polymer-visual 1.0.0

Visualization tools for polymer self-assembly simulation data (SCFT/PSCF)

polymer-visual

Fig. 1: Density profiles generated with polymer-visual showing a double-gyroid morphology.

A Python package for visualizing polymer self-assembly simulation data from PSCF. This is a Python port of the original MATLAB version.

Features

• 3D Isosurface Plots: Visualize individual or composite density profiles
• 1D Line Profiles: Plot composition along any direction through the unit cell
• 2D Contour Plots: Generate contour maps on any plane
• Scattering Profiles: Predict scattering peak intensities
• Interactive Visualization: Using Plotly for interactive 3D graphics
• Command-Line Interface: Easy-to-use CLI for batch processing

Installation

# Using pip
pip install polymer-visual

# Using poetry
poetry add polymer-visual

Quick Start

Command Line

# View file information
polymer-visual info examples/gyr.rf

# Generate all plots
polymer-visual plot examples/gyr.rf -o output/

# Generate specific plot types
polymer-visual plot examples/gyr.rf --composite --individual

# Generate a line profile
polymer-visual line examples/gyr.rf 1 1 1 --start 0 0 0

Python API

from polymer_visual import load_data, plot_all

# Load data from file
data = load_data('examples/gyr.rf')

# Generate all plots
figures = plot_all(data, output_dir='./output', show=True)

# Or use specific plot functions
from polymer_visual import plot_composite_profile, plot_individual_profiles

# Composite profile
plot_composite_profile(
    data['R'], data['x'], data['y'], data['z'],
    save_file='composite.html',
    show_fig=True
)

# Individual profiles for each species
plot_individual_profiles(
    data['R'], data['x'], data['y'], data['z'],
    save_file='individual.html',
    show_fig=True
)

Supported File Formats

The package reads PSCF r-grid files (.rgrid, .rf) containing:

• Crystal system information
• Unit cell parameters
• Grid dimensions
• Volume fraction data for each monomer species

Crystal Systems

Supported crystal systems include:

• Cubic, Tetragonal, Orthorhombic
• Hexagonal
• Triclinic, Monoclinic
• Trigonal/Rhombohedral
• 2D systems: Square, Rectangular, Oblique, Rhombic, Lamellar

Documentation

For detailed documentation, see the docs directory.

Development

# Clone the repository
git clone https://github.com/kdorfmanUMN/polymer_visual.git
cd polymer_visual

# Install development dependencies
poetry install

# Run tests
pytest

# Build package
poetry build

License

This package is licensed under the MIT License. See LICENSE for details.

Authors

• Original MATLAB code by Naveen Pillai, Akash Arora, Ben Magruder
• Python port by polymer-visual team

References

For more information about the underlying science, see:

• PSCF Software
• PSCF Publication