This tool is designed to automate the identification, time-tracking and validation of crystallographic twins within crystal structures using OVITO. The tool is divided into two parts.
Identification_and_tracking.py finds, connects and tracks suspected twin boundaries. Validate_Findings.py validates the findings from the previous part.
The Python script provided here streamlines the process, making it efficient and easy to use.
- Automatic identification of crystallographic twins in crystal structures.
- Time-tracking functionality to monitor twin evolution over time frames.
- Validation of single detected structures, yielding of atomistic data files that allow for comprehensive analysis of results
Python environment with OVITO package installed (OVITO installation: https://www.ovito.org/manual/python/introduction/installation.html).
Download files: Download the contained files to your local machine.
Run the Script: Execute either Python file within a Python environment.
Example: python Identification_and_tracking.py --numfram 6 dump.shear.* would apply the algorithm to 6 frames of the dump file range.
Run python Identification_and_tracking.py -h to see all available flags.
Input Data: Provide crystal structure data as required by the script. Ensure the data format is compatible with OVITO.
Review Results: The tool will automatically identify crystallographic twins and provide time-tracking data if applicable.
Example: python Validate_findings.py twins.dump.* would apply the algorithm to all timesteps, analyzed and exported in part 1.
Input Data: Part 1 creates a new directory "twinfiles" and exports lammps.dump files to the same. These files are the required input for part 2.
A summary of the validation and tracking for each analyzed timestep is provided in the produced TwinSummary.txt text file.
Using for example the free version of OVITO (https://www.ovito.org/about/ovito-pro/) you can visualize the results of 'Identification_and_tracking.py'. Every particle is assigned a new property "twinid" that is either the unique ID of the suspected twin or zero if the atom was not part of a detected structure. You can filter for this property using the expression selection modifier with some expression like „twinid==0“ and delete this selection to be left with all findings. 'Validate_Findings.py' provides lists of "twinid"-entries of validated and not validated findings which make it possible to examine individual findings in more detail.
For testing and demonstration purposes, sample lammps.dump files are included in the 'Testfiles' directory.
Contributions and improvements to this tool are welcome! Feel free to fork this repository or make changes.
This tool is licensed under GNU GPLv3. See the LICENSE file for more details.
For inquiries or suggestions, contact hendrik.ehrich@tuwien.ac.at.