Tutorials

Python API

Usage of ShakeNBreak from a Python API is exemplified in the SnB Python API Tutorial, which includes:

• SnB Python API
  • ShakeNBreak applied to Cd vacancies in CdTe (V_Cd)
  • Table of contents
  • 1. Generate defects with doped/pymatgen
  • 2. Apply the SnB method to your defects
  • 3. Send to HPCs and run relaxations
  • 4. Plot energies vs distortion
  • 5. Optional: Analyse the defect distortions found with SnB
  • 6. Optional: Input File Generation for Other Codes

Command line interface (CLI)

Additionally, the core functionality of the code can be accessed through the command line, with the following commands:

1. Generation of distorted structures and/or their relaxation input files:

   • for a specific defect: snb-generate

   • for all defects present in a directory: snb-generate_all

2. Submitting the geometry optimisations to the HPC scheduler:

   snb-run

3. Parsing of the geometry optimisation results:

   snb-parse

4. Analysis of the energies and structural differences between the relaxed configurations:

   snb-analyse

5. Plotting of energy vs distortions to identify what energy lowering reconstructions have been found:

   snb-plot

6. Identification of defect species undergoing energy-lowering distortions and test these distortions for the other charge states of the defect

   snb-regenerate

7. Saving the ground state structures

   snb-groundstate

All commands are documented in the Python API section, and their use is exemplified in the following pages:

• Structure Generation
  • For a single defect
  • For many defects
• Submitting the geometry optimisations
• Analysis & plotting
  • Parsing
  • Analysis
  • Plotting
  • Second round of structure searching
  • Saving the ground state structures
  • Further Defect Analysis

Getting help

Beyond the documentation, we can get a full list of accepted flags and their description using the --help or -h flag, e.g.:

$ snb-generate --help

> Usage: snb-generate [OPTIONS]
Generate the trial distortions for structure-searching for a given defect.
Options:
-d, --defect FILE               Path to defect structure  [required]
-b, --bulk FILE                 Path to bulk structure  [required]
-c, --charge INTEGER            Defect charge state
--min-charge, --min INTEGER     Minimum defect charge state for which to
--max-charge, --max INTEGER     Maximum defect charge state for which to
                                generate distortions
--defect-index, --idx INTEGER   Index of defect site in defect structure, in
                                case auto site-matching fails
--defect-coords, --def-coords <FLOAT FLOAT FLOAT>...
                                Fractional coordinates of defect site in
                                defect structure, in case auto site-matching
                                fails. In the form 'x y z' (3 arguments)
--code TEXT                     Code to generate relaxation input files for.
                                Options: 'VASP', 'CP2K', 'espresso',
                                'CASTEP', 'FHI-aims'. Defaults to 'VASP'
-n, --name TEXT                 Defect name for folder and metadata
                                generation. Defaults to doped scheme
                                (see tutorials)
--config FILE                   Config file for advanced distortion
                                settings. See example
                                in/input_files/example_generate_config.yaml
-v, --verbose                   Print information about identified defects
                                and generated distortions
-h, --help                      Show this help message and exit