Welcome to the atomID
package! This README will guide you through the initial steps required to start using the AnnotateCrystal
class for annotating crystal structures and defects. Follow the steps outlined below to get started.
To begin, you need to install the atomID
package. This can be done using pip:
pip install atomid
This section provides a step-by-step guide on how to utilise the AnnotateCrystal
class within the atomID
package.
Start by importing the AnnotateCrystal
class from the atomid.annotate
module:
from atomid.annotate import AnnotateCrystal
Next, create an instance of the AnnotateCrystal
class:
crystal = AnnotateCrystal()
Read the crystal structure file by using the read_crystal_structure_file
method. Make sure to replace crystal_data_file_path
with the actual path to your crystal structure file:
crystal.read_crystal_structure_file(crystal_data_file_path, "vasp")
You can now annotate the crystal structure with the annotate_crystal_structure
method:
crystal.annotate_crystal_structure()
To annotate defects, provide a reference file path. Replace ref_file_path
with the actual path to your reference file:
crystal.annotate_defects(ref_file_path, "vasp")
Finally, write the annotated data to a file using the write_to_file
method. Specify the output file name and format:
crystal.write_to_file(output_file_path, "ttl")
Here is a complete example that combines all the steps:
from atomid.annotate import AnnotateCrystal
# Create an instance of AnnotateCrystal
crystal = AnnotateCrystal()
# Read the crystal structure file
crystal.read_crystal_structure_file("path/to/your/interstitial_file.poscar", "vasp")
# Annotate the crystal structure
crystal.annotate_crystal_structure()
# Annotate defects using a reference file
crystal.annotate_defects("path/to/your/reference_file.poscar", "vasp")
# Write the annotated data to a file
crystal.write_to_file("Al_inter.ttl", "ttl")
Detailed documentation for the atomID
package can be found in docs folder.
Please refer to the CONTRIBUTING GUIDE on contributing to the atomID
package.
For any queries or feedback, kindly create an issue on the GitHub repository