├── .gitignore ├── Calculation Status.md ├── IPR workflow ├── 1. Check Modules.ipynb ├── 2. Database Manager.ipynb ├── 3. Workflow Manager.ipynb ├── 3a. Process relaxed crystal results.ipynb ├── README.md ├── old workflow │ ├── 4. Workflow Manager-Copy1.ipynb │ ├── 4. Workflow Manager.ipynb │ ├── Master Prepare Manager - for CTCMS.ipynb │ ├── Master Prepare Manager.ipynb │ ├── master_X_point_defect_mobilities.py │ ├── master_X_point_defects.py │ ├── master_prepare.py │ ├── master_prepare_scripts │ │ ├── README.md │ │ ├── iprhub_on_laptop.in │ │ ├── iprhub_on_ruth.in │ │ └── test_on_desktop.in │ ├── new_prepare.py │ ├── prepare_ctcms.py │ ├── prepare_ctcms2.py │ ├── prepare_desktop.py │ └── prepare_desktop2.py ├── prepare_free_energy.ipynb ├── prepare_free_energy_liquid.ipynb ├── prepare_relax_dynamic_at_temp.ipynb ├── prepare_relax_liquid.ipynb └── process_all_relaxed.py ├── LICENSE.TXT ├── MANIFEST.in ├── README.rst ├── UPDATES.rst ├── bin ├── README.rst ├── add_urls_and_backup.py ├── check_runners.py ├── clean_bad_guys.py ├── emperor │ ├── CTCMSEmperor.py │ ├── CTCMSEmperorPrepare.py │ ├── WSLLaptopEmperor.py │ ├── WSLLaptopEmperorPrepare.py │ ├── ht_pots.in │ ├── make_all_pot_ids.py │ ├── newpot.in │ ├── pool12.in │ └── unfinished_pots.in ├── emperor_15_slurm ├── emperor_16_slurm ├── iprPy ├── iprPy_prepare ├── iprPy_prepare_pool_1 ├── iprPy_prepare_pool_2 ├── iprPy_prepare_pool_3 ├── iprPy_prepare_pool_4 ├── iprPy_prepare_pool_5 ├── iprPy_slurm ├── iprPy_slurm_16 ├── iprPy_slurm_4 ├── iprPy_slurm_8 ├── melt_commander │ ├── Compare with TI.ipynb │ ├── Find bcc.ipynb │ ├── Find hcp.ipynb │ ├── MeltCommander.py │ ├── Melting_temperatures.csv │ ├── Melting_temperatures_bcc.csv │ ├── Melting_temperatures_hcp.csv │ ├── README.md │ ├── Results.ipynb │ ├── Run bcc-Copy1.ipynb │ ├── Run bcc.ipynb │ ├── Run hcp-Copy1.ipynb │ ├── Run hcp.ipynb │ ├── T_melts.csv │ ├── melt_a.in │ ├── melt_b.in │ ├── melt_c.in │ ├── melt_d.in │ ├── melt_e.in │ ├── melt_f.in │ ├── melt_g.in │ ├── melt_h.in │ ├── melt_i.in │ ├── melt_j.in │ └── melt_k.in ├── multi_runner_slurm.py ├── prepare │ ├── master_prepare_ctcms.in │ ├── master_prepare_ctcms_pool_1.in │ ├── master_prepare_ctcms_pool_2.in │ ├── master_prepare_ctcms_pool_3.in │ ├── master_prepare_ctcms_pool_4.in │ ├── master_prepare_ctcms_pool_5.in │ ├── master_prepare_desktop.in │ ├── master_prepare_desktop_wsl.in │ └── master_prepare_laptop_wsl.in ├── prepare_relax_dynamic_at_temp.py ├── relax_commander │ ├── README.md │ ├── Single runner emperor.ipynb │ └── emperor_script.py ├── reposition_orphans.py ├── sf_commander │ └── StackingFaultCommander.py ├── sleep_until_done.py └── targeted_runner.py ├── conda_environment └── conda_iprPy.yml ├── demo ├── 0-files │ ├── .ipynb_checkpoints │ │ ├── 1999--Mishin-Y--Ni--LAMMPS--ipr1-checkpoint.json │ │ └── A1--Cu--fcc--vacancy-vacancy-checkpoint.json │ ├── 1999--Mishin-Y--Ni--A1--Cu--fcc--111sf.json │ ├── 1999--Mishin-Y--Ni--LAMMPS--ipr1.json │ ├── 1999--Mishin-Y--Ni--LAMMPS--ipr1 │ │ ├── Ni99.eam.alloy │ │ └── Ni99_releaseNotes_1.pdf │ ├── A1--Cu--fcc--111.json │ ├── A1--Cu--fcc--111sf.json │ ├── A1--Cu--fcc--a-2-110--90-edge--{100}.json │ ├── A1--Cu--fcc--a-2-110--90-edge--{111}.json │ ├── A1--Cu--fcc--stgb-100-05.72.json │ ├── A1--Cu--fcc--vacancy-vacancy.json │ ├── A1--Cu--fcc--vacancy.json │ ├── A1--Cu--fcc.json │ ├── relax_dynamic_420000.dump │ └── relax_liquid_170000.dump ├── E_vs_r_scan │ └── calc_E_vs_r_scan.in ├── README.md ├── bond_angle_scan │ └── calc_bond_angle_scan.in ├── crystal_space_group │ └── calc_crystal_space_group.in ├── diatom_scan │ └── calc_diatom_scan.in ├── diffusion_liquid │ └── calc_diffusion_liquid.in ├── diffusion_msd │ └── calc_diffusion_msd.in ├── diffusion_vacf │ └── calc_diffusion_vacf.in ├── dislocation_SDVPN │ └── calc_dislocation_SDVPN.in ├── dislocation_monopole │ └── calc_dislocation_monopole.in ├── dislocation_periodic_array │ └── calc_dislocation_periodic_array.in ├── elastic_constants_dynamic │ └── calc_elastic_constants_dynamic.in ├── elastic_constants_static │ └── calc_elastic_constants_static.in ├── energy_check │ └── calc_energy_check.in ├── free_energy │ └── calc_free_energy.in ├── free_energy_liquid │ └── calc_free_energy_liquid.in ├── grain_boundary_grip │ ├── calc_grain_boundary_grip.in │ └── calc_grain_boundary_grip_hodl.in ├── grain_boundary_static │ └── calc_grain_boundary_static.in ├── isolated_atom │ └── calc_isolated_atom.in ├── melting_temperature │ └── calc_melting_temperature.in ├── phonon │ └── calc_phonon.in ├── point_defect_diffusion │ └── calc_point_defect_diffusion.in ├── point_defect_mobility │ └── calc_point_defect_mobility.in ├── point_defect_static │ └── calc_point_defect_static.in ├── relax_box │ └── calc_relax_box.in ├── relax_dynamic │ └── calc_relax_dynamic.in ├── relax_liquid │ └── calc_relax_liquid.in ├── relax_static │ └── calc_relax_static.in ├── runall.bash ├── set_command_paths.py ├── stacking_fault_map_2D │ └── calc_stacking_fault_map_2D.in ├── stacking_fault_static │ └── calc_stacking_fault_static.in ├── surface_energy_static │ └── calc_surface_energy_static.in ├── viscosity_driving │ └── calc_viscosity_driving.in └── viscosity_green_kubo │ └── calc_viscosity_green_kubo.in ├── doc ├── builddoc ├── buildstyledocs.py ├── html │ ├── .buildinfo │ ├── .doctrees │ │ ├── calculation │ │ │ ├── E_vs_r_scan │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── bond_angle_scan │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── crystal_space_group │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── diatom_scan │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── dislocation_SDVPN │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── dislocation_monopole │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── dislocation_periodic_array │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── elastic_constants_static │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── energy_check │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── free_energy │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── free_energy_liquid │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── isolated_atom │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── phonon │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── point_defect_diffusion │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── point_defect_static │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── relax_box │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── relax_dynamic │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── relax_liquid │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── relax_static │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── stacking_fault_map_2D │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ ├── stacking_fault_static │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ │ └── surface_energy_static │ │ │ │ ├── class.doctree │ │ │ │ ├── doc.doctree │ │ │ │ ├── function.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── template.doctree │ │ ├── calculation_styles.doctree │ │ ├── environment.pickle │ │ ├── extend │ │ │ ├── addbuildcombos.doctree │ │ │ ├── addcalculation.doctree │ │ │ ├── addsubset.doctree │ │ │ └── index.doctree │ │ ├── index.doctree │ │ ├── intro.doctree │ │ ├── iprPy │ │ │ ├── calculation.doctree │ │ │ ├── database.doctree │ │ │ ├── index.doctree │ │ │ ├── input.doctree │ │ │ ├── record.doctree │ │ │ └── tools.doctree │ │ ├── nbsphinx │ │ │ ├── notebook │ │ │ │ ├── E_vs_r_scan.ipynb │ │ │ │ ├── bond_angle_scan.ipynb │ │ │ │ ├── crystal_space_group.ipynb │ │ │ │ ├── diatom_scan.ipynb │ │ │ │ ├── dislocation_SDVPN.ipynb │ │ │ │ ├── dislocation_monopole.ipynb │ │ │ │ ├── dislocation_periodic_array.ipynb │ │ │ │ ├── elastic_constants_static.ipynb │ │ │ │ ├── energy_check.ipynb │ │ │ │ ├── isolated_atom.ipynb │ │ │ │ ├── phonon.ipynb │ │ │ │ ├── point_defect_static.ipynb │ │ │ │ ├── relax_box.ipynb │ │ │ │ ├── relax_dynamic.ipynb │ │ │ │ ├── relax_liquid.ipynb │ │ │ │ ├── relax_static.ipynb │ │ │ │ ├── stacking_fault_map_2D.ipynb │ │ │ │ ├── stacking_fault_static.ipynb │ │ │ │ └── surface_energy_static.ipynb │ │ │ ├── notebook_E_vs_r_scan_29_0.png │ │ │ ├── notebook_bond_angle_scan_24_0.png │ │ │ ├── notebook_bond_angle_scan_24_1.png │ │ │ ├── notebook_dislocation_SDVPN_23_0.png │ │ │ ├── notebook_dislocation_SDVPN_24_0.png │ │ │ ├── notebook_dislocation_SDVPN_25_0.png │ │ │ ├── notebook_dislocation_SDVPN_29_0.png │ │ │ ├── notebook_phonon_31_1.png │ │ │ ├── notebook_phonon_33_1.png │ │ │ ├── notebook_phonon_35_0.png │ │ │ ├── notebook_phonon_37_0.png │ │ │ ├── notebook_phonon_41_0.png │ │ │ ├── notebook_phonon_41_1.png │ │ │ ├── notebook_phonon_43_0.png │ │ │ ├── notebook_phonon_43_1.png │ │ │ ├── notebook_phonon_45_0.png │ │ │ ├── notebook_phonon_47_0.png │ │ │ ├── notebook_phonon_49_0.png │ │ │ ├── notebook_relax_liquid_35_0.png │ │ │ ├── notebook_relax_liquid_35_1.png │ │ │ ├── notebook_relax_liquid_38_0.png │ │ │ ├── notebook_relax_liquid_38_1.png │ │ │ ├── notebook_relax_liquid_42_0.png │ │ │ ├── notebook_relax_liquid_42_1.png │ │ │ ├── notebook_relax_liquid_44_0.png │ │ │ ├── notebook_stacking_fault_map_2D_34_0.png │ │ │ ├── notebook_stacking_fault_map_2D_35_0.png │ │ │ └── notebook_stacking_fault_map_2D_36_0.png │ │ ├── notebook │ │ │ ├── E_vs_r_scan.doctree │ │ │ ├── bond_angle_scan.doctree │ │ │ ├── crystal_space_group.doctree │ │ │ ├── diatom_scan.doctree │ │ │ ├── dislocation_SDVPN.doctree │ │ │ ├── dislocation_monopole.doctree │ │ │ ├── dislocation_periodic_array.doctree │ │ │ ├── elastic_constants_static.doctree │ │ │ ├── energy_check.doctree │ │ │ ├── isolated_atom.doctree │ │ │ ├── phonon.doctree │ │ │ ├── point_defect_static.doctree │ │ │ ├── relax_box.doctree │ │ │ ├── relax_dynamic.doctree │ │ │ ├── relax_liquid.doctree │ │ │ ├── relax_static.doctree │ │ │ ├── stacking_fault_map_2D.doctree │ │ │ ├── stacking_fault_static.doctree │ │ │ └── surface_energy_static.doctree │ │ ├── notebook_styles.doctree │ │ ├── overview.doctree │ │ ├── run │ │ │ ├── database_setup.doctree │ │ │ ├── htp.doctree │ │ │ ├── index.doctree │ │ │ ├── notebook.doctree │ │ │ └── single.doctree │ │ └── setup.doctree │ ├── .nojekyll │ ├── _images │ │ ├── notebook_E_vs_r_scan_29_0.png │ │ ├── notebook_bond_angle_scan_24_0.png │ │ ├── notebook_bond_angle_scan_24_1.png │ │ ├── notebook_dislocation_SDVPN_23_0.png │ │ ├── notebook_dislocation_SDVPN_24_0.png │ │ ├── notebook_dislocation_SDVPN_25_0.png │ │ ├── notebook_dislocation_SDVPN_29_0.png │ │ ├── notebook_phonon_31_1.png │ │ ├── notebook_phonon_33_1.png │ │ ├── notebook_phonon_35_0.png │ │ ├── notebook_phonon_37_0.png │ │ ├── notebook_phonon_41_0.png │ │ ├── notebook_phonon_41_1.png │ │ ├── notebook_phonon_43_0.png │ │ ├── notebook_phonon_43_1.png │ │ ├── notebook_phonon_45_0.png │ │ ├── notebook_phonon_47_0.png │ │ ├── notebook_phonon_49_0.png │ │ ├── notebook_relax_liquid_35_0.png │ │ ├── notebook_relax_liquid_35_1.png │ │ ├── notebook_relax_liquid_38_0.png │ │ ├── notebook_relax_liquid_38_1.png │ │ ├── notebook_relax_liquid_42_0.png │ │ ├── notebook_relax_liquid_42_1.png │ │ ├── notebook_relax_liquid_44_0.png │ │ ├── notebook_stacking_fault_map_2D_34_0.png │ │ ├── notebook_stacking_fault_map_2D_35_0.png │ │ └── notebook_stacking_fault_map_2D_36_0.png │ ├── _static │ │ ├── basic.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── nbsphinx-broken-thumbnail.svg │ │ ├── nbsphinx-code-cells.css │ │ ├── nbsphinx-gallery.css │ │ ├── nbsphinx-no-thumbnail.svg │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ └── sphinx_highlight.js │ ├── calculation │ │ ├── E_vs_r_scan │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── bond_angle_scan │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── crystal_space_group │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── diatom_scan │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── dislocation_SDVPN │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── dislocation_monopole │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── dislocation_periodic_array │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── elastic_constants_static │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── energy_check │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── free_energy │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── free_energy_liquid │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── isolated_atom │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── phonon │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── point_defect_diffusion │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── point_defect_static │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── relax_box │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── relax_dynamic │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── relax_liquid │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── relax_static │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── stacking_fault_map_2D │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ ├── stacking_fault_static │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ │ └── surface_energy_static │ │ │ ├── class.html │ │ │ ├── doc.html │ │ │ ├── function.html │ │ │ ├── index.html │ │ │ └── template.html │ ├── calculation_styles.html │ ├── extend │ │ ├── addbuildcombos.html │ │ ├── addcalculation.html │ │ ├── addsubset.html │ │ └── index.html │ ├── genindex.html │ ├── index.html │ ├── intro.html │ ├── iprPy │ │ ├── calculation.html │ │ ├── database.html │ │ ├── index.html │ │ ├── input.html │ │ ├── record.html │ │ └── tools.html │ ├── notebook │ │ ├── E_vs_r_scan.html │ │ ├── E_vs_r_scan.ipynb │ │ ├── bond_angle_scan.html │ │ ├── bond_angle_scan.ipynb │ │ ├── crystal_space_group.html │ │ ├── crystal_space_group.ipynb │ │ ├── diatom_scan.html │ │ ├── diatom_scan.ipynb │ │ ├── dislocation_SDVPN.html │ │ ├── dislocation_SDVPN.ipynb │ │ ├── dislocation_monopole.html │ │ ├── dislocation_monopole.ipynb │ │ ├── dislocation_periodic_array.html │ │ ├── dislocation_periodic_array.ipynb │ │ ├── elastic_constants_static.html │ │ ├── elastic_constants_static.ipynb │ │ ├── energy_check.html │ │ ├── energy_check.ipynb │ │ ├── isolated_atom.html │ │ ├── isolated_atom.ipynb │ │ ├── phonon.html │ │ ├── phonon.ipynb │ │ ├── point_defect_static.html │ │ ├── point_defect_static.ipynb │ │ ├── relax_box.html │ │ ├── relax_box.ipynb │ │ ├── relax_dynamic.html │ │ ├── relax_dynamic.ipynb │ │ ├── relax_liquid.html │ │ ├── relax_liquid.ipynb │ │ ├── relax_static.html │ │ ├── relax_static.ipynb │ │ ├── stacking_fault_map_2D.html │ │ ├── stacking_fault_map_2D.ipynb │ │ ├── stacking_fault_static.html │ │ ├── stacking_fault_static.ipynb │ │ ├── surface_energy_static.html │ │ └── surface_energy_static.ipynb │ ├── notebook_styles.html │ ├── objects.inv │ ├── overview.html │ ├── py-modindex.html │ ├── run │ │ ├── database_setup.html │ │ ├── htp.html │ │ ├── index.html │ │ ├── notebook.html │ │ └── single.html │ ├── search.html │ ├── searchindex.js │ └── setup.html └── source │ ├── calculation │ ├── E_vs_r_scan │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── bond_angle_scan │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── crystal_space_group │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── diatom_scan │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── dislocation_SDVPN │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── dislocation_monopole │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── dislocation_periodic_array │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── elastic_constants_static │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── energy_check │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── free_energy │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── free_energy_liquid │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── isolated_atom │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── phonon │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── point_defect_diffusion │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── point_defect_static │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── relax_box │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── relax_dynamic │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── relax_liquid │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── relax_static │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── stacking_fault_map_2D │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── stacking_fault_static │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ └── surface_energy_static │ │ ├── class.rst │ │ ├── doc.rst │ │ ├── function.rst │ │ ├── index.rst │ │ └── template.rst │ ├── calculation_styles.rst │ ├── conf.py │ ├── extend │ ├── addbuildcombos.rst │ ├── addcalculation.rst │ ├── addsubset.rst │ └── index.rst │ ├── index.rst │ ├── intro.rst │ ├── iprPy │ ├── calculation.rst │ ├── database.rst │ ├── index.rst │ ├── input.rst │ ├── record.rst │ └── tools.rst │ ├── notebook │ ├── E_vs_r_scan.ipynb │ ├── bond_angle_scan.ipynb │ ├── crystal_space_group.ipynb │ ├── diatom_scan.ipynb │ ├── dislocation_SDVPN.ipynb │ ├── dislocation_monopole.ipynb │ ├── dislocation_periodic_array.ipynb │ ├── elastic_constants_static.ipynb │ ├── energy_check.ipynb │ ├── isolated_atom.ipynb │ ├── phonon.ipynb │ ├── point_defect_static.ipynb │ ├── relax_box.ipynb │ ├── relax_dynamic.ipynb │ ├── relax_liquid.ipynb │ ├── relax_static.ipynb │ ├── stacking_fault_map_2D.ipynb │ ├── stacking_fault_static.ipynb │ └── surface_energy_static.ipynb │ ├── notebook_styles.rst │ ├── overview.rst │ ├── run │ ├── database_setup.rst │ ├── htp.rst │ ├── index.rst │ ├── notebook.rst │ └── single.rst │ └── setup.rst ├── iprPy ├── Settings.py ├── VERSION ├── __init__.py ├── analysis │ ├── PropertyProcessor │ │ ├── __init__.py │ │ ├── _crystal.py │ │ ├── _diatom.py │ │ ├── _elastic.py │ │ ├── _empty.py │ │ ├── _evsr.py │ │ ├── _mdliquid.py │ │ ├── _mdsolid.py │ │ ├── _mdthermo.py │ │ ├── _phonon.py │ │ ├── _point.py │ │ ├── _stacking.py │ │ └── _surface.py │ ├── StackingFaultMEPCommander.py │ ├── __init__.py │ ├── add_urls_and_backup.py │ ├── get_isolated_atom_energies.py │ ├── match_reference_prototype.py │ ├── md_solid_properties │ │ ├── __init__.py │ │ ├── _md_solid_properties.py │ │ ├── find_transition_temps.py │ │ ├── load_transition_temp.py │ │ ├── process_0K.py │ │ ├── process_at_temp.py │ │ ├── save_transition_temp.py │ │ └── update_untransformed_flag.py │ ├── process_relaxations.py │ ├── prototype_spg_info.json │ ├── stacking_fault_map_2D_mep.py │ └── thermo │ │ ├── AnalyzeFE.py │ │ ├── AnalyzeMD.py │ │ ├── AnalyzeQHA.py │ │ ├── Thermo.py │ │ ├── ThermoSolid.py │ │ └── __init__.py ├── calculation │ ├── Calculation.py │ ├── E_vs_r_scan │ │ ├── EvsRScan.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_E_vs_r_scan.xsd │ │ ├── calculation_E_vs_r_scan.xsl │ │ ├── calculation_E_vs_r_scan_short.xsl │ │ ├── e_vs_r_scan.py │ │ ├── run0.template │ │ └── theory.md │ ├── __init__.py │ ├── bain_transformation_map │ │ ├── Bain.ipynb │ │ ├── Bain.py │ │ ├── BainTransformationMap.py │ │ ├── __init__.py │ │ ├── calc_bain_transformation_map.py │ │ ├── calculation_bain_transformation_map │ │ │ ├── CalculationBainTransformationMap.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ └── record-calculation-bain-transformation-map.xsd │ │ ├── data_model.py │ │ └── min.template │ ├── bond_angle_scan │ │ ├── BondAngleScan.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── bond_angle_scan.py │ │ ├── bond_scan.template │ │ ├── calculation_bond_angle_scan.xsd │ │ ├── prepare_bond_angle_scan.py │ │ └── theory.md │ ├── crystal_space_group │ │ ├── CrystalSpaceGroup.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_crystal_space_group.xsd │ │ ├── calculation_crystal_space_group.xsl │ │ ├── crystal_space_group.py │ │ └── theory.md │ ├── diatom_scan │ │ ├── DiatomScan.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_diatom_scan.xsd │ │ ├── calculation_diatom_scan.xsl │ │ ├── calculation_diatom_scan_short.xsl │ │ ├── diatom_scan.py │ │ ├── run0.template │ │ └── theory.md │ ├── diffusion_liquid │ │ ├── DiffusionLiquid.py │ │ ├── __init__.py │ │ ├── calculation_diffusion_liquid.xsd │ │ ├── calculation_diffusion_liquid.xsl │ │ ├── diffusion_liquid.py │ │ └── diffusion_liquid.template │ ├── diffusion_msd │ │ ├── DiffusionMSD.py │ │ ├── __init__.py │ │ ├── diffusion_msd.py │ │ └── in.diffusion_msd.template │ ├── diffusion_vacf │ │ ├── DiffusionVACF.py │ │ ├── __init__.py │ │ ├── diffusion_vacf.py │ │ └── in.diffusion_vacf.template │ ├── dislocation_SDVPN │ │ ├── DislocationSDVPN.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_dislocation_SDVPN.xsd │ │ ├── dislocation_SDVPN.py │ │ └── theory.md │ ├── dislocation_SDVPN_stress │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calc_dislocation_Peierls_Nabarro_stress.py │ │ ├── calc_dislocation_Peierls_Nabarro_stress.template │ │ ├── calculation_dislocation_SDVPN_stress │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── buildmodel.py │ │ │ ├── compare_terms.py │ │ │ ├── record-calculation-dislocation-Peierls-Nabarro-stress.xsd │ │ │ ├── schema.py │ │ │ └── todict.py │ │ ├── dislocation_Peierls_Nabarro_stress_template.ipynb │ │ ├── prepare_dislocation_Peierls_Nabarro_stress.py │ │ └── theory.md │ ├── dislocation_dipole │ │ ├── DislocationDipole.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_dislocation_dipole.xsd │ │ ├── calculation_dislocation_dipole.xsl │ │ ├── disl_relax.template │ │ ├── dislocation_dipole.py │ │ └── theory.md │ ├── dislocation_monopole │ │ ├── DislocationMonopole.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_dislocation_monopole.xsd │ │ ├── calculation_dislocation_monopole.xsl │ │ ├── disl_relax.template │ │ ├── dislocation_monopole.py │ │ └── theory.md │ ├── dislocation_monopole_crss │ │ ├── __init__.py │ │ ├── calc_crss.template │ │ ├── calc_dislocation_monopole_crss.py │ │ ├── data_model.py │ │ ├── prepare.py │ │ ├── read_input.py │ │ └── strain_system.template │ ├── dislocation_periodic_array │ │ ├── DislocationPeriodicArray.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_dislocation_periodic_array.xsd │ │ ├── disl_relax.template │ │ ├── dislocation_periodic_array.py │ │ └── theory.md │ ├── dislocation_periodic_array_stress │ │ ├── DislocationPeriodicArrayStress.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calc_dislocation_periodic_array_stress.py │ │ ├── calc_dislocation_periodic_array_stress.template │ │ ├── calculation_dislocation_periodic_array_stress │ │ │ ├── CalculationDislocationPeriodicArrayStress.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ └── record-calculation-dislocation-periodic-array-stress.xsd │ │ ├── dislarray_free_stress.template │ │ ├── dislarray_rigid_stress.template │ │ └── theory.md │ ├── dislocation_vacancy │ │ ├── __init__.py │ │ ├── calc_files │ │ │ ├── 522c8437-eceb-480d-8f0c-77f83cdb3125.json │ │ │ ├── base.dat │ │ │ ├── bcc.json │ │ │ ├── bcc │ │ │ │ ├── 110-edge.json │ │ │ │ ├── 111-screw.json │ │ │ │ └── 112-edge.json │ │ │ ├── calc_dislocation_vacancy.in │ │ │ ├── calc_dislocation_vacancy.py │ │ │ ├── calc_dislocation_vacancy.template │ │ │ ├── create_sys.in │ │ │ ├── disl.dat │ │ │ ├── disl.dump │ │ │ ├── disl_relax.in │ │ │ ├── disl_relax.template │ │ │ ├── disl_relax_notemp.template │ │ │ ├── disl_relax_script.py │ │ │ ├── fcc.json │ │ │ ├── log.lammps │ │ │ └── results.json │ │ ├── data_model.py │ │ ├── prepare.py │ │ └── read_input.py │ ├── elastic_constants_dynamic │ │ ├── ElasticConstantsDynamic.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── born_matrix.template │ │ ├── calculation_elastic_constants_dynamic.xsd │ │ ├── calculation_elastic_constants_dynamic.xsl │ │ ├── elastic_constants_dynamic.py │ │ └── theory.md │ ├── elastic_constants_static │ │ ├── ElasticConstantsStatic.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_elastic_constants_static.xsd │ │ ├── calculation_elastic_constants_static.xsl │ │ ├── cij.template │ │ ├── elastic_constants_static.py │ │ └── theory.md │ ├── energy_check │ │ ├── EnergyCheck.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_energy_check.xsd │ │ ├── energy_check.py │ │ ├── run0.template │ │ └── theory.md │ ├── free_energy │ │ ├── FreeEnergy.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_free_energy.xsd │ │ ├── calculation_free_energy.xsl │ │ ├── free_energy.py │ │ ├── free_energy.template │ │ ├── msd.template │ │ └── theory.md │ ├── free_energy_liquid │ │ ├── FreeEnergyLiquid.py │ │ ├── README.md │ │ ├── UhlenbeckFordModel.py │ │ ├── __init__.py │ │ ├── calculation_free_energy_liquid.xsd │ │ ├── calculation_free_energy_liquid.xsl │ │ ├── free_energy_liquid.py │ │ ├── free_energy_liquid.template │ │ └── theory.md │ ├── grain_boundary_bcc │ │ ├── __init__.py │ │ ├── calc_bcc_grain_boundary.py │ │ ├── calc_bcc_grain_boundary.template │ │ └── grain_boundary.template │ ├── grain_boundary_grip │ │ ├── GrainBoundaryGRIP.py │ │ ├── __init__.py │ │ ├── grain_boundary_grip.py │ │ └── grip_relax.template │ ├── grain_boundary_static │ │ ├── GrainBoundaryStatic.py │ │ ├── __init__.py │ │ ├── gbmin.template │ │ ├── gbmin_periodic.template │ │ ├── grain_boundary_static.py │ │ └── grain_boundary_static_periodic.py │ ├── isolated_atom │ │ ├── IsolatedAtom.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_isolated_atom.xsd │ │ ├── calculation_isolated_atom.xsl │ │ ├── calculation_isolated_atom_short.xsl │ │ ├── isolated_atom.py │ │ ├── run0.template │ │ └── theory.md │ ├── melting_temperature │ │ ├── MeltingTemperature.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── melting_temperature.py │ │ ├── theory.md │ │ └── two_phase_melting_temp.template │ ├── phonon │ │ ├── Phonon.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calc_phonon.py │ │ ├── calculation_phonon.xsd │ │ ├── calculation_phonon.xsl │ │ ├── phonon.template │ │ └── theory.md │ ├── point_defect_diffusion │ │ ├── PointDefectDiffusion.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_point_defect_diffusion.xsd │ │ ├── diffusion.template │ │ ├── point_defect_diffusion.py │ │ └── theory.md │ ├── point_defect_mobility │ │ ├── PointDefectMobility.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_point_defect_mobility.xsd │ │ ├── neb_lammps.template │ │ ├── point_defect_mobility.py │ │ └── theory.md │ ├── point_defect_static │ │ ├── PointDefectStatic.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── calculation_point_defect_static.xsd │ │ ├── calculation_point_defect_static.xsl │ │ ├── min.template │ │ ├── point_defect_static.py │ │ └── theory.md │ ├── relax_box │ │ ├── README.md │ │ ├── RelaxBox.py │ │ ├── __init__.py │ │ ├── calculation_relax_box.xsd │ │ ├── calculation_relax_box.xsl │ │ ├── cij_run0.template │ │ ├── relax_box.py │ │ └── theory.md │ ├── relax_dynamic │ │ ├── README.md │ │ ├── RelaxDynamic.py │ │ ├── __init__.py │ │ ├── calculation_relax_dynamic.xsd │ │ ├── calculation_relax_dynamic.xsl │ │ ├── full_relax.template │ │ ├── full_relax_restart.template │ │ ├── relax_dynamic.py │ │ └── theory.md │ ├── relax_liquid │ │ ├── README.md │ │ ├── RelaxLiquid.py │ │ ├── __init__.py │ │ ├── calculation_relax_liquid.xsd │ │ ├── liquid_ave_pe.template │ │ ├── liquid_ave_te.template │ │ ├── liquid_restart.template │ │ ├── relax_liquid.py │ │ └── theory.md │ ├── relax_liquid_redo │ │ ├── README.md │ │ ├── RelaxLiquid.py │ │ ├── __init__.py │ │ ├── calculation_relax_liquid.xsd │ │ ├── calculation_relax_liquid.xsl │ │ ├── liquid.template │ │ ├── liquid_restart.template │ │ ├── relax_liquid.py │ │ └── theory.md │ ├── relax_static │ │ ├── README.md │ │ ├── RelaxStatic.py │ │ ├── __init__.py │ │ ├── calculation_relax_static.xsd │ │ ├── calculation_relax_static.xsl │ │ ├── minbox.template │ │ ├── relax_static.py │ │ └── theory.md │ ├── stacking_fault_map_2D │ │ ├── README.md │ │ ├── StackingFaultMap2D.py │ │ ├── __init__.py │ │ ├── calculation_stacking_fault_map_2D.xsd │ │ ├── calculation_stacking_fault_map_2D.xsl │ │ ├── sfmin.template │ │ ├── stacking_fault_map_2D.py │ │ └── theory.md │ ├── stacking_fault_static │ │ ├── README.md │ │ ├── StackingFaultStatic.py │ │ ├── __init__.py │ │ ├── calculation_stacking_fault_static.xsd │ │ ├── sfmin.template │ │ ├── stacking_fault_static.py │ │ └── theory.md │ ├── surface_energy_static │ │ ├── README.md │ │ ├── SurfaceEnergyStatic.py │ │ ├── __init__.py │ │ ├── calculation_surface_energy_static.xsd │ │ ├── calculation_surface_energy_static.xsl │ │ ├── min.template │ │ ├── surface_energy_static.py │ │ └── theory.md │ ├── viscosity_driving │ │ ├── ViscosityDriving.py │ │ ├── __init__.py │ │ ├── viscosity_driving.py │ │ └── viscosity_driving.template │ └── viscosity_green_kubo │ │ ├── ViscosityGreenKubo.py │ │ ├── __init__.py │ │ ├── calculation_viscosity_green_kubo.xsd │ │ ├── calculation_viscosity_green_kubo.xsl │ │ ├── viscosity_green_kubo.py │ │ └── viscosity_green_kubo.template ├── calculation_subset │ ├── AtommanElasticConstants.py │ ├── AtommanGammaSurface.py │ ├── AtommanSystemLoad.py │ ├── AtommanSystemManipulate.py │ ├── CalculationSubset.py │ ├── Dislocation.py │ ├── FreeSurface.py │ ├── GRIP.py │ ├── GrainBoundary.py │ ├── LammpsCommands.py │ ├── LammpsMinimize.py │ ├── LammpsNEB.py │ ├── LammpsPotential.py │ ├── PointDefect.py │ ├── PointDefectNEB.py │ ├── StackingFault.py │ ├── Units.py │ └── __init__.py ├── check_modules.py ├── command_line.py ├── database │ ├── BaseEmperorPrepare.py │ ├── CDCSDatabase.py │ ├── IprPyDatabase.py │ ├── LocalDatabase.py │ ├── MongoDatabase.py │ ├── __init__.py │ ├── load_database.py │ ├── master_prepare.py │ ├── prepare.py │ ├── reset_orphans.py │ └── runner.py ├── fix_lammps_versions.py ├── input │ ├── __init__.py │ ├── boolean.py │ ├── buildcombos.py │ ├── buildcombos_functions │ │ ├── README.rst │ │ ├── __init__.py │ │ ├── atomicarchive.py │ │ ├── atomicparent.py │ │ ├── atomicreference.py │ │ ├── crystalprototype.py │ │ ├── defect.py │ │ ├── defectmobility.py │ │ ├── diatom.py │ │ └── lammpspotential.py │ ├── parse.py │ ├── subset_classes │ │ └── pointdefectmobility │ │ │ ├── __init__.py │ │ │ └── pointdefectmobility.py │ ├── termtodict.py │ └── value.py ├── load_run_directory.py ├── quickcheck │ ├── QuickCheck.md │ ├── QuickCheck.py │ ├── QuickCheckCrystal.py │ └── __init__.py ├── record │ ├── MDSolidProperties.py │ ├── PotentialProperties.py │ ├── PotentialPropertiesSubsets │ │ ├── CrystalStructure.py │ │ ├── DiatomScan.py │ │ ├── ElasticConstants.py │ │ ├── EvsRScan.py │ │ ├── FreeSurface.py │ │ ├── MDLiquid.py │ │ ├── MDSolid.py │ │ ├── MDThermo.py │ │ ├── Phonon.py │ │ ├── PointDefect.py │ │ ├── PotentialsPropertiesSubset.py │ │ ├── StackingFault.py │ │ └── __init__.py │ ├── __init__.py │ ├── point_defect_mobility │ │ ├── PointDefectMobility.py │ │ ├── __init__.py │ │ └── record-point-defect-mobility.xsd │ └── xsd │ │ ├── PotentialProperties.xsd │ │ └── __init__.py ├── tools │ ├── __init__.py │ ├── dict_insert.py │ ├── dynamic_import.py │ ├── num_deriv_3_point.py │ └── read_calc_file.py ├── value │ ├── CijValue.py │ ├── __init__.py │ ├── inputvalue │ │ ├── InputValue.py │ │ └── __init__.py │ └── resultvalue │ │ ├── ResultValue.py │ │ └── __init__.py └── workflow │ ├── Emperor.py │ ├── RunRun.py │ ├── __init__.py │ ├── multi_runner_slurm.py │ ├── multi_runners.py │ ├── multiprocessing_runners.py │ └── prepare │ ├── __init__.py │ ├── point_defect_mobility.py │ └── point_defect_static-original.py ├── make_calc_in_files.py ├── notebook ├── E_vs_r_scan │ ├── E_vs_r_scan - Methodology and code.ipynb │ └── E_vs_r_scan - Python class.ipynb ├── README.md ├── bond_angle_scan │ └── bond_angle_scan - Methodology and code.ipynb ├── crystal_space_group │ └── crystal_space_group - Methodology and code.ipynb ├── diatom_scan │ ├── diatom_scan - Methodology and code.ipynb │ └── diatom_scan - Python class.ipynb ├── dislocation_SDVPN │ └── dislocation_SDVPN - Methodology and code.ipynb ├── dislocation_monopole │ └── dislocation_monopole - Methodology and code.ipynb ├── dislocation_periodic_array │ └── dislocation_periodic_array - Methodology and code.ipynb ├── elastic_constants_dynamic │ └── elastic_constants_dynamic - Methodology and code.ipynb ├── elastic_constants_static │ └── elastic_constants_static - Methodology and code.ipynb ├── energy_check │ └── energy_check - Methodology and code.ipynb ├── isolated_atom │ ├── isolated_atom - Methodology and code.ipynb │ └── isolated_atom - Python class.ipynb ├── phonon │ └── phonon - Methodology and code.ipynb ├── point_defect_diffusion │ └── point_defect_diffusion.ipynb ├── point_defect_mobility │ └── point_defect_mobility - Methodology and code.ipynb ├── point_defect_static │ └── point_defect_static - Methodology and code.ipynb ├── relax_box │ └── relax_box - Methodology and code.ipynb ├── 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