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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.18755409 |
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Table of Contents:
- <p>A Python-based kinetic modeling tool for simulating the complete reconstruction of graphene zigzag edges into 57 reconstructed edge domains. The script models the nucleation, growth and coalescence of reconstructed edge domains as well as diffusion and annihilation kinetics of residual defects (57657, 7557, 5775, 75657, and 57675) based on input energy barriers.</p> <p> </p> <p><strong>Features</strong></p> <p>- Stochastic nucleation: Randomly creates 57 seeds at pristine zigzag edge regions.<br>- Domain growth: Simulates the expansion of reconstructed domains into the pristine edge.<br>- Coalescence & merging: Handles the meeting of adjacent domains, including instantaneous annihilation of specific defect configurations.<br>- Annihilation kinetics: Tracks the long-term diffusion and annihilation of residual defects at various temperatures.<br>- Data export: Generates detailed CSV files for domain length distributions and time-resolved defect counts.</p> <p> </p> <p><strong>Prerequisites</strong></p> <p>- Python 3.8 or higher<br>- NumPy</p> <p><br><strong>Usage</strong></p> <p>You can run the script with default parameters or specify custom simulation settings using command-line arguments.</p> <p>Bash</p> <p>python script_domains.py</p> <p>To run a simulation at 900K with a larger system size and redirected output:</p> <p>Bash</p> <p>python script_domains.py --temp 900 --cell_length 3000000 --max_loops 30 > simulation.log</p> <p> </p> <p><strong>Optional Arguments</strong></p> <p>Argument Type Default Description<br>--cell_length int 3000000 Number of polygons at the edge<br>--temp float 1000 Simulation temperature in Kelvin<br>--time_zero_6 float 2000 Number of time steps to setting the concentration of 6 defects to zero<br>--total_time float 100000 Total time limit in time steps for 6 defect diffusion<br>--max_loops int 20 Number of simulation iterations to average</p> <p> </p> <p><strong>Output Files</strong></p> <p>The script generates several files to help analyze the reconstruction process:<br>- domains.out: Real-time log of domain counts and total reconstructed length during the domain growth and coalescence phase.<br>- domains_dist.csv: A histogram of domain lengths across various stages (after initial reconstruction, merging of domains with the same orientation of 57 pairs, simultaneous annihilation of 6 and 7557 defects, etc.).<br>- evolution_[Temp]K_[Loop].csv: Time-resolved defect counts (num_6, num_7557, etc.) for each simulation run.<br>- domains_summary: A text summary containing average lengths, mean squared lengths, and average defect lifetimes.</p> <p><br><strong>License & Copyright</strong></p> <p>Copyright 2026 Irina V. Lebedeva</p> <p>Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at:<br>http://www.apache.org/licenses/LICENSE-2.0</p> <p> </p> <p>IL acknowledges support from the EuroHPC JU under the MAX (Materials design at the Exascale) project (grant no. 101093374), and from the Spanish MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR through grant no. PCI2022-134972-2. ICN2 is supported by the CERCA programme (Generalitat de Catalunya) and the Severo Ochoa Centres of Excellence programme (grant no. CEX2021-001214-S), funded by MCIN/AEI/10.13039/501100011033.</p>