aim2dat.io¶

Subpackage containing functions to read or write files.

Functions¶

Package Contents¶

aim2dat.io.read_cif_file(file_path: str, extract_structures: bool = False, strct_check_chem_formula: bool = True, strct_get_sym_op_from_sg: bool = True, strct_wrap: bool = False) → dict[source]¶

Read cif file.

Parameters:¶

• file_path (str) – Path to the cif file.

• extract_structures (bool (optional)) – Whether to extract alls crystal structures and add them to the output dictionary with the key 'structures'.

• strct_check_chem_formula (bool (optional)) – Check the chemical formula given by field matches with the structure.

• strct_get_sym_op_from_sg (bool (optional)) – Add symmetry operations based on the space group to add symmetry equivalent sites to the structures.

Returns:¶

dict – Output dictionary.

aim2dat.io.read_cp2k_band_structure(file_path: str) → dict[source]¶

Read band structure file from CP2K.

Parameters:¶

file_path (str) – Path of the output-file of CP2K containing the band structure.

Returns:¶

band_structure (dict) – Dictionary containing the k-path and the eigenvalues as well as the occupations.

aim2dat.io.read_cp2k_proj_dos(folder_path: str) → dict[source]¶

Read the atom projected density of states from CP2K.

Parameters:¶

folder_path (str) – Path to the folder of the pdos files.

Returns:¶

pdos (dict) – Dictionary containing the projected density of states for each kind.

aim2dat.io.read_cp2k_restart_structure(folder_path: str) → dict | list[dict][source]¶

Read structures from ‘restart’-files.

Parameters:¶

folder_path (str) – Path to the folder containing the CP2K output-files.

Returns:¶

dict or list – Dictionary or list of dictionaries containing the structural information. In case of a farming job or several calculations have been run in the same folder, a list of dictionaries is returned.

aim2dat.io.read_cp2k_stdout(file_path: str, parser_type: str = 'standard', raise_error: bool = True) → dict[source]¶

Read standard output file of CP2K.

Parameters:¶

• file_path (str) – Path to the output file.

• parser_type (str) – Defines the quantities that are being parsed. Supported options are 'standard', 'partial_charges' and 'trajectory'.

• raise_error (bool) – Whether to raise an error if a flaw is detected in the output file.

Returns:¶

dict – Dictionary containing the parsed values.

aim2dat.io.read_critic2_plane(file_path: str) → dict[source]¶

Read output plane file.

Parameters:¶

file_path (str) – Path to the file.

Returns:¶

dict – plane details.

aim2dat.io.read_critic2_stdout(file_path: str, raise_error: bool = True) → dict[source]¶

Read standard output file.

Parameters:¶

• file_path (str) – Path to the file.

• raise_error (bool) – Whether to raise an error if a flaw is detected in the output file.

Returns:¶

dict – Results.

aim2dat.io.read_fhiaims_band_structure(folder_path: str, soc: bool = False) → dict[source]¶

Read band structure files from FHI-aims. Spin-polarized calculations are not yet supported.

Parameters:¶

• folder_path (str) – Path to the folder of the band structure files.

• soc (bool (optional)) – Whether spin-orbit coupling is activated. The default value is False.

Returns:¶

band_structure (dict) – Dictionary containing the k-path and th eigenvalues as well as the occupations.

aim2dat.io.read_fhiaims_proj_dos(folder_path: str, soc: bool = False, load_raw: bool = False) → dict[source]¶

Read the atom projected density of states from FHI-aims.

Parameters:¶

• folder_path (str) – Path to the folder of the pdos files or list of pdos files or path to a pdos file.

• soc (bool (optional)) – Whether spin-orbit coupling is activated. The default value is False.

• load_raw (bool (optional)) – Load files with appendix ‘raw’. The default value is False.

Returns:¶

pdos (dict) – Dictionary containing the projected density of states for each atom.

aim2dat.io.read_fhiaims_total_dos(file_path: str) → dict[source]¶

Read the total density of states from FHI-aims.

Parameters:¶

file_path (str) – Path of the output-file of FHI-aims containing the total density of states.

Returns:¶

pdos (dict) – Dictionary containing the projected density of states for each atom.

aim2dat.io.read_hdf5_structure(file_path: str) → list[dict][source]¶

Read hdf5 structure file.

Parameters:¶

file_path (str) – Path to hdf5 file.

Returns:¶

list – List of dictionaries, each representing a molecular/crystalline structure.

aim2dat.io.read_phonopy_band_structure(file_path: str, kpath: list, npoints: int, force_sets_file_path: str = None, force_constants_file_path: str = None, path_labels: list = None, phonopy_kwargs: dict = None) → tuple[dict, list][source]¶

Read band structure using phonopy.

Parameters:¶

• file_path (str) – Phonopy yaml-file containing all settings and parameters.

• kpath (list) – Nested list of high-symmetry points.

• npoints (int) – Nr of points on the k-path.

• force_sets_file_path (str or None) – Force sets file. If set to None, force_constants_file_path needs to be set.

• force_constants_file_path (str or None) – Force constants file. If set to None, force_sets_file_path needs to be set.

• path_labels (list or None) – List of labels for the high-symmetry points specified in kpath.

• phonopy_kwargs (dict) – Additional keywords for phonopy.load.

Returns:¶

• output_bands (dict) – Dictionary containing the k-path and the eigenvalues.

• reference_cell (list) – Reference cell.

aim2dat.io.read_phonopy_proj_dos(file_path: str, mesh: int | list = 100, force_sets_file_path: str = None, force_constants_file_path: str = None, phonopy_kwargs: dict = None) → dict[source]¶

Read the atom projected density of phonon states from phonopy.

Parameters:¶

• file_path (str) – Phonopy yaml-file containing all settings and parameters.

• mesh (list) – Number of points in each dimension.

• force_sets_file_path (str or None) – Force sets file. If set to None, force_constants_file_path needs to be set.

• force_constants_file_path (str or None) – Force constants file. If set to None, force_sets_file_path needs to be set.

• phonopy_kwargs (dict) – Additional keywords for phonopy.load.

Returns:¶

dict – Dictionary containing the projected density of states for each kind.

aim2dat.io.read_phonopy_qha_properties(calculation_folder_paths: list = None, thermal_properties_file_paths: list = None, ev_file_path: str = None, stdout_file_path: str = None, mesh: int | list = 100, t_min: int = 0, t_max: int = 1000, t_step: int = 10, phonopy_kwargs: dict = None)[source]¶

Read the outputs from a quasi-harmonic approximation calculation.

Parameters:¶

• calculation_folder_paths (list or None) – Folders containing the calculations of different volumes. If None thermal_properties_file_paths needs to be set instead.

• thermal_properties_file_paths (list or None) – List of thermal properties yaml files generated by phonopy.

• thermal_properties_file_paths (str or None) – File containing volumes and energies.

• ev_file_path (str or None) – Path to the e-V file.

• stdout_file_path (str or None) – File name of the standard output file.

• mesh (list or int) – Number of points in each dimension.

• t_min (int) – Minimum temperature

• t_max (int) – Maximum temperature

• phonopy_kwargs (dict) – Additional keywords for phonopy.load.

Returns:¶

dict – Dictionary containing the qha properties.

aim2dat.io.read_phonopy_thermal_properties(file_path: str, mesh: int | list = 100, t_min: int = 0, t_max: int = 1000, t_step: int = 10, force_sets_file_path: str = None, force_constants_file_path: str = None, phonopy_kwargs: dict = None)[source]¶

Read the thermal properties from phonopy.

Parameters:¶

• file_path (str) – Phonopy yaml-file containing all settings and parameters.

• mesh (list) – Number of points in each dimension.

• t_min (int) – Minimum temperature

• t_max (int) – Maximum temperature

• force_sets_file_path (str or None) – Force sets file. If set to None, force_constants_file_path needs to be set.

• force_constants_file_path (str or None) – Force constants file. If set to None, force_sets_file_path needs to be set.

• phonopy_kwargs (dict) – Additional keywords for phonopy.load.

Returns:¶

dict – Dictionary containing the thermal properties.

aim2dat.io.read_phonopy_total_dos(file_path: str, mesh: int | list = 100, force_sets_file_path: str = None, force_constants_file_path: str = None, phonopy_kwargs: dict = None) → dict[source]¶

Read the total density of phonon states from phonopy.

Parameters:¶

• file_path (str) – Phonopy yaml-file containing all settings and parameters.

• mesh (list) – Number of points in each dimension.

• force_sets_file_path (str or None) – Force sets file. If set to None, force_constants_file_path needs to be set.

• force_constants_file_path (str or None) – Force constants file. If set to None, force_sets_file_path needs to be set.

• phonopy_kwargs (dict) – Additional keywords for phonopy.load.

Returns:¶

dict – Dictionary containing the total density of states.

aim2dat.io.read_qe_band_structure(file_path: str) → dict[source]¶

Read band structure file from Quantum ESPRESSO. Spin-polarized calculations are not yet supported.

Parameters:¶

file_path (str) – Path of the output-file of Quantum ESPRESSO containing the band structure.

Returns:¶

band_structure (dict) – Dictionary containing the k-path and th eigenvalues as well as the occupations.

aim2dat.io.read_qe_input_structure(file_path: str) → dict[source]¶

Read structure from the Quantum ESPRESSO input file. ibrav parameters are not yet fully supported.

Parameters:¶

file_path (str) – Path of the input-file of Quantum ESPRESSO containing structural data.

Returns:¶

dict – Dictionary containing the structural information.

aim2dat.io.read_qe_proj_dos(folder_path)[source]¶

Read the projected density of states from Quantum ESPRESSO.

Parameters:¶

folder_path (str) – Path to the folder containing the pdos ouput-files.

Returns:¶

pdos (dict) – Dictionary containing the projected density of states for each atom.

aim2dat.io.read_qe_total_dos(file_path: str) → dict[source]¶

Read the total density of states from Quantum ESPRESSO.

Parameters:¶

file_path (str) – Path of the output-file of Quantum ESPRESSO containing the total density of states.

Returns:¶

pdos (dict) – Dictionary containing the projected density of states for each atom.

aim2dat.io.read_qe_xml(file_path: str, extract_structures: bool = False, strct_type: str = None, strct_include: list = None, raise_error: bool = True) → dict[source]¶

Read xml output file.

Parameters:¶

• file_path (str) – Path of the xml-file of Quantum ESPRESSO.

• extract_structures (bool) – Whether to extract alls crystal structures and add them to the output dictionary with the key 'structures'.

• strct_type (str) – Type of extracted structure(s). Supported options are 'input', 'output' or 'steps'.

• strct_include (list) – List of dictionary keys that are included in the structure attributes.

• raise_error (bool) – Whether to raise an error if a flaw is detected in the output file.

Returns:¶

dict – Output dictionary.

aim2dat.io.read_xmgrace_band_structure(file_path: str, kpoints: list) → list[source]¶

Read xmgrace band structure file.

Parameters:¶

• file_path (str) – Path to the xmgrace file.

• kpoints (list) – List of tuples containing the label and the k-point.

Returns:¶

band_structures (list) – List of band structures.

aim2dat.io.read_xmgrace_file(file_path: str) → list | tuple[source]¶

Read xmgrace plot filies.

Up to now the functionality is very limited. xy-data is read and grouped by the line-color.

Notes

TODO: Increase functionality and generality.

Parameters:¶

file_path (str) – Path to the xmgrace file.

Returns:¶

• x_values (list) – Nested list of the x-values.

• y_values (list) – Nested list of the y-values.

• tick_labels (tuple) – Tuple of dictionaries containing the position on the x-axis (“pos”) and the label (“label”).

aim2dat.io.read_yaml_file(file_path: str, typ: str = 'safe')[source]¶

Load a yaml-file and returns the content.

Parameters:¶

• file_path (str) – Path to the yaml-file.

• typ (str (optional)) – Typ used to load the yaml-file.

Returns:¶

data – Content of the file.

aim2dat.io.write_hdf5_structure(file_path: str, structures: list[aim2dat.strct.structure.Structure])[source]¶

Write a list of structures to file.

Parameters:¶

• file_path (str) – Path to hdf5 file.

• structures (list) – List of structures.

aim2dat.io.write_yaml_file(file_path: str, content)[source]¶

Write content to a yaml-file.

Parameters:¶

• file_path (str) – Path to the yaml-file.

• content – Content of the file.

aim2dat.io.write_zeo_file(file_path: str, struct_dict: dict)[source]¶

Write structure dictonaryto an input file for zeo++.

Parameters:¶

• file_path (str) – Path to the zeo-file. Possible endings are '.cssr', '.v1', or '.cuc'.

• struct_dict (dict) – Structure which is written to the file.

Raises:¶

ValueError – Invalid file format. Allowed formats are: '.cssr', '.v1', or '.cuc'.