### Example unitcell.yaml Structure Source: https://kumagai-group.github.io/pydefect/tutorial.html An example of the 'unitcell.yaml' file generated by Pydefect, containing system name, band edges, and dielectric constants. ```yaml system: MgAl2O4 vbm: 4.0183 cbm: 9.2376 ele_dielectric_const: - - 3.075988 - 0.0 - -0.0 - - 0.0 - 3.075988 - 0.0 - - -0.0 - -0.0 - 3.075988 ion_dielectric_const: - - 5.042937 - -0.0 - -0.0 - - -0.0 - 5.042937 - 0.0 - - -0.0 - 0.0 - 5.042937 ``` -------------------------------- ### Calculation Summary Table Example Source: https://kumagai-group.github.io/pydefect/tutorial.html An example of the output from `pydefect cs`, presented as a markdown table. It details various properties for each defect, such as symmetry relations and defect types. ```markdown |:---------:|:----------:|:-----------:|:-----------------:|:------------:|:------------------:|:--------------:| | name | Ele. conv. | Ionic conv. | Is energy strange | Same config. | Defect type | Symm. Relation | | Al_i1_-1 | . | . | . | False | unknown | subgroup | | Al_i1_0 | . | . | . | False | unknown | subgroup | | Al_i1_1 | . | . | . | False | unknown | subgroup | | Al_i1_2 | . | . | . | . | . | . | | Al_i1_3 | . | . | . | . | . | . | | Mg_i1_0 | . | . | . | . | . | . | | Mg_i1_1 | . | . | . | . | . | . | | Mg_i1_2 | . | . | . | . | . | . | | O_i1_-1 | . | . | . | . | . | . | | O_i1_-2 | . | . | . | False | interstitial_split | subgroup | ``` -------------------------------- ### Example Directory Structure for Defects Source: https://kumagai-group.github.io/pydefect/tutorial.html Illustrates the directory structure created by Pydefect after processing defect species, showing perfect and various defect configurations. ```text perfect/ Va_O1_0/ Va_O1_1/ Va_O1_2/ ``` -------------------------------- ### Example POSCAR Structure Source: https://kumagai-group.github.io/pydefect/first_principles_calc.html An example of a POSCAR file format, showing lattice parameters, atom types, counts, and direct coordinates. This is the output format after symmetrization. ```vasp Mg7 Al16 O32 1.0 8.105607 0.000000 0.000000 0.000000 8.105607 0.000000 0.000000 0.000000 8.105607 Mg Al O 7 16 32 direct 0.749726 0.749738 0.249693 Mg 0.749726 0.249738 0.749693 Mg ... (truncated for brevity) ... ``` -------------------------------- ### Example Correction Energy Output Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html This is an example of the output from `pydefect_print`, showing the calculated components contributing to the correction energy. ```text +--------------------+ | charge | 0 | | additional charge | 1 | | pc 1st term | 0 | | pc 2nd term | 0.819326 | | alignment 1st term | -0.0953654 | | alignment 2nd term | -0.10711 | | alignment 3rd term | -0 | | correction energy | 0.61685 | +--------------------+------------+ ``` -------------------------------- ### Defect Energy Info YAML Structure Source: https://kumagai-group.github.io/pydefect/tutorial.html An example structure of a `defect_energy_info.yaml` file. Note that `formation_energy` assumes standard state chemical potentials and a Fermi level at 0 eV. Custom energy corrections can be added. ```yaml name: Va_O1 charge: 0 formation_energy: 6.803585744999999 atom_io: O: -1 energy_corrections: pc term: 0.0 alignment term: -0.0 is_shallow: False ``` -------------------------------- ### Defect Energy Summary JSON Structure Source: https://kumagai-group.github.io/pydefect/tutorial.html An example of the `defect_energy_summary.json` content, showing relative chemical potentials, band edge information, and a table summarizing defect properties like charge, energy, and shallow status. ```json title: MgAl₂O₄ rel_chem_pots: -A Al: 0.00 Mg: -0.69 O: -5.25 -B Al: 0.00 Mg: -0.32 O: -5.34 -C Al: -7.87 Mg: -5.94 O: 0.00 -D Al: -8.01 Mg: -5.66 O: 0.00 vbm: 0.00, cbm: 5.22, supercell vbm: -0.03, supercell_cbm: 6.14 name atom_io charge energy correction is_shallow ------ ------------ -------- -------- ------------ ------------ Al_i1 Al: 1 -1 14.958 -0.049 False 0 9.896 0.000 True 1 3.376 0.527 False 2 -0.872 1.814 True 3 -6.994 3.370 False Mg_i1 Mg: 1 0 8.208 0.000 True 1 2.015 0.555 True 2 -4.117 1.534 False O_i1 O: 1 -2 8.122 0.721 False -1 7.055 0.149 False 0 4.566 0.000 False Va_Al1 Al: -1 -3 13.527 3.402 False -2 12.968 1.789 True -1 12.672 0.660 True 0 12.595 0.000 True 1 12.710 -0.232 True Va_Mg1 Mg: -1 -2 10.093 1.524 False -1 9.580 0.578 True 0 9.311 0.000 False Va_MgO O: -1 Mg: -1 0 9.887 0.000 False Va_O1 O: -1 0 6.804 0.000 False 1 3.808 0.166 False 2 0.883 0.845 False ``` -------------------------------- ### Extract Final Atom Energies from VASP OUTCAR Source: https://kumagai-group.github.io/pydefect/tutorial.html This Python script iterates through elements, attempts to open their respective OUTCAR files, and prints their final energies. It requires pymatgen to be installed. ```python from pymatgen.core import Element from pymatgen.io.vasp import Outcar for e in Element: try: o = Outcar(str(e) + "/OUTCAR-finish") name = str(e) + ":" print(f"{name:<3} {o.final_energy:11.8f}") except: pass ``` -------------------------------- ### Prepare Defect Calculation Directory Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html Use this command to set up the directory for defect calculations, including setting NSW to 1 and adjusting the charge state. ```bash vise vs -uis NSW 1 --options charge 1 -d ../ -t defect ``` -------------------------------- ### Create VASP Input Files Source: https://kumagai-group.github.io/pydefect/tutorial.html Iterate through directories and use `vise vs` to create VASP input files for each. This step is part of preparing for VASP calculations. ```bash for i in */; do cd $i; vise vs; cd ../; done ``` -------------------------------- ### Prepare Atom Energies with Vise Source: https://kumagai-group.github.io/pydefect/tutorial.html Use `vise_util map` to prepare atom directories for aligning energy standards. This is a prerequisite for generating composition energies. ```bash vise_util map -e Mg Al O ``` -------------------------------- ### Generate Calculation Summary Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to create a `calc_summary.json` file, which provides a summary of calculations, including information on electronic and ionic convergence, energy strangeness, and defect types. It requires defect directories and perfect supercell calculation results. ```bash pydefect cs -d *_*/ -pcr perfect/calc_results.json ``` -------------------------------- ### Create Defect Energy Summary JSON Source: https://kumagai-group.github.io/pydefect/tutorial.html This command compiles information from individual `defect_energy_info.yaml` files into a single `defect_energy_summary.json`. It requires defect directories, unit cell info, and perfect supercell band edge states. ```bash pydefect des -d *_*/ -u ../unitcell/unitcell.yaml -pbes perfect/perfect_band_edge_state.json -t ../cpd/target_vertices.yaml ``` -------------------------------- ### Generate VASP Input Files for Defect Calculations Source: https://kumagai-group.github.io/pydefect/tutorial.html Loop through defect directories to generate VASP input files using `vise vs -t defect`. Ensure the `-t defect` option is used for defect-specific inputs. Gamma-only VASP is recommended for large supercells with Gamma-point sampling. ```bash for i in */; do cd $i; vise vs -t defect; cd ../; done ``` -------------------------------- ### Generate VESTA Files for Defect Visualization Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `dvf` subcommand from `pydefect_util` to generate `defect.vesta` files for visualizing defect structures in VESTA. ```bash pydefect_util dvf -d *_*/ ``` -------------------------------- ### Create Defect Calculation Directories with pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `defect_entries` subcommand to create directories for each defect, including a `perfect/` directory. Running the command again will skip existing directories. ```bash pydefect_vasp de ``` -------------------------------- ### Generate VASP Input for Band, DOS, and Dielectric Calculations Source: https://kumagai-group.github.io/pydefect/tutorial.html Generate VASP input files for band structure, density of states, and dielectric tensor calculations. Use '-uis' for custom INCAR settings. ```bash vise vs -x pbesol -t band -pd ../structure_opt vise vs -x pbesol -t dos -pd ../structure_opt -uis LVTOT True LAECHG True KPAR 1 vise vs -x pbesol -t dielectric_dfpt -pd ../structure_opt ``` -------------------------------- ### Visualize Convex Hull with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `pc` sub-command to generate a PDF visualization of the convex hull diagram. The output file is named `cpd.pdf`. ```bash pydefect pc ``` -------------------------------- ### Set VASP Environment Variables Source: https://kumagai-group.github.io/pydefect/tutorial.html Configure default functional and VASP pseudopotential directory for Vise. PMG_MAPI_KEY is required for querying POSCAR files and total energies. ```yaml PMG_DEFAULT_FUNCTIONAL: PBE_54 PMG_MAPI_KEY: xxxxxxxxxxxxxxxx PMG_VASP_PSP_DIR: /home/kumagai/potcars/ ``` -------------------------------- ### Display pydefect subcommand help Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the -h flag with any pydefect subcommand to view detailed help information and available arguments. ```bash pydefect s -h ``` -------------------------------- ### Inspect Defect Entry Information Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `pydefect_print` command to inspect the `defect_entry.json` file, which contains information about a point defect prior to first-principles calculations. ```bash pydefect_print defect_entry.json ``` -------------------------------- ### Generate VASP Input for Unit Cell Optimization Source: https://kumagai-group.github.io/pydefect/tutorial.html Use 'vise vasp_set' to generate VASP input files for structure optimization with the PBEsol functional. The default functional is PBE. ```bash vise vasp_set -x pbesol ``` -------------------------------- ### Generate defect_entry.json for Complex Defects Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `pydefect_vasp_util de` subcommand to generate `defect_entry.json` by analyzing structural differences between a defect and a perfect supercell. This is useful for complex defects or analyzing previous calculations. ```bash pydefect_vasp_util de -d . -p ../perfect/POSCAR -n complex_defect ``` -------------------------------- ### Generate Band Edge Orbital Information Source: https://kumagai-group.github.io/pydefect/tutorial.html This command analyzes defect directories to create band_edge_orbital_infos.json files and eigenvalues.pdf plots. It requires the perfect band edge state data as a reference. ```bash pydefect_vasp beoi -d *_* -pbes perfect/perfect_band_edge_state.json ``` -------------------------------- ### Generate Composition Energies File Source: https://kumagai-group.github.io/pydefect/tutorial.html Collect the total energies per formula unit from VASP calculations into a YAML file using the mce sub-command. Specify the directories containing the calculation results. ```bash pydefect_vasp mce -d *_*/ ``` -------------------------------- ### Retrieve Competing Phases with pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to retrieve POSCAR files for competing phases from the Materials Project database. Specify the elements and an energy cutoff above the convex hull. ```bash pydefect_vasp mp -e Mg Al O --e_above_hull 0.0005 ``` -------------------------------- ### Generate Defect Energy Information Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to generate `defect_energy_info.yaml` files for each defect. It requires paths to defect directories, perfect supercell results, unit cell information, and standard phase energies. ```bash pydefect dei -d *_*/ -pcr perfect/calc_results.json -u ../unitcell/unitcell.yaml -s ../cpd/standard_energies.yaml ``` -------------------------------- ### Set Oxidation States with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Manually set oxidation states for elements when constructing defect supercells. This is useful for cases where default inference might be incorrect. ```bash pydefect ds --oxi_states Mg 4 ``` -------------------------------- ### Configure VASP Output Filenames in vise.yaml Source: https://kumagai-group.github.io/pydefect/tutorial.html If VASP output files (vasprun.xml, OUTCAR) are renamed, update the vise.yaml configuration to point to the new filenames for proper parsing. ```yaml vasprun: vasprun-finish.xml OUTCAR: OUTCAR-finish ``` -------------------------------- ### Generate Standard and Relative Energies with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `sre` sub-command to create `standard_energies.yaml` and `relative_energies.yaml` files. The standard energies file contains absolute energies of elements under standard states, while the relative energies file contains energies relative to these standard states. ```bash pydefect sre ``` -------------------------------- ### Identify Interstitial Sites from Charge Density Source: https://kumagai-group.github.io/pydefect/tutorial.html Run this command to find local minima in the charge density, which may indicate favorable interstitial sites. Ensure AECCAR{0,2} files are present. ```bash pydefect_vasp le -v AECCAR{0,2} -i all_electron_charge ``` -------------------------------- ### Generate Composition Energies with Pydefect Utility Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `pydefect_util cefm` command to generate `composition_energies.yaml` from atom energies. This file is used in subsequent CPD calculations. ```bash pydefect_util cefm -a atom_energies.yaml -e Mg Al O ``` -------------------------------- ### Iterative Equilibrium Concentration Calculation Log Source: https://kumagai-group.github.io/pydefect/concentrations.html This log output shows the progress of an iterative calculation to find the equilibrium defect concentration. It indicates the number of iterations and the final pinning levels at a given temperature. ```log INFO: Calc equilibrium concentration: iteration 0 INFO: Calc equilibrium concentration: iteration 1 INFO: Calc equilibrium concentration: iteration 2 INFO: Calc equilibrium concentration: iteration 3 INFO: Calc equilibrium concentration: iteration 4 INFO: Calc equilibrium concentration: iteration 5 INFO: Calc equilibrium concentration: iteration 6 INFO: Equilibrium concentration is found. T: 300 Pinning levels: ----------- ----- ----- Cs_2VCu 3.150 Cs_Cu1 Cs_i1 1.266 Cu_Cs1 Cu_i1 O_i1 Va_Cs1 3.201 Va_Cu-split Va_Cu1 2.796 Va_O1 0.028 ----------- ----- ----- ``` -------------------------------- ### Generate Total DOS for Carrier Concentration Calculation Source: https://kumagai-group.github.io/pydefect/concentrations.html Use this command to generate the total density of states (DOS) file required for carrier concentration calculations. Ensure the path to the VASP output is correct. ```bash pydefect_vasp_util make_total_dos ../unitcell/dos/vasprun.xml -o ../unitcell/dos/OUTCAR ``` -------------------------------- ### Generate Perfect Band Edge State Data Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to generate the initial JSON file containing the band edge states of a perfect supercell. This serves as a reference for defect analysis. ```bash pydefect_vasp pbes -d perfect ``` -------------------------------- ### Construct Convex Hull with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `cv` sub-command to construct the convex hull (CPD) for a target compound. Specify the target compound using the `-t` flag. ```bash pydefect cv -t MgAl2O4 ``` -------------------------------- ### Generate INCAR for WAVECAR Creation Source: https://kumagai-group.github.io/pydefect/first_principles_calc.html This command prepares an INCAR file for a GGA-based calculation to generate a WAVECAR file. It removes LHFCALC and ALGO tags and sets NSW to 1, optimizing for speed in the pre-calculation step. ```bash grep -v LHFCALC INCAR | grep -v ALGO | sed s/"NSW = 50"/"NSW = 1"/ > INCAR-pre ``` -------------------------------- ### Calculate Carrier Concentrations Source: https://kumagai-group.github.io/pydefect/concentrations.html Calculate carrier concentrations (electron and hole) at a specified temperature using the generated total DOS file. The results are saved to a JSON file. ```bash pydefect_util calc_carrier_concentrations -t total_dos.json -T 1000 ``` -------------------------------- ### Gather Unit Cell Information with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Collect bulk properties like band edges and dielectric tensors using the 'pydefect_vasp u' command. This generates a 'unitcell.yaml' file. ```bash pydefect_vasp u -vb band/vasprun-finish.xml -ob band/OUTCAR-finish -odc dielectric/OUTCAR-finish -odi dielectric/OUTCAR-finish -n MgAl2O4 ``` -------------------------------- ### Evaluate Site Degeneracies for Defect Concentration Calculation Source: https://kumagai-group.github.io/pydefect/concentrations.html Determine the degeneracy of equivalent sites in a supercell, which is crucial for accurate defect concentration calculations. This command requires paths to defect and supercell information files. ```bash pydefect_util make_degeneracies -d ../defects/*_*_*/ -s ../defects/supercell_info.json ``` -------------------------------- ### Print Band Edge States Information Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to display the contents of the band_edge_states.json file in a human-readable format. This allows for detailed examination of defect states, including their energy, occupation, and orbital contributions. ```bash pydefect_print band_edge_states.json ``` -------------------------------- ### Parse VASP Calculation Results for Defect Properties Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `calc_results` subcommand to generate `calc_results.json` in all defect directories after VASP calculations are complete. This file contains key results relevant to defect properties. In-progress calculations are automatically skipped. ```bash pydefect_vasp cr -d *_*/ perfect ``` -------------------------------- ### Print Supercell Info from JSON Source: https://kumagai-group.github.io/pydefect/tutorial.html Extracts and displays human-readable information from a `supercell_info.json` file. This provides a summary of the supercell's properties. ```bash pydefect_print supercell_info.json ``` -------------------------------- ### Plot Defect Formation Energies with pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `pydefect pe` command to generate a plot of defect formation energies. Specify the input data file with `-d` and select the chemical potential condition with `-l`. ```bash pydefect pe -d defect_energy_summary.json -l A ``` -------------------------------- ### Print Volumetric Data Local Extrema Source: https://kumagai-group.github.io/pydefect/tutorial.html Use this command to view the contents of the volumetric_data_local_extrema.json file, which details the identified local minima. ```bash pydefect_print volumetric_data_local_extrema.json ``` -------------------------------- ### Generate Calculation Results Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html Execute this command to generate the `calc_results.json` file after VASP has finished running. ```bash pydefect cr -d . ``` -------------------------------- ### Create Supercell with Transformation Matrix Source: https://kumagai-group.github.io/pydefect/tutorial.html Generates a supercell using a specified transformation matrix applied to the conventional unit cell. Be cautious as anisotropic supercells can alter symmetry. ```bash pydefect s -p ../unitcell/structure_opt/CONTCAR-finish --matrix 2 1 1 ``` -------------------------------- ### Analyze Defect Structures with Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html The `dsi` subcommand analyzes local structures around defects, generating `defect_structure_info.json` files. This information can be viewed using `pydefect_print`. ```bash pydefect dsi -d *_*/ ``` ```text -- defect structure info Defect type: vacancy Site symmetry: -3m -> -3m (same) Has same configuration from initial structure: True Drift distance: 0.022 Defect center: ( 0.625, 0.375, 0.372) Removed atoms: 8 Al ( 0.625, 0.375, 0.375) Neighbor max distance 2.472 Displacements Elem Dist Displace Angle Index Initial site Final site Neighbor O 1.9 0.26 160 46 ( 0.639, 0.361, 0.139) -> ( 0.647, 0.353, 0.108) T O 1.92 0.26 160 42 ( 0.639, 0.139, 0.361) -> ( 0.647, 0.110, 0.351) T O 1.92 0.26 160 26 ( 0.861, 0.361, 0.361) -> ( 0.890, 0.353, 0.351) T O 1.92 0.24 170 47 ( 0.389, 0.389, 0.389) -> ( 0.360, 0.396, 0.394) T O 1.93 0.24 170 31 ( 0.611, 0.611, 0.389) -> ( 0.604, 0.639, 0.394) T O 1.94 0.23 160 35 ( 0.611, 0.389, 0.611) -> ( 0.604, 0.396, 0.637) T Al 2.85 0.03 30 14 ( 0.625, 0.125, 0.125) -> ( 0.627, 0.128, 0.127) Al 2.85 0.03 30 21 ( 0.875, 0.375, 0.125) -> ( 0.872, 0.373, 0.127) Al 2.87 0.05 40 16 ( 0.875, 0.125, 0.375) -> ( 0.872, 0.128, 0.372) ``` -------------------------------- ### Add Interstitial Sites from Local Extrema Source: https://kumagai-group.github.io/pydefect/tutorial.html Add specified interstitial sites (by index) from the local extrema file to the supercell_info.json. The --local_extrema flag points to the JSON file. ```bash pydefect_util ai --local_extrema ../unitcell/dos/volumetric_data_local_extrema.json -i 1 2 ``` -------------------------------- ### Define Defect Species and Charge States Source: https://kumagai-group.github.io/pydefect/tutorial.html Creates the `defect_in.yaml` file, which lists defect species and their charge states. This file can be edited manually or modified using options like `--keywords`. ```yaml Al_Mg1: [-1, 0, 1] Al_O1: [-1, 0, 1, 2, 3, 4, 5] Mg_Al1: [-1, 0, 1] O_Al1: [-5, -4, -3, -2, -1, 0, 1] Va_Al1: [-3, -2, -1, 0, 1] Va_Mg1: [-2, -1, 0] Va_O1: [0, 1, 2] ``` -------------------------------- ### Set ENCUT for VASP Calculations Source: https://kumagai-group.github.io/pydefect/tutorial.html Iterate through directories of competing phases to set the ENCUT parameter for VASP calculations using vise. The ENCUT is set to 1.3 times the maximum ENMAX of constituent POTCARs. ```bash for i in *_*/; do cd $i; vise vs -uis ENCUT 520.0 -x pbesol; cd ../; done ``` -------------------------------- ### Symmetrize Defect Structure with pydefect Source: https://kumagai-group.github.io/pydefect/first_principles_calc.html Use the `pydefect_vasp_util rdp` command to symmetrize the atomic positions of a defect structure, creating a new POSCAR file. This is useful when defect relaxation leads to structures that are not obviously symmetric. ```bash pydefect_vasp_util rdp -p Va_Mg1_0/CONTCAR-finish -d Va_Mg1_0/defect_entry.json -n POSCAR_new ``` -------------------------------- ### Calculate Defect Concentrations Source: https://kumagai-group.github.io/pydefect/concentrations.html Calculate defect concentrations at a specific point in the chemical potential diagram, using defect energy summary, degeneracies, and total DOS files. The calculation may involve iterative steps to find equilibrium. ```bash pydefect_util calc_defect_concentrations -d ../defects/defect_energy_summary.json -l A --degeneracies degeneracies.yaml -t total_dos.json ``` -------------------------------- ### Print Correction Energy Details Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html Use this command to display the detailed breakdown of the GKFO correction energy, including various terms and the final correction energy. ```bash pydefect_print ``` -------------------------------- ### Generate Band Edge States Data Source: https://kumagai-group.github.io/pydefect/tutorial.html This subcommand generates the band_edge_states.json file, which contains detailed information about the band edge states for defect calculations. It uses the perfect supercell's band edge states for comparison. ```bash pydefect bes -d *_*/ -pbes perfect/perfect_band_edge_state.json ``` -------------------------------- ### Apply Finite-Size Corrections to Charged Defects Source: https://kumagai-group.github.io/pydefect/tutorial.html Use the `efnv` subcommand to apply finite-size corrections to the total energies of charged defects. This requires static dielectric constants and atomic site potentials of the perfect supercell. Inspect the generated `correction.pdf` for visual verification. ```bash pydefect efnv -d *_*/ -pcr perfect/calc_results.json -u ../unitcell/unitcell.yaml ``` -------------------------------- ### Plot Carrier Concentrations Source: https://kumagai-group.github.io/pydefect/concentrations.html Visualize the calculated carrier concentrations. This command typically uses previously generated data files. ```bash pydefect_util plot_carrier_concentrations ``` -------------------------------- ### Apply GKFO Correction Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html This command applies the GKFO correction and generates `gkfo_correction.pdf` and `gkfo_correction.json`. Ensure the paths to unitcell.yaml and correction.json are correct. ```bash pydefect_util gkfo -u ../../../unitcell/unitcell.yaml -iefnv ../correction.json -icr ../calc_results.json -fcr calc_results.json -cd 1 ``` -------------------------------- ### Create Supercell from CONTCAR Source: https://kumagai-group.github.io/pydefect/tutorial.html Generates a supercell from a given CONTCAR file. Ensure the input structure is a standardized primitive cell to avoid errors. ```bash pydefect s -p ../unitcell/structure_opt/CONTCAR-finish ``` -------------------------------- ### Calculate Absorption Energy Source: https://kumagai-group.github.io/pydefect/vertical_transition_level.html Manual calculation of the absorption energy using the total energies of the initial and final states, CBM, and the calculated correction energy. ```text -411.920 + 405.739 + 9.2376 + 0.61685 = 3.67345 eV ``` -------------------------------- ### View Conventional Unit Cell Source: https://kumagai-group.github.io/pydefect/tutorial.html Displays the conventional unit cell structure. Refer to the help message for additional options. ```bash vise si -p ../unitcell/structure_opt/CONTCAR-finish -c ``` -------------------------------- ### Add Dopants for Defect Set Source: https://kumagai-group.github.io/pydefect/tutorial.html Adds dopant elements, such as Calcium (Ca), to the defect set configuration. This modifies the `defect_in.yaml` file. ```bash pydefect ds -d Ca ``` -------------------------------- ### Filter Defect Types with Regular Expressions in Pydefect Source: https://kumagai-group.github.io/pydefect/tutorial.html Restrict defect calculations to specific defect types using the -k option with a Python regular expression. This helps in focusing on relevant defect configurations. ```bash pydefect ds -k "Va_O[0-9]?_[0-9]+" ``` -------------------------------- ### Remove Interstitial Site Source: https://kumagai-group.github.io/pydefect/tutorial.html Remove a specific interstitial site (by index) from the supercell_info.json file. The -s flag specifies the input file. ```bash pydefect pi -i 1 -s supercell_info.json ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.