| name | structure-tools |
| description | Structure Tools Skills (8 sub-skills: advanced-optimization, format-conversion, input-generation, pdf-analysis, structure-editing, structure-matching, symmetry-analysis, xrd-pattern) |
Structure Tools Skills
Tools for crystal structure preparation, manipulation, symmetry analysis, format conversion, and DFT input generation. This skill group covers the foundational operations needed before running any calculation: getting a structure into the right format, building supercells, analyzing symmetry, and generating complete input files for QE and VASP.
Available Skills
| Skill | Description |
|---|
| advanced-optimization | Advanced structure optimization: quasi-Newton methods (BFGS, SR1, PSB), scipy minimizers (CG, L-BFGS-B, TNC), simultaneous cell+position optimization with Voigt strain, staged optimization for disordered/amorphous materials. |
| input-generation | Generate DFT input files for QE and VASP from CIF/POSCAR/Materials Project. Covers INCAR, KPOINTS, POTCAR, POSCAR generation (VASPKIT 101-109 equivalent), and QE pw.x input generation with automatic pseudopotential selection. |
| structure-editing | Build supercells, fix/move/delete/substitute atoms, redefine lattice vectors, convert between fractional and Cartesian coordinates, sort atoms by element/coordinate. Covers VASPKIT 400-415 equivalent. |
| symmetry-analysis | Find space group, point group, primitive/conventional cell, Wyckoff positions, equivalent atoms, symmetry of relaxed structures, molecular point group. Uses spglib and pymatgen. Covers VASPKIT 601-609 equivalent. |
| format-conversion | Convert between CIF, POSCAR, XYZ, PDB, QE input, LAMMPS data, and extxyz formats. Bidirectional conversion with symmetry preservation. Covers VASPKIT 419 equivalent. |
| xrd-pattern | Simulate powder X-ray diffraction patterns. Supports multiple wavelengths, peak labeling with hkl indices, phase comparison, and Scherrer broadening. |
| pdf-analysis | Pair distribution function g(r) computation. Total and partial (element-specific) PDFs, crystalline vs amorphous comparison, MD trajectory averaging. |
| structure-matching | Structure comparison and matching using pymatgen StructureMatcher. RMSD calculation, site mapping, symmetry comparison with spglib. |
Decision Guide
What do you need to do with a crystal structure?
Advanced structure relaxation (custom optimizers, difficult convergence)?
--> advanced-optimization/SKILL.md
Generate DFT input files?
--> input-generation/SKILL.md
Modify the structure (supercell, substitution, fix atoms)?
--> structure-editing/SKILL.md
Analyze or determine symmetry?
--> symmetry-analysis/SKILL.md
Convert between file formats?
--> format-conversion/SKILL.md
Simulate XRD patterns or compare phases by diffraction?
--> xrd-pattern/SKILL.md
Compute pair distribution function g(r)?
--> pdf-analysis/SKILL.md
Compare or match two structures (RMSD, symmetry, deduplication)?
--> structure-matching/SKILL.md
Common Prerequisites
- Python packages: pymatgen, ASE, spglib, numpy are pre-installed. Install extras with
pip install seekpath as needed.
- Structure files: Start from a CIF, POSCAR, or query Materials Project with
mp-api. All sub-skills show how to load structures from any common format.
- Pseudopotentials: QE input generation requires UPF files (SSSP library recommended). VASP input generation requires POTCAR files from a licensed VASP distribution.
