Site Analysis¶
Access via the Calculate Site Analysis button in the left panel (enabled when crystallization event files are present in the loaded folder).
Site analysis examines the properties of individual lattice sites and characterises when and how they crystallized during the simulation.
Input Data¶
The analysis auto-detects these files in the loaded folder:
| File | Contents |
|---|---|
| Crystallization event files | Which site crystallized at which time step |
| Population/occupation files | Site occupancy over time |
| Count files | Event counting per site |
| Structure file | Site coordinates, energies |
| Simulation parameters | Direction and variable metadata |
What It Computes¶
For each lattice site:
| Property | Description |
|---|---|
| Site number | Unique site identifier |
| File prefix | Simulation run identifier |
| Energy | Site interaction energy |
| Occupation | Fraction of simulation time occupied |
| Coordination | Number of neighbouring occupied sites at crystallization |
| Total events | Number of crystallization/dissolution events |
| Total population | Cumulative occupied time steps |
| Tile type | Crystallographic face/edge/corner classification |
| Interaction patterns | Frequency of each neighbour interaction type |
Filtering¶
The analysis result can be filtered using the Data Filter dialog (accessible from the plotting toolbar).
Data Filters Tab¶
Add conditions on site properties:
| Column | Type | Example |
|---|---|---|
| site_number | Numeric | > 100 |
| energy | Numeric | < -50.0 |
| occupation | Numeric | >= 0.5 |
| coordination | Numeric | == 6 |
| total_events | Numeric | > 10 |
| tile_type | Categorical | == "face" |
Multiple conditions are combined with AND logic.
Interaction Filters Tab¶
Filter sites by the frequency of specific neighbour interaction types. This is useful for finding sites that preferentially form particular crystallographic contacts.
Both tabs can be active simultaneously (all conditions combined with AND).
Hierarchical Clustering¶
The site analysis results can be visualized with hierarchical clustering in the plotting dialog, grouping sites by similarity of their interaction patterns. This reveals structurally distinct site populations within the crystal.
Output¶
Results are saved to aspects_output/:
| File | Contents |
|---|---|
site_analysis.csv |
All computed site properties |
interaction_data.csv |
Interaction frequency per site |
| Site analysis plots | Generated in the plotting dialog |
Workflow¶
- Import a folder containing crystallization event files
- Click Calculate Site Analysis
- The analysis runs in the background with a progress bar
- Results open automatically in the Plotting Dialog
- Use the Data Filter to focus on specific site populations
- Export filtered data or plots from the plotting dialog
Notes¶
- Sites with zero events are included in the output but typically have zero occupation
- Very large simulations may produce large site analysis files; the filter dialog helps narrow the focus
- Hierarchical clustering requires all interaction columns to be numeric and non-null
- Analysis can be cancelled from Tools → Active Threads. Cancellation takes effect at the next checkpoint (typically the start of each file), so there may be a short delay before the task stops.