File Formats¶
Input Formats¶
XYZ Files¶
The primary input format. Each file represents one crystal structure frame (time step).
File extension: .xyz (or .txt with XYZ content)
Structure:
<N> ← number of points
<comment line> ← metadata or blank
<type> <id> <layer> <x> <y> <z> [<site> <energy>]
<type> <id> <layer> <x> <y> <z> [<site> <energy>]
... ← N rows of point data
Columns:
| Column | Name | Description |
|---|---|---|
| 1 | Type | Molecule/atom type identifier |
| 2 | Number | Atom number |
| 3 | Layer | Growth layer index |
| 4 | X | X coordinate (Å) |
| 5 | Y | Y coordinate (Å) |
| 6 | Z | Z coordinate (Å) |
| 7 | Site | Site number (optional) |
| 8 | Energy | Particle energy (optional) |
Multi-frame trajectories: Load an entire folder — each XYZ file in the folder becomes one frame. Files are sorted by filename to determine frame order.
CIF Files¶
Crystallographic Information Files are used to import lattice parameters.
File extension: .cif
CGAspects reads:
- _cell_length_a, _cell_length_b, _cell_length_c
- _cell_angle_alpha, _cell_angle_beta, _cell_angle_gamma
CrystoGen Structure File¶
The simulation structure file produced by CrystoGen. Contains lattice parameters and optionally crystallographic direction information.
Auto-loaded if present in the data folder.
Size File (size.csv)¶
Contains crystal dimensions along each crystallographic direction at each time step. Used for Growth Rate Analysis.
Format: CSV with columns for time and each direction's size measurement.
Simulation Parameters File¶
A text file (.txt) produced by CrystoGen containing:
- List of crystallographic directions used in the simulation
- Supersaturation levels
- Other simulation metadata
Auto-detected in the data folder.
Crystallization Event Files¶
Binary or text files recording when each lattice site crystallized during the simulation. Used for Site Analysis.
Population / Occupation Files¶
Record the occupancy fraction of each site over simulation time. Used for site analysis.
Count Files¶
Record the number of crystallization/dissolution events per site. Used for site analysis.
CSV Files (for Plotting)¶
Any CSV file with a header row and numerical data can be loaded for plotting:
Load via File → Import CSV for Plotting or File → Import CSV from Clipboard.
Output Formats¶
CSV Analysis Results¶
All analysis outputs are saved as CSV files in aspects_output/ inside the data folder:
| File | Analysis | Contents |
|---|---|---|
aspect_ratios.csv |
Aspect Ratio | S, M, L dimensions, ratios, shape, SA, Vol per frame |
cda_results.csv |
Aspect Ratio (CDA) | Crystal extent along each direction per frame |
growth_rates.csv |
Growth Rate | Size vs time per direction |
site_analysis.csv |
Site Analysis | All site properties |
interaction_data.csv |
Site Analysis | Interaction frequencies per site |
Plot Images¶
Plots are saved to aspects_output/CGPlots/:
| Format | Extension | Description |
|---|---|---|
| PNG | .png |
Raster image, 300 DPI by default |
.pdf |
Vector, scalable, publication-ready | |
| EPS | .eps |
Vector, for LaTeX inclusion |
| SVG | .svg |
Vector, web-friendly |
XYZ Export¶
File → Export XYZ (Ctrl+Shift+E) saves the current point cloud to an XYZ file, including any deletions made in the viewport.
3D Mesh Export¶
The viewport geometry can be exported as a 3D mesh:
| Format | Extension | Notes |
|---|---|---|
| OBJ | .obj |
Wavefront, includes normals |
| STL | .stl |
Binary, suitable for 3D printing |
| PLY | .ply |
Stanford PLY |
| GLB | .glb |
glTF binary, for web/game engines |
Rendered Image¶
File → Render (Ctrl+R) saves the current 3D viewport as a PNG image at 1×, 2×, or 4× resolution.
Log File¶
The application log is written to a platform-specific location. Access it via View → Open Log File.