IO module

IO.find_gb_location(filepath)[source]

Determines the location of a grain boundary based on centro-symmetry parameter.

Parameters:

filepath (str) – Path to the LAMMPS dump file.

Returns:

  • average_gb_loc (float): Average z-location of the grain boundary.

  • extreme_gb_loc_hi (float): Upper bound of GB atom positions.

  • extreme_gb_loc_lo (float): Lower bound of GB atom positions.

Return type:

tuple

IO.read_LAMMPS_datafile(path_r, mode=1)[source]

Reads a LAMMPS data file and extracts atom positions and box dimensions.

Parameters:

  • path_r (str) – Path to the data file.

  • mode (int, optional) – Parsing mode. - 1: Expecting 5 columns per atom line. - 2: Expecting 8 columns per atom line.

Returns:

A list containing:

  • number of atoms (int)

  • number of types (int)

  • box dimensions (3x2 np.ndarray)

  • atom positions (np.ndarray)

Return type:

list

IO.read_LAMMPS_dumpfile(path_r)[source]

Reads atomic configurations from a LAMMPS dump file.

Parameters:

path_r (str) – Path to the LAMMPS dump file.

Returns:

A list of snapshots, each containing:

  • timestep (float)

  • number of atoms (int)

  • box dimensions (3x2 np.ndarray)

  • atomic data (np.ndarray of shape [n_atoms, 7])

Return type:

list

IO.read_gridsearch_results(filepath)[source]

Reads grid search results from a custom text file (displacements and GB energy).

Parameters:

filepath (str) – Path to the results file.

Returns:

Array with columns [dispy, dispz, GB_energy].

Return type:

np.ndarray

IO.read_neb_output_data(path_r, mode)[source]

Reads output from a NEB (nudged elastic band) LAMMPS simulation.

Parameters:

  • path_r (str) – Path to NEB output dump file.

  • mode (int) – Determines number of atom attributes to read (7 or 8 columns).

Returns:

A list of snapshots, each with:

  • timestep (float)

  • number of atoms (int)

  • box dimensions (3x2 np.ndarray)

  • atomic data (np.ndarray of shape [n_atoms, N])

Return type:

list

IO.write_LAMMPSoutput_tstep(natoms, Atoms, box, folder, file, tstep)[source]

Writes a single timestep’s atomic configuration to a LAMMPS trajectory file.

Parameters:

  • natoms (int) – Total number of atoms.

  • Atoms (np.ndarray) – Array of atomic data (id, type, x, y, z, PotEng, CentroSym).

  • box (np.ndarray) – Box dimensions (3x2).

  • folder (str) – Output folder.

  • file (str) – File name.

  • tstep (int) – Timestep to write.

Returns:

Path to the output trajectory file.

Return type:

str

IO.write_gridsearch_results(filepath, data)[source]

Writes displacements and GB energy to a tabulated results file.

Parameters:

  • filepath (str) – Output file path.

  • data (np.ndarray) – Array of shape (N, 3) containing: - dispy (float) - dispz (float) - GB energy (float)

IO.write_lammps_datafile(folder, file, suffix, g_A, g_B, input_box, mode=2)[source]

Writes a LAMMPS data file for a bicrystal configuration.

Parameters:

  • folder (str) – Path to output folder.

  • file (str) – File name prefix.

  • suffix (str) – File suffix (e.g., ‘min_shuffle’).

  • g_A (np.ndarray) – Atom positions for grain A.

  • g_B (np.ndarray) – Atom positions for grain B.

  • input_box (np.ndarray) – Original box dimensions (3x3).

  • mode (int, optional) – Determines which box vector to expand for bicrystal. Default is 2 (z-direction).

Returns:

Path to the generated data file.

Return type:

str