[Force Balance 2](force_balance/plot_force_balance_2.html.md)
Force Balance 2
[Force Balance](force_balance/plot_force_balance.html.md)
Force Balance
[Polydispersity Study](force_balance/plot_polydispersity_study.html.md)
Polydispersity Study
[Deformation Experiment](force_balance/plot_fb_deformation_exp.html.md)
Deformation Experiment
[Maximum Entropy Homogenization Procedure (MEHP)](force_balance/plot_force_relaxation.html.md)
Maximum Entropy Homogenization Procedure (MEHP)
## Network Generation
pylimer-tools includes a powerful Monte Carlo-based network generator for creating realistic polymer systems.
This tools is particularly useful for generating quick initial configurations for molecular dynamics simulations,
or for doing fast predictions of the viscoelasticity using the [`NormalModeAnalyzer`](../api/pylimer_tools_cpp.NormalModeAnalyzer.html.md#pylimer_tools_cpp.NormalModeAnalyzer) or the
[`pylimer_tools_cpp.MEHPForceBalance`](../api/pylimer_tools_cpp.MEHPForceBalance.html.md#pylimer_tools_cpp.MEHPForceBalance) and its variants.
For more options, examples and advanced usage, see the [test suite](https://github.com/GenieTim/pylimer-tools/tree/main/tests)
and the modules API reference, particularly of the [`MCUniverseGenerator`](../api/pylimer_tools_cpp.MCUniverseGenerator.html.md#pylimer_tools_cpp.MCUniverseGenerator) class.
The network generation system allows you to:
- Create end-linked and vulcanized polymer networks with controllable topology
- Generate solvent chains and background molecules
- Control crosslinking degree and functionality
- Set realistic bead distances and box sizes
The [`MCUniverseGenerator`](../api/pylimer_tools_cpp.MCUniverseGenerator.html.md#pylimer_tools_cpp.MCUniverseGenerator) class is the main interface for network generation.
The initial method was introduced in Gusev [[Gus19](../acknowledgements.html.md#id8)],
the current implementation is more powerful, as needed for Bernhard and Gusev [[BG25](../acknowledgements.html.md#id12)].
[Save Generated Network](network_generator/plot_save_network.html.md)
Save Generated Network
[Simple Crosslinked Network](network_generator/plot_simple_crosslinked_network.html.md)
Simple Crosslinked Network
[Adding Topology Information](network_generator/plot_add_angles.html.md)
Adding Topology Information
[Generate a Polydisperse Polymer Network](network_generator/plot_polydisperse_system.html.md)
Generate a Polydisperse Polymer Network
[Multi-Component System](network_generator/plot_multi_component_system.html.md)
Multi-Component System
[Monte Carlo Configuration](network_generator/plot_monte_carlo_configuration.html.md)
Monte Carlo Configuration
[Generate Vulcanized Networks](network_generator/plot_vulcanized_network.html.md)
Generate Vulcanized Networks
[Custom Crosslinking with Callback Functions](network_generator/plot_custom_crosslinking_callback.html.md)
Custom Crosslinking with Callback Functions
[Tetra-PEG Network Generation](network_generator/plot_tetra_peg_network.html.md)
Tetra-PEG Network Generation
## Normal Mode Analysis
pylimer-tools provides a normal mode analysis (NMA) implementation to predict the loss and storage modulus of polymer networks
as published in Gusev and Bernhard [[GB24](../acknowledgements.html.md#id7)].
This is useful for understanding the viscoelastic properties of the network.
The corresponding class is [`NormalModeAnalyzer`](../api/pylimer_tools_cpp.NormalModeAnalyzer.html.md#pylimer_tools_cpp.NormalModeAnalyzer).
[Unit Conversion](readers_writers/plot_unit_conversion.html.md)
Unit Conversion
[pylimer-tools Output Reader](readers_writers/plot_pylimer_tools_output_reader.html.md)
pylimer-tools Output Reader
[Correlated Averages Reader](readers_writers/plot_correlated_averages_reader.html.md)
Correlated Averages Reader
[Histogram Reader](readers_writers/plot_histogram_reader.html.md)
Histogram Reader
[Performance and Caching](readers_writers/plot_performance_caching.html.md)
Performance and Caching
[Extract Trajectory Frame to Data File](readers_writers/plot_convert_trajectory_to_frame.html.md)
Extract Trajectory Frame to Data File
[Log & Thermo File Reader](readers_writers/plot_log_thermo_file_reader.html.md)
Log & Thermo File Reader
[Dump File Reader](readers_writers/plot_dump_file_reader.html.md)
Dump File Reader
[Time-Averaged Data Reader](readers_writers/plot_time_averaged_data_reader.html.md)
Time-Averaged Data Reader
[Convert for Bond Swapping](readers_writers/plot_convert_for_bond_swapping.html.md)
Convert for Bond Swapping
[Data File Reader](readers_writers/plot_data_file_reader.html.md)
Data File Reader
[Memory-Efficient Dump File Reading](readers_writers/plot_memory_efficient_dump_file_reading.html.md)
Memory-Efficient Dump File Reading
[Data File Writer](readers_writers/plot_data_file_writer.html.md)
Data File Writer
## Structure Analysis
pylimer-tools offers various tools to manipulate and analyze the topology of polymer networks.
Here you can find examples of some of the functionality provided by the package.
### Decomposing Crosslinked Networks to Chains
There are a number of ways how a given [`Universe`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) can be decomposed.
The most common use case is to decompose a crosslinked network into its constituent chains, which can then be used for further analysis or processing.
To find the chains, there are two main approaches:
- Removing the crosslinkers and analysing the remaining polymer strands using [`get_molecules()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_molecules)
- Decomposing the network to chains, but keeping the crosslinkers in place, possibly being repeated in all the chains it is associated with. This decomposition can be done using the [`get_chains_with_crosslinker()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_chains_with_crosslinker) method.
pylimer-tools provides two more advanced methods for decomposing networks:
- If you removed the junctions yourself, you can use [`get_clusters()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_clusters)
If you want even more control, you could assemble your own decomposition algorithm using the [`Universe`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) class and its methods, such as [`get_atoms_connected_to()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_atoms_connected_to).
### Finding Loops
You can also find loops in the network using the [`find_loops()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.find_loops) method.
If you want to count the number of loops present in the network, as a function of their length, you can use the [`count_loop_lengths()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.count_loop_lengths) method.
Finally, to find the shortest loop a specific atom is involved in, you can use the [`find_minimal_order_loop_from()`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.find_minimal_order_loop_from) method.
#### CAUTION
There are exponentially many paths between two crosslinkers of a network,
and you may run out of memory when using these functions, if your network is lattice-like.
[Decompose/Split Structure](structure_analysis/plot_decompose_structure.html.md)
Decompose/Split Structure
[Loop Finding and Analysis](structure_analysis/plot_loop_analysis.html.md)
Loop Finding and Analysis
[End-to-End Distribution](structure_analysis/plot_end_to_end_distribution.html.md)
End-to-End Distribution
[Extract Synthesis Parameters](structure_analysis/plot_structure_analysis.html.md)
Extract Synthesis Parameters
## Trajectory Analysis
pylimer-tools provides advanced tools for analyzing molecular dynamics trajectories, particularly for polymer systems.
This includes reading trajectory data and computing various properties.
For more information, refer to the documentation of the [`UniverseSequence`](../api/pylimer_tools_cpp.UniverseSequence.html.md#pylimer_tools_cpp.UniverseSequence) class and the [`Universe`](../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) class for a list of methods available for property computations.