GBKineticsRunController module

src.GBKineticsRunController.runGBkinetics(sig, mis, inc, lat_par, lat_Vec, axis, size_y, size_z, elem, reg_parameter, max_iters, lammps_location, mpi_location, folder, potential, dispy, dispz, oilab_output_file, choose_disconnection=True, run_neb=False, neb_mode=1, partitions=40)[source]

Run a grain boundary kinetics simulation using input parameters and LAMMPS.

Parameters:

  • sigma (int) – Sigma value of the grain boundary.

  • misorientation (float) – Misorientation angle in degrees.

  • inclination (float) – Inclination angle in degrees.

  • lattice_parameter (float) – Lattice parameter of the element.

  • lattice_vector (np.ndarray) – Lattice vectors for the crystal (3x3 matrix).

  • axis (list[int]) – Tilt axis vector.

  • size_y (int) – System size along the GB period (in 2×CSL units).

  • size_z (int) – System size along the tilt axis (in 2×CSL units).

  • element (str) – Chemical element symbol (e.g., “Cu”).

  • reg (float) – Regularization parameter for the min-shuffle algorithm.

  • iterMax (int) – Maximum number of iterations for the min-shuffle algorithm.

  • lammps_location (str) – Path to the directory containing LAMMPS binaries.

  • mpi_location (str) – Path to the directory containing the MPI executable.

  • output_folder (str) – Root folder where output data will be stored.

  • lammps_potential (str) – Full path to the LAMMPS potential file.

  • disp_along_gb (float) – Displacement along the grain boundary direction.

  • disp_along_tilt (float) – Displacement along the tilt axis direction.

  • oilab_output_file (str) – Path to the bicrystallographic data file from oILAB.

  • choose_disconnection (bool) – Whether to manually choose the disconnection mode.

  • run_neb (bool) – Whether to run NEB calculations.

  • neb_mode (int) – NEB mode.

  • partitions (int) – Number of intermediate images used for NEB calculations.

Returns:

Path to the folder containing the simulation results.

Return type:

str

src.GBKineticsRunController.runGridSearch(sig, mis, inc, lat_par, lat_Vec, axis, size_y, size_z, elem, lammps_location, mpi_location, folder, potential, oilab_output_file, choose_disconnection=False, number_of_cores=6, step_increments=0.1, limit=1, output_setting=0)[source]

Run a grid search to identify minimum energy configurations of a grain boundary structure.

This function builds a bicrystal based on bicrystallographic parameters and performs a systematic grid search using LAMMPS simulations to evaluate different GB displacements.

Parameters:

  • sig (int) – Sigma value of the grain boundary.

  • mis (float) – Misorientation angle in degrees.

  • inc (float) – Inclination angle in degrees.

  • lat_par (float) – Lattice parameter of the element.

  • lat_Vec (np.ndarray) – Lattice vectors (3x3 matrix) for the crystal.

  • axis (list[int]) – Tilt axis vector of the grain boundary.

  • size_y (int) – System size along the grain boundary period (in 2×CSL units).

  • size_z (int) – System size along the tilt axis (in 2×CSL units).

  • elem (str) – Chemical symbol of the element (e.g., “Cu”).

  • lammps_location (str) – Path to the directory containing LAMMPS binaries.

  • mpi_location (str) – Path to the directory containing the MPI executable.

  • folder (str) – Root folder to store all output data.

  • potential (str) – Full path to the LAMMPS potential file.

  • oilab_output_file (str) – Path to the bicrystallographic data file from oILAB.

  • choose_disconnection (bool, optional) – Whether to manually select a disconnection mode. Defaults to False.

  • number_of_cores (int, optional) – Number of processor cores to use for LAMMPS. Defaults to 6.

  • step_increments (float, optional) – Step size (in lattice units) for displacement search. Defaults to 0.1.

  • limit (float, optional) – Maximum displacement range to search (in lattice units). Defaults to 1.

  • output_setting (int, optional) – Output format/type flag for LAMMPS scripts. Defaults to 0.

Returns:

Output from the grid search post-processing routine (usually energy data or selected configuration).

Return type:

Any