runLAMMPS module

class src.runLAMMPS.run_LAMMPS(folder, element, lattice_parameter, sigma, misorientation, inclination, size_along_gb_period, potential, mpi_location, lammps_location)[source]

Bases: object

A class to set up, run, and post-process LAMMPS simulations for grain boundary disconnection energy calculations.

folder

Directory for simulation input/output files.

Type:

str

element

Chemical element symbol (e.g. ‘Cu’).

Type:

str

lattice_parameter

Lattice parameter for the element.

Type:

float

sigma

Sigma value for grain boundary.

Type:

int

misorientation

Misorientation angle.

Type:

float

inclination

Grain boundary inclination.

Type:

float

size_along_gb_period

Size along grain boundary periodicity.

Type:

int

potential

Path to interatomic potential file.

Type:

str

mpi_location

Path to MPI binaries.

Type:

str

lammps_location

Path to LAMMPS binaries.

Type:

str

output_filename_gridsearch

Filename for grid search output.

Type:

str or None

gridsearch_output_setting

Grid search output setting flag.

Type:

int or None

gridsearch_output_folder

Folder for grid search outputs.

Type:

str or None

lammps_input_filename

Filename of the current LAMMPS input script.

Type:

str or None

neb_images

Number of NEB images (partitions).

Type:

int or None

number_of_images_provided

Number of images in NEB calculation.

Type:

int or None

burgers_vec

Burgers vector magnitude.

Type:

float or None

step_height

Step height used in NEB calculation.

Type:

float or None

neb_output_folder

Folder for NEB output files.

Type:

str or None

__init__(folder, element, lattice_parameter, sigma, misorientation, inclination, size_along_gb_period, potential, mpi_location, lammps_location)[source]

Initializes the run_LAMMPS instance with simulation parameters.

Parameters:

  • folder (str) – Directory to store simulation files.

  • element (str) – Chemical element symbol.

  • lattice_parameter (float) – Lattice parameter.

  • sigma (int) – Sigma value for grain boundary.

  • misorientation (float) – Misorientation angle in degrees.

  • inclination (float) – Grain boundary inclination angle.

  • size_along_gb_period (int) – Size along grain boundary period.

  • potential (str) – Path to interatomic potential file.

  • mpi_location (str) – Path to MPI binaries.

  • lammps_location (str) – Path to LAMMPS binaries.

post_process_gridsearch_data(plot_decision=False)[source]

Post-processes grid search results, sorting and optionally plotting the GB energy surface.

Parameters:

plot_decision (bool, optional) – If True, generates and saves contour plots (default: False).

post_process_neb_output(outfolder, plot_decision=False)[source]

Post-processes the NEB output dump files and optionally plots the energy profile.

Parameters:

  • outfolder (str) – Folder to write processed output files.

  • plot_decision (bool, optional) – If True, generates and saves energy plot (default: False).

Runs a grid search of displacements using MPI-parallelized LAMMPS.

Parameters:

  • infile (str) – Input data filename.

  • outfolder (str) – Output folder for results.

  • number_of_cores (int, optional) – Number of MPI cores to use (default: 6).

  • step_increments (float, optional) – Step size for grid search increments (default: 0.1).

  • limit (float, optional) – Maximum displacement limit (default: 1).

  • output_setting (int, optional) – Output verbosity setting (default: 0).

Returns:

Filename of the grid search results.

Return type:

str

Raises:

RuntimeError – If the grid search LAMMPS run fails.

run_minimization(file_name, disp_along_gb_period, disp_along_tilt_axis, minimization_along_gb_directions=False, number_of_cores=6)[source]

Runs a minimization calculation using LAMMPS.

Parameters:

  • file_name (str) – Base filename for input/output files.

  • disp_along_gb_period (float) – Displacement along grain boundary period.

  • disp_along_tilt_axis (float) – Displacement along tilt axis.

  • minimization_along_gb_directions (bool, optional) – Whether to perform box relaxations (default: False).

Returns:

Filename of the minimized structure output.

Return type:

str

Raises:

RuntimeError – If the minimization LAMMPS run fails.

run_neb_calc(burgers_vector, step_height, number_of_steps, partitions=40, mode=1)[source]

Runs the NEB calculation using MPI-parallelized LAMMPS.

Parameters:

  • burgers_vector (float) – Burgers vector magnitude.

  • step_height (float) – Step height.

  • number_of_steps (int) – Number of NEB steps.

  • partitions (int, optional) – Number of parallel partitions (default: 40).

  • mode (int, optional) – Mode flag for NEB input script generation (default: 1).

Raises:

RuntimeError – If the NEB LAMMPS run fails.

write_lammps_gridsearch_input(infile, outfolder, step_increments, limit, output_setting=0)[source]

Writes a LAMMPS input script for performing a grid search over displacements.

Parameters:

  • infile (str) – Name of the input data file.

  • outfolder (str) – Output folder to store results.

  • step_increments (float) – Incremental displacement step size.

  • limit (float) – Maximum displacement limit in both directions.

  • output_setting (int) – Flag to enable detailed output; 1 enables additional dumps.

write_lammps_neb_input_script(burgers_vector, step_height, num_steps, partitions, mode=1)[source]

Writes a LAMMPS input script for Nudged Elastic Band (NEB) calculations.

Parameters:

  • burgers_vector (float) – Burgers vector magnitude for disconnection.

  • step_height (float) – Step height for the disconnection mode.

  • num_steps (int) – Number of NEB images (steps).

  • partitions (int) – Number of parallel partitions for NEB.

  • mode (int) – Mode flag controlling file naming and step count behavior.

Returns:

Path to the output folder for NEB calculation results.

Return type:

str

write_minimization_input(file_name, dispy, dispz, minimization_along_gb_directions=False)[source]

Writes a LAMMPS input script for energy minimization with optional box relaxation.

Parameters:

  • file_name (str) – Base filename for input/output.

  • dispy (float) – Displacement along grain boundary periodic direction.

  • dispz (float) – Displacement along tilt axis.

  • minimization_along_gb_directions (bool) – If True, performs additional minimization steps with box relaxation along y and z directions.