pyGND

Geometrically Necessary Dislocation calculations for TriBeam 3D microstructures

PyGND is a Python package for calculating geometrically necessary dislocation (GND) densities from EBSD (Electron Backscatter Diffraction) data using Nye's dislocation theory. The code was originally developed in MATLAB by Wyatt Witzen and has been reimplemented in Python for improved performance and accessibility.

THIS CODE IS UNDER ACTIVE DEVELOPMENT AND IS PROVIDED AS_IS. Please submit an issue if any problems arise.

Features

• Multiple crystal structures: FCC, BCC, and HCP
• Flexible slip system selection: Choose specific slip systems or use all available
• Optimized calculations: Parallel processing with configurable CPU cores
• Multiple minimization methods: L1 and L2 minimization
• Multiple input formats: Support for ANG files and DREAM.3D formats
• Progress tracking: Built-in progress bars for long calculations
• Memory efficient: Configurable chunking for large datasets
• Desktop GUI and a command line interface, in addition to the Python API

Installation

From PyPI

pip install pygnd

From source

git clone https://github.com/lambjames18/pyGND.git
cd pyGND

pip install -e .

If you use uv (the toolchain this project develops with), uv sync will set up an editable install with all dependencies resolved from pyproject.toml. Using uv is the recommended route, especially if planning to contribute to the project.

Quick Start

Python API

import pygnd

# Calculate GND from an .ang file
pygnd.calculate_and_save_ang(
    "path/to/data.ang",
    cs=1,  # 1=FCC, 2=BCC, 3=HCP
    burgers=2.48e-10,  # Burgers vector magnitude in meters
    grain_ids_path="path/to/grain_data.txt",
    minimization=["l2", "l1"],
    slip_systems="all",
    n_cpus=4,
    progress_bar=True,
)

# Calculate GND from a DREAM.3D file and save the results back into it
pygnd.calculate_and_save_dream3d(
    "path/to/data.dream3d",
    ids_name="FeatureIds",
    euler_name="EulerAngles",
    cs=2,  # BCC
    burgers=2.48e-10,
    minimization="l2",
    slip_systems="screw+110",
    n_cpus=8,
    chunk_size=5000,
)

See examples/ for complete runnable scripts, and the API documentation for the full parameter reference (including pygnd.get_linear_operator, the pygnd.rotations/pygnd.quaternions conversion utilities, and lower-level functions in pygnd.core).

Command line

Installing the package also provides three console scripts:

# Print the version, logo, and a summary of the entry points below
pygnd

# Run the same calculation as above from the command line
pygnd_calculate ang path/to/data.ang --cs 1 --burgers 2.48e-10 --grain-ids-path path/to/grain_data.txt
pygnd_calculate dream3d path/to/data.dream3d --ids-name FeatureIds --euler-name EulerAngles --cs 2 --burgers 2.48e-10

# Validate a file's shape/spacing before queuing a large job, without running the calculation
pygnd_calculate ang path/to/data.ang --dry-run

# Launch the desktop GUI
pygnd_gui

Run pygnd_calculate --help, pygnd_calculate ang --help, or pygnd_calculate dream3d --help for the full list of options (minimization scheme, CPU/chunk-size controls, slip systems, etc.) — these mirror the Python API parameters below.

Crystal Structures and Slip Systems

FCC (cs=1)

• Slip systems: Always uses all slip systems

BCC (cs=2)

Available slip system options:

• "screw+110" - Screw dislocations on {110} planes
• "screw+112" - Screw dislocations on {112} planes
• "screw+123" - Screw dislocations on {123} planes
• "screw+110+112" - Combined {110} and {112}
• "screw+110+123" - Combined {110} and {123}
• "screw+112+123" - Combined {112} and {123}
• "all" - All available slip systems

HCP (cs=3)

Available slip system options:

• "basal" - Basal slip
• "prismatic" - Prismatic slip
• "pyramidal" - Pyramidal slip
• "basal+prismatic" - Combined basal and prismatic
• "basal+pyramidal" - Combined basal and pyramidal
• "prismatic+pyramidal" - Combined prismatic and pyramidal
• "all" - All available slip systems

For HCP with a mixed basal/prismatic + pyramidal slip-system combination, burgers must be a (basal/prismatic, pyramidal) tuple of the two Burgers vector magnitudes.

Main Functions

• calculate_and_save_ang(ang_path, cs, burgers, grain_ids_path=None, ...) — calculate from an .ang file, saving results as .npy files and preview images next to it.
• calculate_and_save_dream3d(dream3d_path, ids_name, euler_name, cs, burgers, ...) — calculate from a DREAM.3D file, saving results back into it (falling back to .npy files if the DREAM.3D write fails).
• calculate_and_save(...) — a deprecated combined-argument entry point kept for backwards compatibility; prefer the two functions above.

Both functions share the following parameters:

• cs (int): Crystal structure (1=FCC, 2=BCC, 3=HCP)
• burgers (float or tuple): Burgers vector magnitude(s) in meters (see above for HCP mixed slip systems)
• slip_systems (str): Slip system selection (see above)
• minimization (str or list): "l1", "l2", or both ["l1", "l2"]
• n_cpus (int): Number of CPU cores to use for L1 minimization (-1 uses all available)
• chunk_size (int): Data points per processing chunk
• progress_bar (bool): Show a progress bar during L1 minimization

See the API documentation for the complete, per-function parameter reference.

Output

The package saves results in .npy files by default. If a DREAM.3D file is used, it will attempt to add the output to the DREAM.3D file directly. In the case of an ANG file, images of the result are saved in addition to the .npy raw data. Raw data is saved in the following format:

• gnd_l1.npy or gnd_l2.npy: shape (n_slip_systems, Z, Y, X), to get the full GND density, sum across the first (n_slip_systems) axis.
• fdm.npy: shape (3, Z, Y, X), to get the average finite difference misorientation, take the mean along the first axis.

Dependencies

Runtime dependencies (see pyproject.toml for the authoritative, unpinned list): numpy, scipy, h5py, matplotlib, tqdm, joblib.

Documentation

• API documentation (built with pdoc)
• Test coverage report

Contributing

Contributions are welcome! Please feel free to submit a Pull Request. Before submitting:

1. Ensure all tests pass: uv run pytest
2. Add tests for new features
3. Follow the existing code style
4. Update documentation as needed

See CONTRIBUTING.md for more details.

Uses in the literature

A few papers that have used this code are provided below.

1. Lamb, J.D. et al. On the role of geometrically necessary dislocations in void formation and growth in response to shock loading conditions in wrought and additively manufactured Ta. DOI: 10.1016/j.jmrt.2024.07.003

2. Lamb, J.D. et al. Quantification of melt pool dynamics and microstructure during simulated additive manufacturing. DOI: 10.1016/j.scriptamat.2024.116036

3. Witzen, W.A. et al. Resolving crystallographic geometrically necessary dislocations in three dimensions in a hexagonal close packed titanium alloy. DOI: 10.1088/1361-651x/ad64f4

License

This project is licensed under the MIT License - see the LICENSE file for details.

Authors

• James Lamb - Python implementation
• Wyatt Witzen - Original MATLAB implementation and methodology