Merge pull request #10 from Materials-Data-Science-and-Informatics/mo…

…ve_to_class

Move to Annotate Crystal class

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "atomID"
-version = "0.2.2"
+version = "0.3.2"
 description = "Python package to identify and annotate crystal structure data files"
 authors = ["Ninad Bhat"]
 readme = "README.md"

src/atomid/annotate.py

@@ -0,0 +1,112 @@
+"""Annotate crystal class."""
+
+import atomrdf as ardf
+from ase.io import read as ase_read
+
+from atomid.crystal.structure_identification import (
+    find_lattice_parameter,
+    get_crystal_structure_using_cna,
+)
+from atomid.point_defect_analysis.wigner_seitz_method import analyze_defects
+
+
+class AnnotateCrystal:
+    """Annotate crystal object."""
+
+    def __init__(self) -> None:
+        self.system = ardf.System()
+        self.kg = ardf.KnowledgeGraph()
+
+    def read_crystal_structure_file(self, data_file: str, format: str) -> None:
+        """Read the crystal structure file.
+
+        Parameters
+        ----------
+        data_file : str
+            The name of the file to read
+        format : str
+            The format of the file. If None, the format is guessed from the file extension
+        """
+        crystal_data = ase_read(data_file, format=format)
+        kg = ardf.KnowledgeGraph()
+        crystal_structure = ardf.System.read.file(
+            filename=crystal_data, format="ase", graph=kg
+        )
+
+        self.kg = kg
+        self.system = crystal_structure
+
+    def annotate_crystal_structure(self) -> None:
+        """Identify and annotate the crystal structure.
+
+        This method identifies the crystal structure using Common Neighbour Analysis
+        and lattice constant using radial distribution function.
+        """
+        crystal_structure = get_crystal_structure_using_cna(self.system)
+
+        if crystal_structure != "others":
+            lattice_constants = find_lattice_parameter(self.system, crystal_structure)
+            self.system = ardf.System.read.file(
+                crystal_structure,
+                format="ase",
+                graph=self.kg,
+                lattice=crystal_structure,
+                lattice_constant=lattice_constants,
+            )
+
+    def identify_defects(self, reference_data_file: str, ref_format: str) -> dict:
+        """Identify defects in the crystal structure using the reference data file.
+
+        Parameters
+        ----------
+        reference_data_file : str
+            The name of the file to read
+        ref_format : str
+            The format of the file. If None, the format is guessed from the file extension
+
+        Returns
+        -------
+        defects : dict
+            A dictionary containing the vacancy and interstitial defects.
+        """
+        actual_positions = self.system.atoms.positions
+        ref_ase = ase_read(reference_data_file, format=ref_format)
+        ref_positions = ref_ase.positions
+
+        defects: dict[str, dict[str, float]] = analyze_defects(
+            reference_positions_list=ref_positions,
+            actual_positions_list=actual_positions,
+        )
+        return defects
+
+    def annotate_defects(self, reference_data_file: str, ref_format: str) -> None:
+        """Annotate defects in the crystal structure using the reference data file.
+
+        Parameters
+        ----------
+        reference_data_file : str
+            The name of the file to read
+        ref_format : str
+            The format of the file. If None, the format is guessed from the file extension
+
+        """
+        defects = self.identify_defects(reference_data_file, ref_format)
+
+        vacancies = defects.get("Vacancies", {"count": 0, "fraction": 0})
+
+        if vacancies["count"] > 0:
+            self.system.add_vacancy(
+                concentration=vacancies["fraction"], number=vacancies["count"]
+            )
+
+    def write_to_file(self, filename: str, format: str = "ttl") -> None:
+        """Write the annotated system to a file.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file to write
+        format : str
+            The format of the file. If None, the format is guessed from the file extension
+        """
+        self.kg.write(filename, format=format)

src/atomid.py → src/atomid/atomid.py

@@ -6,12 +6,13 @@
 import ase
 from ase.io import read as ase_read
 from atomrdf import KnowledgeGraph, System
-from crystal_analysis.structure_identification import (
+from rdflib import Namespace
+
+from atomid.crystal.structure_identification import (
     find_lattice_parameter,
     get_crystal_structure_using_cna,
 )
-from point_defect_analysis.wigner_seitz_method import analyze_defects
-from rdflib import Namespace
+from atomid.point_defect_analysis.wigner_seitz_method import analyze_defects
 
 CMSO = Namespace("http://purls.helmholtz-metadaten.de/cmso/")
 PODO = Namespace("http://purls.helmholtz-metadaten.de/podo/")
@@ -57,7 +58,7 @@ def identify_defects_in_crystal_structure(
     ref_positions = ref_ase.positions
 
     defects: dict[str, dict[str, float]] = analyze_defects(
-        reference_positions=ref_positions, actual_positions=actual_positions
+        reference_positions_list=ref_positions, actual_positions_list=actual_positions
     )
 
     return defects