Generators

Run Dynamics

The imeall.slabmaker the imeall.run_dyn modules are responsible for generating the canonical imeall.gb_models.GrainBoundary structures and a representative spanning set of microscopic initializations of the imeall.gb_models.SubGrainBoundary structures for atomistic relaxation.

Both modules also runs as a command line tool. To see the command line documentation:
python run_dyn.py -h
class imeall.run_dyn.Capturing[source]

Capturing wraps a function to capture output for redirection.

class imeall.run_dyn.ImeallIO[source]

ImeallIO contains methods for searching the Imeall Directory tree, and creating new imeall.gb_models.GrainBoundary and imeall.gb_models.SubGrainBoundary directories. Each SubGrainBoundary directory contains supercells of the parent canonical GrainBoundary.

find_subdir(target_dir, calc_suffix)[source]

Find if named directory is in target directory. :param target_dir: directory to search. :type target_dir: str :param calc_suffix: name of directory to look for. :type calc_suffix: str

Returns:directory location and name.
load_json(json_file)[source]

Helper function to return gb_data as dict.

Parameters:json_file (str) – name of gb.json or subgb.json file.
Returns:grain boundary data dictionary.
Return type:dict
make_dir(target_dir, dir_name)[source]

Create GrainBoundary directory if it does not exist and return the concatenated string name.

Parameters:
  • target_dir (str) – target directory.
  • dir_name (str) – name of new directory in target directory.
Returns:

target directory name.
Return type:

str

Relaxation

The imeall.relax module handles relaxation of a SubGrainBoundary. This module also runs as a command line tool.

imeall.relax.relax_gb(gb_file='file_name', traj_steps=120, total_steps=1200, force_tol=0.05)[source]

Method to relax a grain_boundary bicrystal structure.

Parameters:
  • gb_file (str) – gbid.
  • traj_steps (int) – number of steps between print trajectories.
  • total_steps (int) – total number of force relaxation steps.
  • force_tol (float) – Force relaxation criterion in ev/A.
Returns:

ase.Atoms Object