Features

Nexus-CAT provides a wide range of features for cluster analysis in atomistic simulations. Below is an overview of the key features:

Cluster Analysis

Multiple Clustering Strategies: Nexus-CAT supports several strategies for defining clusters:
- Distance Strategy: Connects nodes based on a simple distance cutoff.
- Bonding Strategy: Identifies clusters based on a three-node bonding pattern (e.g., Si-O-Si).
- Coordination Strategy: Extends the bonding pattern by adding constraints on the coordination number of the nodes.
- Shared Strategy: A more advanced strategy that connects nodes based on a minimum number of shared neighbors, useful for analyzing polyhedral linkages.

Average Cluster Size: Calculate the average size of clusters in the system.
Largest Cluster Size: Identify the largest cluster in the system.
Spanning Cluster Size: Exclude percolating clusters and calculate the largest remaining cluster.
Gyration Radius: Measure the spatial extent of clusters.
Correlation Length: Calculate the correlation length of clusters.
Percolation Probability: Determine the probability of clusters percolating in 1D, 2D, or 3D.
Cluster Size Distribution: Computes the distribution of cluster sizes, n(s), for each connectivity type.
Concentration: Computes the concentration of clusters for each connectivity type.

Customize cluster connectivity criterion and polyhedra.
The use of factories (StrategyFactory, AnalyzerFactory, ReaderFactory, WriterFactory) allows for easy extension of the package with new algorithms and file formats.

XYZ Cluster Exporter: The ClustersWriter generates XYZ files containing the unwrapped atomic coordinates of the clusters, which can be used for visualization in other software.
Performance Metrics: The PerformanceWriter saves detailed performance metrics, which can be useful for benchmarking and optimization.

For a complete list of features, refer to the API Reference.