pyiron.vasp.structure module

pyiron.vasp.structure.atoms_from_string(string, read_velocities=False, species_list=None)[source]

Routine to convert a string list read from a input/output structure file and convert into Atoms instance

Parameters:
  • string (list) – A list of strings (lines) read from the POSCAR/CONTCAR/CHGCAR/LOCPOT file
  • read_velocities (bool) – True if the velocities from a CONTCAR file should be read (predictor corrector)
  • species_list (list/numpy.ndarray) – A list of species of the atoms
Returns:

The required structure object

Return type:

pyiron.atomistics.structure.atoms.Atoms

pyiron.vasp.structure.get_species_list_from_potcar(filename='POTCAR')[source]

Generates the species list from a POTCAR type file

Parameters:filename (str) – Input filename
Returns:A list of species symbols
Return type:list
pyiron.vasp.structure.manip_contcar(filename, new_filename, add_pos)[source]

Manipulate a CONTCAR/POSCAR file by adding something to the positions

Parameters:
  • filename (str) – Filename/path of the input file
  • new_filename (str) – Filename/path of the output file
  • add_pos (list/numpy.ndarray) – Array of values to be added to the positions of the input
pyiron.vasp.structure.read_atoms(filename='CONTCAR', return_velocities=False, species_list=None, species_from_potcar=False)[source]

Routine to read structural static from a POSCAR type file

Parameters:
  • filename (str) – Input filename
  • return_velocities (bool) – True if the predictor corrector velocities are read (only from MD output)
  • species_list (list/numpy.ndarray) – A list of the species (if not present in the POSCAR file or a POTCAR in the
  • directory) (same) –
  • species_from_potcar (bool) – True if the species list should be read from the POTCAR file in the same directory
Returns:

The generated structure object

Return type:

pyiron.atomistics.structure.atoms.Atoms

pyiron.vasp.structure.vasp_sorter(structure)[source]

Routine to sort the indices of a structure as it would be when written to a POSCAR file

Parameters:structure (pyiron.atomistics.structure.atoms.Atoms) – The structure whose indices need to be sorted
Returns:A list of indices which is sorted by the corresponding species for writing to POSCAR
Return type:list
pyiron.vasp.structure.write_poscar(structure, filename='POSCAR', write_species=True, cartesian=True)[source]

Writes a POSCAR type file from a structure object

Parameters:
  • structure (pyiron.atomistics.structure.atoms.Atoms) – The structure instance to be written to the POSCAR format
  • filename (str) – Output filename
  • write_species (bool) – True if the species should be written to the file
  • cartesian (bool) – True if the positions are written in Cartesian coordinates