diff --git a/doped/analysis.py b/doped/analysis.py index ece15084..aa8130e3 100644 --- a/doped/analysis.py +++ b/doped/analysis.py @@ -711,6 +711,9 @@ def __init__( f"files are present and/or specify `bulk_path` manually." ) + # remove trailing '/.' from bulk_path if present: + self.bulk_path = self.bulk_path.rstrip("/.") + self.defect_dict = {} self.bulk_corrections_data = { # so we only load and parse bulk data once "bulk_locpot_dict": None, @@ -912,6 +915,15 @@ def _mention_bulk_path_subfolder_for_correction_warnings(warning: str) -> str: if defect_list: warnings.warn(f"Defects: {defect_list} each encountered the same warning:\n{warning}") + if not parsed_defect_entries: + subfolder_string = f" and `subfolder`: '{self.subfolder}'" if self.subfolder != "." else "" + raise ValueError( + f"No defect calculations in `output_path` '{self.output_path}' were successfully parsed, " + f"using `bulk_path`: {self.bulk_path}{subfolder_string}. Please check the correct " + f"defect/bulk paths and subfolder are being set, and that the folder structure is as " + f"expected (see `DefectsParser` docstring)." + ) + # get any defect entries in parsed_defect_entries that share the same name (without charge): # first get any entries with duplicate names: entries_to_rename = [ # TODO: Add test for this: diff --git a/doped/utils/plotting.py b/doped/utils/plotting.py index 123d51e7..9043ab6a 100644 --- a/doped/utils/plotting.py +++ b/doped/utils/plotting.py @@ -727,7 +727,7 @@ def _get_formation_energy_lines(defect_thermodynamics, dft_chempots, xlim): def _get_ylim_from_y_range_vals(y_range_vals, ymin=0, auto_labels=False): - window = max(y_range_vals) - min(y_range_vals) + window = max(y_range_vals) - min(*y_range_vals, ymin) spacer = 0.1 * window ylim = (ymin, max(y_range_vals) + spacer) if auto_labels: # need to manually set xlim or ylim if labels cross axes!! diff --git a/examples/CdTe/CdTe_example_thermo.json b/examples/CdTe/CdTe_example_thermo.json index 8383bb3f..0ad2f653 100644 --- a/examples/CdTe/CdTe_example_thermo.json +++ b/examples/CdTe/CdTe_example_thermo.json @@ -1 +1 @@ -{"@module": "doped.thermodynamics", "@class": "DefectThermodynamics", "defect_entries": [{"defect": {"@module": "doped.core", "@class": "Vacancy", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[13.086768, 0.0, 0.0], [0.0, 13.086768, 0.0], [0.0, 0.0, 13.086768]], "pbc": [true, true, true], "a": 13.086768, "b": 13.086768, "c": 13.086768, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 2241.2856479961474}, "properties": {}, "sites": [{"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.0, 0.5], "xyz": [0.0, 0.0, 6.543384], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.5, 0.0], "xyz": [0.0, 6.543384, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.5, 0.5], "xyz": [0.0, 6.543384, 6.543384], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.5, 0.0, 0.0], "xyz": [6.543384, 0.0, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.5, 0.0, 0.5], "xyz": [6.543384, 0.0, 6.543384], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.5, 0.5, 0.0], "xyz": [6.543384, 6.543384, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [6.543384, 6.543384, 6.543384], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.25, 0.25], "xyz": [0.0, 3.271692, 3.271692], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.25, 0.75], "xyz": [0.0, 3.271692, 9.815076], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.75, 0.25], "xyz": [0.0, 9.815076, 3.271692], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.0, 0.75, 0.75], "xyz": [0.0, 9.815076, 9.815076], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "spin": null, "occu": 1}], "abc": [0.5, 0.25, 0.25], "xyz": [6.543384, 3.271692, 3.271692], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "oxidation_state": 2.0, 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20.578592749120002], "properties": {}, "label": "O"}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.0, 0.49999999999999994, 0.598984], "xyz": [0.0, 1.8784539999999998, 13.680387250879999], "properties": {}, "label": "O"}], "@version": null}, "_BilbaoCS_conv_cell_vector_mapping": [0, 1, 2], "@version": null} \ No newline at end of file diff --git a/tests/test_analysis.py b/tests/test_analysis.py index 2ae957c4..87e35b40 100644 --- a/tests/test_analysis.py +++ b/tests/test_analysis.py @@ -442,7 +442,26 @@ def test_DefectsParser_corrections_errors_warning(self): style=f"{module_path}/../doped/utils/doped.mplstyle", savefig_kwargs={"transparent": True, "bbox_inches": "tight"}, ) - def test_DefectsParser_YTOS(self): + def test_DefectsParser_YTOS_default_bulk(self): + # bulk path needs to be specified for YTOS as it's not the default name: + dp = DefectsParser( + output_path=self.YTOS_EXAMPLE_DIR, + dielectric=self.ytos_dielectric, + ) + self._check_DefectsParser(dp) + thermo = dp.get_defect_thermodynamics() + dumpfn( + thermo, os.path.join(self.YTOS_EXAMPLE_DIR, "YTOS_example_thermo.json") + ) # for test_plotting + return thermo.plot() # no chempots for YTOS formation energy plot test + + @pytest.mark.mpl_image_compare( + baseline_dir=f"{data_dir}/remote_baseline_plots", + filename="YTOS_example_defects_plot.png", + style=f"{module_path}/../doped/utils/doped.mplstyle", + savefig_kwargs={"transparent": True, "bbox_inches": "tight"}, + ) + def test_DefectsParser_YTOS_explicit_bulk(self): # bulk path needs to be specified for YTOS as it's not the default name: dp = DefectsParser( output_path=self.YTOS_EXAMPLE_DIR, @@ -456,6 +475,16 @@ def test_DefectsParser_YTOS(self): ) # for test_plotting return thermo.plot() # no chempots for YTOS formation energy plot test + def test_DefectsParser_no_defects_parsed_error(self): + with self.assertRaises(ValueError) as exc: + DefectsParser(output_path=self.YTOS_EXAMPLE_DIR, subfolder="vasp_gam") + assert ( + f"No defect calculations in `output_path` '{self.YTOS_EXAMPLE_DIR}' were successfully parsed, " + f"using `bulk_path`: {self.YTOS_EXAMPLE_DIR}/Bulk and `subfolder`: 'vasp_gam'. Please check " + f"the correct defect/bulk paths and subfolder are being set, and that the folder structure is " + f"as expected (see `DefectsParser` docstring)." in str(exc.exception) + ) + @pytest.mark.mpl_image_compare( baseline_dir=f"{data_dir}/remote_baseline_plots", filename="O_Se_example_defects_plot.png", diff --git a/tests/test_generation.py b/tests/test_generation.py index b64e553b..47d7f6b0 100644 --- a/tests/test_generation.py +++ b/tests/test_generation.py @@ -983,11 +983,11 @@ def _check_editing_defect_gen(self, random_defect_entry_name, defect_gen): def _generate_and_test_no_warnings(self, structure, min_image_distance=None, **kwargs): original_stdout = sys.stdout # Save a reference to the original standard output sys.stdout = StringIO() # Redirect standard output to a stringIO object. + w = None try: with warnings.catch_warnings(record=True) as w: warnings.resetwarnings() defect_gen = DefectsGenerator(structure, **kwargs) - print([str(warning.message) for warning in w]) # for debugging if min_image_distance is None: assert not w else: @@ -1003,6 +1003,9 @@ def _generate_and_test_no_warnings(self, structure, min_image_distance=None, **k finally: sys.stdout = original_stdout # Reset standard output to its original value. + if w: + print([str(warning.message) for warning in w]) # for debugging + return defect_gen, output def test_extrinsic(self):