pdyna.io module

pdyna.io: The collection of I/O functions to various input formats.

pdyna.io.chemical_from_formula(struct)[source]

Get the chemical formula from the structure object. Only recorded a limited range of structures.

Parameters:

struct (Structure) – The structure object.

Returns:

The chemical formula.

Return type:

str

pdyna.io.construct_cell(diagdisp, offdiag)[source]

Help function to create an ASE-cell with displacement vector from the lammps coordination system parameters.

Parameters:

  • diagdisp (tuple) – The diagonal displacement vector.

  • offdiag (tuple) – The off-diagonal displacement vector.

Returns:

The cell matrix and the displacement vector.

Return type:

tuple

pdyna.io.display_A_sites(A_sites)[source]

Display the A-site occupancy in the structure.

pdyna.io.get_max_index(index)[source]

Get the maximum index from a slice object or integer.

pdyna.io.lammps_data_to_ase_atoms(data, colnames, cell, celldisp, pbc=False, atomsobj=<class 'ase.atoms.Atoms'>, order=True, specorder=None, prismobj=None, units='metal')[source]

Extract positions and other per-atom parameters and create Atoms Taken directly from ASE

Parameters:

  • data (numpy.ndarray) – The LAMMPS data block.

  • colnames (list) – The column names.

  • cell (numpy.ndarray) – The lattice matrix.

  • celldisp (numpy.ndarray) – The lattice displacement.

  • pbc (bool) – The periodic boundary conditions.

  • atomsobj (class) – The atoms object class.

  • order (bool) – Order the atoms.

  • specorder (list) – The order of atomic species.

  • prismobj (class) – The prism object.

Returns:

The atomic structure in ASE.Atoms format.

Return type:

ase.Atoms

pdyna.io.print_time(times)[source]

Print the elapsed time for each step in the calculation.

pdyna.io.process_lammps_data(data, colnames, cell, celldisp, order=True, specorder=None, units='metal')[source]

Extract positions and other per-atom parameters from block of LAMMPS data. Modified from ASE functions

Parameters:

  • data (numpy.ndarray) – The LAMMPS data block.

  • colnames (list) – The column names.

  • cell (numpy.ndarray) – The lattice matrix.

  • celldisp (numpy.ndarray) – The lattice displacement.

  • order (bool) – Order the atoms.

  • specorder (list) – The order of atomic species.

  • units (str) – The LAMMPS units.

Returns:

The atomic symbols, lattices, and atomic positions.

Return type:

tuple

pdyna.io.process_lat(m)[source]

Convert lattice matrix to abc and three angles.

Parameters:

m (numpy.ndarray) – The lattice matrix.

Returns:

The abc lattice vectors and three angles.

Return type:

numpy.ndarray

pdyna.io.process_lat_reverse(cellpar)[source]

Convert abc and three angles to lattice matrix. Modified from ASE functions.

Parameters:

cellpar (numpy.ndarray) – The abc lattice vectors and three angles.

Returns:

The lattice matrix.

Return type:

numpy.ndarray

pdyna.io.read_ase_md_settings(fdir)[source]

Read the ASE MD input file and extract the simulation settings.

Parameters:

fdir (str) – The directory path.

Returns:

The simulation settings

Return type:

tuple

pdyna.io.read_ase_traj(filepath)[source]

Read the ASE internal trajectory file and extract the atomic symbols, lattices, and atomic positions. Modified from ASE original trajectory reading functions

Parameters:

filepath (str) – The ASE trajectory file.

Returns:

The atomic symbols, lattices, and atomic positions

Return type:

tuple

pdyna.io.read_lammps_dir(fdir, allow_multi=False)[source]

Read the LAMMPS input files in the directory and extract the simulation settings.

Parameters:

  • fdir (str) – The directory path.

  • allow_multi (bool) – Allow multiple LAMMPS input files in the directory.

Returns:

The simulation settings.

Return type:

dict or list of dict

pdyna.io.read_lammps_dump(filepath, specorder=None)[source]

Read the LAMMPS trajectory file and extract the atomic symbols, lattices, and atomic positions. Modified from ASE LAMMPS reading functions

Parameters:

  • filepath (str) – The LAMMPS trajectory file.

  • specorder (list) – The order of atomic species.

Returns:

The atomic symbols, lattices, and atomic positions.

Return type:

tuple

pdyna.io.read_lammps_settings(infile)[source]

Read the LAMMPS input file and extract the simulation settings.

Parameters:

infile (str) – The LAMMPS input file.

Returns:

The simulation settings

Return type:

dict

pdyna.io.read_pdb(filepath)[source]

Read the protein data bank (PDB) trajectory file and extract the atomic symbols, lattices, and atomic positions. Modified from Pymatgen xyz reading functions

Parameters:

filepath (str) – The PDB file.

Returns:

The atomic symbols, lattices, and atomic positions.

Return type:

tuple

pdyna.io.read_xdatcar(filename, natom)[source]

Read the VASP XDATCAR file and extract the atomic symbols, lattices, and atomic positions.

Parameters:

  • filename (str) – The XDATCAR file.

  • natom (int) – The number of atoms.

Returns:

The atomic symbols, lattices, and atomic positions.

Return type:

tuple

pdyna.io.read_xyz(filepath)[source]

Read the XYZ format trajectory file and extract the atomic symbols, lattices, and atomic positions. Modified from Pymatgen xyz reading functions

Parameters:

filepath (str) – The XYZ format file.

Returns:

The atomic symbols, lattices, and atomic positions.

Return type:

tuple