Add calc_displacements_ellipsoid function
#87
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Outside diff range, codebase verification and nitpick comments (9)
doped/utils/displacements.py (9)
604-604: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- marker=dict(color="black", size=3), + marker={"color": "black", "size": 3},Tools
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dictcall (rewrite as a literal)Rewrite as a literal
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609-611: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- scene=dict( - aspectmode="data", - ), + scene={"aspectmode": "data"},Tools
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638-638: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- line=dict(color="black", width=2), + line={"color": "black", "width": 2},Tools
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744-753: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- marker=dict( - size=10, - opacity=0.5, - color=anisotropy_info_df["the_longest_radius"], # Set color according to column "a" - colorscale="rainbow", - colorbar=dict( - title="The longest radius of ellipsoid", - titleside="right", - ), - ), + marker={ + "size": 10, + "opacity": 0.5, + "color": anisotropy_info_df["the_longest_radius"], # Set color according to column "a" + "colorscale": "rainbow", + "colorbar": { + "title": "The longest radius of ellipsoid", + "titleside": "right", + }, + },Tools
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761-761: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- line=dict(color="black", dash="dash"), + line={"color": "black", "dash": "dash"},Tools
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771-771: Optimize dictionary creation.Rewrite the
dictcall as a literal for better performance and readability.- title_font=dict(size=10), + title_font={"size": 10},Tools
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Files selected for processing (1)
- doped/utils/displacements.py (3 hunks)
Additional context used
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doped/utils/displacements.py
604-604: Unnecessary
dictcall (rewrite as a literal)Rewrite as a literal
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Additional comments not posted (2)
doped/utils/displacements.py (2)
35-35: LGTM!The changes to
calc_site_displacementsimprove clarity and modularity. The function is well-structured and handles edge cases appropriately.
985-985: LGTM!The repositioning of
_get_bulk_struct_with_defectimproves the modularity of the code. The function is well-documented and handles different defect types appropriately.
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@teruya7 this looks very nice, thank you very much for adding to the code! 🙌 Some small things on the checklist to get this merged:
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Also following the CodeRabbit suggestions above; could you change the |
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@kavanase |
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@teruya7 that was quick! 🙌 |
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Added some other fixes and cleanup there. One issue, for the cell axes in the I think this is probably due to my refactoring of that part of the code to try make it a bit more succinct. Would you be able to find the issue with this and fix it? 🙏 |
| @@ -126,6 +126,22 @@ def test_plot_site_displacements_error(self): | |||
| with pytest.raises(ValueError): | |||
| defect_entry.plot_site_displacements(vector_to_project_on=[0, 0, 1], relative_to_defect=True) | |||
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| def test_calc_displacements_ellipsoid(self): | |||
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Nice!
Could you add some quick image comparison tests (for the plotting functions, using matplotlib) here too, like the tests at the bottom of this module?
For this you just need to add @custom_mpl_image_compare(filename="...") above the test function as for the others, where filename is the name of the reference file to compare to in tests/data/remote_baseline_plots, and your test function returns the matplotlib Figure object. Would be good to do some quick tests for the different possible combinations of options.
Then maybe a quick test each like you've done here for the outputs of the function with a substitution and interstitial defect please? (Best to test each type of defect when possible). There's an example of this in test_calc_site_displacements
| bulk_sc, defect_sc_with_site, defect_site_index = _get_bulk_struct_with_defect(defect_entry) | ||
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| # Map sites in defect supercell to bulk supercell | ||
| mappings = get_site_mapping_indices(defect_sc_with_site, bulk_sc) | ||
| mappings_dict = {i[1]: i[2] for i in mappings} # {defect_sc_index: bulk_sc_index} | ||
| # Loop over sites in defect sc | ||
| disp_dict = { # mapping defect site index (in defect sc) to displacement | ||
| "Index (defect)": [], | ||
| "Species": [], | ||
| "Species_with_index": [], | ||
| "Displacement": [], | ||
| "Displacement Norm": [], | ||
| "Distance to defect": [], | ||
| "X sites in cartesian coordinate (defect)": [], | ||
| "Y sites in cartesian coordinate (defect)": [], | ||
| "Z sites in cartesian coordinate (defect)": [], | ||
| } # type: dict | ||
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| sc_defect_frac_coords = _get_defect_supercell_bulk_site_coords(defect_entry) | ||
| if sc_defect_frac_coords is None: | ||
| raise ValueError( | ||
| "The relaxed defect position (`DefectEntry.sc_defect_frac_coords`) has not been parsed. " | ||
| "Please use `DefectsParser`/`DefectParser` to parse relaxed defect positions before " | ||
| "calculating site displacements." | ||
| ) | ||
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| for i, site in enumerate(defect_sc_with_site): | ||
| bulk_sc_index = mappings_dict[i] # Map to bulk sc | ||
| bulk_site = bulk_sc[bulk_sc_index] # Get site in bulk sc | ||
| # Calculate displacement (need to account for pbc!) | ||
| # First final point, then initial point | ||
| frac_disp = pbc_diff(site.frac_coords, bulk_site.frac_coords) # in fractional coords | ||
| disp = bulk_sc.lattice.get_cartesian_coords(frac_disp) # in Angstroms | ||
| # Distance to defect site (last site in defect sc) | ||
| distance = defect_sc_with_site.get_distance(i, defect_site_index) # len(defect_sc_with_site) - 1) | ||
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| disp_dict["Index (defect)"].append(i) | ||
| disp_dict["Displacement"].append(disp) | ||
| disp_dict["Displacement Norm"].append(np.linalg.norm(disp, ord=2)) | ||
| disp_dict["Distance to defect"].append(distance) | ||
| disp_dict["Species_with_index"].append(f"{site.specie.name}({i})") | ||
| disp_dict["Species"].append(site.specie.name) | ||
| disp_dict["X sites in cartesian coordinate (defect)"].append( | ||
| _shift_defect_site_to_center_of_the_supercell( | ||
| site.frac_coords, sc_defect_frac_coords, bulk_sc | ||
| )[0] | ||
| ) | ||
| disp_dict["Y sites in cartesian coordinate (defect)"].append( | ||
| _shift_defect_site_to_center_of_the_supercell( | ||
| site.frac_coords, sc_defect_frac_coords, bulk_sc | ||
| )[1] | ||
| ) | ||
| disp_dict["Z sites in cartesian coordinate (defect)"].append( | ||
| _shift_defect_site_to_center_of_the_supercell( | ||
| site.frac_coords, sc_defect_frac_coords, bulk_sc | ||
| )[2] | ||
| ) | ||
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| with warnings.catch_warnings(): | ||
| warnings.filterwarnings("ignore", "invalid value encountered in scalar divide") | ||
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| # sort each list in disp dict by index of species in bulk element list, then by distance to defect: | ||
| element_list = [ | ||
| el.symbol for el in defect_entry.defect.structure.composition.elements | ||
| ] # host elements | ||
| element_list += sorted( | ||
| [ # extrinsic elements, sorted alphabetically for deterministic ordering in output: | ||
| el.symbol | ||
| for el in defect_entry.defect.defect_structure.composition.elements | ||
| if el.symbol not in element_list | ||
| ] | ||
| ) | ||
| # Combine the lists into a list of tuples, then sort, then unpack: | ||
| combined = list(zip(*disp_dict.values())) | ||
| combined.sort( | ||
| key=lambda x: (element_list.index(x[1]), x[4], x[0]) | ||
| ) # Sort by species, then distance, then index | ||
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| ( | ||
| disp_dict["Index (defect)"], | ||
| disp_dict["Species"], | ||
| disp_dict["Species_with_index"], | ||
| disp_dict["Displacement"], | ||
| disp_dict["Displacement Norm"], | ||
| disp_dict["Distance to defect"], | ||
| disp_dict["X sites in cartesian coordinate (defect)"], | ||
| disp_dict["Y sites in cartesian coordinate (defect)"], | ||
| disp_dict["Z sites in cartesian coordinate (defect)"], | ||
| ) = zip(*combined) |
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A good chunk of this code is duplicated from the calc_site_displacements function. It would be best for code efficiency and maintenance if this is pulled out into a helper function that then is used in both functions (with flags for relative_to_defect, vector_to_project_on and ellipsoid to determine which disp_dict data is needed?).
Could you implement this please?
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I also updated the functions to return the |
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Thank you for checking! |
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