pylimer-tools Documentation¶
Welcome to pylimer-tools, a comprehensive Python library for working with bead-spring polymer systems and for analyzing LAMMPS molecular dynamics simulation output. This library provides powerful tools for reading, processing, and analyzing polymer networks with a focus on performance and ease of use.
🚀 Quick Start¶
Install pylimer-tools with pip:
pip install pylimer-tools
Basic usage example:
import numpy as np
from pylimer_tools_cpp import UniverseSequence
# Load a LAMMPS data file
filePath = "your_lammps_data_file.structure.out"
universeSequence = UniverseSequence()
universeSequence.initialize_from_data_sequence([filePath])
universe = universeSequence.at_index(0)
# Analyze the system
print(f"System size: {universe.get_size()}")
print(f"Volume: {universe.get_volume()} u³")
print(f"Mean bond length: {np.mean(universe.compute_bond_lengths())} u")
📚 Documentation Sections¶
🔧 Key Features¶
Polymer Analysis: Calculate radius of gyration, end-to-end distances, molecular weights, bond and loop statistics
Network Generation: Monte Carlo network generators for polymer systems with highly flexible parameters
Force Balance: Reduce polymer networks to their minimum energy, maximum entropy homogenized state, predict the equilibrium shear modulus
Normal Mode Analysis: Predict the loss and storage modulus of polymer networks
Dissipative Particle Dynamics: Simulate coarse-grained polymer systems with slip-springs and DPD
High Performance: C++ backend with Python bindings for optimal performance on large polymer structures
LAMMPS Integration: Seamlessly read and write LAMMPS data and dump files with memory-efficient streaming
Comprehensive: Support for angles, dihedrals, crosslinkers, velocities, charges, and custom polymer properties
Trajectory Analysis: Advanced tools for analyzing molecular dynamics trajectories
Batch Processing: Efficient tools for processing multiple files and time series data