.gitattributes
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CHANGELOG.rst
CITATIONS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
.github/workflows/build_and_test.yml
.github/workflows/lint.yml
.github/workflows/pip_install_test.yml
.github/workflows/release.yml
SnB_input_files/castep.param
SnB_input_files/cp2k_input.inp
SnB_input_files/default_POTCARs.yaml
SnB_input_files/example_generate_all_config.yaml
SnB_input_files/example_generate_config.yaml
SnB_input_files/incar.yaml
SnB_input_files/qe_input.yaml
docs/Analysis.rst
docs/Code_Compatibility.rst
docs/Contributing.rst
docs/Generation.rst
docs/Installation.rst
docs/Makefile
docs/ShakeNBreak_Example_Workflow.ipynb
docs/SnB_CLI.gif
docs/SnB_Supercell_Schematic_PES_2sec_Compressed.gif
docs/Tips.rst
docs/Tutorials.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/modules.rst
docs/paper.bib
docs/paper.md
docs/requirements.txt
docs/shakenbreak.analysis.rst
docs/shakenbreak.bib
docs/shakenbreak.cli.rst
docs/shakenbreak.distortions.rst
docs/shakenbreak.energy_lowering_distortions.rst
docs/shakenbreak.input.rst
docs/shakenbreak.io.rst
docs/shakenbreak.plotting.rst
docs/shakenbreak.rst
docs/shakenbreak.vasp.rst
docs/toc.png
docs/v_Cd_s0_0.svg
docs/v_Cd_s0_0_colorbar.svg
figures/Figure_joss.png
fonts/Montserrat-Regular.ttf
shakenbreak/__init__.py
shakenbreak/analysis.py
shakenbreak/cli.py
shakenbreak/distortions.py
shakenbreak/energy_lowering_distortions.py
shakenbreak/input.py
shakenbreak/io.py
shakenbreak/plotting.py
shakenbreak/shakenbreak.mplstyle
shakenbreak/vasp.py
shakenbreak.egg-info/PKG-INFO
shakenbreak.egg-info/SOURCES.txt
shakenbreak.egg-info/dependency_links.txt
shakenbreak.egg-info/entry_points.txt
shakenbreak.egg-info/not-zip-safe
shakenbreak.egg-info/requires.txt
shakenbreak.egg-info/top_level.txt
shakenbreak/__pycache__/__init__.cpython-39.pyc
shakenbreak/__pycache__/analysis.cpython-39.pyc
shakenbreak/__pycache__/cli.cpython-39.pyc
shakenbreak/__pycache__/distortions.cpython-39.pyc
shakenbreak/__pycache__/energy_lowering_distortions.cpython-39.pyc
shakenbreak/__pycache__/input.cpython-39.pyc
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shakenbreak/__pycache__/plotting.cpython-39.pyc
shakenbreak/__pycache__/vasp.cpython-39.pyc
shakenbreak/scripts/SnB_run.sh
shakenbreak/scripts/save_vasp_files.sh
tests/__init__.py
tests/test_analysis.py
tests/test_cli.py
tests/test_distortions.py
tests/test_energy_lowering_distortions.py
tests/test_input.py
tests/test_io.py
tests/test_local.py
tests/test_plotting.py
tests/test_shakenbreak.py
tests/data/README
tests/data/castep/POSCAR
tests/data/castep/Si2-cellopt-aniso.castep
tests/data/castep/castep_mod.param
tests/data/castep/vac_1_Cd_0/test_vac_1_Cd_0.yaml
tests/data/castep/vac_1_Cd_0/Bond_Distortion_30.0%/castep.cell
tests/data/castep/vac_1_Cd_0/Bond_Distortion_30.0%/castep.param
tests/data/castep/vac_1_Cd_0/Bond_Distortion_30.0%/castep_user_parameters.param
tests/data/castep/vac_1_Cd_0/Bond_Distortion_30.0%/geom.castep
tests/data/cp2k/POSCAR
tests/data/cp2k/cp2k.restart
tests/data/cp2k/cp2k_input_mod.inp
tests/data/cp2k/vac_1_Cd_0/test_vac_1_Cd_0.yaml
tests/data/cp2k/vac_1_Cd_0/Bond_Distortion_30.0%/cp2k_input.inp
tests/data/cp2k/vac_1_Cd_0/Bond_Distortion_30.0%/cp2k_input_user_parameters.inp
tests/data/cp2k/vac_1_Cd_0/Bond_Distortion_30.0%/relax.out
tests/data/cp2k/vac_1_Cd_0/Bond_Distortion_30.0%/structure.cif
tests/data/example_results/v_Cd_s0_-1/v_Cd_s0_-1.yaml
tests/data/example_results/v_Cd_s0_-1/v_Cd_s0_-1_additional_distortions.yaml
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-10.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-20.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-30.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-40.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-50.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_-60.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_0.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_10.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_20.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_30.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_40.0%/CONTCAR
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tests/data/example_results/v_Cd_s0_-1/Bond_Distortion_60.0%/CONTCAR
tests/data/example_results/v_Cd_s0_-1/Unperturbed/CONTCAR
tests/data/example_results/v_Cd_s0_-2/v_Cd_s0_-2.yaml
tests/data/example_results/v_Cd_s0_-2/v_Cd_s0_-2_additional_distortions.yaml
tests/data/example_results/v_Cd_s0_-2/Rattled/CONTCAR
tests/data/example_results/v_Cd_s0_-2/Unperturbed/CONTCAR
tests/data/example_results/v_Cd_s0_0/v_Cd_s0_0.yaml
tests/data/example_results/v_Cd_s0_0/v_Cd_s0_0_additional_distortions.yaml
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-10.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-20.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-30.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-40.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-50.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_-60.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_0.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_10.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_20.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_30.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_40.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_50.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Bond_Distortion_60.0%/CONTCAR
tests/data/example_results/v_Cd_s0_0/Unperturbed/CONTCAR
tests/data/example_results/v_Ti_0/Bond_Distortion_-40.0%/CONTCAR
tests/data/example_results/v_Ti_0/Bond_Distortion_-40.0%/OUTCAR
tests/data/example_results/v_Ti_0/Unperturbed/CONTCAR
tests/data/example_results/v_Ti_0/Unperturbed/OUTCAR
tests/data/fhi_aims/.aims.out.swp
tests/data/fhi_aims/POSCAR
tests/data/fhi_aims/POSCAR_geom
tests/data/fhi_aims/Si_opt.out
tests/data/fhi_aims/control.in
tests/data/fhi_aims/geometry.in
tests/data/fhi_aims/vac_1_Cd_0/test_vac_1_Cd_0.yaml
tests/data/fhi_aims/vac_1_Cd_0/Bond_Distortion_30.0%/aims.out
tests/data/fhi_aims/vac_1_Cd_0/Bond_Distortion_30.0%/control.in
tests/data/fhi_aims/vac_1_Cd_0/Bond_Distortion_30.0%/control_user_parameters.in
tests/data/fhi_aims/vac_1_Cd_0/Bond_Distortion_30.0%/geometry.in
tests/data/local_baseline_plots/vac_1_Cd_0_cli_default.png
tests/data/local_baseline_plots/vac_1_Ti_0_cli_colorbar_disp.png
tests/data/quantum_espresso/espresso_structure.cif
tests/data/quantum_espresso/qe.in
tests/data/quantum_espresso/vac_1_Cd_0/test_vac_1_Cd_0.yaml
tests/data/quantum_espresso/vac_1_Cd_0/Bond_Distortion_30.0%/espresso.out
tests/data/quantum_espresso/vac_1_Cd_0/Bond_Distortion_30.0%/espresso.pwi
tests/data/quantum_espresso/vac_1_Cd_0/Bond_Distortion_30.0%/espresso_structure.pwi
tests/data/quantum_espresso/vac_1_Cd_0/Bond_Distortion_30.0%/espresso_user_parameters.pwi
tests/data/remote_baseline_plots/Cd_Te_s32c_2_displacement.png
tests/data/remote_baseline_plots/Int_Se_1_6.png
tests/data/remote_baseline_plots/vac_1_Cd_-1.png
tests/data/remote_baseline_plots/vac_1_Cd_-2.png
tests/data/remote_baseline_plots/vac_1_Cd_-2_only_rattled.png
tests/data/remote_baseline_plots/vac_1_Cd_-2_only_rattled_and_rattled_dist_from_other_charges_states.png
tests/data/remote_baseline_plots/vac_1_Cd_-2_rattled_other_charge_states.png
tests/data/remote_baseline_plots/vac_1_Cd_0.png
tests/data/remote_baseline_plots/vac_1_Cd_0_colors.png
tests/data/remote_baseline_plots/vac_1_Cd_0_displacement.png
tests/data/remote_baseline_plots/vac_1_Cd_0_fake_defect_name.png
tests/data/remote_baseline_plots/vac_1_Cd_0_include_site_num_in_name.png
tests/data/remote_baseline_plots/vac_1_Cd_0_max_dist.png
tests/data/remote_baseline_plots/vac_1_Cd_0_maxdist_title_linecolor_label.png
tests/data/remote_baseline_plots/vac_1_Cd_0_not_enough_markers.png
tests/data/remote_baseline_plots/vac_1_Cd_0_notitle.png
tests/data/remote_baseline_plots/vac_1_Cd_0_other_charge_states.png
tests/data/remote_baseline_plots/vac_1_Cd_0_plot_defect_add_colorbar_max_dist.png
tests/data/remote_baseline_plots/vac_1_Cd_0_plot_defect_with_unrecognised_name.png
tests/data/remote_baseline_plots/vac_1_Cd_0_plot_defect_without_colorbar.png
tests/data/remote_baseline_plots/vac_1_Cd_0_plot_defect_without_title_units_meV.png
tests/data/vasp/Cu_prim_POSCAR
tests/data/vasp/rTiO2_vac_2_O_0_nupdown_0.yaml
tests/data/vasp/rTiO2_vac_2_O_0_nupdown_2.yaml
tests/data/vasp/CdTe/CdTe_Bulk_Conventional_POSCAR
tests/data/vasp/CdTe/CdTe_Bulk_Primitive_POSCAR
tests/data/vasp/CdTe/CdTe_Bulk_Supercell_POSCAR
tests/data/vasp/CdTe/CdTe_Int_Cd_2_-60%_Distortion_NN_10_POSCAR
tests/data/vasp/CdTe/CdTe_Int_Cd_2_-60%_Distortion_Rattled_POSCAR
tests/data/vasp/CdTe/CdTe_Int_Cd_2_-60%_Distortion_Unrattled_POSCAR
tests/data/vasp/CdTe/CdTe_Int_Cd_2_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-1_vgam_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Distortion_Rattled_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Distortion_Unrattled_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Distortion_local_rattle_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Distortion_stdev0.1_Rattled_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Distortion_stdev0pt1_Rattled_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_-50%_Kwarged_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_0_30%_local_rattle_POSCAR
tests/data/vasp/CdTe/CdTe_V_Cd_POSCAR
tests/data/vasp/CdTe/CdTe_as_1_Te_on_Cd_-2_DX_Relaxed_CONTCAR
tests/data/vasp/CdTe/CdTe_defects_dict.json
tests/data/vasp/CdTe/CdTe_extrinsic_defects_dict.json
tests/data/vasp/CdTe/CdTe_sub_1_In_on_Cd_1.yaml
tests/data/vasp/CdTe/CdTe_vac_1_Cd_0_stdev_0.05.yaml
tests/data/vasp/CdTe/CdTe_vac_1_Cd_0_stdev_0.15.yaml
tests/data/vasp/CdTe/CdTe_vac_1_Cd_0_stdev_0.25.yaml
tests/data/vasp/CdTe/CdTe_vac_1_Cd_0_stdev_0.25_no_unperturbed.yaml
tests/data/vasp/CdTe/Int_Cd_2_0_minus0pt6_struc_rattle_seed_0_stdev_0.28_POSCAR
tests/data/vasp/CdTe/Int_Cd_2_2_tailed_off_rattle_POSCAR
tests/data/vasp/CdTe/Int_Cd_2_2_tailed_off_rattle_seed_0_stdev_0.28_POSCAR
tests/data/vasp/CdTe/distortion_metadata.json
tests/data/vasp/CdTe/doped_Te_i_dict.json
tests/data/vasp/CdTe/doped_V_Cd_0_dict.json
tests/data/vasp/CdTe/doped_defect_dict.json
tests/data/vasp/CdTe/fake_V_Cd_-2_from_other_charge_states.yaml
tests/data/vasp/CdTe/vac_1_Cd_-2.yaml
tests/data/vasp/CdTe/vac_1_Cd_0_-30.0%_Distortion_tailed_off_rattle_POSCAR
tests/data/vasp/CdTe/vacancies_dist_defect_dict.json
tests/data/vasp/CdTe/vacancies_dist_metadata.json
tests/data/vasp/CdTe/vac_1_Cd_0/fake_vac_1_Cd_0.yaml
tests/data/vasp/CdTe/vac_1_Cd_0/vac_1_Cd_0.yaml
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-10.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-10.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-12.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-12.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-15.0%/CONTCAR
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tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-17.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-17.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-2.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-2.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-20.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-20.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-22.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-22.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-25.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-25.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-27.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-27.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-30.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-30.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-32.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-32.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-35.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-35.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-37.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-37.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-40.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-40.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-42.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-42.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-45.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-45.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-47.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-47.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-5.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-5.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-50.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-50.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-52.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-52.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-55.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-55.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-57.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-57.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-60.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-60.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-7.5%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_-7.5%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_0.0%/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Bond_Distortion_0.0%/POSCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Unperturbed/CONTCAR
tests/data/vasp/CdTe/vac_1_Cd_0/Unperturbed/POSCAR
tests/data/vasp/vac_1_Ti_0/Bond_Distortion_-40.0%/CONTCAR
tests/data/vasp/vac_1_Ti_0/Bond_Distortion_10.0%/CONTCAR
tests/data/vasp/vac_1_Ti_0/Unperturbed/CONTCAR
tutorials/ShakeNBreak_Example_Interstitials.ipynb
tutorials/ShakeNBreak_Example_Workflow.ipynb