Options for generating simulations: makesims.yml

stage

Sets options which detemine where on the local machine the simulations should be generated

path (string)

The absolute path on the local machine in which the simulaton series directory will be generated.

method (string: "castep" | "lammps")

Sets the modelling software to use.

base_structure

Parameterises the AtomisticStructure upon which all structures in the series will be based.

boundary_vac_args

Sets arguments which are passed to apply_boundary_vac method.

vac_thickness (float)

Sets the length of vacuum to be applied to the GB supercell in the GB normal direction. Vacuum is distributed according to a Sigmoid function.

boundary_vac_flat_args

Sets arguments which are passed to apply_boundary_vac_flat method.

vac_thickness (float)

Sets the length of vacuum to be applied to the GB supercell in the GB normal direction. Vacuum is distributed according to a step function.

boundary_vac_linear_args

Sets arguments which are passed to apply_boundary_vac_linear method.

vac_thickness (float)

Sets the length of vacuum to be applied to the GB supercell in the GB normal direction. Vacuum is distributed according to a linear function.

overlap_tol (float)

Sets the distance tolerance used in check.atoms_overlap .

import

Sets options for importing an AtomisticStructure from a previous simulation series.

id (string)

Sets the ID of the simulation series in which the structure to import can be found.

sim_idx (int)

Sets the index of the simulation within the series in which the structure to import can be found.

opt_step (int)

Sets the optimisation step from which to import the structure. Negative indices count back from the final step, which would be -1.

check

For each `check`, if "all", the check is performed after the generation of both the base structure and the series structures. If "base", the check is performed after the generation of the base structure only. If "series", the check is performed after the generation of each series structure. If "none", the check is not performed at all.

atoms_overlap (string: "all" | "base" | "series" | "none")

Determines when to check if any atoms are closer than the distance defined in base_structure.overlap_tol .

bicrystal_inversion_symmetry (string: "all" | "base" | "series" | "none")

Determines when to check if the generated bicrystal exhibits inversion symmetry through the centre of one of its crystals.