Agent skill
bonding-analysis
Install this agent skill to your Project
npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/other/other/bonding-analysis
SKILL.md
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
baderbinary (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.
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