#### NOTE [Go to the end](#sphx-glr-download-auto-examples-structure-analysis-plot-decompose-structure-py) to download the full example code. # Decompose/Split Structure This example demonstrates how to decompose a crosslinked polymer network into chains and analyze its structure using pylimer-tools. The following approaches are shown: - Removing crosslinkers and analyzing polymer strands - Decomposing the network to chains while keeping crosslinkers - Finding clusters after manual junction removal ```none Number of chains (without crosslinkers): 100 Number of chains (with crosslinkers): 100 Number of clusters: 3 ```
```Python import os from pathlib import Path import matplotlib.pyplot as plt from pylimer_tools.io.read_lammps_output_file import read_data_file from pylimer_tools_cpp import Universe # Replace with your crosslinker type crosslinker_type = 2 # Load your network (replace path accordingly) 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() universe = read_data_file( str(_fixtures_dir / "structure/network_100_a_46.structure.out") ) assert isinstance(universe, Universe) # 1. Decompose by removing crosslinkers chains = universe.get_molecules(crosslinker_type) print(f"Number of chains (without crosslinkers): {len(chains)}") # 2. Decompose keeping crosslinkers in all chains chains_with_xl = universe.get_chains_with_crosslinker(crosslinker_type) print(f"Number of chains (with crosslinkers): {len(chains_with_xl)}") # 3. Find clusters (if you removed junctions yourself) clusters = universe.get_clusters() print(f"Number of clusters: {len(clusters)}") # Plot the weights of the clusters, chains and molecules plt.figure(figsize=(10, 6)) plt.bar( ["Clusters", "Chains (with XL)", "Chains (no XL)"], [len(clusters), len(chains_with_xl), len(chains)], ) plt.xlabel("Type") plt.ylabel("Count") plt.show() ``` **Total running time of the script:** (0 minutes 0.044 seconds) [`Download Jupyter notebook: plot_decompose_structure.ipynb`](_downloads/31ed97ac7fa37613360dae14352db5c0/plot_decompose_structure.ipynb) [`Download Python source code: plot_decompose_structure.py`](_downloads/9aee77b743bc8aa54912cb3246f7e56b/plot_decompose_structure.py) [`Download zipped: plot_decompose_structure.zip`](_downloads/a98179068a66220f8278f60c78a997c8/plot_decompose_structure.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)