diff --git a/.gitignore b/.gitignore index e0a4a4cc..82ee5e70 100755 --- a/.gitignore +++ b/.gitignore @@ -150,4 +150,4 @@ snb_test.ipynb conda_packaging.md .pytest_cache/ shakenbreak/__pycache__/ -tests/__pycache__/ \ No newline at end of file +tests/__pycache__/ diff --git a/.pytest_cache/.gitignore b/.pytest_cache/.gitignore deleted file mode 100755 index bc1a1f61..00000000 --- a/.pytest_cache/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -# Created by pytest automatically. -* diff --git a/.pytest_cache/CACHEDIR.TAG b/.pytest_cache/CACHEDIR.TAG deleted file mode 100755 index fce15ad7..00000000 --- a/.pytest_cache/CACHEDIR.TAG +++ /dev/null @@ -1,4 +0,0 @@ -Signature: 8a477f597d28d172789f06886806bc55 -# This file is a cache directory tag created by pytest. -# For information about cache directory tags, see: -# https://bford.info/cachedir/spec.html diff --git a/.pytest_cache/README.md b/.pytest_cache/README.md deleted file mode 100755 index b89018ce..00000000 --- a/.pytest_cache/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# pytest cache directory # - -This directory contains data from the pytest's cache plugin, -which provides the `--lf` and `--ff` options, as well as the `cache` fixture. - -**Do not** commit this to version control. - -See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information. diff --git a/.pytest_cache/v/cache/lastfailed b/.pytest_cache/v/cache/lastfailed deleted file mode 100755 index 3519943b..00000000 --- a/.pytest_cache/v/cache/lastfailed +++ /dev/null @@ -1,33 +0,0 @@ -{ - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd_Dimer": true, - "tests/test_input.py::InputTestCase::test_Distortions_initialisation": true, - "tests/test_input.py::InputTestCase::test_Distortions_intermetallic": true, - "tests/test_input.py::InputTestCase::test_Distortions_single_atom_primitive": true, - "tests/test_input.py::InputTestCase::test_apply_distortions": true, - "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_Int_Cd_2": true, - "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_V_Cd": true, - "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_V_Cd_dimer": true, - "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_kwargs": true, - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_Int_Cd_2": true, - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd": true, - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_kwargs": true, - "tests/test_input.py::InputTestCase::test_calc_number_electrons": true, - "tests/test_input.py::InputTestCase::test_calc_number_neighbours": true, - "tests/test_input.py::InputTestCase::test_create_vasp_input": true, - "tests/test_input.py::InputTestCase::test_default_rattle_stdev_and_seed": true, - "tests/test_input.py::InputTestCase::test_from_structures": true, - "tests/test_input.py::InputTestCase::test_generate_defect_object": true, - "tests/test_input.py::InputTestCase::test_get_bulk_comp": true, - "tests/test_input.py::InputTestCase::test_get_sc_defect_coords": true, - "tests/test_input.py::InputTestCase::test_local_rattle": true, - "tests/test_input.py::InputTestCase::test_most_common_oxi": true, - "tests/test_input.py::InputTestCase::test_with_non_UTF_8_encoding": true, - "tests/test_input.py::InputTestCase::test_write_castep_files": true, - "tests/test_input.py::InputTestCase::test_write_cp2k_files": true, - "tests/test_input.py::InputTestCase::test_write_espresso_files": true, - "tests/test_input.py::InputTestCase::test_write_fhi_aims_files": true, - "tests/test_input.py::InputTestCase::test_write_vasp_files": true, - "tests/test_input.py::InputTestCase::test_write_vasp_files_from_doped_defect_gen": true, - "tests/test_input.py::InputTestCase::test_write_vasp_files_from_doped_dict": true, - "tests/test_input.py::InputTestCase::test_write_vasp_files_from_list": true -} \ No newline at end of file diff --git a/.pytest_cache/v/cache/nodeids b/.pytest_cache/v/cache/nodeids deleted file mode 100755 index 96101dfd..00000000 --- a/.pytest_cache/v/cache/nodeids +++ /dev/null @@ -1,40 +0,0 @@ -[ - "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_V_Cd_dimer", - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd_Dimer", - "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd_dimer", - "tests/test_plotting.py::PlottingDefectsTestCase::test_cast_energies_to_floats", - "tests/test_plotting.py::PlottingDefectsTestCase::test_change_energy_units_to_meV", - "tests/test_plotting.py::PlottingDefectsTestCase::test_format_axis", - "tests/test_plotting.py::PlottingDefectsTestCase::test_format_defect_name", - "tests/test_plotting.py::PlottingDefectsTestCase::test_format_ticks", - "tests/test_plotting.py::PlottingDefectsTestCase::test_get_displacement_dict", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_incorrect_output_path", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_min_e_diff", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_nonexistent_defect_folder", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_SnB_naming_w_site_num", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_displacement", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_fake_defect_name", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_legend_label_linecolor_title_saveplot", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_max_distance", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_with_rattled_and_imported", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_from_other_charge_states", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_keywords", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_not_enough_markers", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_only_rattled", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_only_rattled_and_rattled_dist_from_other_charge_states", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_rattled_and_dist_from_other_chargestates", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_value_error", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_without_saving", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_add_colorbar", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_fake_output_directories", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_include_site_num_in_name", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_missing_unperturbed_energy", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_unrecognised_name", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_without_colorbar", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_without_title_units_in_meV", - "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defects_output", - "tests/test_plotting.py::PlottingDefectsTestCase::test_purge_data_dict", - "tests/test_plotting.py::PlottingDefectsTestCase::test_remove_high_energy_points", - "tests/test_plotting.py::PlottingDefectsTestCase::test_save_plot", - "tests/test_plotting.py::PlottingDefectsTestCase::test_verify_data_directories_exist" -] \ No newline at end of file diff --git a/.pytest_cache/v/cache/stepwise b/.pytest_cache/v/cache/stepwise deleted file mode 100755 index 0637a088..00000000 --- a/.pytest_cache/v/cache/stepwise +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e9558658..c654c5f0 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,7 +1,7 @@ Change Log ========== -v3.2.4 +v3.3.0 ---------- - Add Dimer distortion as a targeted distortion for dimer reconstructions. It pushes two of the defect NN to a distance of 2 A. @@ -17,6 +17,7 @@ v3.2.4 the user about this (i.e. only `Unperturbed`) - Update `snb-run` to add early-on detection of distortions that are stuck in high energy basins and rename them to "High_Energy" to avoid continuing their relaxation +- Miscellaneous efficiency improvements and bug fixes v3.2.3 ---------- diff --git a/MANIFEST.in b/MANIFEST.in index 25b7a27f..78b4bd66 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1 @@ -include parse* -recursive-include shakenbreak * -recursive-include data * \ No newline at end of file +recursive-include shakenbreak * \ No newline at end of file diff --git a/README.md b/README.md index fdef22ed..e869e4d3 100644 --- a/README.md +++ b/README.md @@ -127,7 +127,8 @@ Automatic testing is run on the master and develop branches using Github Actions `ShakeNBreak` has benefitted from feedback from many members of the Walsh and Scanlon research groups who have used / are using it in their work, including Adair Nicolson, Xinwei Wang, Katarina Brlec, Joe Willis, Zhenzhu Li, Jiayi Cen, Lavan Ganeshkumar, Daniel Sykes, Luisa Herring-Rodriguez, Alex Squires, Sabrine Hachmioune and Chris Savory. ## Studies using `ShakeNBreak` - + +- X. Wang et al. [_arXiv_](https://arxiv.org/abs/2402.04434) 2024 - I. Mosquera-Lois et al. [_arXiv_](https://doi.org/10.48550/arXiv.2401.12127) 2024 - K. Li et al. [_ChemRxiv_](https://chemrxiv.org/engage/chemrxiv/article-details/65846b8366c1381729bc5f23) 2023 - X. Wang et al. [_Physical Review B_](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102) 2023 @@ -139,10 +140,12 @@ Automatic testing is run on the master and develop branches using Github Actions - I. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon [_npj Computational Materials_](https://doi.org/10.1038/s41524-023-00973-1) 2023 - Y. T. Huang & S. R. Kavanagh et al. [_Nature Communications_](https://www.nature.com/articles/s41467-022-32669-3) 2022 - S. R. Kavanagh, D. O. Scanlon, A. Walsh, C. Freysoldt [_Faraday Discussions_](https://doi.org/10.1039/D2FD00043A) 2022 +- Y-S. Choi et al. [_ACS Appl. Energy Mater._](https://doi.org/10.1021/acsaem.2c03466) 2022 (early version) - S. R. Kavanagh, D. O. Scanlon, A. Walsh [_ACS Energy Letters_](https://pubs.acs.org/doi/full/10.1021/acsenergylett.1c00380) 2021 - C. J. Krajewska et al. [_Chemical Science_](https://doi.org/10.1039/D1SC03775G) 2021 (early version) - (News & Views): A. Mannodi-Kanakkithodi [_Nature Physics_](https://doi.org/10.1038/s41567-023-02049-9) 2023 ([Free-to-read link](https://t.co/EetpnRgjzh)) + diff --git a/docs/conf.py b/docs/conf.py index a5ba945f..6e25c040 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -25,7 +25,7 @@ author = 'Irea Mosquera-Lois, Seán R. Kavanagh' # The full version, including alpha/beta/rc tags -release = '3.2.4' +release = '3.3.0' # -- General configuration --------------------------------------------------- diff --git a/docs/distortion_metadata.json b/docs/distortion_metadata.json deleted file mode 100644 index 642409b8..00000000 --- a/docs/distortion_metadata.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - }, - "defects": { - "v_Cd_s0": { - "unique_site": [ - 0.0, - 0.0, - 0.0 - ], - "charges": { - "-3": { - "num_nearest_neighbours": 1, - "distorted_atoms": [ - [ - 33, - "Te" - ] - ], - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - } - }, - "-2": { - "num_nearest_neighbours": 0, - "distorted_atoms": null, - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - } - }, - "-1": { - "num_nearest_neighbours": 1, - "distorted_atoms": [ - [ - 33, - "Te" - ] - ], - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - } - }, - "0": { - "num_nearest_neighbours": 2, - "distorted_atoms": [ - [ - 33, - "Te" - ], - [ - 42, - "Te" - ] - ], - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - } - }, - "1": { - "num_nearest_neighbours": 3, - "distorted_atoms": [ - [ - 33, - "Te" - ], - [ - 42, - "Te" - ], - [ - 52, - "Te" - ] - ], - "distortion_parameters": { - "distortion_increment": 0.1, - "bond_distortions": [ - -0.6, - -0.5, - -0.4, - -0.3, - -0.2, - -0.1, - 0.0, - 0.1, - 0.2, - 0.3, - 0.4, - 0.5, - 0.6 - ], - "local_rattle": false, - "mc_rattle_parameters": { - "stdev": 0.28333683853583164 - } - } - } - } - } - } -} \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 8d5c8905..4094aa8b 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -211,6 +211,7 @@ run tests and add new tests for any new features whenever submitting pull reques Studies using ``ShakeNBreak`` ============================= +- X\. Wang et al. `arXiv `_ 2024 - I\. Mosquera-Lois et al. `arXiv `_ 2024 - K\. Li et al. `ChemRxiv `_ 2024 - X\. Wang et al. `Physical Review B `_ 2023 @@ -222,12 +223,13 @@ Studies using ``ShakeNBreak`` - I\. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon `npj Computational Materials`_ 2023 - Y\. T. Huang & S. R. Kavanagh et al. `Nature Communications`_ 2022 - S\. R. Kavanagh, D. O. Scanlon, A. Walsh, C. Freysoldt `Faraday Discussions`_ 2022 +- Y-S\. Choi et al. `ACS Appl. Energy Mater. `__ 2022 (early version) - S\. R. Kavanagh, D. O. Scanlon, A. Walsh `ACS Energy Letters`_ 2021 - C\. J. Krajewska et al. `Chemical Science`_ 2021 (early version) - (News & Views): A. Mannodi-Kanakkithodi `Nature Physics`_ 2023 (`Free-to-read link `__) .. Se -.. Xinwei, Wenzhen early 2024 papers +.. Wenzhen paper .. Oba book .. BiOI .. Kumagai collab paper diff --git a/docs/v_Cd_s0_0.svg b/docs/v_Cd_0.svg similarity index 100% rename from docs/v_Cd_s0_0.svg rename to docs/v_Cd_0.svg diff --git a/docs/v_Cd_s0_0_colorbar.svg b/docs/v_Cd_0_colorbar.svg similarity index 100% rename from docs/v_Cd_s0_0_colorbar.svg rename to docs/v_Cd_0_colorbar.svg diff --git a/docs/vac_1_Cd_0.svg b/docs/vac_1_Cd_0.svg deleted file mode 100644 index 22bf7c25..00000000 --- a/docs/vac_1_Cd_0.svg +++ /dev/null @@ -1,1312 +0,0 @@ - - - - - - - - 2022-09-02T17:11:02.373800 - image/svg+xml - - - Matplotlib v3.5.1, https://matplotlib.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docs/vac_1_Cd_0_colorbar.svg b/docs/vac_1_Cd_0_colorbar.svg deleted file mode 100644 index 01b18855..00000000 --- a/docs/vac_1_Cd_0_colorbar.svg +++ /dev/null @@ -1,1531 +0,0 @@ - - - - - - - - 2022-09-02T17:11:56.271636 - image/svg+xml - - - Matplotlib v3.5.1, https://matplotlib.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/setup.py b/setup.py index ca2b3fcd..db6ed38f 100644 --- a/setup.py +++ b/setup.py @@ -31,40 +31,44 @@ def _install_custom_font(): mpl_fonts_dir = os.path.join(mpl_data_dir, "fonts", "ttf") # Copy the font file to matplotlib's True Type font directory - fonts_dir = f"{path_to_file}/fonts/" + fonts_dir = f"{path_to_file}/shakenbreak/" + ttf_fonts = [ + file_name for file_name in os.listdir(fonts_dir) if ".ttf" in file_name + ] try: - for file_name in os.listdir(fonts_dir): - if ".ttf" in file_name: # must be in ttf format for matplotlib - old_path = os.path.join(fonts_dir, file_name) - new_path = os.path.join(mpl_fonts_dir, file_name) - shutil.copyfile(old_path, new_path) - print("Copying " + old_path + " -> " + new_path) - else: - print(f"No ttf fonts found in the {fonts_dir} directory.") + for font in ttf_fonts: # must be in ttf format for matplotlib + old_path = os.path.join(fonts_dir, font) + new_path = os.path.join(mpl_fonts_dir, font) + shutil.copyfile(old_path, new_path) + print("Copying " + old_path + " -> " + new_path) + if not ttf_fonts: + print(f"No ttf fonts found in the {fonts_dir} directory.") except Exception: pass # Try to delete matplotlib's fontList cache mpl_cache_dir = mpl.get_cachedir() mpl_cache_dir_ls = os.listdir(mpl_cache_dir) - if "fontList.cache" in mpl_cache_dir_ls: - fontList_path = os.path.join(mpl_cache_dir, "fontList.cache") - if fontList_path: - os.remove(fontList_path) - print("Deleted the matplotlib fontList.cache.") - else: + for file_name in mpl_cache_dir_ls: + if "fontlist" in file_name.lower(): + fontList_path = os.path.join(mpl_cache_dir, file_name) + if os.path.exists(fontList_path): + os.remove(fontList_path) + print("Deleted the matplotlib fontList cache.") + if not any("fontlist" in file_name.lower() for file_name in mpl_cache_dir_ls): print("Couldn't find matplotlib cache, so will continue.") # Add fonts - for font in os.listdir(fonts_dir): + for font in ttf_fonts: matplotlib.font_manager._load_fontmanager(try_read_cache=False) matplotlib.font_manager.fontManager.addfont(f"{fonts_dir}/{font}") print(f"Adding {font} font to matplotlib fonts.") except Exception: - warning_msg = """WARNING: An issue occured while installing the custom font for ShakeNBreak. - The widely available Helvetica font will be used instead.""" - warnings.warn(warning_msg) + warnings.warn( + "An issue occured while installing the custom font for ShakeNBreak. The widely available " + "Helvetica font will be used instead." + ) class PostInstallCommand(install): @@ -116,13 +120,12 @@ def run(self): def package_files(directory): """Include package data.""" paths = [] - for (path, directories, filenames) in os.walk(directory): + for path, directories, filenames in os.walk(directory): paths.extend(os.path.join("..", path, filename) for filename in filenames) return paths input_files = package_files("SnB_input_files/") -fonts = package_files("fonts/") with open("README.md", "r", encoding="utf-8") as file: long_description = file.read() @@ -130,7 +133,7 @@ def package_files(directory): setup( name="shakenbreak", - version="3.2.4", + version="3.3.0", description="Package to generate and analyse distorted defect structures, in order to " "identify ground-state and metastable defect configurations.", long_description=long_description, @@ -191,7 +194,7 @@ def package_files(directory): }, # Specify any non-python files to be distributed with the package package_data={ - "shakenbreak": ["shakenbreak/*"] + input_files + fonts, + "shakenbreak": ["shakenbreak/*"] + input_files, }, include_package_data=True, # Specify the custom installation class diff --git a/fonts/Montserrat-Regular.ttf b/shakenbreak/Montserrat-Regular.ttf similarity index 100% rename from fonts/Montserrat-Regular.ttf rename to shakenbreak/Montserrat-Regular.ttf diff --git a/shakenbreak/scripts/SnB_run.sh b/shakenbreak/SnB_run.sh similarity index 92% rename from shakenbreak/scripts/SnB_run.sh rename to shakenbreak/SnB_run.sh index d4141444..cd89bb01 100755 --- a/shakenbreak/scripts/SnB_run.sh +++ b/shakenbreak/SnB_run.sh @@ -20,7 +20,6 @@ job_filepath=${2:-"job"} # jobscript path job_filename=$(basename "${job_filepath}") # jobscript name job_name_option=${3:-"-N"} # job name option -DIR="$(dirname "${BASH_SOURCE[0]}")" if [ $single_defect = true ]; then defect_name=${PWD##*/}/ # Use current directory name fi @@ -33,7 +32,7 @@ else fi if [ ! -f "$job_filepath" ]; then - echo "Job file '$job_filepath' not found, so will only submit jobs in folders with '$job_filename' present" + echo "Job file '$job_filepath' not found, so will only save files and submit jobs in folders with '$job_filename' present" job_in_cwd=false fi @@ -188,6 +187,12 @@ SnB_run_loop() { fi echo "${i%?} not (fully) relaxed, saving files and rerunning" + # save_vasp_files: + current_time=$(date +%H_%M_%Son%d_%m_%y) + for vasp_file in {CONTCAR,OUTCAR,XDATCAR,POSCAR,INCAR,OSZICAR,vasprun.xml}; do + cp ${vasp_file} ${vasp_file}_${current_time} + done + gzip vasprun.xml_${current_time} # gzip to save file space if [[ -f "CONTCAR" ]] && [[ $(wc -l < "CONTCAR") -ge 9 ]]; then # CONTCAR exists and greater than 9 lines "cp" CONTCAR POSCAR @@ -200,14 +205,17 @@ SnB_run_loop() { fi fi fi + if [ -f "./${job_filename}" ]; then echo "Running job for ${i%?}" folder_shortname="${i#*_*_}" # Remove % from folder_shortname as messes with some HPC schedulers - if "${job_submit_command}" "${job_name_option}" "${defect_name%?}"_"${folder_shortname%?}" "${job_filename}" 2>/dev/null || \ - "${job_submit_command}" "${job_name_option}" "${defect_name%?}"_"${folder_shortname%??}" "${job_filename}"; then - bash "${DIR}"/save_vasp_files.sh # only save over files if job submit command is successful (to prevent unwanted duplication of files) + if ! ( "${job_submit_command}" "${job_name_option}" "${defect_name%?}"_"${folder_shortname%?}" "${job_filename}" 2>/dev/null || \ + "${job_submit_command}" "${job_name_option}" "${defect_name%?}"_"${folder_shortname%??}" "${job_filename}" ); then + rm *_"${current_time}" # only save over files if job submit command is successful (to prevent unwanted duplication of files) fi + else + rm *_"${current_time}" # only save over files if job successfully submitted fi builtin cd .. || return else @@ -239,4 +247,4 @@ fi if [ ! $shopt_enabled = true ]; then shopt -u extglob # disable extended globbing (pattern matching) if it was disabled at start -fi \ No newline at end of file +fi diff --git a/shakenbreak/analysis.py b/shakenbreak/analysis.py index 8e178c01..e961e1cc 100644 --- a/shakenbreak/analysis.py +++ b/shakenbreak/analysis.py @@ -117,15 +117,15 @@ def _get_distortion_filename(distortion) -> str: distortion_label = f"Bond_Distortion_{distortion:.1f}%" elif isinstance(distortion, str): if "_from_" in distortion and ( - "Rattled" not in distortion - and "Dimer" not in distortion + "Rattled" not in distortion and "Dimer" not in distortion ): distortion_label = f"Bond_Distortion_{distortion}" # runs from other charge states elif ( "Rattled_from_" in distortion or "Dimer_from" in distortion - or distortion in [ + or distortion + in [ "Unperturbed", "Rattled", "Dimer", @@ -194,9 +194,8 @@ def _format_distortion_names( ): return float(distortion_label.split("Bond_Distortion_")[-1].split("%")[0]) / 100 elif ( - ("Dimer" in distortion_label or "Rattled" in distortion_label) - and "High_Energy" in distortion_label - ): + "Dimer" in distortion_label or "Rattled" in distortion_label + ) and "High_Energy" in distortion_label: return distortion_label else: return "Label_not_recognized" @@ -505,7 +504,10 @@ def get_structures( distortion_subdirectories = [ i for i in next(os.walk(f"{output_path}/{defect_species}"))[1] - if ("Bond_Distortion" in i) or ("Unperturbed" in i) or ("Rattled" in i) or ("Dimer" in i) + if ("Bond_Distortion" in i) + or ("Unperturbed" in i) + or ("Rattled" in i) + or ("Dimer" in i) ] # distortion subdirectories if not distortion_subdirectories: raise FileNotFoundError( @@ -787,10 +789,10 @@ def calculate_struct_comparison( distortion ] = None # algorithm couldn't match lattices. Set comparison # metric to None - warnings.warn( - f"pymatgen StructureMatcher could not match lattices between " - f"{ref_name} and {distortion} structures." - ) + # warnings.warn( + # f"pymatgen StructureMatcher could not match lattices between " + # f"{ref_name} and {distortion} structures." + # ) # Unnecessary warning, occurs often with highly-distorted/disordered structures return disp_dict @@ -1000,8 +1002,10 @@ def get_homoionic_bonds( homoionic neighbours and distances (A) (e.g. {'O(1)': {'O(2)': '2.0 A', 'O(3)': '2.0 A'}}) """ - if isinstance(elements, str): # For backward compatibility - elements = [elements,] + if isinstance(elements, str): # For backward compatibility + elements = [ + elements, + ] structure = structure.copy() structure.remove_oxidation_states() for element in elements: @@ -1012,11 +1016,13 @@ def get_homoionic_bonds( # Search for homoionic bonds in the whole structure sites = [] for element in elements: - sites.extend([ - (site_index, site) - for site_index, site in enumerate(structure) - if site.species_string == element - ]) + sites.extend( + [ + (site_index, site) + for site_index, site in enumerate(structure) + if site.species_string == element + ] + ) homoionic_bonds = {} for site_index, site in sites: neighbours = structure.get_neighbors(site, r=radius) @@ -1040,9 +1046,9 @@ def get_homoionic_bonds( if neighbour[0] == element } if f"{site.species_string}({site_index})" in homoionic_bonds: - homoionic_bonds[ - f"{site.species_string}({site_index})" - ].update(homoionic_neighbours) + homoionic_bonds[f"{site.species_string}({site_index})"].update( + homoionic_neighbours + ) else: homoionic_bonds[ f"{site.species_string}({site_index})" diff --git a/shakenbreak/cli.py b/shakenbreak/cli.py index 08f800a2..b7f40996 100644 --- a/shakenbreak/cli.py +++ b/shakenbreak/cli.py @@ -10,8 +10,8 @@ import click from doped.generation import get_defect_name_from_entry -from doped.utils.plotting import _format_defect_name from doped.utils.parsing import get_outcar +from doped.utils.plotting import _format_defect_name # Monty and pymatgen from monty.serialization import dumpfn, loadfn @@ -813,7 +813,7 @@ def run(submit_command, job_script, job_name_option, all, verbose): job_name_option = "-N" call( - f"{os.path.dirname(__file__)}/scripts/SnB_run.sh {optional_flags} {submit_command} {job_script} " + f"{os.path.dirname(__file__)}/SnB_run.sh {optional_flags} {submit_command} {job_script} " f"{job_name_option}", shell=True, ) diff --git a/shakenbreak/distortions.py b/shakenbreak/distortions.py index 39815736..4e527b69 100644 --- a/shakenbreak/distortions.py +++ b/shakenbreak/distortions.py @@ -10,10 +10,10 @@ _probability_mc_rattle, generate_mc_rattled_structures, ) -from pymatgen.analysis.local_env import MinimumDistanceNN +from pymatgen.analysis.local_env import CrystalNN, MinimumDistanceNN from pymatgen.core.structure import Structure from pymatgen.io.ase import AseAtomsAdaptor -from pymatgen.analysis.local_env import CrystalNN + def _warning_on_one_line(message, category, filename, lineno, file=None, line=None): """Format warnings output""" @@ -89,7 +89,9 @@ def distort( if distorted_atoms and len(distorted_atoms) >= num_nearest_neighbours: nearest = [ ( - round(input_structure_ase.get_distance(atom_number, index, mic=True), 4), + round( + input_structure_ase.get_distance(atom_number, index, mic=True), 4 + ), index + 1, input_structure_ase.get_chemical_symbols()[index], ) @@ -106,7 +108,9 @@ def distort( ) distances = [ # Get all distances between the selected atom and all other atoms ( - round(input_structure_ase.get_distance(atom_number, index, mic=True), 4), + round( + input_structure_ase.get_distance(atom_number, index, mic=True), 4 + ), index + 1, # Indices start from 1 symbol, ) @@ -124,7 +128,9 @@ def distort( ): # filter the neighbours that match the element criteria and are # closer than 4.5 Angstroms nearest = [] # list of nearest neighbours - for dist, index, element in distances[1:]: # starting from 1 to exclude defect atom + for dist, index, element in distances[ + 1: + ]: # starting from 1 to exclude defect atom if ( element == distorted_element and dist < 4.5 @@ -228,7 +234,7 @@ def apply_dimer_distortion( if site_index is not None: # site_index can be 0 atom_number = site_index - 1 # Align atom number with python 0-indexing - elif type(frac_coords) in [list, tuple, np.ndarray]: # Only for vacancies! + elif type(frac_coords) in [list, tuple, np.ndarray]: # Only for vacancies! input_structure_ase.append("V") # fake "V" at vacancy input_structure_ase.positions[-1] = np.dot( frac_coords, input_structure_ase.cell @@ -243,20 +249,22 @@ def apply_dimer_distortion( # Get defect nn struct = aaa.get_structure(input_structure_ase) cnn = CrystalNN() - sites = [d['site'] for d in cnn.get_nn_info(struct, atom_number)] + sites = [d["site"] for d in cnn.get_nn_info(struct, atom_number)] # Get distances between NN distances = {} for i, site in enumerate(sites): - for other_site in sites[i+1:]: + for other_site in sites[i + 1 :]: distances[(site.index, other_site.index)] = site.distance(other_site) - # Get defect NN with smallest distance - site_indexes = min(distances, key=distances.get) + # Get defect NN with smallest distance and lowest indices: + site_indexes = min( + distances, key=lambda k: (round(distances.get(k, 10), 3), k[0], k[1]) + ) # Set their distance to 2 A input_structure_ase.set_distance( a0=site_indexes[0], a1=site_indexes[1], distance=2.0, fix=0.5, mic=True ) - if type(frac_coords) in [list, tuple, np.ndarray]: + if type(frac_coords) in [list, tuple, np.ndarray]: input_structure_ase.pop(-1) # remove fake V from vacancy structure distorted_structure = aaa.get_structure(input_structure_ase) diff --git a/shakenbreak/input.py b/shakenbreak/input.py index cb314e21..41268caa 100644 --- a/shakenbreak/input.py +++ b/shakenbreak/input.py @@ -258,7 +258,7 @@ def _create_vasp_input( match_found = not any( any( x in i - for i in os.listdir(dir) + for i in os.listdir(os.path.join(output_path, dir)) for x in ["Unperturbed", "Rattled", "Bond_Distortion"] ) for dir in matching_dirs @@ -776,7 +776,9 @@ def identify_defect( Returns: :obj:`Defect` """ - # identify defect site, structural information, and create defect object + # Note: Could replace much of the code in this function with the defect_from_structures function from + # doped if we wanted, but works fine as is. + # identify defect site, structural information, and create defect object: try: defect_type, comp_diff = get_defect_type_and_composition_diff( bulk_structure, defect_structure @@ -1257,6 +1259,7 @@ def _apply_rattle_bond_distortions( active_atoms: Optional[list] = None, distorted_element: Optional[str] = None, distorted_atoms: Optional[list] = None, + oxidation_states: Optional[dict] = None, verbose: bool = False, **mc_rattle_kwargs, ) -> dict: @@ -1332,6 +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 + 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!) @@ -1360,7 +1365,10 @@ def _apply_rattle_bond_distortions( # unit cell is conserved in the supercell frac_coords = None # only for vacancies if defect_site_index is not None: - if isinstance(distortion_factor, str) and distortion_factor.lower() == "dimer": + if ( + isinstance(distortion_factor, str) + and distortion_factor.lower() == "dimer" + ): bond_distorted_defect = distortions.apply_dimer_distortion( structure=defect_structure, site_index=defect_site_index, @@ -1431,6 +1439,7 @@ def apply_snb_distortions( distorted_element: Optional[str] = None, distorted_atoms: Optional[list] = None, verbose: bool = False, + oxidation_states: Optional[dict] = None, **mc_rattle_kwargs, ) -> dict: """ @@ -1536,6 +1545,7 @@ def apply_snb_distortions( distorted_atoms=distorted_atoms, verbose=verbose, seed=seed, + oxidation_states=oxidation_states, **mc_rattle_kwargs, ) distorted_defect_dict["distortions"][ @@ -1566,16 +1576,21 @@ def apply_snb_distortions( distorted_atoms=distorted_atoms, verbose=verbose, seed=seed, + oxidation_states=oxidation_states, **mc_rattle_kwargs, ) - distorted_defect_dict["distortions"]["Dimer"] = ( - bond_distorted_defect["distorted_structure"] + distorted_defect_dict["distortions"]["Dimer"] = bond_distorted_defect[ + "distorted_structure" + ] + distorted_defect_dict["distortion_parameters"].update( + { + "unique_site": bulk_supercell_site.frac_coords, + "num_distorted_neighbours_in_dimer": 2, # Dimer distortion only affects 2 atoms + "distorted_atoms_in_dimer": bond_distorted_defect[ + "distorted_atoms" + ], + } ) - distorted_defect_dict["distortion_parameters"].update({ - "unique_site": bulk_supercell_site.frac_coords, - "num_distorted_neighbours_in_dimer": 2, # Dimer distortion only affects 2 atoms - "distorted_atoms_in_dimer": bond_distorted_defect["distorted_atoms"], - }) if defect_site_index: # only add site index if not vacancy distorted_defect_dict["distortion_parameters"][ "defect_site_index" @@ -1635,11 +1650,15 @@ def apply_snb_distortions( distorted_defect_dict["distortions"]["Dimer"] = bond_distorted_defect[ "distorted_structure" ] - distorted_defect_dict["distortion_parameters"].update({ - "unique_site": bulk_supercell_site.frac_coords, - "num_distorted_neighbours_in_dimer": 2, # Dimer distortion only affects 2 atoms - "distorted_atoms_in_dimer": bond_distorted_defect["distorted_atoms"], - }) + distorted_defect_dict["distortion_parameters"].update( + { + "unique_site": bulk_supercell_site.frac_coords, + "num_distorted_neighbours_in_dimer": 2, # Dimer distortion only affects 2 atoms + "distorted_atoms_in_dimer": bond_distorted_defect[ + "distorted_atoms" + ], + } + ) return distorted_defect_dict @@ -1961,9 +1980,9 @@ def guess_oxidation_states(bulk_comp): self.bond_distortions.append("Dimer") bond_distortions.remove("Dimer") - self.bond_distortions.extend(list( - np.around(bond_distortions, 3) - )) # round to 3 decimal places + self.bond_distortions.extend( + list(np.around(bond_distortions, 3)) + ) # round to 3 decimal places else: # If the user does not specify bond_distortions, use # distortion_increment: @@ -2123,7 +2142,7 @@ def _print_distortion_info( ) -> None: """Print applied bond distortions and rattle standard deviation.""" rounded_distortions = [ - f'{round(i,3)+0}' if isinstance(i, float) else i for i in bond_distortions + f"{round(i,3)+0}" if isinstance(i, float) else i for i in bond_distortions ] print( "Applying ShakeNBreak...", @@ -2230,24 +2249,12 @@ def _setup_distorted_defect_dict( ) pristine_site = _get_bulk_defect_site(defect_entry) - try: - distorted_defect_dict = { - "defect_type": defect_type, - "defect_site": defect_site, - "defect_supercell_site": pristine_site, # original site in pristine supercell - "defect_multiplicity": defect.get_multiplicity(), - "charges": {int(charge): {} for charge in user_charges}, - } # General info about (neutral) defect - except NotImplementedError: # interstitial - distorted_defect_dict = { - "defect_type": defect_type, - "defect_site": defect_site, - "defect_supercell_site": pristine_site, - "defect_multiplicity": _get_voronoi_multiplicity( - defect.site, defect.structure - ), - "charges": {int(charge): {} for charge in user_charges}, - } # General info about (neutral) defect + distorted_defect_dict = { + "defect_type": defect_type, + "defect_site": defect_site, + "defect_supercell_site": pristine_site, # original site in pristine supercell + "charges": {int(charge): {} for charge in user_charges}, + } # General info about (neutral) defect if defect_type == "substitution": # substitutions and antisites sub_site_in_bulk = defect.defect_site distorted_defect_dict[ @@ -2370,6 +2377,7 @@ def apply_distortions( distorted_element=distorted_element, distorted_atoms=self.distorted_atoms, verbose=verbose, + oxidation_states=self.oxidation_states, **self._mc_rattle_kwargs, ) @@ -2469,6 +2477,8 @@ def write_vasp_files( tuple of dictionaries with new defects_dict (containing the distorted structures) and defect distortion parameters. """ + # Note: If input file generation was becoming too slow, could try to profile deeper / possibly + # implement multiprocessing. distorted_defects_dict, self.distortion_metadata = self.apply_distortions( verbose=verbose, ) diff --git a/shakenbreak/io.py b/shakenbreak/io.py index 7294254d..ec311b4d 100644 --- a/shakenbreak/io.py +++ b/shakenbreak/io.py @@ -368,7 +368,7 @@ def parse_fhi_aims_energy(defect_dir, dist, energy, aims_out): "Bond_Distortion", "Rattled", "Unperturbed", - "Dimer", + "Dimer", ] ) and "High_Energy" in dir diff --git a/shakenbreak/plotting.py b/shakenbreak/plotting.py index 7466c41a..b169bccd 100644 --- a/shakenbreak/plotting.py +++ b/shakenbreak/plotting.py @@ -37,39 +37,46 @@ def _install_custom_font(): print("Trying to install ShakeNBreak custom font...") try: # Copy the font file to matplotlib's True Type font directory - fonts_dir = f"{MODULE_DIR}/../fonts/" + fonts_dir = MODULE_DIR + ttf_fonts = [ + file_name for file_name in os.listdir(fonts_dir) if ".ttf" in file_name + ] try: - for file_name in os.listdir(fonts_dir): - if ".ttf" in file_name: # must be in ttf format for matplotlib - old_path = os.path.join(fonts_dir, file_name) - new_path = os.path.join(mpl_fonts_dir, file_name) - shutil.copyfile(old_path, new_path) - print("Copying " + old_path + " -> " + new_path) - else: - print(f"No ttf fonts found in the {fonts_dir} directory.") + for font in ttf_fonts: # must be in ttf format for matplotlib + old_path = os.path.join(fonts_dir, font) + new_path = os.path.join(mpl_fonts_dir, font) + shutil.copyfile(old_path, new_path) + print("Copying " + old_path + " -> " + new_path) + if not ttf_fonts: + print(f"No ttf fonts found in the {fonts_dir} directory.") except Exception: pass # Try to delete matplotlib's fontList cache mpl_cache_dir = mpl.get_cachedir() mpl_cache_dir_ls = os.listdir(mpl_cache_dir) - if "fontList.cache" in mpl_cache_dir_ls: - fontList_path = os.path.join(mpl_cache_dir, "fontList.cache") - if fontList_path: - os.remove(fontList_path) - print("Deleted the matplotlib fontList.cache.") - else: + for file_name in mpl_cache_dir_ls: + if "fontlist" in file_name.lower(): + fontList_path = os.path.join(mpl_cache_dir, file_name) + if os.path.exists(fontList_path): + os.remove(fontList_path) + print("Deleted the matplotlib fontList cache.") + if not any( + "fontlist" in file_name.lower() for file_name in mpl_cache_dir_ls + ): print("Couldn't find matplotlib cache, so will continue.") # Add font to MAtplotlib Fontmanager - for font in os.listdir(fonts_dir): + for font in ttf_fonts: font_manager._load_fontmanager(try_read_cache=False) font_manager.fontManager.addfont(f"{fonts_dir}/{font}") print(f"Adding {font} font to matplotlib fonts.") + except Exception: - warning_msg = """WARNING: An issue occured while installing the custom font for ShakeNBreak. - The widely available Helvetica font will be used instead.""" - warnings.warn(warning_msg) + warnings.warn( + "An issue occured while installing the custom font for ShakeNBreak. The widely available " + "Helvetica font will be used instead." + ) def _get_backend(save_format: str) -> Optional[str]: @@ -412,7 +419,7 @@ def _format_datapoints_from_other_chargestates( elif entry == "Rattled": # add 0.0 for Rattled # (to avoid problems when sorting distortions) keys.append(0.0) - elif entry == "Dimer": # add 0.0 for Dimer + elif entry == "Dimer": # add 0.0 for Dimer # (to avoid problems when sorting distortions) keys.append(0.0) else: @@ -1340,7 +1347,7 @@ def plot_colorbar( energies_dict["distortions"]["Dimer"], c=disp_dict["Dimer"], s=50, - marker="s", #default_style_settings["marker"], + marker="s", # default_style_settings["marker"], label="Dimer", cmap=colormap, norm=norm, @@ -1728,15 +1735,14 @@ def plot_datasets( dataset["distortions"]["Dimer"], c=colors[dataset_number], s=50, - marker="s", #default_style_settings["marker"], + marker="s", # default_style_settings["marker"], label="Dimer", ) if len(sorted_distortions) > 0 and [ - - key for key in dataset["distortions"] - if (key != "Rattled" and key != "Dimer") - + key + for key in dataset["distortions"] + if (key != "Rattled" and key != "Dimer") ]: # more than just Rattled if imported_indices: # Exclude datapoints from other charge states non_imported_sorted_indices = [ diff --git a/shakenbreak/scripts/save_vasp_files.sh b/shakenbreak/scripts/save_vasp_files.sh deleted file mode 100644 index bb2367aa..00000000 --- a/shakenbreak/scripts/save_vasp_files.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -# Script to save important VASP output files for future reference, -# likely before beginning a continuation job in the same directory. - -current_time=$(date +%H_%M_%Son%d_%m_%y) -for i in {CONTCAR,OUTCAR,XDATCAR,POSCAR,INCAR,OSZICAR,vasprun.xml}; do - cp $i ${i}_${current_time} -done -gzip vasprun.xml_${current_time} # gzip to save file space diff --git a/tests/Test_Dimer.ipynb b/tests/Test_Dimer.ipynb index a53eb1d6..e175cac9 100644 --- a/tests/Test_Dimer.ipynb +++ b/tests/Test_Dimer.ipynb @@ -9,31 +9,36 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.446525Z", + "start_time": "2024-02-12T18:13:53.896207Z" + } + }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "Generating DefectEntry objects: 100.0%|██████████| [00:06, 14.43it/s]" + "Generating DefectEntry objects: 100.0%|██████████| [00:06, 14.75it/s] " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Vacancies Charge States Conv. Cell Coords Wyckoff\n", - "----------- --------------- ------------------- ---------\n", - "v_Cd [-2,-1,0,+1] [0.000,0.000,0.000] 4a\n", - "v_Te [-1,0,+1,+2] [0.250,0.250,0.250] 4c\n", + "Vacancies Guessed Charges Conv. Cell Coords Wyckoff\n", + "----------- ----------------- ------------------- ---------\n", + "v_Cd [-2,-1,0,+1] [0.000,0.000,0.000] 4a\n", + "v_Te [-1,0,+1,+2] [0.250,0.250,0.250] 4c\n", "\n", - "Substitutions Charge States Conv. Cell Coords Wyckoff\n", + "Substitutions Guessed Charges Conv. Cell Coords Wyckoff\n", "--------------- --------------------- ------------------- ---------\n", "Cd_Te [0,+1,+2,+3,+4] [0.250,0.250,0.250] 4c\n", "Te_Cd [-4,-3,-2,-1,0,+1,+2] [0.000,0.000,0.000] 4a\n", "\n", - "Interstitials Charge States Conv. Cell Coords Wyckoff\n", + "Interstitials Guessed Charges Conv. Cell Coords Wyckoff\n", "--------------- --------------------- ------------------- ---------\n", "Cd_i_C3v [0,+1,+2] [0.625,0.625,0.625] 16e\n", "Cd_i_Td_Cd2.83 [0,+1,+2] [0.750,0.750,0.750] 4d\n", @@ -58,22 +63,25 @@ "from pymatgen.core.structure import Structure\n", "from doped.generation import DefectsGenerator\n", "\n", - "bulk = Structure.from_file(\"./tests/data/vasp/CdTe/CdTe_Bulk_Primitive_POSCAR\") # CdTe\n", - "defect_gen = DefectsGenerator(bulk)" + "bulk = Structure.from_file(\"data/vasp/CdTe/CdTe_Bulk_Primitive_POSCAR\") # CdTe\n", + "defect_gen = DefectsGenerator(bulk, supercell_gen_kwargs={\"min_atoms\": 64})" ] }, { "cell_type": "code", - "execution_count": 4, - "metadata": {}, + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.453232Z", + "start_time": "2024-02-12T18:14:06.449086Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "dict_keys(['v_Cd_-2', 'v_Cd_-1', 'v_Cd_0', 'v_Cd_+1', 'v_Te_-1', 'v_Te_0', 'v_Te_+1', 'v_Te_+2', 'Cd_Te_0', 'Cd_Te_+1', 'Cd_Te_+2', 'Cd_Te_+3', 'Cd_Te_+4', 'Te_Cd_-4', 'Te_Cd_-3', 'Te_Cd_-2', 'Te_Cd_-1', 'Te_Cd_0', 'Te_Cd_+1', 'Te_Cd_+2', 'Cd_i_C3v_0', 'Cd_i_C3v_+1', 'Cd_i_C3v_+2', 'Cd_i_Td_Cd2.83_0', 'Cd_i_Td_Cd2.83_+1', 'Cd_i_Td_Cd2.83_+2', 'Cd_i_Td_Te2.83_0', 'Cd_i_Td_Te2.83_+1', 'Cd_i_Td_Te2.83_+2', 'Te_i_C3v_-2', 'Te_i_C3v_-1', 'Te_i_C3v_0', 'Te_i_C3v_+1', 'Te_i_C3v_+2', 'Te_i_C3v_+3', 'Te_i_C3v_+4', 'Te_i_Td_Cd2.83_-2', 'Te_i_Td_Cd2.83_-1', 'Te_i_Td_Cd2.83_0', 'Te_i_Td_Cd2.83_+1', 'Te_i_Td_Cd2.83_+2', 'Te_i_Td_Cd2.83_+3', 'Te_i_Td_Cd2.83_+4', 'Te_i_Td_Te2.83_-2', 'Te_i_Td_Te2.83_-1', 'Te_i_Td_Te2.83_0', 'Te_i_Td_Te2.83_+1', 'Te_i_Td_Te2.83_+2', 'Te_i_Td_Te2.83_+3', 'Te_i_Td_Te2.83_+4'])" - ] + "text/plain": "dict_keys(['v_Cd_-2', 'v_Cd_-1', 'v_Cd_0', 'v_Cd_+1', 'v_Te_-1', 'v_Te_0', 'v_Te_+1', 'v_Te_+2', 'Cd_Te_0', 'Cd_Te_+1', 'Cd_Te_+2', 'Cd_Te_+3', 'Cd_Te_+4', 'Te_Cd_-4', 'Te_Cd_-3', 'Te_Cd_-2', 'Te_Cd_-1', 'Te_Cd_0', 'Te_Cd_+1', 'Te_Cd_+2', 'Cd_i_C3v_0', 'Cd_i_C3v_+1', 'Cd_i_C3v_+2', 'Cd_i_Td_Cd2.83_0', 'Cd_i_Td_Cd2.83_+1', 'Cd_i_Td_Cd2.83_+2', 'Cd_i_Td_Te2.83_0', 'Cd_i_Td_Te2.83_+1', 'Cd_i_Td_Te2.83_+2', 'Te_i_C3v_-2', 'Te_i_C3v_-1', 'Te_i_C3v_0', 'Te_i_C3v_+1', 'Te_i_C3v_+2', 'Te_i_C3v_+3', 'Te_i_C3v_+4', 'Te_i_Td_Cd2.83_-2', 'Te_i_Td_Cd2.83_-1', 'Te_i_Td_Cd2.83_0', 'Te_i_Td_Cd2.83_+1', 'Te_i_Td_Cd2.83_+2', 'Te_i_Td_Cd2.83_+3', 'Te_i_Td_Cd2.83_+4', 'Te_i_Td_Te2.83_-2', 'Te_i_Td_Te2.83_-1', 'Te_i_Td_Te2.83_0', 'Te_i_Td_Te2.83_+1', 'Te_i_Td_Te2.83_+2', 'Te_i_Td_Te2.83_+3', 'Te_i_Td_Te2.83_+4'])" }, - "execution_count": 4, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -84,8 +92,13 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": {}, + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.461636Z", + "start_time": "2024-02-12T18:14:06.452870Z" + } + }, "outputs": [], "source": [ "defects = {\n", @@ -97,8 +110,13 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, + "execution_count": 4, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.627532Z", + "start_time": "2024-02-12T18:14:06.458210Z" + } + }, "outputs": [ { "name": "stdout", @@ -119,16 +137,19 @@ }, { "cell_type": "code", - "execution_count": 7, - "metadata": {}, + "execution_count": 5, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.630883Z", + "start_time": "2024-02-12T18:14:06.627969Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "['Dimer']" - ] + "text/plain": "['Dimer']" }, - "execution_count": 7, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -139,20 +160,19 @@ }, { "cell_type": "code", - "execution_count": 8, - "metadata": {}, + "execution_count": 6, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.635543Z", + "start_time": "2024-02-12T18:14:06.630576Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "{'distortion_parameters': {'distortion_increment': None,\n", - " 'bond_distortions': ['Dimer'],\n", - " 'local_rattle': False,\n", - " 'mc_rattle_parameters': {'stdev': 0.28333683853583175}},\n", - " 'defects': {}}" - ] + "text/plain": "{'distortion_parameters': {'distortion_increment': None,\n 'bond_distortions': ['Dimer'],\n 'local_rattle': False,\n 'mc_rattle_parameters': {'stdev': 0.28333683853583175}},\n 'defects': {}}" }, - "execution_count": 8, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -163,8 +183,13 @@ }, { "cell_type": "code", - "execution_count": 9, - "metadata": {}, + "execution_count": 7, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:06.771362Z", + "start_time": "2024-02-12T18:14:06.636681Z" + } + }, "outputs": [ { "name": "stdout", @@ -172,9 +197,9 @@ "text": [ "Applying ShakeNBreak... Will apply the following bond distortions: ['Dimer']. Then, will rattle with a std dev of 0.28 Å \n", "\n", - "\u001b[1m\n", - "Defect: v_Cd\u001b[0m\n", - "\u001b[1mNumber of missing electrons in neutral state: 2\u001b[0m\n", + "\u001B[1m\n", + "Defect: v_Cd\u001B[0m\n", + "\u001B[1mNumber of missing electrons in neutral state: 2\u001B[0m\n", "\n", "Defect v_Cd in charge state: 0. Number of distorted neighbours: 2\n", "\n", @@ -182,14 +207,6 @@ "\n", "Defect v_Cd in charge state: -2. Number of distorted neighbours: 0\n" ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "local_env.py:4133: UserWarning: No oxidation states specified on sites! For better results, set the site oxidation states in the structure.\n", - "local_env.py:3927: UserWarning: CrystalNN: cannot locate an appropriate radius, covalent or atomic radii will be used, this can lead to non-optimal results.\n" - ] } ], "source": [ @@ -198,8 +215,13 @@ }, { "cell_type": "code", - "execution_count": 10, - "metadata": {}, + "execution_count": 8, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:20.414687Z", + "start_time": "2024-02-12T18:14:20.070908Z" + } + }, "outputs": [ { "name": "stdout", @@ -207,9 +229,9 @@ "text": [ "Applying ShakeNBreak... Will apply the following bond distortions: ['Dimer']. Then, will rattle with a std dev of 0.28 Å \n", "\n", - "\u001b[1m\n", - "Defect: v_Cd\u001b[0m\n", - "\u001b[1mNumber of missing electrons in neutral state: 2\u001b[0m\n", + "\u001B[1m\n", + "Defect: v_Cd\u001B[0m\n", + "\u001B[1mNumber of missing electrons in neutral state: 2\u001B[0m\n", "\n", "Defect v_Cd in charge state: 0. Number of distorted neighbours: 2\n", "\n", @@ -220,541 +242,9 @@ }, { "data": { - "text/plain": [ - "({'v_Cd': {'defect_type': 'vacancy',\n", - " 'defect_site': PeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5],\n", - " 'defect_supercell_site': PeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5],\n", - " 'defect_multiplicity': 1,\n", - " 'charges': {0: {'structures': {'Unperturbed': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n", - " 'distortions': {'Dimer': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 5.836, 5.836) [0.375, 0.446, 0.446]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 7.25, 7.25) [0.375, 0.554, 0.554]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]}}},\n", - " -1: {'structures': {'Unperturbed': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n", - " 'distortions': {'Dimer': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 5.836, 5.836) [0.375, 0.446, 0.446]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 7.25, 7.25) [0.375, 0.554, 0.554]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]}}},\n", - " -2: {'structures': {'Unperturbed': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n", - " 'distortions': {'Rattled': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.776, 0.2499, 0.02026) [0.5178, 0.0191, 0.001548]\n", - " PeriodicSite: Cd (10.22, 3.208, 0.1487) [0.7808, 0.2452, 0.01136]\n", - " PeriodicSite: Cd (9.794, -0.02858, 2.947) [0.7484, -0.002184, 0.2252]\n", - " PeriodicSite: Cd (-0.4122, 0.2974, -0.271) [-0.0315, 0.02272, -0.02071]\n", - " PeriodicSite: Cd (3.102, 3.192, -0.2704) [0.237, 0.2439, -0.02066]\n", - " PeriodicSite: Cd (6.627, 6.82, -0.4001) [0.5064, 0.5211, -0.03057]\n", - " PeriodicSite: Cd (9.298, 10.15, -0.1669) [0.7105, 0.7759, -0.01275]\n", - " PeriodicSite: Cd (3.115, 0.2455, 2.9) [0.238, 0.01876, 0.2216]\n", - " PeriodicSite: Cd (6.431, 2.639, 3.331) [0.4914, 0.2016, 0.2546]\n", - " PeriodicSite: Cd (9.74, 6.329, 3.538) [0.7442, 0.4836, 0.2703]\n", - " PeriodicSite: Cd (6.552, 0.4754, 6.299) [0.5007, 0.03633, 0.4813]\n", - " PeriodicSite: Cd (10.06, 3.335, 6.281) [0.7686, 0.2548, 0.4799]\n", - " PeriodicSite: Cd (9.92, 0.03925, 10.4) [0.758, 0.002999, 0.7947]\n", - " PeriodicSite: Cd (0.07354, 6.813, 0.1364) [0.00562, 0.5206, 0.01042]\n", - " PeriodicSite: Cd (2.996, 9.608, 0.3128) [0.229, 0.7342, 0.0239]\n", - " PeriodicSite: Cd (-0.1834, 3.351, 3.096) [-0.01401, 0.2561, 0.2366]\n", - " PeriodicSite: Cd (3.596, 6.429, 3.2) [0.2747, 0.4913, 0.2445]\n", - " PeriodicSite: Cd (6.726, 10.07, 2.916) [0.5139, 0.7697, 0.2228]\n", - " PeriodicSite: Cd (-0.1172, -0.5479, 6.693) [-0.008952, -0.04187, 0.5115]\n", - " PeriodicSite: Cd (3.484, 3.394, 6.358) [0.2662, 0.2594, 0.4858]\n", - " PeriodicSite: Cd (10.22, 9.907, 6.423) [0.7809, 0.757, 0.4908]\n", - " PeriodicSite: Cd (2.698, -0.1605, 9.745) [0.2061, -0.01226, 0.7447]\n", - " PeriodicSite: Cd (6.688, 3.501, 9.61) [0.5111, 0.2675, 0.7343]\n", - " PeriodicSite: Cd (9.894, 6.283, 9.413) [0.756, 0.4801, 0.7193]\n", - " PeriodicSite: Cd (0.5605, 9.386, 3.213) [0.04283, 0.7172, 0.2455]\n", - " PeriodicSite: Cd (0.3798, 6.835, 6.403) [0.02902, 0.5223, 0.4893]\n", - " PeriodicSite: Cd (3.531, 9.717, 7.051) [0.2698, 0.7425, 0.5388]\n", - " PeriodicSite: Cd (0.237, 3.409, 9.94) [0.01811, 0.2605, 0.7596]\n", - " PeriodicSite: Cd (3.199, 6.578, 9.722) [0.2445, 0.5026, 0.7429]\n", - " PeriodicSite: Cd (6.451, 10.2, 9.833) [0.4929, 0.7792, 0.7514]\n", - " PeriodicSite: Cd (0.09249, 9.932, 10.49) [0.007067, 0.7589, 0.8013]\n", - " PeriodicSite: Te (11.27, 4.808, 4.497) [0.8613, 0.3674, 0.3436]\n", - " PeriodicSite: Te (1.733, 8.144, 4.834) [0.1325, 0.6223, 0.3694]\n", - " PeriodicSite: Te (1.686, 4.691, 7.752) [0.1288, 0.3585, 0.5924]\n", - " PeriodicSite: Te (4.88, 5.177, 4.987) [0.3729, 0.3956, 0.3811]\n", - " PeriodicSite: Te (8.005, 8.466, 5.166) [0.6117, 0.6469, 0.3948]\n", - " PeriodicSite: Te (11.48, 11.33, 4.578) [0.8774, 0.8656, 0.3498]\n", - " PeriodicSite: Te (1.671, 1.887, 5.189) [0.1277, 0.1442, 0.3965]\n", - " PeriodicSite: Te (8.019, 4.856, 7.997) [0.6127, 0.371, 0.6111]\n", - " PeriodicSite: Te (11.2, 8.312, 8.001) [0.856, 0.6351, 0.6114]\n", - " PeriodicSite: Te (1.64, 11.29, 7.71) [0.1253, 0.8625, 0.5892]\n", - " PeriodicSite: Te (11.91, 4.654, 11.25) [0.9102, 0.3556, 0.8596]\n", - " PeriodicSite: Te (1.838, 8.228, 11.35) [0.1404, 0.6287, 0.8675]\n", - " PeriodicSite: Te (2.336, 4.438, 1.636) [0.1785, 0.3391, 0.125]\n", - " PeriodicSite: Te (4.821, 11.3, 5.306) [0.3684, 0.8637, 0.4054]\n", - " PeriodicSite: Te (8.258, 1.897, 5.124) [0.631, 0.145, 0.3915]\n", - " PeriodicSite: Te (5.353, 8.218, 7.731) [0.409, 0.628, 0.5908]\n", - " PeriodicSite: Te (8.514, 11.36, 8.754) [0.6506, 0.8681, 0.6689]\n", - " PeriodicSite: Te (11.76, 1.627, 7.887) [0.8986, 0.1243, 0.6026]\n", - " PeriodicSite: Te (5.274, 4.923, 11.51) [0.403, 0.3762, 0.8792]\n", - " PeriodicSite: Te (8.407, 8.179, 11.37) [0.6424, 0.625, 0.8686]\n", - " PeriodicSite: Te (11.59, 11.47, 11.38) [0.8853, 0.8768, 0.8696]\n", - " PeriodicSite: Te (1.702, 1.79, 11.34) [0.1301, 0.1368, 0.8665]\n", - " PeriodicSite: Te (8.427, 4.601, 1.687) [0.644, 0.3516, 0.1289]\n", - " PeriodicSite: Te (11.55, 8.273, 2.054) [0.8827, 0.6322, 0.1569]\n", - " PeriodicSite: Te (1.701, 11.74, 1.646) [0.13, 0.8973, 0.1258]\n", - " PeriodicSite: Te (5.031, 2.14, 7.997) [0.3844, 0.1635, 0.6111]\n", - " PeriodicSite: Te (4.478, 11.68, 11.37) [0.3422, 0.8921, 0.8687]\n", - " PeriodicSite: Te (8.217, 1.229, 11.53) [0.6279, 0.09388, 0.8807]\n", - " PeriodicSite: Te (4.878, 8.331, 1.851) [0.3728, 0.6366, 0.1415]\n", - " PeriodicSite: Te (8.098, 11.73, 1.492) [0.6188, 0.8966, 0.114]\n", - " PeriodicSite: Te (11.11, 1.918, 1.833) [0.8487, 0.1465, 0.14]\n", - " PeriodicSite: Te (5.421, 1.7, 1.446) [0.4143, 0.1299, 0.1105],\n", - " 'Dimer': Structure Summary\n", - " Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - " PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - " PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - " PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n", - " PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - " PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - " PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - " PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - " PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - " PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - " PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - " PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - " PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - " PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - " PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - " PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - " PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - " PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - " PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - " PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - " PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - " PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - " PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - " PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - " PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - " PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - " PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - " PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - " PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - " PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - " PeriodicSite: Te (4.908, 5.836, 5.836) [0.375, 0.446, 0.446]\n", - " PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - " PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - " PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - " PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - " PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - " PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - " PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - " PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - " PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - " PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - " PeriodicSite: Te (4.908, 7.25, 7.25) [0.375, 0.554, 0.554]\n", - " PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - " PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - " PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - " PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n", - " PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - " PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - " PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - " PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - " PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - " PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - " PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - " PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - " PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - " PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]}}}}}},\n", - " {'distortion_parameters': {'distortion_increment': None,\n", - " 'bond_distortions': ['Dimer'],\n", - " 'local_rattle': False,\n", - " 'mc_rattle_parameters': {'stdev': 0.28333683853583175}},\n", - " 'defects': {'v_Cd': {'unique_site': [0.5, 0.5, 0.5],\n", - " 'charges': {0: {'num_nearest_neighbours': 2,\n", - " 'distorted_atoms': None,\n", - " 'distortion_parameters': {'distortion_increment': None,\n", - " 'bond_distortions': ['Dimer'],\n", - " 'local_rattle': False,\n", - " 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}},\n", - " -1: {'num_nearest_neighbours': 1,\n", - " 'distorted_atoms': None,\n", - " 'distortion_parameters': {'distortion_increment': None,\n", - " 'bond_distortions': ['Dimer'],\n", - " 'local_rattle': False,\n", - " 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}},\n", - " -2: {'num_nearest_neighbours': 0,\n", - " 'distorted_atoms': None,\n", - " 'distortion_parameters': {'distortion_increment': None,\n", - " 'bond_distortions': ['Dimer'],\n", - " 'local_rattle': False,\n", - " 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}}}}}})" - ] + "text/plain": "({'v_Cd': {'defect_type': 'vacancy',\n 'defect_site': PeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5],\n 'defect_supercell_site': PeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5],\n 'charges': {0: {'structures': {'Unperturbed': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n 'distortions': {'Dimer': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd2+ (6.911, 0.07044, 0.1085) [0.5281, 0.005382, 0.008289]\n PeriodicSite: Cd2+ (9.892, 3.456, -0.2653) [0.7558, 0.2641, -0.02027]\n PeriodicSite: Cd2+ (9.499, -0.1927, 3.262) [0.7258, -0.01473, 0.2492]\n PeriodicSite: Cd2+ (-0.1171, -0.1694, -0.06195) [-0.00895, -0.01295, -0.004734]\n PeriodicSite: Cd2+ (3.159, 3.541, 0.3778) [0.2414, 0.2706, 0.02887]\n PeriodicSite: Cd2+ (6.596, 6.63, -0.246) [0.504, 0.5066, -0.0188]\n PeriodicSite: Cd2+ (9.695, 10.6, -0.0988) [0.7408, 0.8102, -0.00755]\n PeriodicSite: Cd2+ (2.954, -0.1659, 2.694) [0.2257, -0.01267, 0.2058]\n PeriodicSite: Cd2+ (6.481, 3.258, 3.175) [0.4952, 0.2489, 0.2426]\n PeriodicSite: Cd2+ (9.942, 6.815, 2.709) [0.7597, 0.5208, 0.207]\n PeriodicSite: Cd2+ (6.367, 0.007261, 6.381) [0.4865, 0.0005548, 0.4876]\n PeriodicSite: Cd2+ (10.22, 3.857, 7.161) [0.7806, 0.2947, 0.5472]\n PeriodicSite: Cd2+ (9.627, -0.4261, 9.811) [0.7356, -0.03256, 0.7497]\n PeriodicSite: Cd2+ (0.344, 6.112, -0.3731) [0.02628, 0.467, -0.02851]\n PeriodicSite: Cd2+ (3.258, 9.812, 0.05336) [0.249, 0.7498, 0.004077]\n PeriodicSite: Cd2+ (-0.2757, 3.273, 2.741) [-0.02107, 0.2501, 0.2094]\n PeriodicSite: Cd2+ (3.349, 6.826, 2.764) [0.2559, 0.5216, 0.2112]\n PeriodicSite: Cd2+ (6.598, 10.01, 3.126) [0.5042, 0.765, 0.2388]\n PeriodicSite: Cd2+ (-0.1604, -0.1492, 6.562) [-0.01226, -0.0114, 0.5014]\n PeriodicSite: Cd2+ (3.344, 4.038, 6.443) [0.2556, 0.3085, 0.4924]\n PeriodicSite: Cd2+ (10.16, 10.08, 6.317) [0.7761, 0.7702, 0.4827]\n PeriodicSite: Cd2+ (3.307, 0.147, 9.738) [0.2527, 0.01124, 0.7441]\n PeriodicSite: Cd2+ (6.975, 3.796, 9.69) [0.533, 0.29, 0.7404]\n PeriodicSite: Cd2+ (9.164, 7.162, 9.342) [0.7002, 0.5473, 0.7138]\n PeriodicSite: Cd2+ (0.07552, 9.585, 3.039) [0.005771, 0.7324, 0.2322]\n PeriodicSite: Cd2+ (0.08003, 6.422, 6.503) [0.006116, 0.4907, 0.4969]\n PeriodicSite: Cd2+ (2.931, 9.849, 6.473) [0.2239, 0.7526, 0.4946]\n PeriodicSite: Cd2+ (-0.2122, 2.91, 9.847) [-0.01621, 0.2224, 0.7525]\n PeriodicSite: Cd2+ (3.336, 6.504, 9.485) [0.2549, 0.497, 0.7248]\n PeriodicSite: Cd2+ (6.984, 9.808, 9.416) [0.5337, 0.7495, 0.7195]\n PeriodicSite: Cd2+ (-0.4375, 9.586, 9.687) [-0.03343, 0.7325, 0.7402]\n PeriodicSite: Te2- (11.28, 4.997, 4.59) [0.8617, 0.3818, 0.3507]\n PeriodicSite: Te2- (1.621, 8.016, 5.115) [0.1239, 0.6125, 0.3909]\n PeriodicSite: Te2- (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te2- (5.836, 5.836, 4.908) [0.446, 0.446, 0.375]\n PeriodicSite: Te2- (7.722, 7.611, 5.044) [0.59, 0.5816, 0.3855]\n PeriodicSite: Te2- (11.59, 11.67, 4.631) [0.8859, 0.8919, 0.3539]\n PeriodicSite: Te2- (1.431, 1.563, 5.388) [0.1093, 0.1195, 0.4117]\n PeriodicSite: Te2- (8.324, 4.972, 8.098) [0.6361, 0.3799, 0.6188]\n PeriodicSite: Te2- (11.65, 7.812, 8.592) [0.8899, 0.5969, 0.6565]\n PeriodicSite: Te2- (1.283, 11.08, 7.65) [0.09806, 0.8469, 0.5845]\n PeriodicSite: Te2- (11.43, 5.08, 11.32) [0.8734, 0.3882, 0.8654]\n PeriodicSite: Te2- (1.846, 8.798, 10.89) [0.1411, 0.6723, 0.832]\n PeriodicSite: Te2- (1.183, 5.168, 2.353) [0.09041, 0.3949, 0.1798]\n PeriodicSite: Te2- (4.95, 11.37, 4.694) [0.3783, 0.869, 0.3587]\n PeriodicSite: Te2- (8.254, 1.274, 5.127) [0.6307, 0.09734, 0.3917]\n PeriodicSite: Te2- (4.464, 8.267, 8.207) [0.3411, 0.6317, 0.6271]\n PeriodicSite: Te2- (8.015, 11.53, 7.91) [0.6125, 0.8811, 0.6044]\n PeriodicSite: Te2- (11.2, 1.249, 8.246) [0.8557, 0.09541, 0.6301]\n PeriodicSite: Te2- (4.618, 4.601, 10.88) [0.3529, 0.3516, 0.831]\n PeriodicSite: Te2- (7.802, 8.407, 11.38) [0.5962, 0.6424, 0.8697]\n PeriodicSite: Te2- (11.37, 11.91, 11.31) [0.8685, 0.9098, 0.8642]\n PeriodicSite: Te2- (1.265, 1.85, 12.02) [0.09667, 0.1413, 0.9185]\n PeriodicSite: Te2- (8.129, 5.28, 1.445) [0.6212, 0.4035, 0.1104]\n PeriodicSite: Te2- (11.31, 8.118, 0.7387) [0.8639, 0.6203, 0.05645]\n PeriodicSite: Te2- (2.113, 11.22, 1.652) [0.1614, 0.8571, 0.1263]\n PeriodicSite: Te2- (5.077, 1.312, 7.827) [0.3879, 0.1003, 0.5981]\n PeriodicSite: Te2- (4.793, 11.5, 11.54) [0.3663, 0.8789, 0.8818]\n PeriodicSite: Te2- (8.366, 1.348, 11.45) [0.6393, 0.103, 0.8749]\n PeriodicSite: Te2- (4.696, 8.215, 1.171) [0.3588, 0.6278, 0.08945]\n PeriodicSite: Te2- (8.366, 11.74, 1.517) [0.6393, 0.8972, 0.1159]\n PeriodicSite: Te2- (11.42, 1.543, 1.465) [0.8729, 0.1179, 0.1119]\n PeriodicSite: Te2- (5.198, 1.69, 1.849) [0.3972, 0.1291, 0.1413]}}},\n -1: {'structures': {'Unperturbed': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n 'distortions': {'Dimer': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd2+ (6.511, 0.3501, 0.006629) [0.4975, 0.02675, 0.0005065]\n PeriodicSite: Cd2+ (9.476, 3.745, -0.2978) [0.7241, 0.2862, -0.02276]\n PeriodicSite: Cd2+ (10.03, 0.07665, 3.522) [0.7663, 0.005857, 0.2691]\n PeriodicSite: Cd2+ (-0.3469, 0.1869, 0.2339) [-0.0265, 0.01428, 0.01787]\n PeriodicSite: Cd2+ (2.978, 3.589, -0.3454) [0.2276, 0.2742, -0.02639]\n PeriodicSite: Cd2+ (6.424, 6.882, -0.05259) [0.4908, 0.5259, -0.004018]\n PeriodicSite: Cd2+ (10.07, 10.35, -0.1553) [0.7698, 0.7912, -0.01187]\n PeriodicSite: Cd2+ (2.88, 0.1304, 3.389) [0.2201, 0.009965, 0.2589]\n PeriodicSite: Cd2+ (6.709, 3.079, 3.541) [0.5127, 0.2352, 0.2706]\n PeriodicSite: Cd2+ (9.661, 6.571, 2.86) [0.7382, 0.5021, 0.2185]\n PeriodicSite: Cd2+ (6.273, 0.1163, 6.466) [0.4793, 0.008889, 0.4941]\n PeriodicSite: Cd2+ (9.341, 3.314, 6.351) [0.7137, 0.2532, 0.4853]\n PeriodicSite: Cd2+ (9.69, -0.08397, 10.29) [0.7405, -0.006417, 0.786]\n PeriodicSite: Cd2+ (-0.2574, 6.573, -0.2869) [-0.01967, 0.5022, -0.02192]\n PeriodicSite: Cd2+ (3.56, 9.868, -0.1456) [0.2721, 0.7541, -0.01113]\n PeriodicSite: Cd2+ (-0.0911, 3.578, 3.249) [-0.006961, 0.2734, 0.2483]\n PeriodicSite: Cd2+ (3.114, 6.59, 3.292) [0.238, 0.5035, 0.2515]\n PeriodicSite: Cd2+ (6.48, 9.626, 3.709) [0.4952, 0.7355, 0.2834]\n PeriodicSite: Cd2+ (-0.2055, 0.3768, 6.844) [-0.0157, 0.0288, 0.523]\n PeriodicSite: Cd2+ (3.518, 3.606, 6.941) [0.2688, 0.2755, 0.5304]\n PeriodicSite: Cd2+ (9.361, 9.722, 6.761) [0.7153, 0.7429, 0.5166]\n PeriodicSite: Cd2+ (3.072, -0.05131, 9.776) [0.2347, -0.003921, 0.747]\n PeriodicSite: Cd2+ (6.43, 3.426, 9.759) [0.4913, 0.2618, 0.7457]\n PeriodicSite: Cd2+ (10.01, 6.935, 9.82) [0.7652, 0.5299, 0.7504]\n PeriodicSite: Cd2+ (0.1845, 9.867, 2.995) [0.0141, 0.7539, 0.2289]\n PeriodicSite: Cd2+ (-0.434, 6.518, 6.2) [-0.03316, 0.4981, 0.4738]\n PeriodicSite: Cd2+ (3.29, 9.678, 6.913) [0.2514, 0.7395, 0.5283]\n PeriodicSite: Cd2+ (-0.1434, 3.143, 10.18) [-0.01096, 0.2402, 0.7779]\n PeriodicSite: Cd2+ (3.238, 6.272, 10.01) [0.2474, 0.4792, 0.765]\n PeriodicSite: Cd2+ (6.848, 9.915, 10.19) [0.5233, 0.7576, 0.7786]\n PeriodicSite: Cd2+ (0.6591, 10.13, 9.976) [0.05036, 0.7738, 0.7623]\n PeriodicSite: Te2- (11.32, 4.62, 4.505) [0.8652, 0.3531, 0.3442]\n PeriodicSite: Te2- (1.277, 7.841, 4.889) [0.09759, 0.5992, 0.3736]\n PeriodicSite: Te2- (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te2- (5.836, 5.836, 4.908) [0.446, 0.446, 0.375]\n PeriodicSite: Te2- (7.205, 7.542, 5.245) [0.5505, 0.5763, 0.4008]\n PeriodicSite: Te2- (11.31, 11.64, 4.804) [0.8644, 0.8892, 0.3671]\n PeriodicSite: Te2- (1.453, 2.132, 5.154) [0.111, 0.1629, 0.3938]\n PeriodicSite: Te2- (8.665, 5.289, 8.472) [0.6621, 0.4042, 0.6474]\n PeriodicSite: Te2- (11.25, 8.416, 8.537) [0.8598, 0.6431, 0.6524]\n PeriodicSite: Te2- (2.042, 11.58, 7.928) [0.156, 0.885, 0.6058]\n PeriodicSite: Te2- (11.57, 4.657, 11.42) [0.8837, 0.3559, 0.873]\n PeriodicSite: Te2- (1.295, 8.371, 11.16) [0.09893, 0.6397, 0.8529]\n PeriodicSite: Te2- (1.204, 4.912, 1.967) [0.09201, 0.3753, 0.1503]\n PeriodicSite: Te2- (4.848, 11.23, 4.826) [0.3705, 0.8584, 0.3688]\n PeriodicSite: Te2- (8.416, 2.166, 4.653) [0.6431, 0.1655, 0.3555]\n PeriodicSite: Te2- (4.695, 7.987, 8.843) [0.3588, 0.6103, 0.6757]\n PeriodicSite: Te2- (8.328, 11.3, 8.215) [0.6364, 0.8635, 0.6277]\n PeriodicSite: Te2- (11.4, 1.565, 8.469) [0.8715, 0.1196, 0.6471]\n PeriodicSite: Te2- (5.063, 5.103, 11.92) [0.3869, 0.3899, 0.9106]\n PeriodicSite: Te2- (8.584, 8.115, 11.45) [0.6559, 0.6201, 0.8753]\n PeriodicSite: Te2- (11.73, 11.78, 11.4) [0.8966, 0.9002, 0.8709]\n PeriodicSite: Te2- (2.056, 1.592, 11.65) [0.1571, 0.1216, 0.8903]\n PeriodicSite: Te2- (8.249, 4.681, 1.526) [0.6303, 0.3577, 0.1166]\n PeriodicSite: Te2- (11.82, 7.839, 1.656) [0.9036, 0.599, 0.1265]\n PeriodicSite: Te2- (1.513, 11.52, 1.713) [0.1156, 0.8801, 0.1309]\n PeriodicSite: Te2- (4.776, 1.38, 8.583) [0.3649, 0.1055, 0.6559]\n PeriodicSite: Te2- (5.15, 11.62, 11.56) [0.3935, 0.8877, 0.8831]\n PeriodicSite: Te2- (7.811, 1.555, 11.06) [0.5968, 0.1188, 0.8453]\n PeriodicSite: Te2- (5.335, 8.341, 1.625) [0.4076, 0.6373, 0.1241]\n PeriodicSite: Te2- (8.377, 11.54, 2.23) [0.6401, 0.8819, 0.1704]\n PeriodicSite: Te2- (11.76, 1.509, 1.705) [0.8984, 0.1153, 0.1303]\n PeriodicSite: Te2- (4.764, 1.935, 1.298) [0.3641, 0.1479, 0.09916]}}},\n -2: {'structures': {'Unperturbed': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n PeriodicSite: Cd (Cd2+) (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n PeriodicSite: Cd (Cd2+) (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n PeriodicSite: Cd (Cd2+) (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n PeriodicSite: Cd (Cd2+) (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n PeriodicSite: Cd (Cd2+) (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n PeriodicSite: Cd (Cd2+) (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n PeriodicSite: Cd (Cd2+) (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n PeriodicSite: Cd (Cd2+) (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n PeriodicSite: Te (Te2-) (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n PeriodicSite: Te (Te2-) (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n PeriodicSite: Te (Te2-) (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n PeriodicSite: Te (Te2-) (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n PeriodicSite: Te (Te2-) (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n PeriodicSite: Te (Te2-) (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n PeriodicSite: Te (Te2-) (4.908, 1.636, 1.636) [0.375, 0.125, 0.125],\n 'distortions': {'Rattled': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd2+ (6.776, 0.2499, 0.02026) [0.5178, 0.0191, 0.001548]\n PeriodicSite: Cd2+ (10.22, 3.208, 0.1487) [0.7808, 0.2452, 0.01136]\n PeriodicSite: Cd2+ (9.794, -0.02858, 2.947) [0.7484, -0.002184, 0.2252]\n PeriodicSite: Cd2+ (-0.4122, 0.2974, -0.271) [-0.0315, 0.02272, -0.02071]\n PeriodicSite: Cd2+ (3.102, 3.192, -0.2704) [0.237, 0.2439, -0.02066]\n PeriodicSite: Cd2+ (6.627, 6.82, -0.4001) [0.5064, 0.5211, -0.03057]\n PeriodicSite: Cd2+ (9.298, 10.15, -0.1669) [0.7105, 0.7759, -0.01275]\n PeriodicSite: Cd2+ (3.115, 0.2455, 2.9) [0.238, 0.01876, 0.2216]\n PeriodicSite: Cd2+ (6.431, 2.639, 3.331) [0.4914, 0.2016, 0.2546]\n PeriodicSite: Cd2+ (9.74, 6.329, 3.538) [0.7442, 0.4836, 0.2703]\n PeriodicSite: Cd2+ (6.552, 0.4754, 6.299) [0.5007, 0.03633, 0.4813]\n PeriodicSite: Cd2+ (10.06, 3.335, 6.281) [0.7686, 0.2548, 0.4799]\n PeriodicSite: Cd2+ (9.92, 0.03925, 10.4) [0.758, 0.002999, 0.7947]\n PeriodicSite: Cd2+ (0.07354, 6.813, 0.1364) [0.00562, 0.5206, 0.01042]\n PeriodicSite: Cd2+ (2.996, 9.608, 0.3128) [0.229, 0.7342, 0.0239]\n PeriodicSite: Cd2+ (-0.1834, 3.351, 3.096) [-0.01401, 0.2561, 0.2366]\n PeriodicSite: Cd2+ (3.596, 6.429, 3.2) [0.2747, 0.4913, 0.2445]\n PeriodicSite: Cd2+ (6.726, 10.07, 2.916) [0.5139, 0.7697, 0.2228]\n PeriodicSite: Cd2+ (-0.1172, -0.5479, 6.693) [-0.008952, -0.04187, 0.5115]\n PeriodicSite: Cd2+ (3.484, 3.394, 6.358) [0.2662, 0.2594, 0.4858]\n PeriodicSite: Cd2+ (10.22, 9.907, 6.423) [0.7809, 0.757, 0.4908]\n PeriodicSite: Cd2+ (2.698, -0.1605, 9.745) [0.2061, -0.01226, 0.7447]\n PeriodicSite: Cd2+ (6.688, 3.501, 9.61) [0.5111, 0.2675, 0.7343]\n PeriodicSite: Cd2+ (9.894, 6.283, 9.413) [0.756, 0.4801, 0.7193]\n PeriodicSite: Cd2+ (0.5605, 9.386, 3.213) [0.04283, 0.7172, 0.2455]\n PeriodicSite: Cd2+ (0.3798, 6.835, 6.403) [0.02902, 0.5223, 0.4893]\n PeriodicSite: Cd2+ (3.531, 9.717, 7.051) [0.2698, 0.7425, 0.5388]\n PeriodicSite: Cd2+ (0.237, 3.409, 9.94) [0.01811, 0.2605, 0.7596]\n PeriodicSite: Cd2+ (3.199, 6.578, 9.722) [0.2445, 0.5026, 0.7429]\n PeriodicSite: Cd2+ (6.451, 10.2, 9.833) [0.4929, 0.7792, 0.7514]\n PeriodicSite: Cd2+ (0.09249, 9.932, 10.49) [0.007067, 0.7589, 0.8013]\n PeriodicSite: Te2- (11.27, 4.808, 4.497) [0.8613, 0.3674, 0.3436]\n PeriodicSite: Te2- (1.733, 8.144, 4.834) [0.1325, 0.6223, 0.3694]\n PeriodicSite: Te2- (1.686, 4.691, 7.752) [0.1288, 0.3585, 0.5924]\n PeriodicSite: Te2- (4.88, 5.177, 4.987) [0.3729, 0.3956, 0.3811]\n PeriodicSite: Te2- (8.005, 8.466, 5.166) [0.6117, 0.6469, 0.3948]\n PeriodicSite: Te2- (11.48, 11.33, 4.578) [0.8774, 0.8656, 0.3498]\n PeriodicSite: Te2- (1.671, 1.887, 5.189) [0.1277, 0.1442, 0.3965]\n PeriodicSite: Te2- (8.019, 4.856, 7.997) [0.6127, 0.371, 0.6111]\n PeriodicSite: Te2- (11.2, 8.312, 8.001) [0.856, 0.6351, 0.6114]\n PeriodicSite: Te2- (1.64, 11.29, 7.71) [0.1253, 0.8625, 0.5892]\n PeriodicSite: Te2- (11.91, 4.654, 11.25) [0.9102, 0.3556, 0.8596]\n PeriodicSite: Te2- (1.838, 8.228, 11.35) [0.1404, 0.6287, 0.8675]\n PeriodicSite: Te2- (2.336, 4.438, 1.636) [0.1785, 0.3391, 0.125]\n PeriodicSite: Te2- (4.821, 11.3, 5.306) [0.3684, 0.8637, 0.4054]\n PeriodicSite: Te2- (8.258, 1.897, 5.124) [0.631, 0.145, 0.3915]\n PeriodicSite: Te2- (5.353, 8.218, 7.731) [0.409, 0.628, 0.5908]\n PeriodicSite: Te2- (8.514, 11.36, 8.754) [0.6506, 0.8681, 0.6689]\n PeriodicSite: Te2- (11.76, 1.627, 7.887) [0.8986, 0.1243, 0.6026]\n PeriodicSite: Te2- (5.274, 4.923, 11.51) [0.403, 0.3762, 0.8792]\n PeriodicSite: Te2- (8.407, 8.179, 11.37) [0.6424, 0.625, 0.8686]\n PeriodicSite: Te2- (11.59, 11.47, 11.38) [0.8853, 0.8768, 0.8696]\n PeriodicSite: Te2- (1.702, 1.79, 11.34) [0.1301, 0.1368, 0.8665]\n PeriodicSite: Te2- (8.427, 4.601, 1.687) [0.644, 0.3516, 0.1289]\n PeriodicSite: Te2- (11.55, 8.273, 2.054) [0.8827, 0.6322, 0.1569]\n PeriodicSite: Te2- (1.701, 11.74, 1.646) [0.13, 0.8973, 0.1258]\n PeriodicSite: Te2- (5.031, 2.14, 7.997) [0.3844, 0.1635, 0.6111]\n PeriodicSite: Te2- (4.478, 11.68, 11.37) [0.3422, 0.8921, 0.8687]\n PeriodicSite: Te2- (8.217, 1.229, 11.53) [0.6279, 0.09388, 0.8807]\n PeriodicSite: Te2- (4.878, 8.331, 1.851) [0.3728, 0.6366, 0.1415]\n PeriodicSite: Te2- (8.098, 11.73, 1.492) [0.6188, 0.8966, 0.114]\n PeriodicSite: Te2- (11.11, 1.918, 1.833) [0.8487, 0.1465, 0.14]\n PeriodicSite: Te2- (5.421, 1.7, 1.446) [0.4143, 0.1299, 0.1105],\n 'Dimer': Structure Summary\n Lattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\n PeriodicSite: Cd2+ (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n PeriodicSite: Cd2+ (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n PeriodicSite: Cd2+ (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n PeriodicSite: Cd2+ (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]\n PeriodicSite: Cd2+ (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n PeriodicSite: Cd2+ (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n PeriodicSite: Cd2+ (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n PeriodicSite: Cd2+ (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n PeriodicSite: Cd2+ (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n PeriodicSite: Cd2+ (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n PeriodicSite: Cd2+ (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n PeriodicSite: Cd2+ (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n PeriodicSite: Cd2+ (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n PeriodicSite: Cd2+ (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n PeriodicSite: Cd2+ (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n PeriodicSite: Cd2+ (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n PeriodicSite: Cd2+ (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n PeriodicSite: Cd2+ (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n PeriodicSite: Cd2+ (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n PeriodicSite: Cd2+ (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n PeriodicSite: Cd2+ (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n PeriodicSite: Cd2+ (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n PeriodicSite: Cd2+ (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n PeriodicSite: Cd2+ (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n PeriodicSite: Cd2+ (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n PeriodicSite: Cd2+ (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n PeriodicSite: Cd2+ (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n PeriodicSite: Cd2+ (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n PeriodicSite: Cd2+ (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n PeriodicSite: Cd2+ (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n PeriodicSite: Cd2+ (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n PeriodicSite: Te2- (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n PeriodicSite: Te2- (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n PeriodicSite: Te2- (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n PeriodicSite: Te2- (5.836, 5.836, 4.908) [0.446, 0.446, 0.375]\n PeriodicSite: Te2- (7.25, 7.25, 4.908) [0.554, 0.554, 0.375]\n PeriodicSite: Te2- (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n PeriodicSite: Te2- (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n PeriodicSite: Te2- (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n PeriodicSite: Te2- (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n PeriodicSite: Te2- (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n PeriodicSite: Te2- (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n PeriodicSite: Te2- (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n PeriodicSite: Te2- (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n PeriodicSite: Te2- (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n PeriodicSite: Te2- (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n PeriodicSite: Te2- (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n PeriodicSite: Te2- (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n PeriodicSite: Te2- (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n PeriodicSite: Te2- (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n PeriodicSite: Te2- (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n PeriodicSite: Te2- (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]\n PeriodicSite: Te2- (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n PeriodicSite: Te2- (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n PeriodicSite: Te2- (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n PeriodicSite: Te2- (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n PeriodicSite: Te2- (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n PeriodicSite: Te2- (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n PeriodicSite: Te2- (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n PeriodicSite: Te2- (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n PeriodicSite: Te2- (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n PeriodicSite: Te2- (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n PeriodicSite: Te2- (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]}}}}}},\n {'distortion_parameters': {'distortion_increment': None,\n 'bond_distortions': ['Dimer'],\n 'local_rattle': False,\n 'mc_rattle_parameters': {'stdev': 0.28333683853583175}},\n 'defects': {'v_Cd': {'unique_site': [0.5, 0.5, 0.5],\n 'charges': {0: {'num_nearest_neighbours': 2,\n 'distorted_atoms': None,\n 'distortion_parameters': {'distortion_increment': None,\n 'bond_distortions': ['Dimer'],\n 'local_rattle': False,\n 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}},\n -1: {'num_nearest_neighbours': 1,\n 'distorted_atoms': None,\n 'distortion_parameters': {'distortion_increment': None,\n 'bond_distortions': ['Dimer'],\n 'local_rattle': False,\n 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}},\n -2: {'num_nearest_neighbours': 0,\n 'distorted_atoms': None,\n 'distortion_parameters': {'distortion_increment': None,\n 'bond_distortions': ['Dimer'],\n 'local_rattle': False,\n 'mc_rattle_parameters': {'stdev': 0.28333683853583175}}}}}}})" }, - "execution_count": 10, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -763,6 +253,14 @@ "Dist.write_vasp_files()" ] }, + { + "cell_type": "code", + "outputs": [], + "source": [], + "metadata": { + "collapsed": false + } + }, { "cell_type": "markdown", "metadata": {}, @@ -781,15 +279,20 @@ }, { "cell_type": "code", - "execution_count": 1, - "metadata": {}, + "execution_count": 10, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:40.452191Z", + "start_time": "2024-02-12T18:14:40.348171Z" + } + }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "local_env.py:4141: UserWarning: No oxidation states specified on sites! For better results, set the site oxidation states in the structure.\n", - "local_env.py:3934: UserWarning: CrystalNN: cannot locate an appropriate radius, covalent or atomic radii will be used, this can lead to non-optimal results.\n" + "local_env.py:4135: UserWarning: No oxidation states specified on sites! For better results, set the site oxidation states in the structure.\n", + "local_env.py:3928: UserWarning: CrystalNN: cannot locate an appropriate radius, covalent or atomic radii will be used, this can lead to non-optimal results.\n" ] } ], @@ -798,23 +301,26 @@ "from pymatgen.core.structure import Structure\n", "import os\n", "\n", - "VASP_CDTE_DATA_DIR= \"./tests/data/vasp/CdTe\"\n", + "VASP_CDTE_DATA_DIR= \"data/vasp/CdTe\"\n", "struc = Structure.from_file(os.path.join(VASP_CDTE_DATA_DIR, \"CdTe_V_Cd_POSCAR\"))\n", "output = apply_dimer_distortion(struc, frac_coords=[0,0,0])" ] }, { "cell_type": "code", - "execution_count": 2, - "metadata": {}, + "execution_count": 12, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:56.822023Z", + "start_time": "2024-02-12T18:14:56.746909Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "dict_keys(['distorted_structure', 'num_distorted_neighbours', 'distorted_atoms', 'undistorted_structure', 'defect_frac_coords'])" - ] + "text/plain": "dict_keys(['distorted_structure', 'num_distorted_neighbours', 'distorted_atoms', 'undistorted_structure', 'defect_frac_coords'])" }, - "execution_count": 2, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } @@ -825,16 +331,19 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, + "execution_count": 13, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:14:57.912833Z", + "start_time": "2024-02-12T18:14:57.905600Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "(2, [(62, 'Te'), (51, 'Te')])" - ] + "text/plain": "(2, [(32, 'Te'), (41, 'Te')])" }, - "execution_count": 3, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -845,87 +354,19 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, + "execution_count": 14, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:15:11.574290Z", + "start_time": "2024-02-12T18:15:11.471991Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "Structure Summary\n", - "Lattice\n", - " abc : 13.086768 13.086768 13.086768\n", - " angles : 90.0 90.0 90.0\n", - " volume : 2241.2856479961474\n", - " A : 13.086768 0.0 0.0\n", - " B : 0.0 13.086768 0.0\n", - " C : 0.0 0.0 13.086768\n", - " pbc : True True True\n", - "PeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\n", - "PeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\n", - "PeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\n", - "PeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\n", - "PeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\n", - "PeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\n", - "PeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5]\n", - "PeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\n", - "PeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\n", - "PeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\n", - "PeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\n", - "PeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\n", - "PeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\n", - "PeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\n", - "PeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\n", - "PeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\n", - "PeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\n", - "PeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\n", - "PeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\n", - "PeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\n", - "PeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\n", - "PeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\n", - "PeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\n", - "PeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\n", - "PeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\n", - "PeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\n", - "PeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\n", - "PeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\n", - "PeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\n", - "PeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\n", - "PeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\n", - "PeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\n", - "PeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\n", - "PeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\n", - "PeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\n", - "PeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\n", - "PeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\n", - "PeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\n", - "PeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\n", - "PeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\n", - "PeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\n", - "PeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\n", - "PeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\n", - "PeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\n", - "PeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\n", - "PeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\n", - "PeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\n", - "PeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]\n", - "PeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\n", - "PeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\n", - "PeriodicSite: Te (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\n", - "PeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\n", - "PeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\n", - "PeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\n", - "PeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\n", - "PeriodicSite: Te (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\n", - "PeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\n", - "PeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\n", - "PeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\n", - "PeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\n", - "PeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\n", - "PeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\n", - "PeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]" - ] + "text/plain": "Structure Summary\nLattice\n abc : 13.086768 13.086768 13.086768\n angles : 90.0 90.0 90.0\n volume : 2241.2856479961474\n A : 13.086768 0.0 0.0\n B : 0.0 13.086768 0.0\n C : 0.0 0.0 13.086768\n pbc : True True True\nPeriodicSite: Cd (0.0, 0.0, 6.543) [0.0, 0.0, 0.5]\nPeriodicSite: Cd (0.0, 6.543, 0.0) [0.0, 0.5, 0.0]\nPeriodicSite: Cd (0.0, 6.543, 6.543) [0.0, 0.5, 0.5]\nPeriodicSite: Cd (6.543, 0.0, 0.0) [0.5, 0.0, 0.0]\nPeriodicSite: Cd (6.543, 0.0, 6.543) [0.5, 0.0, 0.5]\nPeriodicSite: Cd (6.543, 6.543, 0.0) [0.5, 0.5, 0.0]\nPeriodicSite: Cd (6.543, 6.543, 6.543) [0.5, 0.5, 0.5]\nPeriodicSite: Cd (0.0, 3.272, 3.272) [0.0, 0.25, 0.25]\nPeriodicSite: Cd (0.0, 3.272, 9.815) [0.0, 0.25, 0.75]\nPeriodicSite: Cd (0.0, 9.815, 3.272) [0.0, 0.75, 0.25]\nPeriodicSite: Cd (0.0, 9.815, 9.815) [0.0, 0.75, 0.75]\nPeriodicSite: Cd (6.543, 3.272, 3.272) [0.5, 0.25, 0.25]\nPeriodicSite: Cd (6.543, 3.272, 9.815) [0.5, 0.25, 0.75]\nPeriodicSite: Cd (6.543, 9.815, 3.272) [0.5, 0.75, 0.25]\nPeriodicSite: Cd (6.543, 9.815, 9.815) [0.5, 0.75, 0.75]\nPeriodicSite: Cd (3.272, 0.0, 3.272) [0.25, 0.0, 0.25]\nPeriodicSite: Cd (3.272, 0.0, 9.815) [0.25, 0.0, 0.75]\nPeriodicSite: Cd (3.272, 6.543, 3.272) [0.25, 0.5, 0.25]\nPeriodicSite: Cd (3.272, 6.543, 9.815) [0.25, 0.5, 0.75]\nPeriodicSite: Cd (9.815, 0.0, 3.272) [0.75, 0.0, 0.25]\nPeriodicSite: Cd (9.815, 0.0, 9.815) [0.75, 0.0, 0.75]\nPeriodicSite: Cd (9.815, 6.543, 3.272) [0.75, 0.5, 0.25]\nPeriodicSite: Cd (9.815, 6.543, 9.815) [0.75, 0.5, 0.75]\nPeriodicSite: Cd (3.272, 3.272, 0.0) [0.25, 0.25, 0.0]\nPeriodicSite: Cd (3.272, 3.272, 6.543) [0.25, 0.25, 0.5]\nPeriodicSite: Cd (3.272, 9.815, 0.0) [0.25, 0.75, 0.0]\nPeriodicSite: Cd (3.272, 9.815, 6.543) [0.25, 0.75, 0.5]\nPeriodicSite: Cd (9.815, 3.272, 0.0) [0.75, 0.25, 0.0]\nPeriodicSite: Cd (9.815, 3.272, 6.543) [0.75, 0.25, 0.5]\nPeriodicSite: Cd (9.815, 9.815, 0.0) [0.75, 0.75, 0.0]\nPeriodicSite: Cd (9.815, 9.815, 6.543) [0.75, 0.75, 0.5]\nPeriodicSite: Te (1.636, 1.636, 4.908) [0.125, 0.125, 0.375]\nPeriodicSite: Te (1.636, 1.636, 11.45) [0.125, 0.125, 0.875]\nPeriodicSite: Te (1.636, 8.179, 4.908) [0.125, 0.625, 0.375]\nPeriodicSite: Te (1.636, 8.179, 11.45) [0.125, 0.625, 0.875]\nPeriodicSite: Te (8.179, 1.636, 4.908) [0.625, 0.125, 0.375]\nPeriodicSite: Te (8.179, 1.636, 11.45) [0.625, 0.125, 0.875]\nPeriodicSite: Te (8.179, 8.179, 4.908) [0.625, 0.625, 0.375]\nPeriodicSite: Te (8.179, 8.179, 11.45) [0.625, 0.625, 0.875]\nPeriodicSite: Te (1.636, 4.908, 1.636) [0.125, 0.375, 0.125]\nPeriodicSite: Te (1.636, 4.908, 8.179) [0.125, 0.375, 0.625]\nPeriodicSite: Te (1.636, 11.45, 1.636) [0.125, 0.875, 0.125]\nPeriodicSite: Te (1.636, 11.45, 8.179) [0.125, 0.875, 0.625]\nPeriodicSite: Te (8.179, 4.908, 1.636) [0.625, 0.375, 0.125]\nPeriodicSite: Te (8.179, 4.908, 8.179) [0.625, 0.375, 0.625]\nPeriodicSite: Te (8.179, 11.45, 1.636) [0.625, 0.875, 0.125]\nPeriodicSite: Te (8.179, 11.45, 8.179) [0.625, 0.875, 0.625]\nPeriodicSite: Te (4.908, 1.636, 1.636) [0.375, 0.125, 0.125]\nPeriodicSite: Te (4.908, 1.636, 8.179) [0.375, 0.125, 0.625]\nPeriodicSite: Te (4.908, 8.179, 1.636) [0.375, 0.625, 0.125]\nPeriodicSite: Te (4.908, 8.179, 8.179) [0.375, 0.625, 0.625]\nPeriodicSite: Te (11.45, 1.636, 1.636) [0.875, 0.125, 0.125]\nPeriodicSite: Te (11.45, 1.636, 8.179) [0.875, 0.125, 0.625]\nPeriodicSite: Te (11.45, 8.179, 1.636) [0.875, 0.625, 0.125]\nPeriodicSite: Te (11.45, 8.179, 8.179) [0.875, 0.625, 0.625]\nPeriodicSite: Te (4.908, 4.908, 4.908) [0.375, 0.375, 0.375]\nPeriodicSite: Te (4.908, 4.908, 11.45) [0.375, 0.375, 0.875]\nPeriodicSite: Te (4.908, 11.45, 4.908) [0.375, 0.875, 0.375]\nPeriodicSite: Te (4.908, 11.45, 11.45) [0.375, 0.875, 0.875]\nPeriodicSite: Te (11.45, 4.908, 4.908) [0.875, 0.375, 0.375]\nPeriodicSite: Te (11.45, 4.908, 11.45) [0.875, 0.375, 0.875]\nPeriodicSite: Te (11.45, 11.45, 4.908) [0.875, 0.875, 0.375]\nPeriodicSite: Te (11.45, 11.45, 11.45) [0.875, 0.875, 0.875]" }, - "execution_count": 3, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -936,16 +377,19 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, + "execution_count": 15, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:15:17.298050Z", + "start_time": "2024-02-12T18:15:17.274374Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "'Cd31 Te32\\n1.0\\n 13.0867679999999993 0.0000000000000000 0.0000000000000000\\n 0.0000000000000000 13.0867679999999993 0.0000000000000000\\n 0.0000000000000000 0.0000000000000000 13.0867679999999993\\nCd Te\\n31 32\\ndirect\\n 0.0000000000000000 0.0000000000000000 0.5000000000000000 Cd\\n 0.0000000000000000 0.5000000000000000 0.0000000000000000 Cd\\n 0.0000000000000000 0.5000000000000000 0.5000000000000000 Cd\\n 0.5000000000000000 0.0000000000000000 0.0000000000000000 Cd\\n 0.5000000000000000 0.0000000000000000 0.5000000000000000 Cd\\n 0.5000000000000000 0.5000000000000000 0.0000000000000000 Cd\\n 0.5000000000000000 0.5000000000000000 0.5000000000000000 Cd\\n 0.0000000000000000 0.2500000000000000 0.2500000000000000 Cd\\n 0.0000000000000000 0.2500000000000000 0.7500000000000000 Cd\\n 0.0000000000000000 0.7500000000000000 0.2500000000000000 Cd\\n 0.0000000000000000 0.7500000000000000 0.7500000000000000 Cd\\n 0.5000000000000000 0.2500000000000000 0.2500000000000000 Cd\\n 0.5000000000000000 0.2500000000000000 0.7500000000000000 Cd\\n 0.5000000000000000 0.7500000000000000 0.2500000000000000 Cd\\n 0.5000000000000000 0.7500000000000000 0.7500000000000000 Cd\\n 0.2500000000000000 0.0000000000000000 0.2500000000000000 Cd\\n 0.2500000000000000 0.0000000000000000 0.7500000000000000 Cd\\n 0.2500000000000000 0.5000000000000000 0.2500000000000000 Cd\\n 0.2500000000000000 0.5000000000000000 0.7500000000000000 Cd\\n 0.7500000000000000 0.0000000000000000 0.2500000000000000 Cd\\n 0.7500000000000000 0.0000000000000000 0.7500000000000000 Cd\\n 0.7500000000000000 0.5000000000000000 0.2500000000000000 Cd\\n 0.7500000000000000 0.5000000000000000 0.7500000000000000 Cd\\n 0.2500000000000000 0.2500000000000000 0.0000000000000000 Cd\\n 0.2500000000000000 0.2500000000000000 0.5000000000000000 Cd\\n 0.2500000000000000 0.7500000000000000 0.0000000000000000 Cd\\n 0.2500000000000000 0.7500000000000000 0.5000000000000000 Cd\\n 0.7500000000000000 0.2500000000000000 0.0000000000000000 Cd\\n 0.7500000000000000 0.2500000000000000 0.5000000000000000 Cd\\n 0.7500000000000000 0.7500000000000000 0.0000000000000000 Cd\\n 0.7500000000000000 0.7500000000000000 0.5000000000000000 Cd\\n 0.1250000000000000 0.1250000000000000 0.3750000000000000 Te\\n 0.1250000000000000 0.1250000000000000 0.8749999999999999 Te\\n 0.1250000000000000 0.6250000000000000 0.3750000000000000 Te\\n 0.1250000000000000 0.6250000000000000 0.8749999999999999 Te\\n 0.6250000000000000 0.1250000000000000 0.3750000000000000 Te\\n 0.6250000000000000 0.1250000000000000 0.8749999999999999 Te\\n 0.6250000000000000 0.6250000000000000 0.3750000000000000 Te\\n 0.6250000000000000 0.6250000000000000 0.8749999999999999 Te\\n 0.1250000000000000 0.3750000000000000 0.1250000000000000 Te\\n 0.1250000000000000 0.3750000000000000 0.6250000000000000 Te\\n 0.1250000000000000 0.8749999999999999 0.1250000000000000 Te\\n 0.1250000000000000 0.8749999999999999 0.6250000000000000 Te\\n 0.6250000000000000 0.3750000000000000 0.1250000000000000 Te\\n 0.6250000000000000 0.3750000000000000 0.6250000000000000 Te\\n 0.6250000000000000 0.8749999999999999 0.1250000000000000 Te\\n 0.6250000000000000 0.8749999999999999 0.6250000000000000 Te\\n 0.3750000000000000 0.1250000000000000 0.1250000000000000 Te\\n 0.3750000000000000 0.1250000000000000 0.6250000000000000 Te\\n 0.3750000000000000 0.6250000000000000 0.1250000000000000 Te\\n 0.3750000000000000 0.6250000000000000 0.6250000000000000 Te\\n 0.8749999999999999 0.0540321935245239 0.0540321935245239 Te\\n 0.8749999999999999 0.1250000000000000 0.6250000000000000 Te\\n 0.8749999999999999 0.6250000000000000 0.1250000000000000 Te\\n 0.8749999999999999 0.6250000000000000 0.6250000000000000 Te\\n 0.3750000000000000 0.3750000000000000 0.3750000000000000 Te\\n 0.3750000000000000 0.3750000000000000 0.8749999999999999 Te\\n 0.3750000000000000 0.8749999999999999 0.3750000000000000 Te\\n 0.3750000000000000 0.8749999999999999 0.8749999999999999 Te\\n 0.8749999999999999 0.3750000000000000 0.3750000000000000 Te\\n 0.8749999999999999 0.3750000000000000 0.8749999999999999 Te\\n 0.8749999999999999 0.8749999999999999 0.3750000000000000 Te\\n 0.8749999999999999 0.9459678064754760 0.9459678064754760 Te\\n'" - 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"execution_count": 6, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -956,16 +400,19 @@ }, { "cell_type": "code", - "execution_count": 8, - "metadata": {}, + "execution_count": 16, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:15:30.217363Z", + "start_time": "2024-02-12T18:15:30.193203Z" + } + }, "outputs": [ { "data": { - "text/plain": [ - "63" - ] + "text/plain": "63" }, - "execution_count": 8, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -976,24 +423,26 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": {}, + "execution_count": 17, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:15:31.992512Z", + "start_time": "2024-02-12T18:15:31.945862Z" + } + }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Te(51): {'Te(62)': '2.0 A'} \n", - "\n" + "Te(32): {'Te(41)': '2.0 A'} \n" ] }, { "data": { - "text/plain": [ - "{'Te(51)': {'Te(62)': '2.0 A'}}" - ] + "text/plain": "{'Te(32)': {'Te(41)': '2.0 A'}}" }, - "execution_count": 5, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -1013,22 +462,32 @@ }, { "cell_type": "code", - "execution_count": 26, - "metadata": {}, + "execution_count": 18, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:15:55.413924Z", + "start_time": "2024-02-12T18:15:55.355726Z" + } + }, "outputs": [], "source": [ "from shakenbreak.distortions import apply_dimer_distortion\n", "from pymatgen.core.structure import Structure\n", "import os\n", "\n", - "VASP_CDTE_DATA_DIR= \"./tests/data/vasp/CdTe\"\n", + "VASP_CDTE_DATA_DIR= \"data/vasp/CdTe\"\n", "struc = Structure.from_file(os.path.join(VASP_CDTE_DATA_DIR, \"CdTe_V_Cd_POSCAR\"))" ] }, { "cell_type": "code", - "execution_count": 27, - "metadata": {}, + "execution_count": 19, + "metadata": { + "ExecuteTime": { + "end_time": "2024-02-12T18:16:05.677110Z", + "start_time": "2024-02-12T18:15:56.588227Z" + } + }, "outputs": [], "source": [ "from shakenbreak import input\n", @@ -1649,9 +1108,9 @@ "text": [ "Applying ShakeNBreak... Will apply the following bond distortions: ['Dimer']. Then, will rattle with a std dev of 0.25 Å \n", "\n", - "\u001b[1m\n", - "Defect: v_Cd_Td_Te2.83\u001b[0m\n", - "\u001b[1mNumber of missing electrons in neutral state: 2\u001b[0m\n", + "\u001B[1m\n", + "Defect: v_Cd_Td_Te2.83\u001B[0m\n", + "\u001B[1mNumber of missing electrons in neutral state: 2\u001B[0m\n", "\n", "Defect v_Cd_Td_Te2.83 in charge state: 0. Number of distorted neighbours: 2\n" ] @@ -2156,26 +1615,26 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[0;31mSignature:\u001b[0m\n", - "\u001b[0mplot_defect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mdefect_species\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0menergies_dict\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mdict\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'.'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mneighbour_atom\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - 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"\u001b[0;34m\u001b[0m \u001b[0minclude_site_info_in_name\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mbool\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0my_label\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'Energy (eV)'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0madd_title\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mbool\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mline_color\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - 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"\u001b[0;31mFile:\u001b[0m /mnt/c/Users/Irea/OneDrive - Imperial College London/07_Python_Packages/ShakeNBreak_remote/shakenbreak/plotting.py\n", - "\u001b[0;31mType:\u001b[0m function" + "\u001B[0;31mFile:\u001B[0m /mnt/c/Users/Irea/OneDrive - Imperial College London/07_Python_Packages/ShakeNBreak_remote/shakenbreak/plotting.py\n", + "\u001B[0;31mType:\u001B[0m function" ] } ], @@ -2349,10 +1808,10 @@ "evalue": "'PathCollection' object has no attribute 'get_marker'", "output_type": "error", "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[26], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43max\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_legend_handles_labels\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_marker\u001b[49m()\n", - "\u001b[0;31mAttributeError\u001b[0m: 'PathCollection' object has no attribute 'get_marker'" + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mAttributeError\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[26], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[43max\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget_legend_handles_labels\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m]\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget_marker\u001B[49m()\n", + "\u001B[0;31mAttributeError\u001B[0m: 'PathCollection' object has no attribute 'get_marker'" ] } ], @@ -2741,9 +2200,9 @@ "Oxidation states were not explicitly set, thus have been guessed as {'Cd': 2.0, 'Te': -2.0, 'Se': -2.0}. If this is unreasonable you should manually set oxidation_states\n", "Applying ShakeNBreak... Will apply the following bond distortions: ['-0.2']. Then, will rattle with a std dev of 0.27 Å \n", "\n", - "\u001b[1m\n", - "Defect: v_Cd_C1_Se2.68\u001b[0m\n", - "\u001b[1mNumber of missing electrons in neutral state: 2\u001b[0m\n", + "\u001B[1m\n", + "Defect: v_Cd_C1_Se2.68\u001B[0m\n", + "\u001B[1mNumber of missing electrons in neutral state: 2\u001B[0m\n", "\n", "Defect v_Cd_C1_Se2.68 in charge state: 0. Number of distorted neighbours: 2\n" ] @@ -2814,9 +2273,9 @@ "Oxidation states were not explicitly set, thus have been guessed as {'Cd': 2.0, 'Te': -2.0, 'Se': -2.0}. If this is unreasonable you should manually set oxidation_states\n", "Applying ShakeNBreak... Will apply the following bond distortions: ['-0.2']. Then, will rattle with a std dev of 0.27 Å \n", "\n", - "\u001b[1m\n", - "Defect: v_Cd_C1_Se2.68\u001b[0m\n", - "\u001b[1mNumber of missing electrons in neutral state: 2\u001b[0m\n", + "\u001B[1m\n", + "Defect: v_Cd_C1_Se2.68\u001B[0m\n", + "\u001B[1mNumber of missing electrons in neutral state: 2\u001B[0m\n", "\n", "Defect v_Cd_C1_Se2.68 in charge state: 0. Number of distorted neighbours: 2\n" ] diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Distortion_Unrattled_POSCAR b/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Distortion_Unrattled_POSCAR index 47838418..0664ca71 100644 --- a/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Distortion_Unrattled_POSCAR +++ b/tests/data/vasp/CdTe/CdTe_V_Cd_Dimer_Distortion_Unrattled_POSCAR @@ -1,4 +1,4 @@ -V1 Cd31 Te32 +Cd31 Te32 1.0 13.0867679999999993 0.0000000000000000 0.0000000000000000 0.0000000000000000 13.0867679999999993 0.0000000000000000 @@ -38,7 +38,7 @@ direct 0.7500000000000000 0.7500000000000000 0.0000000000000000 Cd 0.7500000000000000 0.7500000000000000 0.5000000000000000 Cd 0.1250000000000000 0.1250000000000000 0.3750000000000000 Te - 0.1250000000000000 0.1250000000000000 0.8749999999999999 Te + 0.1250000000000000 0.0540321935245239 0.9459678064754760 Te 0.1250000000000000 0.6250000000000000 0.3750000000000000 Te 0.1250000000000000 0.6250000000000000 0.8749999999999999 Te 0.6250000000000000 0.1250000000000000 0.3750000000000000 Te @@ -47,7 +47,7 @@ direct 0.6250000000000000 0.6250000000000000 0.8749999999999999 Te 0.1250000000000000 0.3750000000000000 0.1250000000000000 Te 0.1250000000000000 0.3750000000000000 0.6250000000000000 Te - 0.1250000000000000 0.8749999999999999 0.1250000000000000 Te + 0.1250000000000000 0.9459678064754760 0.0540321935245239 Te 0.1250000000000000 0.8749999999999999 0.6250000000000000 Te 0.6250000000000000 0.3750000000000000 0.1250000000000000 Te 0.6250000000000000 0.3750000000000000 0.6250000000000000 Te @@ -57,7 +57,7 @@ direct 0.3750000000000000 0.1250000000000000 0.6250000000000000 Te 0.3750000000000000 0.6250000000000000 0.1250000000000000 Te 0.3750000000000000 0.6250000000000000 0.6250000000000000 Te - 0.8749999999999999 0.0540321935245239 0.0540321935245239 Te + 0.8749999999999999 0.1250000000000000 0.1250000000000000 Te 0.8749999999999999 0.1250000000000000 0.6250000000000000 Te 0.8749999999999999 0.6250000000000000 0.1250000000000000 Te 0.8749999999999999 0.6250000000000000 0.6250000000000000 Te @@ -68,4 +68,4 @@ direct 0.8749999999999999 0.3750000000000000 0.3750000000000000 Te 0.8749999999999999 0.3750000000000000 0.8749999999999999 Te 0.8749999999999999 0.8749999999999999 0.3750000000000000 Te - 0.8749999999999999 0.9459678064754760 0.9459678064754760 Te + 0.8749999999999999 0.8749999999999999 0.8749999999999999 Te 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 860c8c78..fd982b95 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 96953739..d3cbdb1f 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", 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{"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_cli.py b/tests/test_cli.py index c9efa015..0227abfa 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1702,8 +1702,8 @@ def test_run(self): ) out = str(proc.communicate()[0]) self.assertIn( - "Job file 'job' not found, so will only submit jobs in folders with " - "'job' present", + "Job file 'job' not found, so will only save files and submit jobs in folders with 'job' " + "present", out, ) self.assertIn("Bond_Distortion_-40.0% fully relaxed", out) @@ -1721,7 +1721,7 @@ def test_run(self): ) # setting 'job command' to 'echo' to out = str(proc.communicate()[0]) self.assertNotIn( - "Job file 'job_file' not found, so will only submit jobs in folders with " + "Job file 'job_file' not found, so will only save files and submit jobs in folders with " "'job_file' present", out, ) @@ -1747,7 +1747,7 @@ def test_run(self): ) # setting 'job command' to 'echo' to out = str(proc.communicate()[0]) self.assertNotIn( - "Job file '../job_file' not found, so will only submit jobs in folders with " + "Job file '../job_file' not found, so will only save files and submit jobs in folders with " "'job_file' present", out, ) @@ -1769,8 +1769,7 @@ def test_run(self): for file in os.listdir("Bond_Distortion_10.0%") if "CAR_" in file and "on" in file ] - for file in car_files: - # remove + for file in car_files: # remove os.remove(f"Bond_Distortion_10.0%/{file}") with open("Bond_Distortion_10.0%/OUTCAR", "w") as fp: @@ -1787,13 +1786,52 @@ def test_run(self): for file in os.listdir("Bond_Distortion_10.0%") if "on" in file and "CAR_" in file ] # contcar and outcar - self.assertEqual(len(saved_files), 2) # CONTCAR, OUTCAR + self.assertEqual( + len(saved_files), 0 + ) # no saved files, because submit command will fail + + # with job file present, but failing job submit command (no file saving) + with open("job", "w") as fp: + fp.write("Test pop") + proc = subprocess.Popen(["snb-run", "-v"], stdout=subprocess.PIPE, stderr=subprocess.PIPE) + out = str(proc.communicate()[0]) + self.assertIn( + "Bond_Distortion_10.0% not (fully) relaxed, saving files and rerunning", out + ) + saved_files = [ + file + for file in os.listdir("Bond_Distortion_10.0%") + if "on" in file and "CAR_" in file + ] + self.assertEqual( + len(saved_files), 0 + ) # no saved files, because submit command fails + + # with working (fake) job submit command: + proc = subprocess.Popen( + ["snb-run", "-s echo", "-n this"], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + out = str(proc.communicate()[0]) + self.assertIn( + "Bond_Distortion_10.0% not (fully) relaxed, saving files and rerunning", out + ) + saved_files = [ + file + for file in os.listdir("Bond_Distortion_10.0%") + if "on" in file and "CAR_" in file + ] # poscar, contcar and outcar + self.assertEqual(len(saved_files), 3) # POSCAR, CONTCAR, OUTCAR + self.assertEqual(len([i for i in saved_files if "POSCAR" in i]), 1) self.assertEqual(len([i for i in saved_files if "CONTCAR" in i]), 1) self.assertEqual(len([i for i in saved_files if "OUTCAR" in i]), 1) for i in saved_files: os.remove(f"Bond_Distortion_10.0%/{i}") os.remove("Bond_Distortion_10.0%/OUTCAR") os.remove("Bond_Distortion_10.0%/POSCAR") + if_present_rm("Bond_Distortion_10.0%/job") + if_present_rm("job") # test "--all" option os.chdir("..") @@ -1832,14 +1870,11 @@ def test_run(self): for f in os.listdir("v_Ge_s16_0/Bond_Distortion_50.0%_High_Energy") if "OUTCAR" in f ] - print("OUTCARS for v_Ge_s16_0/Bond_Distortion_50.0%_High_Energy:", outcars) - self.assertTrue( - len(outcars) == 6 - ) # last OUTCAR not saved cause high energy distortion + assert len(outcars) == 6 # last OUTCAR not saved cause high energy distortion outcars = [ f for f in os.listdir("v_Ge_s16_0/Bond_Distortion_40.0%") if "OUTCAR" in f ] - self.assertTrue(len(outcars) == 4) # last OUTCAR saved + assert len(outcars) == 3 # last OUTCAR saved # Clean up; rename high energy directories os.rename( "v_Ge_s16_0/Bond_Distortion_50.0%_High_Energy", @@ -1956,7 +1991,7 @@ def test_run(self): for file in os.listdir("Bond_Distortion_10.0%") if "on" in file and "CAR_" in file ] - for i in car_files: + for i in car_files: # remove os.remove(f"Bond_Distortion_10.0%/{i}") proc = subprocess.Popen( ["snb-run", "-v", "-s echo", "-n this", "-j job_file"], @@ -2311,6 +2346,14 @@ def _test_OUTCAR_error(error_string): with open("Bond_Distortion_10.0%/INCAR", "w") as fp: fp.write("ALGO = Fast") + car_files = [ + file + for file in os.listdir("Bond_Distortion_10.0%") + if "CAR_" in file and "on" in file + ] + for file in car_files: + os.remove(f"Bond_Distortion_10.0%/{file}") + proc = subprocess.Popen( ["snb-run", "-v", "-s echo", "-n this", "-j job_file"], stdout=subprocess.PIPE, @@ -2425,7 +2468,7 @@ def _test_OUTCAR_error(error_string): ["snb-run", "-v", "-s echo", "-n this", "-j job_file"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, - ) # setting 'job command' to 'echo' to + ) # setting 'job command' to 'echo' out = str(proc.communicate()[0]) self.assertIn("Bond_Distortion_-40.0% fully relaxed", out) self.assertNotIn("Unperturbed fully relaxed", out) @@ -2440,7 +2483,7 @@ def _test_OUTCAR_error(error_string): self.assertIn( "ISPIN = 2", incar_string ) # no change in INCAR as run was fully converged - self.assertEqual(len(os.listdir(f"Bond_Distortion_-40.0%")), 3) # no new files + self.assertEqual(len(os.listdir("Bond_Distortion_-40.0%")), 3) # no new files with open(f"Unperturbed/INCAR", "r") as fp: incar_string = fp.read() @@ -2713,9 +2756,6 @@ def test_parse(self): ] ) ) - if os.path.exists("./example_results.yaml"): - # Print contents - tmp = loadfn("./example_results.yaml") self.assertFalse( any(os.path.exists(i) for i in os.listdir() if i.endswith(".yaml")) ) diff --git a/tests/test_distortions.py b/tests/test_distortions.py index 76a7373c..f5560439 100644 --- a/tests/test_distortions.py +++ b/tests/test_distortions.py @@ -386,13 +386,13 @@ def test_apply_dimer_distortion(self): self.assertEqual(output["undistorted_structure"], self.V_Cd_struc) self.assertEqual(output["num_distorted_neighbours"], 2) self.assertEqual( - set(output["distorted_atoms"]), set([(62, 'Te'), (51, 'Te')]) + set(output["distorted_atoms"]), set([(32, 'Te'), (41, 'Te')]) ) # Check that 2 Te are separated by 2 A homo_bonds = analysis.get_homoionic_bonds( output['distorted_structure'], elements=["Te",] ) - self.assertEqual(homo_bonds, {"Te(51)": {'Te(62)': '2.0 A'}}) + self.assertEqual(homo_bonds, {"Te(32)": {'Te(41)': '2.0 A'}}) if __name__ == "__main__": unittest.main() diff --git a/tests/test_energy_lowering_distortions.py b/tests/test_energy_lowering_distortions.py index 5f36bd71..35e62408 100644 --- a/tests/test_energy_lowering_distortions.py +++ b/tests/test_energy_lowering_distortions.py @@ -544,18 +544,9 @@ def test_get_energy_lowering_distortions(self): self.defect_charges_dict, self.VASP_CDTE_DATA_DIR, stol=0.01 ) ) # same call as before, but with stol - # many warnings due to difficulty in structure matching (20) – with small stol - # (confirming stol has been passed to compare_structures), and no data parsed from - # Int_Cd_2_+1 (1) + # no data parsed from Int_Cd_2_+1 (1) for warning in w: self.assertEqual(warning.category, UserWarning) - warning_message = ( - "pymatgen StructureMatcher could not match lattices between specified " - "ref_structure (Cd31 Te32) and -0.475 structures." - ) - self.assertTrue( - any([str(warning.message) == warning_message for warning in w]) - ) # test no defects specified and write_input_files = True for fake_distortion_dir in ["Bond_Distortion_-7.5%", "Unperturbed"]: diff --git a/tests/test_input.py b/tests/test_input.py index c92d9042..077651e8 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) @@ -3306,6 +3306,9 @@ def test_apply_distortions(self): fake_hydrogen_V_Cd_dict["charges"] = [0] fake_hydrogen_bulk = copy.copy(self.cdte_doped_defect_dict["bulk"]) fake_hydrogen_bulk["supercell"]["structure"][4].species = "H" + fake_hydrogen_bulk["supercell"]["structure"].add_oxidation_state_by_element( + {"Cd": +2, "Te": -2, "H": +1} + ) fake_hydrogen_V_Cd = input.generate_defect_object( fake_hydrogen_V_Cd_dict, fake_hydrogen_bulk, @@ -3316,7 +3319,6 @@ def test_apply_distortions(self): ] dist = input.Distortions( {"vac_1_Cd": fake_hydrogen_V_Cd_entries}, - oxidation_states=oxidation_states, bond_distortions=bond_distortions, ) distortion_defect_dict, distortion_metadata = dist.apply_distortions(