 +725,7 @@ def _add_unit_cell(self):
-------
"""

unit_cell = self.graph.add_node(f'{self._name}_UnitCell', CMSO.UnitCell)
unit_cell = self.graph.create_node(f'{self._name}_UnitCell', CMSO.UnitCell)
self.graph.add((self.crystal_structure, CMSO.hasUnitCell, unit_cell))
self.unit_cell = unit_cell

Expand All @@ -748,13 +748,13 @@ def _add_lattice_properties(self, lattice_parameter_value, lattice_angle_value):
Returns
-------
"""
lattice_parameter = self.graph.add_node(f'{self._name}_LatticeParameter', CMSO.LatticeParameter)
lattice_parameter = self.graph.create_node(f'{self._name}_LatticeParameter', CMSO.LatticeParameter)
self.graph.add((self.unit_cell, CMSO.hasLatticeParameter, lattice_parameter))
self.graph.add((lattice_parameter, CMSO.hasLength_x, Literal(lattice_parameter_value[0], datatype=XSD.float)))
self.graph.add((lattice_parameter, CMSO.hasLength_y, Literal(lattice_parameter_value[1], datatype=XSD.float)))
self.graph.add((lattice_parameter, CMSO.hasLength_z, Literal(lattice_parameter_value[2], datatype=XSD.float)))

lattice_angle = self.graph.add_node(f'{self._name}_LatticeAngle', CMSO.LatticeAngle)
lattice_angle = self.graph.create_node(f'{self._name}_LatticeAngle', CMSO.LatticeAngle)
self.graph.add((self.unit_cell, CMSO.hasAngle, lattice_angle))
self.graph.add((lattice_angle, CMSO.hasAngle_alpha, Literal(lattice_angle_value[0], datatype=XSD.float)))
self.graph.add((lattice_angle, CMSO.hasAngle_beta, Literal(lattice_angle_value[1], datatype=XSD.float)))
Expand Down Expand Up @@ -804,14 +804,14 @@ def _add_atoms(self):
outfile = self._save_atom_attributes(position_identifier, species_identifier)

if "positions" in self.atoms.keys():
position = self.graph.add_node(f'{self._name}_Position', CMSO.AtomAttribute)
position = self.graph.create_node(f'{self._name}_Position', CMSO.AtomAttribute)
self.graph.add((self.sample, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasAttribute, position))
self.graph.add((position, CMSO.hasName, Literal('Position', datatype=XSD.string)))
self.graph.add((position, CMSO.hasIdentifier, Literal(position_identifier, datatype=XSD.string)))
self.graph.add((position, CMSO.hasPath, Literal(outfile, datatype=XSD.string)))

if "species" in self.atoms.keys():
species = self.graph.add_node(f'{self._name}_Species', CMSO.AtomAttribute)
species = self.graph.create_node(f'{self._name}_Species', CMSO.AtomAttribute)
self.graph.add((self.sample, Namespace("http://purls.helmholtz-metadaten.de/cmso/").hasAttribute, species))
self.graph.add((species, CMSO.hasName, Literal('Species', datatype=XSD.string)))
self.graph.add((species, CMSO.hasIdentifier, Literal(species_identifier, datatype=XSD.string)))
Expand Down Expand Up @@ -858,7 +858,7 @@ def add_vacancy(self, concentration, number=None):
if self.graph is None:
return

vacancy = self.graph.add_node(f'{self._name}_Vacancy', PODO.Vacancy)
vacancy = self.graph.create_node(f'{self._name}_Vacancy', PODO.Vacancy)
self.graph.add((self.material, CMSO.hasDefect, vacancy))
self.graph.add((self.simulation_cell, PODO.hasVacancyConcentration, Literal(concentration, datatype=XSD.float)))
if number is not None:
Expand All @@ -885,19 +885,19 @@ def add_gb(self, gb_dict):
return

if gb_dict["GBType"] is None:
plane_defect = self.graph.add_node(f'{self._name}_GrainBoundary')
plane_defect = self.graph.create_node(f'{self._name}_GrainBoundary')

elif gb_dict["GBType"] == "Twist":
plane_defect = self.graph.add_node(f'{self._name}_TwistGrainBoundary', PLDO.TwistGrainBoundary)
plane_defect = self.graph.create_node(f'{self._name}_TwistGrainBoundary', PLDO.TwistGrainBoundary)

elif gb_dict["GBType"] == "Tilt":
plane_defect = self.graph.add_node(f'{self._name}_TiltGrainBoundary', PLDO.TiltGrainBoundary)
plane_defect = self.graph.create_node(f'{self._name}_TiltGrainBoundary', PLDO.TiltGrainBoundary)

elif gb_dict["GBType"] == "Symmetric Tilt":
plane_defect = self.graph.add_node(f'{self._name}_SymmetricalTiltGrainBoundary', PLDO.SymmetricalTiltGrainBoundary)
plane_defect = self.graph.create_node(f'{self._name}_SymmetricalTiltGrainBoundary', PLDO.SymmetricalTiltGrainBoundary)

elif gb_dict["GBType"] == "Mixed":
plane_defect = self.graph.add_node(f'{self._name}_MixedGrainBoundary', PLDO.MixedGrainBoundary)
plane_defect = self.graph.create_node(f'{self._name}_MixedGrainBoundary', PLDO.MixedGrainBoundary)

self.graph.add((self.material, CMSO.hasDefect, plane_defect))
self.graph.add((plane_defect, PLDO.hasSigmaValue, Literal(gb_dict["sigma"], datatype=XSD.integer)))
Expand Down
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