# unknown

> This skill automates the complete workflow for running VASP DFT calculations on structures generated by [OgreInterface](https://github.com/caizefeng/OgreInterface), from setup to energy extraction.

- Author: Chenbo Min
- Repository: chamber523/ogre-dft-workflow-skill
- Version: 20260130122646
- Stars: 0
- Forks: 0
- Last Updated: 2026-02-06
- Source: https://github.com/chamber523/ogre-dft-workflow-skill
- Web: https://mule.run/skillshub/@@chamber523/ogre-dft-workflow-skill~unknown:20260130122646

---

# Ogre DFT Workflow Skill

A DFT calculation workflow designed for **Vibe Coding**. Built on top of [OgreInterface](https://github.com/caizefeng/OgreInterface) for epitaxial interface modeling.

## Overview

Run DFT calculations for all structure files generated by OgreInterface located in:
- `PES/poscars`
- `zdist/poscars`
- `reference/poscars`

Extract the final energies from the calculations and save them into the corresponding `energies.npy` files. The order of the energies in each `.npy` file matches the order of the POSCAR file suffixes.

**Note:** For `reference/energies.npy`, the array is structured as `[E1, E2, E3, E4]` where:
- E1 = film slab
- E2 = substrate slab
- E3 = film double slab
- E4 = substrate double slab

## Directory Structure

```
ogre-dft-workflow/
├── scripts/
│   ├── 1_setup_calculations.sh      # Setup calculation directories
│   ├── 2_update_dipol.py            # Update DIPOL values
│   ├── 3_submit_jobs.sh             # Submit jobs to SLURM
│   ├── 4_extract_energies.py        # Extract energies from OUTCAR
│   ├── 5_create_npy.py              # Create NPY array
│   ├── setup_reference_folders.py   # Setup reference calculations (E1-E4)
│   └── sort_poscar_elements.py      # Sort POSCAR atoms by element type
└── templates/                        # Reference files for your system
    ├── POTCAR                        # Your pseudopotential file
    ├── INCAR_template                # Your INCAR with DIPOL = PLACEHOLDER_DIPOL, MAGMOM = (manual)
    ├── KPOINTS_template              # Your KPOINTS settings
    └── job_template.slurm            # Your SLURM script
```

## Vibe Coding Usage

This workflow is designed for AI-assisted coding tools like **Claude Code**, **Cursor**, etc.

### Typical Workflow

1. Use [vaspkit](https://vaspkit.com/) to prepare template files (`POTCAR`, `KPOINTS`, `INCAR_template`)

2. Drag your calculation folder (`pes` or `zdist`) into the AI coding environment

3. ni> "Setup calculation folders, update DIPOL, and submit jobs"

The AI will execute the appropriate scripts automatically.

## Script Details

### 1_setup_calculations.sh
- Creates calc_XXXX directories
- Copies files from `templates/` to each directory
- Usage: `./1_setup_calculations.sh <type> <poscars_dir>`
  - `<type>`: "pes" or "zdist"
  - `<poscars_dir>`: Directory containing POSCAR_0000, POSCAR_0001, etc.

### 2_update_dipol.py
- Calculates mass-weighted center of mass from POSCAR
- Updates DIPOL tag in all INCAR files
- Options: `--force`, `--verbose`, `--dry-run`

### 3_submit_jobs.sh
- Submits jobs to SLURM queue
- Options: `--dry-run`, `--delay N`, `--check-dipol`

### 4_extract_energies.py
- Extracts energies from OUTCAR files
- Outputs: `energies_YYYYMMDD_HHMMSS.csv`

### 5_create_npy.py
- Creates `energies.npy` from extracted energies

### setup_reference_folders.py
- Creates reference calculation directories (calc_0000 to calc_0003)
- Interface energy formula: `E_interface = E_total - (E1 + E2) + 0.5*(E3 + E4)`

### sort_poscar_elements.py
- Sorts POSCAR files to group atoms by element type

## Workflow Summary

```
OgreInterface                    This Workflow
     │                                │
     ▼                                ▼
Generate POSCARs ──────────► 1. Setup calculations
                             2. Update DIPOL
                             3. Submit VASP jobs
                             4. Wait for completion
                             5. Extract energies → energies.npy
```

## License

MIT

## Acknowledgments

- [OgreInterface](https://github.com/caizefeng/OgreInterface) - Epitaxial interface generation