ShakeNBreak Package

See the doped DeepWiki site for an overview of the codebase and workflow diagrams.

Module contents

ShakeNBreak is a defect structure-searching method employing chemically-guided bond distortions to locate ground-state and metastable structures of point defects in solid materials.

Submodules

• shakenbreak.input module
  • Distortions
    • Distortions.apply_distortions()
    • Distortions.from_structures()
    • Distortions.write_castep_files()
    • Distortions.write_cp2k_files()
    • Distortions.write_distortion_metadata()
    • Distortions.write_espresso_files()
    • Distortions.write_fhi_aims_files()
    • Distortions.write_vasp_files()
  • apply_snb_distortions()
  • bold_print()
  • distort_and_rattle_defect_entry()
  • generate_defect_object()
  • identify_defect()
• shakenbreak.distortions module
  • apply_dimer_distortion()
  • distort()
  • distort_and_rattle()
  • get_dimer_bond_length()
  • local_mc_rattle()
  • rattle()
• shakenbreak.io module
  • parse_energies()
  • parse_fhi_aims_input()
  • parse_qe_input()
  • parse_structure()
  • read_structure_w_ase()
  • read_vasp_structure()
• shakenbreak.analysis module
  • analyse_defect_site()
  • analyse_structure()
  • calculate_struct_comparison()
  • compare_structures()
  • get_energies()
  • get_gs_distortion()
  • get_homoionic_bonds()
  • get_site_magnetizations()
  • get_structures()
• shakenbreak.plotting module
  • plot_all_defects()
  • plot_defect()
  • plot_colorbar()
  • plot_datasets()
• shakenbreak.energy_lowering_distortions module
  • compare_struct_to_distortions()
  • get_energy_lowering_distortions()
  • read_defects_directories()
  • write_groundstate_structure()
  • write_retest_inputs()
• shakenbreak.cli module
  • Commands
    • snb
      • analyse
      • generate
      • generate_all
      • groundstate
      • mag
      • parse
      • plot
      • regenerate
      • run
    • CommandWithConfigFile()