asr.setup.defects¶
Summary¶
This is the documentation for asr.setup.defects-recipe.
This recipe is comprised of a single instruction, namely:
Run this recipe through the CLI interface
$ asr run asr.setup.defects
or as a python module
$ python -m asr.setup.defects
Detailed description¶
Generate defective atomic structures.
Steps¶
asr.setup.defects¶
- asr.setup.defects.main(atomfile='unrelaxed.json', chargestates=3, supercell=(3, 3, 3), maxsize=None, intrinsic=True, extrinsic='NO', vacancies=True, double=False, uniform_vacuum=False, halfinteger=False, general_algorithm=None)[source]¶
Set up defect structures for a given host.
Recipe setting up all possible defects within a reasonable supercell as well as the respective pristine system for a given input structure. Defects include: vacancies, intrinsic substitutional defects. For a given primitive input structure this recipe will create a directory tree in the following way (for the example of MoS2):
There has to be a ‘unrelaxed.json’ file with the primitive structure of the desired system in the folder you run setup.defects. The tree structure will then look like this:
. ‘ ├── general_parameters.json ‘ ├── MoS2_331.v_S ‘ │ ├── charge_0 ‘ │ │ ├── params.json ‘ │ │ └── unrelaxed.json ‘ │ ├── charge_1 ‘ │ │ ├── params.json ‘ │ │ └── unrelaxed.json -> ./../charge_0/structure.json ‘ │ . ‘ │ ‘ ├── MoS2_231.Mo_S ‘ │ ├── charge_0 ‘ . . ‘ . ‘ ├── pristine_sc ‘ │ ├── params.json ‘ │ └── structure.json ‘ ├── results_setup.defects.json ‘ └── unrelaxed.json ‘
Here, the notation for the defects is the following: ‘formula_supercellsize.defect_sustitutionposition’ where ‘v’ denotes a vacancy
When the general algorithm is used to set up symmetry broken supercells, the foldernames will contain ‘000’ instead of the supersize.
In the resulting folders you can find the unrelaxed structures, as well as a ‘params.json’ file which contains specific parameters as well as the charge states of the different defect structures.