Folder hierarchy

├── <system-type>/                       # Layer 1: surface, edge, or bilayer
│   ├── <specific-system>/               # Layer 2: e.g. HB, HB_unitcell, acHB
│   │   ├── analytics.log                # Build log for this dataset
│   │   ├── structure.vasp *.poscar      # Optimised geometry (VASP/POSCAR)
│   │   ├── ir/                          # Raw energy and force files (for Hessian)
│   │   └── dataset/                     # Layer 3: vibrational analytics outputs
│   │       ├── VibrationData.json                 # ASE VibrationData export
│   │       ├── vibration_summary.csv              # Frequency and IR intensity data
│   │       ├── vibration_summary.txt              # Tabulated and formatted summary in plain text
│   │       ├── structure.xyz *.vasp *.traj        # Geometry in XYZ/VASP/TRAJ format
│   │       ├── ModeDistribution.json              # Mode distribution data
│   │       ├── ir_spectrum.dat                    # Interpolated IR spectrum
│   │       ├── graph_ir.png                       # IR spectrum plot
│   │       ├── graph_vdos.png                     # Vibrational DOS plot
│   │       ├── graph_mode_location.png            # Discrete mode-location plot
│   │       └── mode_visualization/                # Mode animations and vectors
│   │           ├── visual_asforce_*/                       # Mode represented as displacement vectors in TRAJ/XYZ format
│   │           └── visual_trajectory_*/                    # Animated motions (GIF, HTML, TRAJ, XYZ)


General directory structure:

- Layer 1: System-type (surface, bilayer, and edges) layer 
- Layer 2: Specific system layer, for example in surface, there are `HB`, `HB_unitcell` etc.
  - `analytics.log`: Log file for the dataset generation
  - `*.vasp` or `*.poscar`: The structure file in VASP format
  - `ir`: The directory containing the energy and force data
  - `dataset`: The directory containing the dataset

The `dataset` directory contents:

- `VibrationData.json`: The VibrationData object (ASE) exported to JSON format
- `vibration_summary.csv` and `vibration_summary.txt`: Get a summary of the vibrational frequencies and infrared intensities
- `structure.xyz`, `structure.vasp`, `structure.traj`: The structure file in XYZ, VASP, and trajectory format
- `ModeDistribution.json`: The mode distribution data
- `ir_spectrum.dat`: The interpolated IR spectrum data
- `graph_ir.png`: The graph of the IR spectrum
- `graph_mode_location.png`: The graph of the mode location
- `graph_vdos.png`: The graph of the vibrational density of states
- `mode_visualization`: The directory containing the mode visualizations. Sub-folders provide two representation styles—asforce (displacement vectors) and trajectory (animated motion)—exported in multiple formats (TRAJ, XYZ, GIF, HTML) for broad compatibility.