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.
1---2name: structure-tools3description: 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.4---5
6---
7name: structure-tools
8description: Structure Tools Skills (8 sub-skills: advanced-optimization, format-conversion, input-generation, pdf-analysis, structure-editing, structure-matching, symmetry-analysis, xrd-pattern)
9---
10
11# Structure Tools Skills
12
13Tools 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.
14
15## Available Skills
16
17| Skill | Description |
18|-------|-------------|
19| [advanced-optimization](advanced-optimization/SKILL.md) | 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. |
20| [input-generation](input-generation/SKILL.md) | 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. |
21| [structure-editing](structure-editing/SKILL.md) | 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. |
22| [symmetry-analysis](symmetry-analysis/SKILL.md) | 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. |
23| [format-conversion](format-conversion/SKILL.md) | Convert between CIF, POSCAR, XYZ, PDB, QE input, LAMMPS data, and extxyz formats. Bidirectional conversion with symmetry preservation. Covers VASPKIT 419 equivalent. |
24| [xrd-pattern](xrd-pattern/SKILL.md) | Simulate powder X-ray diffraction patterns. Supports multiple wavelengths, peak labeling with hkl indices, phase comparison, and Scherrer broadening. |
25| [pdf-analysis](pdf-analysis/SKILL.md) | Pair distribution function g(r) computation. Total and partial (element-specific) PDFs, crystalline vs amorphous comparison, MD trajectory averaging. |
26| [structure-matching](structure-matching/SKILL.md) | Structure comparison and matching using pymatgen StructureMatcher. RMSD calculation, site mapping, symmetry comparison with spglib. |
27
28## Decision Guide
29
30```
31What do you need to do with a crystal structure?
32
33Advanced structure relaxation (custom optimizers, difficult convergence)?
34 --> advanced-optimization/SKILL.md
35
36Generate DFT input files?
37 --> input-generation/SKILL.md
38
39Modify the structure (supercell, substitution, fix atoms)?
40 --> structure-editing/SKILL.md
41
42Analyze or determine symmetry?
43 --> symmetry-analysis/SKILL.md
44
45Convert between file formats?
46 --> format-conversion/SKILL.md
47
48Simulate XRD patterns or compare phases by diffraction?
49 --> xrd-pattern/SKILL.md
50
51Compute pair distribution function g(r)?
52 --> pdf-analysis/SKILL.md
53
54Compare or match two structures (RMSD, symmetry, deduplication)?
55 --> structure-matching/SKILL.md
56```
57
58## Common Prerequisites
59
60- **Python packages**: pymatgen, ASE, spglib, numpy are pre-installed. Install extras with `pip install seekpath` as needed.
61- **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.
62- **Pseudopotentials**: QE input generation requires UPF files (SSSP library recommended). VASP input generation requires POTCAR files from a licensed VASP distribution.
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