#### NOTE [Go to the end](#sphx-glr-download-auto-examples-network-generator-plot-polydisperse-system-py) to download the full example code. # Generate a Polydisperse Polymer Network This example demonstrates how to use the [`MCUniverseGenerator`](../../api/pylimer_tools_cpp.MCUniverseGenerator.html.md#pylimer_tools_cpp.MCUniverseGenerator) to create a polydisperse end-linked polymer network with varying strand lengths. For strand length distribution, in this example, we show how to use the log-normal distribution as proposed by Tsimouri *et al.* [[TCG21](../../acknowledgements.html.md#id24)]. Alternatives were proposed as well, such as the inverse Gaussian or a ternary distribution. ```Python import math import random import matplotlib.pyplot as plt from pylimer_tools.io.bead_spring_parameter_provider import ( ParameterType, get_parameters_for_polymer, ) from pylimer_tools_cpp import MCUniverseGenerator # Get parameters for PDMS polymer density, bead distance, and # characteristic ratio params = get_parameters_for_polymer( "PDMS", parameter_type=ParameterType.GAUSSIAN) C_inf = params.get_characteristic_ratio() # setup strand lengths n_strands = 1000 average_length = 50 polydispersity = 1.25 # Calculate parameters for log-normal distribution s = math.sqrt(math.log(polydispersity)) m = math.log(average_length) - 0.5 * s**2 # sample strand lengths from log-normal distribution strand_lengths = [int(random.lognormvariate(m, s)) for _ in range(n_strands)] n_atoms_total = sum(strand_lengths) + 0.5 * n_strands # add crosslinker sites volume = n_atoms_total / params.get_bead_density() generator = MCUniverseGenerator( volume ** (1 / 3), volume ** (1 / 3), volume ** (1 / 3), ) generator.set_bead_distance( params.get("").to(params.get("distance_units")).magnitude ) generator.add_strands(nr_of_strands=n_strands, strand_lengths=strand_lengths) # 4-functional crosslinkers generator.add_crosslinkers( int(0.5 * n_strands), crosslinker_functionality=4, crosslinker_type=2 ) generator.link_strands_to_conversion( crosslinker_conversion=0.925, # 92.5% of crosslinker sites used ) universe = generator.get_universe() universe.set_masses({1: 1.0, 2: 1.0}) # Set masses for LAMMPS assert math.isclose( universe.compute_polydispersity_index(2), polydispersity, rel_tol=0.1, ) ``` Refer to [File I/O: Readers & Writers](../readers_writers/index.html.md#sphx-glr-auto-examples-readers-writers) for how you can save the universe to a file. For now, we will show that this produces a variety of different strand lengths: ```Python strand_lengths = [m.get_nr_of_atoms() for m in universe.get_chains_with_crosslinker(2)] # Plot the distribution of strand lengths plt.figure() plt.hist(strand_lengths, bins=50, alpha=0.5, label="Strand Lengths") plt.xlabel("Strand Length") plt.ylabel("Frequency") plt.title("Distribution of Strand Lengths in Polydisperse Network") plt.show() ``` **Total running time of the script:** (0 minutes 6.610 seconds) [`Download Jupyter notebook: plot_polydisperse_system.ipynb`](_downloads/e553e202e2ab4659d7d6656402682c89/plot_polydisperse_system.ipynb) [`Download Python source code: plot_polydisperse_system.py`](_downloads/18a5a519189fe3448555dd1bae70d560/plot_polydisperse_system.py) [`Download zipped: plot_polydisperse_system.zip`](_downloads/e44d44775dac690411169184092b0185/plot_polydisperse_system.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)