#### NOTE [Go to the end](#sphx-glr-download-auto-examples-readers-writers-plot-convert-for-bond-swapping-py) to download the full example code. # Convert for Bond Swapping LAMMPS bond swapping can significantly speed up equilibration for polymer networks. However, to preserve the strand lengths, you need to ensure that the molecule indices are set correctly. Here’s how you could re-set the molecule indices for bond swapping with constant chain lengths. ```Python import os from pathlib import Path from pylimer_tools_cpp import DataFileWriter, UniverseSequence if not os.path.exists("generated_structures"): os.makedirs("generated_structures") # Load original system def _find_fixtures_dir() -> Path: for cur in ( [Path(__file__).resolve().parent] if "__file__" in globals() else [] ) + [Path.cwd()]: for p in [cur] + list(cur.parents): candidate = p / "tests" / "pylimer_tools" / "fixtures" if candidate.is_dir(): return candidate return Path("tests/pylimer_tools/fixtures").resolve() _fixtures_dir = _find_fixtures_dir() input_file = str(_fixtures_dir / "structure/melt_83_a_100.structure.out") sequence = UniverseSequence() sequence.initialize_from_data_sequence([input_file]) universe = sequence.at_index(0) # Configure for optimal chain length distribution output_file = os.path.join( os.getcwd(), "generated_structures", "for_swap_" + os.path.basename(input_file) ) writer = DataFileWriter(universe) writer.config_include_angles(True) writer.config_crosslinker_type(2) # Needed for decomposition to chains writer.config_molecule_idx_for_swap(True) # Key setting writer.write_to_file(output_file) print(f"Optimized system capable of bond swapping written to: {output_file}") ``` ```none Optimized system capable of bond swapping written to: /home/runner/work/pylimer-tools/pylimer-tools/examples/readers_writers/generated_structures/for_swap_melt_83_a_100.structure.out ``` To convert it back to the molecule index relating to their current connectivity, simply repeat the process with `config_molecule_idx_for_swap(False)` **Total running time of the script:** (0 minutes 0.030 seconds) [`Download Jupyter notebook: plot_convert_for_bond_swapping.ipynb`](_downloads/2e728147fc88d45b5ad914954901a029/plot_convert_for_bond_swapping.ipynb) [`Download Python source code: plot_convert_for_bond_swapping.py`](_downloads/953551f7c6d4f4b2c609a6c736192bf7/plot_convert_for_bond_swapping.py) [`Download zipped: plot_convert_for_bond_swapping.zip`](_downloads/5b38566522fb42b8edf867d14577716d/plot_convert_for_bond_swapping.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)