shakenbreak.io module#
Module to parse input and output files for VASP, Quantum Espresso, FHI-aims, CASTEP and CP2K.
- shakenbreak.io.parse_energies(defect: str, path: str | None = '.', code: str | None = 'vasp', filename: str | None = 'OUTCAR', verbose: bool = False) None[source]#
Parse final energy for all distortions present in the given defect directory and write them to a yaml file in the defect directory. Returns the energies_file path.
- Parameters:
defect (
str) – Name of defect to parse, including charge state. Should match the name of the defect folder.( (path) – obj: str): Path to the top-level directory containing the defect folder. Defaults to current directory (“.”).
code (
str) – Name of ab-initio code used to run the geometry optimisations, case insensitive. Options include: “vasp”, “cp2k”, “espresso”, “castep” and “fhi-aims”. Defaults to “vasp”.filename (
str) – Filename of the output file, if different from the ShakeNBreak defaults that are defined in the default input files: (i.e. vasp: “OUTCAR”, cp2k: “relax.out”, espresso: “espresso.out”, castep: “*.castep”, fhi-aims: “aims.out”) Default to the ShakeNBreak default filenames.verbose (
bool) – If True, print information about renamed/saved-over files. Defaults to False.
Returns: energies_file path.
- shakenbreak.io.parse_fhi_aims_input(path: str) dict[source]#
Parse the input file of FHI-aims and return it as a dictionary of the parameters.
- Parameters:
path (
str) – Path to the Quantum Espresso input file.
Returns:
dict
- shakenbreak.io.parse_qe_input(path: str) dict[source]#
Parse the input file of Quantum Espresso and return it as a dictionary of the parameters.
- Parameters:
path (
str) – Path to the Quantum Espresso input file.
Returns:
dict
- shakenbreak.io.parse_structure(code: str, structure_path: str, structure_filename: str) Structure | str[source]#
Parses the output structure from different codes (VASP, CP2K, Quantum Espresso, CATSEP, FHI-aims) and converts it to a pymatgen Structure object.
- Parameters:
code (
str) – Code used for geometry optimizations. Valid code names are: “vasp”, “espresso”, “cp2k”, “castep” and “fhi-aims” (case insensitive).structure_path (
str) – Path to directory containing the structure file.structure_filename (
str) – Name of the structure file or the output file containing the optimized structure. If not set, the following values will be used for each code: vasp: “CONTCAR”, cp2k: “cp2k.restart” (The restart file is used), Quantum espresso: “espresso.out”, castep: “castep.castep” (castep output file is used) fhi-aims: geometry.in.next_step
- Returns:
pymatgen Structure object
- Return type:
Structure
- shakenbreak.io.read_castep_structure(filename: str) Structure | str[source]#
Reads a structure from CASTEP output (.castep) file and returns it as a pymatgen Structure.
- Parameters:
filename (
str) – Path to the CASTEP output file.- Returns:
pymatgen Structure object
- Return type:
Structure
- shakenbreak.io.read_cp2k_structure(filename: str) Structure | str[source]#
Reads a structure from CP2K restart file and returns it as a pymatgen Structure.
- Parameters:
filename (
str) – Path to the cp2k restart file.- Returns:
pymatgen Structure object
- Return type:
Structure
- shakenbreak.io.read_espresso_structure(filename: str) Structure | str[source]#
Reads a structure from Quantum Espresso output and returns it as a pymatgen Structure.
- Parameters:
filename (
str) – Path to the Quantum Espresso output file.- Returns:
pymatgen Structure object
- Return type:
Structure
- shakenbreak.io.read_fhi_aims_structure(filename: str, format='aims') Structure | str[source]#
Reads a structure from FHI-aims output and returns it as a pymatgen Structure.
- Parameters:
filename (
str) – Path to the FHI-aims output file.format (
str) – either aims-output (output file) aims (geometry file)
- Returns:
pymatgen Structure object
- Return type:
Structure