Hongyu-yu/pymatgen-phonon
skills/pymatgen-phonon/SKILL.md
Use for phonon band structure/DOS, Gruneisen, and IR spectra analysis with pymatgen.phonon and phonopy-compatible outputs.
$ install --global
skillsauthnpx skillsauth add Hongyu-yu/matsci-ai-skills pymatgen-phononInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
3
Scanners Passed
9
Scanners in report
Clean
TrivyContainer and dependency vulnerability scanner
95%
Clean
SemgrepStatic code analysis for vulnerabilities
95%
Clean
mcp-scan (Snyk)Model Context Protocol security validation
95%
Skipped
Snyk (dep)Open source security scanning
50%
Skipped
Socket.devSupply chain security analysis
50%
Skipped
VirusTotalMulti-engine malware detection
50%
Skipped
CrowdStrikeAdvanced threat intelligence
50%
Skipped
OSV-ScannerOpen Source Vulnerability database check
50%
Skipped
OWASP Dep-Check
50%
Last scanned: Apr 23, 2026, 2:58 AM180.7s3 files scanned
SKILL.md
- name:
- pymatgen-phonon
- description:
- Use for phonon band structure/DOS, Gruneisen, and IR spectra analysis with pymatgen.phonon and phonopy-compatible outputs.
- short-description:
- pymatgen phonon
Pymatgen Phonon
Overview
Pymatgen phonon tools analyze phonon band structures, DOS, Gruneisen parameters, and IR spectra, often from Phonopy outputs.
Required Python Environment
Ensure pymatgen and phonopy are installed in your Python environment:
pip install pymatgen phonopy
# or
conda install -c conda-forge pymatgen phonopy
Example usage pattern:
from pymatgen.phonon.bandstructure import PhononBandStructure
# your code here
When to Use This Skill
- Analyze phonon band structures, DOS, or spectra
- Work with Gruneisen parameters or phonopy outputs
Core Capabilities
1. Phonon Data Loading
- Load phonon band structure and DOS from YAML
2. Plotting
- Phonon dispersion and DOS plotting utilities
3. Gruneisen and IR
- Gruneisen parameters and IR spectra utilities
Quick Workflow
- Load phonopy outputs or phonon objects.
- Compute or plot band structure/DOS/spectra.
- Export figures or derived data.
Resources
scripts/
Executable examples in the scripts/ directory:
2016-09-25-Plotting_phonon_bandstructure_and_dos.py- Phonon band structure and DOS plotting.
references/
Detailed reference material (load as needed):
references/phonon-workflows.md- Phonon workflows and examplesreferences/docs/- Local API docs forpymatgen.phonon
Related Skills
Hongyu-yu/xlsx
tools
VerifiedTrustedCommunity
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
10SKILL.mdUpdated Apr 23, 2026
Hongyu-yu/vasp
tools
VerifiedTrustedCommunity
Expert assistant for VASP (Vienna Ab initio Simulation Package) calculations - input file generation, parameter selection, workflow setup, and best practices for accurate DFT calculations
10SKILL.mdUpdated Apr 23, 2026
Hongyu-yu/transformers
data-ai
VerifiedTrustedCommunity
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
10SKILL.mdUpdated Apr 23, 2026
Hongyu-yu/torch-geometric
tools
VerifiedTrustedCommunity
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
10SKILL.mdUpdated Apr 23, 2026