diff --git a/shakenbreak/input.py b/shakenbreak/input.py index 3ee4cb7..41268ca 100644 --- a/shakenbreak/input.py +++ b/shakenbreak/input.py @@ -1335,7 +1335,8 @@ def _apply_rattle_bond_distortions( defect_type = defect_object.defect_type.name.lower() bulk_supercell_site = _get_bulk_defect_site(defect_entry) defect_structure = defect_entry.sc_entry.structure - defect_structure.add_oxidation_state_by_element(oxidation_states) + if oxidation_states is not None: + defect_structure.add_oxidation_state_by_element(oxidation_states) if defect_type == "vacancy": # for vacancies, we need to use fractional coordinates # (no atom site in structure!) diff --git a/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Rattled_0pt25_POSCAR b/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Rattled_0pt25_POSCAR index 860c8c7..fd982b9 100644 --- a/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Rattled_0pt25_POSCAR +++ b/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Rattled_0pt25_POSCAR @@ -6,66 +6,66 @@ Cd31 Te32 Cd Te 31 32 direct - 0.0156871194840353 0.0168499172361065 0.5013659606570436 Cd2+ - 0.0271500115668686 0.4957262246093266 0.0100224763679073 Cd2+ - -0.0014495703722099 0.4980731524352150 0.4781192167960491 Cd2+ - 0.4722094233480639 0.0200506294364088 -0.0182692230473816 Cd2+ - 0.4885585281400621 -0.0053878728738825 0.4817673004644190 Cd2+ - 0.5056282073490231 0.5186277985499153 -0.0269746115858607 Cd2+ - 0.4801688502186689 0.5257243960661042 0.5248055377787585 Cd2+ - -0.0348316368950783 0.2728944316714810 0.2387460475061252 Cd2+ - -0.0105745472528089 0.2665553322767636 0.7249704332381200 Cd2+ - -0.0075690729980406 0.7073232895687733 0.2540302118175998 Cd2+ - -0.0050910397377601 0.7355423155760010 0.7679544090557621 Cd2+ - 0.5005816366983870 0.2820536382478840 0.2335402909392014 Cd2+ - 0.5164511376504562 0.2542450219488173 0.7322823716342084 Cd2+ - 0.5070828585054892 0.7526462759552357 0.2894765820190052 Cd2+ - 0.5049584993998797 0.7681671971948304 0.7591942235932660 Cd2+ - 0.2314439007613033 -0.0139691580327037 0.2710898637591607 Cd2+ - 0.2376369130393935 0.0053687944240744 0.7381653011727750 Cd2+ - 0.2718374045812695 0.4922892243165773 0.2451784226567301 Cd2+ - 0.2622947472228113 0.5173549697162710 0.7260213390066484 Cd2+ - 0.7421013906143455 -0.0369394254180139 0.2601101761807642 Cd2+ - 0.7643010257290317 0.0082559723869255 0.7375144675771959 Cd2+ - 0.7772298637541588 0.5061737877891480 0.2418884425731874 Cd2+ - 0.7112919524310897 0.4891818031292686 0.7452862206392076 Cd2+ - 0.2597626037064264 0.2654750359385809 -0.0138178746240745 Cd2+ - 0.2856911389734074 0.2667607419061732 0.4824379442736103 Cd2+ - 0.2553308492327366 0.7324121579095495 -0.0270836224755171 Cd2+ - 0.2877874281235570 0.7210962747120893 0.4960596434321737 Cd2+ - 0.7756092046801939 0.2696741257630375 -0.0094615087069471 Cd2+ - 0.7674603327148890 0.2433936502088358 0.5342582586445987 Cd2+ - 0.7659806984052299 0.7592741823626890 0.0084426299687161 Cd2+ - 0.7451092426178079 0.7523250438453772 0.4937354606915620 Cd2+ - 0.1187568485774295 0.1507937162676332 0.3762100856753475 Te2- - 0.1312359429836720 0.1328551962041555 0.9202598135720425 Te2- - 0.1128884079346265 0.6182951658040680 0.3473039496781265 Te2- - 0.1315797807618614 0.6225939184343635 0.8700339946167042 Te2- - 0.6283847628206453 0.1104322706926303 0.3462095332815449 Te2- - 0.6231233285696897 0.1431785472589133 0.8803636878306192 Te2- - 0.6132648937495118 0.6443581611601850 0.3924510477913719 Te2- - 0.6271436363496584 0.6167078405828447 0.8527871928487835 Te2- - 0.1273727892891333 0.3919108640973764 0.1439967743041993 Te2- - 0.1141821228674018 0.3715100179204548 0.6127261640254006 Te2- - 0.1173411386799441 0.8870697863654669 0.0681915310744819 Te2- - 0.1575630076145119 0.8519631496831680 0.5913649039501945 Te2- - 0.6082245405973820 0.3839467110079552 0.1129579011512159 Te2- - 0.6252520424249853 0.3639435370678827 0.5933896303873651 Te2- - 0.6560941606888189 0.8579088993238950 0.1114096916911318 Te2- - 0.6386215189674254 0.8782996437744818 0.6183416726189549 Te2- - 0.3691659245140350 0.1150467855183059 0.1518612689124705 Te2- - 0.3803128561907226 0.1426243580437952 0.6395882828468022 Te2- - 0.3947428748509966 0.6398822065520391 0.0971153956045202 Te2- - 0.3750000000000000 0.6250000000000000 0.6250000000000000 Te2- - 0.8975517329778733 0.0479069033959441 0.0927849932342861 Te2- - 0.8958653442608970 0.1243931913490970 0.6052705997044724 Te2- - 0.8662709695677386 0.6264704742842300 0.1299247251675607 Te2- - 0.8694061068288607 0.6014102855379397 0.6172289000223002 Te2- - 0.3903631884266203 0.3750040440301268 0.3693633479218935 Te2- - 0.3840986630527822 0.3765797318809899 0.8701975112891386 Te2- - 0.3794827130771702 0.8854032160195859 0.3674836864650987 Te2- - 0.3917242540183349 0.8543409397301263 0.8784352524394520 Te2- - 0.8817775378020919 0.3813543713889261 0.4031743957535139 Te2- - 0.8794108581844571 0.3946822747640026 0.8757006722884800 Te2- - 0.8749999999999999 0.8749999999999999 0.3750000000000000 Te2- - 0.8539818238484530 0.9657359971042676 0.9006515870041598 Te2- + 0.0156871194840353 0.0168499172361065 0.5013659606570436 Cd + 0.0271500115668686 0.4957262246093266 0.0100224763679073 Cd + -0.0014495703722099 0.4980731524352150 0.4781192167960491 Cd + 0.4722094233480639 0.0200506294364088 -0.0182692230473816 Cd + 0.4885585281400621 -0.0053878728738825 0.4817673004644190 Cd + 0.5056282073490231 0.5186277985499153 -0.0269746115858607 Cd + 0.4801688502186689 0.5257243960661042 0.5248055377787585 Cd + -0.0348316368950783 0.2728944316714810 0.2387460475061252 Cd + -0.0105745472528089 0.2665553322767636 0.7249704332381200 Cd + -0.0075690729980406 0.7073232895687733 0.2540302118175998 Cd + -0.0050910397377601 0.7355423155760010 0.7679544090557621 Cd + 0.5005816366983870 0.2820536382478840 0.2335402909392014 Cd + 0.5164511376504562 0.2542450219488173 0.7322823716342084 Cd + 0.5070828585054892 0.7526462759552357 0.2894765820190052 Cd + 0.5049584993998797 0.7681671971948304 0.7591942235932660 Cd + 0.2314439007613033 -0.0139691580327037 0.2710898637591607 Cd + 0.2376369130393935 0.0053687944240744 0.7381653011727750 Cd + 0.2718374045812695 0.4922892243165773 0.2451784226567301 Cd + 0.2622947472228113 0.5173549697162710 0.7260213390066484 Cd + 0.7421013906143455 -0.0369394254180139 0.2601101761807642 Cd + 0.7643010257290317 0.0082559723869255 0.7375144675771959 Cd + 0.7772298637541588 0.5061737877891480 0.2418884425731874 Cd + 0.7112919524310897 0.4891818031292686 0.7452862206392076 Cd + 0.2597626037064264 0.2654750359385809 -0.0138178746240745 Cd + 0.2856911389734074 0.2667607419061732 0.4824379442736103 Cd + 0.2553308492327366 0.7324121579095495 -0.0270836224755171 Cd + 0.2877874281235570 0.7210962747120893 0.4960596434321737 Cd + 0.7756092046801939 0.2696741257630375 -0.0094615087069471 Cd + 0.7674603327148890 0.2433936502088358 0.5342582586445987 Cd + 0.7659806984052299 0.7592741823626890 0.0084426299687161 Cd + 0.7451092426178079 0.7523250438453772 0.4937354606915620 Cd + 0.1250000000000000 0.1250000000000000 0.3750000000000000 Te + 0.1187568485774295 0.0798259097921571 0.9471778921508236 Te + 0.1312359429836720 0.6328551962041555 0.4202598135720426 Te + 0.1128884079346265 0.6182951658040680 0.8473039496781265 Te + 0.6315797807618615 0.1225939184343634 0.3700339946167043 Te + 0.6283847628206453 0.1104322706926303 0.8462095332815449 Te + 0.6231233285696897 0.6431785472589133 0.3803636878306193 Te + 0.6132648937495118 0.6443581611601850 0.8924510477913717 Te + 0.1139339894586364 0.3681844242533567 0.1518017271048436 Te + 0.1250000000000000 0.3750000000000000 0.6250000000000000 Te + 0.1106383255258450 0.9486769885987631 0.0905073922219817 Te + 0.1252520424249854 0.8639435370678826 0.5933896303873651 Te + 0.6560941606888189 0.3579088993238951 0.1114096916911318 Te + 0.6386215189674254 0.3782996437744819 0.6183416726189549 Te + 0.6721889309442109 0.8433628919160479 0.1250367613866258 Te + 0.6191659245140352 0.8650467855183057 0.6518612689124705 Te + 0.3578307244804382 0.1464941555012161 0.0876090610972016 Te + 0.3803128561907226 0.1426243580437952 0.6395882828468022 Te + 0.3947428748509966 0.6398822065520391 0.0971153956045202 Te + 0.3975517329778734 0.6188747098714201 0.6637527997097622 Te + 0.8958653442608970 0.1243931913490970 0.1052705997044723 Te + 0.8997301454086939 0.1260280502017524 0.6286909690625229 Te + 0.8662709695677386 0.6264704742842300 0.1299247251675607 Te + 0.8694061068288607 0.6014102855379397 0.6172289000223002 Te + 0.3903631884266203 0.3750040440301268 0.3693633479218935 Te + 0.3840986630527822 0.3765797318809899 0.8701975112891386 Te + 0.3794827130771702 0.8854032160195859 0.3674836864650987 Te + 0.3917242540183349 0.8543409397301263 0.8784352524394520 Te + 0.8817775378020919 0.3813543713889261 0.4031743957535139 Te + 0.8794108581844571 0.3946822747640026 0.8757006722884800 Te + 0.8832990018766742 0.9089615994988091 0.3627269241214383 Te + 0.8460654184237592 0.8901079778386413 0.8694308400251983 Te diff --git a/tests/data/vasp/CdTe/vacancies_dist_defect_dict.json b/tests/data/vasp/CdTe/vacancies_dist_defect_dict.json index 9695373..d3cbdb1 100644 --- a/tests/data/vasp/CdTe/vacancies_dist_defect_dict.json +++ b/tests/data/vasp/CdTe/vacancies_dist_defect_dict.json @@ -1 +1 @@ -{"v_Cd_Td_Te2.83": {"defect_type": "vacancy", "defect_site": {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.0, 0.0], "lattice": {"@module": "pymatgen.core.lattice", "@class": "Lattice", "matrix": [[13.086768, 0.0, 0.0], [0.0, 13.086768, 0.0], [0.0, 0.0, 13.086768]], "pbc": [true, true, true]}, "@module": "pymatgen.core.sites", "@class": "PeriodicSite", "properties": {}, "@version": null}, "defect_supercell_site": {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.0, 0.0], "lattice": {"@module": "pymatgen.core.lattice", "@class": "Lattice", "matrix": [[13.086768, 0.0, 0.0], [0.0, 13.086768, 0.0], [0.0, 0.0, 13.086768]], "pbc": [true, true, true]}, "@module": "pymatgen.core.sites", "@class": "PeriodicSite", "properties": {}, "@version": null}, "defect_multiplicity": 32, "charges": {"0": {"structures": {"Unperturbed": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": -2.0, "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}, "sites": [{"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.0, 0.5], "xyz": [0.0, 0.0, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.5, 0.0], "xyz": [0.0, 6.543384, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.5, 0.5], "xyz": [0.0, 6.543384, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.0, 0.0], "xyz": [6.543384, 0.0, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.0, 0.5], "xyz": [6.543384, 0.0, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.5, 0.0], "xyz": [6.543384, 6.543384, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [6.543384, 6.543384, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.25, 0.25], "xyz": [0.0, 3.271692, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.25, 0.75], "xyz": [0.0, 3.271692, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.75, 0.25], "xyz": [0.0, 9.815076, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.0, 0.75, 0.75], "xyz": [0.0, 9.815076, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.25, 0.25], "xyz": [6.543384, 3.271692, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.25, 0.75], "xyz": [6.543384, 3.271692, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.75, 0.25], "xyz": [6.543384, 9.815076, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.5, 0.75, 0.75], "xyz": [6.543384, 9.815076, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.0, 0.25], "xyz": [3.271692, 0.0, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.0, 0.75], "xyz": [3.271692, 0.0, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.5, 0.25], "xyz": [3.271692, 6.543384, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.5, 0.75], "xyz": [3.271692, 6.543384, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.0, 0.25], "xyz": [9.815076, 0.0, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.0, 0.75], "xyz": [9.815076, 0.0, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.5, 0.25], "xyz": [9.815076, 6.543384, 3.271692], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.5, 0.75], "xyz": [9.815076, 6.543384, 9.815076], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.25, 0.0], "xyz": [3.271692, 3.271692, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.25, 0.5], "xyz": [3.271692, 3.271692, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.75, 0.0], "xyz": [3.271692, 9.815076, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.25, 0.75, 0.5], "xyz": [3.271692, 9.815076, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.25, 0.0], "xyz": [9.815076, 3.271692, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.25, 0.5], "xyz": [9.815076, 3.271692, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.75, 0.0], "xyz": [9.815076, 9.815076, 0.0], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Cd", "oxidation_state": 2.0, "occu": 1}], "abc": [0.75, 0.75, 0.5], "xyz": [9.815076, 9.815076, 6.543384], "label": "Cd2+", "properties": {}}, {"species": [{"element": "Te", "oxidation_state": -2.0, "occu": 1}], "abc": [0.125, 0.125, 0.375], "xyz": [1.635846, 1.635846, 4.907538], "label": "Te2-", "properties": {}}, {"species": [{"element": "Te", "oxidation_state": -2.0, "occu": 1}], "abc": [0.125, 0.125, 0.8749999999999999], "xyz": [1.635846, 1.635846, 11.450921999999998], "label": "Te2-", 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0.39518376205924294, 0.8849706124942863], "xyz": [11.61896413820635, 5.1716782114365145, 11.581405092530625], "properties": {}, "label": "Te2-"}, {"species": [{"element": "Te", "oxidation_state": -2.0, "spin": null, "occu": 1}], "abc": [0.8794827130771701, 0.8854032160195859, 0.36748368646509866], "xyz": [11.509586226051491, 11.587066474502205, 4.809173748553486], "properties": {}, "label": "Te2-"}, {"species": [{"element": "Te", "oxidation_state": -2.0, "spin": null, "occu": 1}], "abc": [0.8917242540183349, 0.8543409397301263, 0.878435252439452], "xyz": [11.669788432311016, 11.180561671150144, 11.495878351696541], "properties": {}, "label": "Te2-"}], "@version": null}}}}}}} \ No newline at end of file diff --git a/tests/test_input.py b/tests/test_input.py index 63df98c..077651e 100644 --- a/tests/test_input.py +++ b/tests/test_input.py @@ -786,7 +786,7 @@ def test_apply_rattle_bond_distortions_V_Cd_dimer(self): ) # Shouldn't match because rattling not done yet rattling_atom_indices = np.arange(0, 63) - idx = np.in1d(rattling_atom_indices, [i - 1 for i in [62, 51]]) + idx = np.in1d(rattling_atom_indices, [i - 1 for i in [41, 32]]) rattling_atom_indices = rattling_atom_indices[ ~idx ] # removed distorted Te indices @@ -1021,7 +1021,7 @@ def test_apply_snb_distortions_V_Cd_dimer(self): self.assertEqual(distortion_parameters_dict["num_distorted_neighbours_in_dimer"], 2) self.assertEqual( set(distortion_parameters_dict["distorted_atoms_in_dimer"]), - set([(62, "Te"), (51, "Te")]) # order of elements not important + set([(41, "Te"), (32, "Te")]) # order of elements not important ) self.assertEqual(self.V_Cd_dimer_struc_0pt25_rattled, distorted_V_Cd_struc)