name: bonding-analysis
description: Bonding Analysis (10 sub-skills: bader2pqr, bader-charge, charge-density, charge-density-difference, charge-format-conversion, elf-analysis, lobster-cohp, orbital-projection, planar-charge, stm-simula
Bonding Analysis
Chemical bonding analysis using Quantum ESPRESSO and Python post-processing tools.
Sub-Skills
| Sub-Skill | Directory | Description |
|---|
| Charge Density Analysis | charge-density/ | Total charge, charge difference, deformation density plots (2D slices, 1D profiles) via pp.x |
| ELF Analysis | elf-analysis/ | Electron Localization Function for bond character identification (covalent/ionic/metallic) |
| Bader Charge Analysis | bader-charge/ | Bader charge partitioning for charge transfer and oxidation states; includes Lowdin charge fallback via projwfc.x |
| Orbital Projection | orbital-projection/ | Projected DOS, fat bands, orbital hybridization, and crystal field splitting via projwfc.x |
General Workflow
All bonding analyses follow the same initial step:
- SCF calculation with
pw.x (self-consistent field)
- Post-processing with
pp.x, projwfc.x, or external tools
- Visualization / quantification with Python (matplotlib, numpy)
Prerequisites
- Quantum ESPRESSO 7.5 (
pw.x, pp.x, projwfc.x)
- Python packages:
numpy, scipy, matplotlib, pymatgen, ase
- For Bader analysis: Henkelman group
bader binary (pip install or download)
- Pseudopotential files appropriate for your system
When to Use
- Charge density: Visualize where electrons accumulate; compare bonded vs isolated atoms.
- ELF: Identify bond types -- covalent bonds show ELF near 1, metallic bonds near 0.5.
- Bader charges: Quantify charge transfer between atoms; estimate oxidation states.
- Orbital projection: Understand which orbitals participate in bonding; identify hybridization and crystal field effects.
