Merge pull request #29 from Materials-Data-Science-and-Informatics/se…

…t_point_defects

Add feature to set point defects

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 Most important changes in each released version.
 
+## v0.3.11
+
+* Add options to manually set point defect concetration and number.
+
+## v0.3.10
+
+* Add option to manually set crystal structure parameters (lattice constant and crytal type).
+
 ## v0.3.9
 
 * Add Dislocation identification and Grain identification.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "atomID"
-version = "0.3.9"
+version = "0.3.11"
 description = "Python package to identify and annotate crystal structure data files"
 authors = ["Ninad Bhat"]
 readme = "README.md"

src/atomid/annotate.py

@@ -235,76 +235,137 @@ def identify_point_defects(
             species_ref=species_reference,
             species_actual=species_actual,
         )
+
+        if hasattr(self, "defects") is False:
+            self.defects = dict()
+
+        self.defects.update(defects)
+
         return defects
 
-    def identify_line_defects(self) -> tuple[list, list]:
-        """Identify line defects in the crystal structure.
+    def add_vacancy_information(self, concentration: float, number: int) -> None:
+        """Add vacancy information to the system.
+
+        Parameters
+        ----------
+        concentration : float
+            The concentration of vacancies.
+        number : int
+            The number of vacancies.
 
         Returns
         -------
-        tuple[list, list]
-            A tuple containing the burgers vectors and lengths of the dislocations.
+        None
         """
-        (burgers_vectors, lengths) = identify_dislocations(self.ovito_pipeline)
+        if hasattr(self, "defects") is False:
+            self.defects = {}
 
-        if len(burgers_vectors) == 0:
-            print("\033[91mNo dislocations found.\033[0m")
-            return None, None
+        self.defects.update(
+            {"vacancies": {"concentration": concentration, "count": number}}
+        )
 
-        return burgers_vectors, lengths
+    def add_interstitial_information(self, concentration: float, number: int) -> None:
+        """Add interstitial information to the system.
 
-    def identify_grains(self) -> tuple[list, list]:
-        """Identify grains in the crystal structure.
+        Parameters
+        ----------
+        concentration : float
+            The concentration of interstitials.
+        number : int
+            The number of interstitials.
 
         Returns
         -------
-        tuple[list, list]
-            A tuple containing the orientations and angles of the grains.
+        None
         """
-        orientations, angles = identify_grain_orientations(self.ovito_pipeline)
+        if hasattr(self, "defects") is False:
+            self.defects = {}
 
-        return orientations, angles
+        self.defects.update(
+            {"interstitials": {"concentration": concentration, "count": number}}
+        )
 
-    def annotate_point_defects(
-        self, reference_data_file: str, ref_format: str, method: Optional[str] = None
-    ) -> None:
-        """Annotate defects in the crystal structure using the reference data file.
+    def add_substitution_information(self, concentration: float, number: int) -> None:
+        """Add substitution information to the system.
 
         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
-        method : str
-            The method to use for defect identification
+        concentration : float
+            The concentration of substitutions.
+        number : int
+            The number of substitutions.
 
         Returns
         -------
         None
         """
-        defects = self.identify_point_defects(reference_data_file, ref_format, method)
+        if hasattr(self, "defects") is False:
+            self.defects = {}
+
+        self.defects.update(
+            {"substitutions": {"concentration": concentration, "count": number}}
+        )
 
-        vacancies = defects.get("vacancies", {"count": 0, "fraction": 0})
-        interstitials = defects.get("interstitials", {"count": 0, "fraction": 0})
-        substitutions = defects.get("substitutions", {"count": 0, "fraction": 0})
+    def annotate_point_defects(self) -> None:
+        """Annotate defects in the crystal structure using the reference data file.
+
+        Returns
+        -------
+        None
+        """
+        if hasattr(self, "defects") is False:
+            self.defects = {}
+
+        defects = self.defects
+
+        vacancies = defects.get("vacancies", {"count": 0, "concentration": 0})
+        interstitials = defects.get("interstitials", {"count": 0, "concentration": 0})
+        substitutions = defects.get("substitutions", {"count": 0, "concentration": 0})
         if vacancies["count"] > 0:
             self.system.add_vacancy(
-                concentration=vacancies["fraction"], number=vacancies["count"]
+                concentration=vacancies["concentration"], number=vacancies["count"]
             )
 
         if interstitials["count"] > 0:
             self.system.add_triples_for_interstitial_impurities(
-                conc_of_impurities=interstitials["fraction"],
+                conc_of_impurities=interstitials["concentration"],
                 no_of_impurities=interstitials["count"],
             )
 
         if substitutions["count"] > 0:
             self.system.add_triples_for_substitutional_impurities(
-                conc_of_impurities=substitutions["fraction"],
+                conc_of_impurities=substitutions["concentration"],
                 no_of_impurities=substitutions["count"],
             )
 
+    def identify_line_defects(self) -> tuple[list, list]:
+        """Identify line defects in the crystal structure.
+
+        Returns
+        -------
+        tuple[list, list]
+            A tuple containing the burgers vectors and lengths of the dislocations.
+        """
+        (burgers_vectors, lengths) = identify_dislocations(self.ovito_pipeline)
+
+        if len(burgers_vectors) == 0:
+            print("\033[91mNo dislocations found.\033[0m")
+            return None, None
+
+        return burgers_vectors, lengths
+
+    def identify_grains(self) -> tuple[list, list]:
+        """Identify grains in the crystal structure.
+
+        Returns
+        -------
+        tuple[list, list]
+            A tuple containing the orientations and angles of the grains.
+        """
+        orientations, angles = identify_grain_orientations(self.ovito_pipeline)
+
+        return orientations, angles
+
     def write_to_file(self, filename: str, format: str = "ttl") -> None:
         """Write the annotated system to a file.
 

src/atomid/point_defect_analysis/wigner_seitz_method.py

@@ -32,7 +32,7 @@ def analyze_defects(
     Returns
     -------
     dict
-        A dictionary containing the counts and fractions of vacancies, interstitials, and substitutions.
+        A dictionary containing the counts and concentration of vacancies, interstitials, and substitutions.
     """
     reference_array = np.array(reference_positions)
     actual_array = np.array(actual_positions)
@@ -93,7 +93,7 @@ def calculate_defects(
     atom_position_count: np.ndarray,
     substitution_count: np.ndarray,
 ) -> Dict:
-    """Calculate the number and fraction of vacancies, interstitials, and substitutions.
+    """Calculate the number and concentration of vacancies, interstitials, and substitutions.
 
     Parameters
     ----------
@@ -107,7 +107,7 @@ def calculate_defects(
     Returns
     -------
     dict
-        A dictionary containing the counts and fractions of vacancies, interstitials, and substitutions.
+        A dictionary containing the counts and concentration of vacancies, interstitials, and substitutions.
     """
     vacancies = [
         (i, tuple(pos))
@@ -128,15 +128,15 @@ def calculate_defects(
     return {
         "vacancies": {
             "count": len(vacancies),
-            "fraction": len(vacancies) / len(reference_array),
+            "concentration": len(vacancies) / len(reference_array),
         },
         "interstitials": {
             "count": len(interstitials),
-            "fraction": len(interstitials) / len(reference_array),
+            "concentration": len(interstitials) / len(reference_array),
         },
         "substitutions": {
             "count": len(substitutions) - len(interstitials),
-            "fraction": (len(substitutions) - len(interstitials))
+            "concentration": (len(substitutions) - len(interstitials))
             / len(reference_array),
         },
     }

tests/test_main.py

@@ -7,7 +7,7 @@
 from utils.compare_rdf import compare_graphs
 
 
-class TestAnnotatePointDefects:
+class TestAnnotateSystemTest:
     """Tests for the AnnotateCrystal class for Point defects."""
 
     testing_dict = {
@@ -92,7 +92,7 @@ def test_write_defects(
         annotate_crystal.identify_point_defects(
             reference_crystal_file, ref_format="vasp"
         )
-
+        annotate_crystal.annotate_point_defects()
         annotate_crystal.write_to_file(f"{tmp_path}/annotated_output.ttl", "ttl")
 
         assert os.path.exists(f"{tmp_path}/annotated_output.ttl")
@@ -110,9 +110,10 @@ def test_output_annotation(
         annotate_crystal.identify_crystal_structure()
         annotate_crystal.annotate_crystal_structure()
 
-        annotate_crystal.annotate_point_defects(
+        annotate_crystal.identify_point_defects(
             reference_crystal_file, ref_format="vasp"
         )
+        annotate_crystal.annotate_point_defects()
         annotate_crystal.write_to_file(f"{tmp_path}/annotated_output.ttl", "ttl")
 
         assert os.path.exists(f"{tmp_path}/annotated_output.ttl")
@@ -127,6 +128,10 @@ def test_output_annotation(
 
         assert result
 
+
+class TestAnnotatePointDefects:
+    """Tests for the AnnotateCrystal class for Point defects."""
+
     def test_set_lattice_constant(self) -> None:
         annotate_crystal = AnnotateCrystal(
             "tests/data/fcc/Al/no_defect/initial/Al.poscar", "vasp"
@@ -141,19 +146,60 @@ def test_set_crystal_structure(self) -> None:
         annotate_crystal.set_crystal_structure("fcc")
         assert annotate_crystal.crystal_type == "fcc"
 
-    def test_annotate_crystal_returns_error(self) -> None:
+    def test_annotate_returns_error_no_lattice_constant(self) -> None:
         annotate_crystal = AnnotateCrystal()
         annotate_crystal.read_crystal_structure_file(
             "tests/data/fcc/Al/no_defect/initial/Al.poscar", format="vasp"
         )
+        annotate_crystal.set_crystal_structure("fcc")
 
         with pytest.raises(ValueError):
             annotate_crystal.annotate_crystal_structure()
 
+    def test_annotate_returns_error_no_crystal_type(self) -> None:
+        annotate_crystal = AnnotateCrystal()
+        annotate_crystal.read_crystal_structure_file(
+            "tests/data/fcc/Al/no_defect/initial/Al.poscar", format="vasp"
+        )
+        annotate_crystal.set_lattice_constant(3.5)
         with pytest.raises(ValueError):
-            annotate_crystal.set_crystal_structure("other")
             annotate_crystal.annotate_crystal_structure()
 
+    def test_add_vacancy(self) -> None:
+        annotate_crystal = AnnotateCrystal()
+        annotate_crystal.read_crystal_structure_file(
+            "tests/data/fcc/Al/defect/vacancy/initial/Al_vacancy.poscar", format="vasp"
+        )
+        annotate_crystal.identify_crystal_structure()
+        annotate_crystal.annotate_crystal_structure()
+        annotate_crystal.add_vacancy_information(concentration=0.1, number=40)
+        assert annotate_crystal.defects["vacancies"]["count"] == 40
+        assert annotate_crystal.defects["vacancies"]["concentration"] == 0.1
+
+    def test_add_interstitial(self) -> None:
+        annotate_crystal = AnnotateCrystal()
+        annotate_crystal.read_crystal_structure_file(
+            "tests/data/fcc/Al/defect/interstitial/initial/Al_interstitial.poscar",
+            format="vasp",
+        )
+        annotate_crystal.identify_crystal_structure()
+        annotate_crystal.annotate_crystal_structure()
+        annotate_crystal.add_interstitial_information(concentration=0.1, number=40)
+        assert annotate_crystal.defects["interstitials"]["count"] == 40
+        assert annotate_crystal.defects["interstitials"]["concentration"] == 0.1
+
+    def test_add_substitution(self) -> None:
+        annotate_crystal = AnnotateCrystal()
+        annotate_crystal.read_crystal_structure_file(
+            "tests/data/fcc/Al/defect/substitution/initial/Al_substitution.poscar",
+            format="vasp",
+        )
+        annotate_crystal.identify_crystal_structure()
+        annotate_crystal.annotate_crystal_structure()
+        annotate_crystal.add_substitution_information(concentration=0.1, number=40)
+        assert annotate_crystal.defects["substitutions"]["count"] == 40
+        assert annotate_crystal.defects["substitutions"]["concentration"] == 0.1
+
 
 class TestAnnotateGrains:
     """Tests for the AnnotateCrystal class for Grain boundaries."""

tests/test_point_defect_identification.py

@@ -37,7 +37,7 @@ def test_analyze_defects_vacacy() -> None:
     )
 
     assert defects["vacancies"]["count"] == 1
-    assert defects["vacancies"]["fraction"] == 0.2
+    assert defects["vacancies"]["concentration"] == 0.2
 
 
 def test_analyze_defects_interstitial() -> None:
@@ -59,7 +59,7 @@ def test_analyze_defects_interstitial() -> None:
         reference_positions=reference_position, actual_positions=actual_position
     )
     assert defects["interstitials"]["count"] == 1
-    assert defects["interstitials"]["fraction"] == 0.25
+    assert defects["interstitials"]["concentration"] == 0.25
 
 
 def test_analyze_defects_substitution() -> None:
@@ -83,7 +83,7 @@ def test_analyze_defects_substitution() -> None:
         reference_positions, actual_positions, species_ref, species_actual
     )
     assert defects["substitutions"]["count"] == 1
-    assert defects["substitutions"]["fraction"] == 0.25
+    assert defects["substitutions"]["concentration"] == 0.25
 
 
 def test_create_index_finder_euclidean(reference_array: np.ndarray) -> None: