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@kavanase
kavanase committed Jan 21, 2025
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9 changes: 8 additions & 1 deletion doped/thermodynamics.py
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Expand Up @@ -377,7 +377,14 @@ def group_defects_by_distance(
)
)

defect_site_dict[name][equiv_site_tuple] = [entry]
if equiv_site_tuple not in defect_site_dict[name]:
defect_site_dict[name][equiv_site_tuple] = [entry]
else: # possibly dist_tol = 0
num_matching_names = sum(
1 for defect_name in defect_site_dict if defect_name.startswith(name)
)
defect_site_dict[f"{name}_{chr(96 + num_matching_names)}"] = {}
defect_site_dict[f"{name}_{chr(96+num_matching_names)}"][equiv_site_tuple] = [entry]

return defect_site_dict

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2 changes: 1 addition & 1 deletion examples/CdTe/CdTe_test_soc_band_edge_states.json
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{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 580, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 1.7812, "orbitals": {"Cd": [0.0, 0.028, 0.062, 0.0], "Te": [0.0, 0.527, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.032033651512700205}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 582, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.3135, "orbitals": {"Cd": [0.293, 0.0, 0.001, 0.0], "Te": [0.221, 0.002, 0.001, 0.0]}, "occupation": 0.0, "participation_ratio": 0.06803247004252029}}, "vbm_orbital_diff": 0.014423076923076922, "cbm_orbital_diff": 0.02111324376199616, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 581, "ave_energy": 2.59455, "occupation": 0.0, "orbitals": {"Cd": [0.008375, 0.013999999999999999, 0.0205, 0.0], "Te": [0.009125, 0.46975, 0.003375, 0.0]}, "participation_ratio": 0.755263198306604, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 580, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 1.7812, "orbitals": {"Cd": [0.0, 0.028, 0.062, 0.0], "Te": [0.0, 0.527, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.032033651512700205}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 582, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.3135, "orbitals": {"Cd": [0.293, 0.0, 0.001, 0.0], "Te": [0.221, 0.002, 0.001, 0.0]}, "occupation": 0.0, "participation_ratio": 0.06803247004252029}}, "vbm_orbital_diff": 0.014423076923076922, "cbm_orbital_diff": 0.02111324376199616, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 581, "ave_energy": 2.59455, "occupation": 0.0, "orbitals": {"Cd": [0.067, 0.11199999999999999, 0.164, 0.0], "Te": [0.073, 3.758, 0.027, 0.0]}, "participation_ratio": 0.755263198306604, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
2 changes: 1 addition & 1 deletion examples/Cu2SiSe3/Cu2SiSe3_int_band_edge_states.json
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{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 352, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.6647, "orbitals": {"Cu": [0.002, 0.021, 0.34, 0.0], "Se": [0.005, 0.321, 0.005, 0.0], "Si": [0.017, 0.016, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.11717032967032967}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 355, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 5.349, "orbitals": {"Cu": [0.09, 0.007, 0.021, 0.0], "Se": [0.185, 0.121, 0.008, 0.0], "Si": [0.132, 0.029, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.020942408376963352}}, "vbm_orbital_diff": 0.12364130434782608, "cbm_orbital_diff": 0.09950248756218906, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 353, "ave_energy": 3.94005, "occupation": 1.0, "orbitals": {"Cu": [0.009125000000000001, 0.027375, 0.245, 0.0], "Se": [0.0175, 0.23412499999999997, 0.0075, 0.0], "Si": [0.04562499999999999, 0.083125, 0.0, 0.0]}, "participation_ratio": 0.49546802087270597, "radius": null, "center": null}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 354, "ave_energy": 4.5089749999999995, "occupation": 1.0, "orbitals": {"Cu": [0.019124999999999996, 0.042124999999999996, 0.172125, 0.0], "Se": [0.016875, 0.166, 0.013, 0.0], "Si": [0.01325, 0.14437499999999998, 0.0, 0.0]}, "participation_ratio": 0.5050764162866771, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 352, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.7174, "orbitals": {"Cu": [0.002, 0.021, 0.347, 0.0], "Se": [0.003, 0.342, 0.004, 0.0], "Si": [0.012, 0.005, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.07615939072487418}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 354, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 5.3524, "orbitals": {"Cu": [0.089, 0.007, 0.021, 0.0], "Se": [0.184, 0.122, 0.007, 0.0], "Si": [0.132, 0.029, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.021258646870254767}}, "vbm_orbital_diff": 0.05978260869565217, "cbm_orbital_diff": 0.10281923714759536, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 353, "ave_energy": 4.083975000000001, "occupation": 1.0, "orbitals": {"Cu": [0.009500000000000001, 0.0295, 0.2545, 0.0], "Se": [0.02, 0.21225000000000002, 0.008624999999999999, 0.0], "Si": [0.054875, 0.081625, 0.0, 0.0]}, "participation_ratio": 0.5579097586972654, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 352, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.6647, "orbitals": {"Cu": [0.002, 0.021, 0.34, 0.0], "Se": [0.005, 0.321, 0.005, 0.0], "Si": [0.017, 0.016, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.11717032967032967}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 355, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 5.349, "orbitals": {"Cu": [0.09, 0.007, 0.021, 0.0], "Se": [0.185, 0.121, 0.008, 0.0], "Si": [0.132, 0.029, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.020942408376963352}}, "vbm_orbital_diff": 0.12364130434782608, "cbm_orbital_diff": 0.09950248756218906, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 353, "ave_energy": 3.94005, "occupation": 1.0, "orbitals": {"Cu": [0.07300000000000001, 0.219, 1.96, 0.0], "Se": [0.14, 1.8729999999999998, 0.06, 0.0], "Si": [0.36499999999999994, 0.665, 0.0, 0.0]}, "participation_ratio": 0.49546802087270597, "radius": null, "center": null}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 354, "ave_energy": 4.5089749999999995, "occupation": 1.0, "orbitals": {"Cu": [0.15299999999999997, 0.33699999999999997, 1.377, 0.0], "Se": [0.135, 1.328, 0.104, 0.0], "Si": [0.106, 1.1549999999999998, 0.0, 0.0]}, "participation_ratio": 0.5050764162866771, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 352, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.7174, "orbitals": {"Cu": [0.002, 0.021, 0.347, 0.0], "Se": [0.003, 0.342, 0.004, 0.0], "Si": [0.012, 0.005, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.07615939072487418}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 354, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 5.3524, "orbitals": {"Cu": [0.089, 0.007, 0.021, 0.0], "Se": [0.184, 0.122, 0.007, 0.0], "Si": [0.132, 0.029, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.021258646870254767}}, "vbm_orbital_diff": 0.05978260869565217, "cbm_orbital_diff": 0.10281923714759536, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 353, "ave_energy": 4.083975000000001, "occupation": 1.0, "orbitals": {"Cu": [0.07600000000000001, 0.236, 2.036, 0.0], "Se": [0.16, 1.6980000000000002, 0.06899999999999999, 0.0], "Si": [0.439, 0.653, 0.0, 0.0]}, "participation_ratio": 0.5579097586972654, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
2 changes: 1 addition & 1 deletion examples/MgO/Defects/Pre_Calculated_Results/Mg_O_1_band_edge_states.json
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{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 427, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.1491, "orbitals": {"Mg": [0.0, 0.015, 0.0, 0.0], "O": [0.0, 0.749, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.00942161737764983}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 430, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 7.9948, "orbitals": {"Mg": [0.226, 0.007, 0.002, 0.0], "O": [0.251, 0.011, 0.0, 0.0]}, "occupation": 0.0099, "participation_ratio": 0.03764847996778739}}, "vbm_orbital_diff": 0.017994858611825194, "cbm_orbital_diff": 0.10039370078740156, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 428, "ave_energy": 4.8125, "occupation": 1.0, "orbitals": {"Mg": [0.072375, 0.07175, 0.01825, 0.0], "O": [0.012999999999999998, 0.264875, 0.0, 0.0]}, "participation_ratio": 0.3972692972623906, "radius": null, "center": null}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 429, "ave_energy": 7.7985875, "occupation": 0.9987624999999999, "orbitals": {"Mg": [0.08512499999999999, 0.106875, 0.030125, 0.0], "O": [0.048874999999999995, 0.16699999999999998, 0.0, 0.0]}, "participation_ratio": 0.47197675198689754, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0012375}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 427, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.1513, "orbitals": {"Mg": [0.0, 0.015, 0.0, 0.0], "O": [0.0, 0.749, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.010086455331412104}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 429, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 8.0018, "orbitals": {"Mg": [0.226, 0.007, 0.002, 0.0], "O": [0.25, 0.011, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.035483870967741936}}, "vbm_orbital_diff": 0.017994858611825194, "cbm_orbital_diff": 0.10236220472440945, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 428, "ave_energy": 5.150875, "occupation": 1.0, "orbitals": {"Mg": [0.078125, 0.073, 0.018, 0.0], "O": [0.01575, 0.23812499999999998, 0.0, 0.0]}, "participation_ratio": 0.3923540535557629, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeStates", "@version": "0.9.5", "states": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 427, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.1491, "orbitals": {"Mg": [0.0, 0.015, 0.0, 0.0], "O": [0.0, 0.749, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.00942161737764983}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 430, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 7.9948, "orbitals": {"Mg": [0.226, 0.007, 0.002, 0.0], "O": [0.251, 0.011, 0.0, 0.0]}, "occupation": 0.0099, "participation_ratio": 0.03764847996778739}}, "vbm_orbital_diff": 0.017994858611825194, "cbm_orbital_diff": 0.10039370078740156, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 428, "ave_energy": 4.8125, "occupation": 1.0, "orbitals": {"Mg": [0.579, 0.574, 0.146, 0.0], "O": [0.10399999999999998, 2.119, 0.0, 0.0]}, "participation_ratio": 0.3972692972623906, "radius": null, "center": null}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 429, "ave_energy": 7.7985875, "occupation": 0.9987624999999999, "orbitals": {"Mg": [0.6809999999999999, 0.855, 0.241, 0.0], "O": [0.39099999999999996, 1.3359999999999999, 0.0, 0.0]}, "participation_ratio": 0.47197675198689754, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0012375}, {"@module": "pydefect.analyzer.band_edge_states", "@class": "BandEdgeState", "@version": "0.9.5", "vbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 427, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 3.1513, "orbitals": {"Mg": [0.0, 0.015, 0.0, 0.0], "O": [0.0, 0.749, 0.0, 0.0]}, "occupation": 1.0, "participation_ratio": 0.010086455331412104}}, "cbm_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "EdgeInfo", "@version": "0.9.5", "band_idx": 429, "kpt_coord": [0.0, 0.0, 0.0], "orbital_info": {"@module": "pydefect.analyzer.band_edge_states", "@class": "OrbitalInfo", "@version": "0.9.5", "energy": 8.0018, "orbitals": {"Mg": [0.226, 0.007, 0.002, 0.0], "O": [0.25, 0.011, 0.0, 0.0]}, "occupation": 0.0, "participation_ratio": 0.035483870967741936}}, "vbm_orbital_diff": 0.017994858611825194, "cbm_orbital_diff": 0.10236220472440945, "localized_orbitals": [{"@module": "pydefect.analyzer.band_edge_states", "@class": "LocalizedOrbital", "@version": "0.9.5", "band_idx": 428, "ave_energy": 5.150875, "occupation": 1.0, "orbitals": {"Mg": [0.625, 0.584, 0.144, 0.0], "O": [0.126, 1.9049999999999998, 0.0, 0.0]}, "participation_ratio": 0.3923540535557629, "radius": null, "center": null}], "vbm_hole_occupation": 0.0, "cbm_electron_occupation": 0.0}]}
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