1_data_prepare/README.md

# Diamond – Step 1: Data Preparation

Generate displaced supercell configurations, run QE DFT, transform to AO basis,
and verify band structure reconstruction.

## Prerequisites

1. **QE pseudopotential**: Place `C.upf` in `../pseudos/`
2. **Siesta pseudopotential**: Place `C.psml` (or appropriate file) in `../aobasis/`
3. **QE on PATH**: Source `~/scripts/tools/qe.sh` or set manually
4. **Conda environments**: `hpro` (HPRO), `deeph` (DeepH)

## Workflow

```bash
# 1. Create input files and directory structure
python prepare.py

# 2. Run QE calculations (SCF + pw2bgw + bands)
python run.py

# 3. Transform Hamiltonians to AO basis via HPRO
python reconstruct.py

# 4. Compare QE and reconstructed band structures
python compare_bands.py
```

## Output

```
data/
  disp-01/ .. disp-50/    displaced 2×2×2 supercell SCF + reconstruction
  bands/
    uc/                   pristine unit cell bands
    sc/                   pristine 2×2×2 supercell bands
    kpath.json            k-path used for band calculations
band_compare_uc.png       QE vs HPRO comparison for unit cell
band_compare_sc.png       QE vs HPRO comparison for supercell
```

## Parameters (params.json)

| Key | Description |
|-----|-------------|
| `supercell_size` | Supercell dimensions (default 2×2×2) |
| `n_displacements` | Number of displaced configs (default 50) |
| `displacement_groups` | Amplitude groups in Angstrom |
| `reconstruction.method` | `"original"` (real-space H(R)) |
| `reconstruction.nbnd` | Bands to include in reconstruction comparison |
| `cluster.run_sh` | Path to cluster submission script (null = local) |