Habilidades pymatgen
🔬

pymatgen

Seguro ⚡ Contém scripts⚙️ Comandos externos📁 Acesso ao sistema de arquivos🌐 Acesso à rede🔑 Variáveis de ambiente

Analisar estruturas cristalinas com pymatgen

Também disponível em: davila7

Trabalhe com estruturas cristalinas e dados de materiais. Converta formatos de arquivo, compute diagramas de fase, analise simetria e acesse o banco de dados do Materials Project para pesquisa em ciência de materiais computacional.

Suporta: Claude Codex Code(CC)
🥉 75 Bronze
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Testar

A utilizar "pymatgen". Read structure from POSCAR and show its properties

Resultado esperado:

  • Formula: Fe2O3 (hematite)
  • Lattice: a=5.04 Å, b=5.04 Å, c=13.77 Å
  • Space group: R-3c (#167)
  • Crystal system: trigonal
  • Density: 5.27 g/cm³
  • Number of sites: 10

A utilizar "pymatgen". Convert CIF to POSCAR format

Resultado esperado:

  • Successfully converted structure.cif to converted.POSCAR
  • Structure contains 10 atoms (Fe4 O6)
  • Format: POSCAR (VASP format)

A utilizar "pymatgen". Query Materials Project for perovskites

Resultado esperado:

  • Found 23 stable perovskite structures
  • Example: SrTiO3 (mp-5229) - band gap 3.2 eV
  • Example: BaTiO3 (mp-2987) - band gap 2.8 eV
  • Energy above hull: all < 0.01 eV/atom

Auditoria de Segurança

Seguro
v4 • 1/17/2026

All 537 static findings are false positives. The static analyzer incorrectly flagged markdown documentation syntax (code blocks, inline code formatting) as shell commands and cryptographic terms in documentation text as weak algorithms. The actual Python code uses secure patterns for API key management (environment variables) and performs legitimate materials science file I/O operations. No malicious code, data exfiltration, or security risks found.

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Arquivos analisados
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Linhas analisadas
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achados
4
Total de auditorias

Fatores de risco

⚡ Contém scripts (6)
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⚙️ Comandos externos (447)
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📁 Acesso ao sistema de arquivos (10)
references/core_classes.md:269 references/io_formats.md:115 references/io_formats.md:122 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:414 scripts/structure_analyzer.py:251 scripts/structure_analyzer.py:258
🌐 Acesso à rede (14)
references/materials_project_api.md:19 references/materials_project_api.md:504 references/materials_project_api.md:505 references/materials_project_api.md:506 references/materials_project_api.md:507 scripts/phase_diagram_generator.py:42 skill-report.json:6 skill-report.json:207 SKILL.md:370 SKILL.md:675 SKILL.md:676 SKILL.md:677 SKILL.md:678 SKILL.md:679
🔑 Variáveis de ambiente (23)
references/materials_project_api.md:26 references/materials_project_api.md:26 references/materials_project_api.md:44 scripts/phase_diagram_generator.py:39 scripts/phase_diagram_generator.py:37 scripts/phase_diagram_generator.py:39 scripts/phase_diagram_generator.py:39 scripts/phase_diagram_generator.py:40 scripts/phase_diagram_generator.py:41 scripts/phase_diagram_generator.py:43 scripts/phase_diagram_generator.py:45 scripts/phase_diagram_generator.py:56 scripts/phase_diagram_generator.py:56 scripts/phase_diagram_generator.py:64 scripts/phase_diagram_generator.py:175 skill-report.json:46 skill-report.json:191 skill-report.json:207 SKILL.md:70 SKILL.md:70 SKILL.md:371 SKILL.md:655 SKILL.md:657
Auditado por: claude Ver Histórico de Auditoria →

Pontuação de qualidade

68
Arquitetura
100
Manutenibilidade
85
Conteúdo
20
Comunidade
100
Segurança
78
Conformidade com especificações

O Que Você Pode Construir

Pesquisar compostos estáveis

Construa diagramas de fase e identifique materiais estáveis usando dados do banco de dados do Materials Project.

Converter formatos de estrutura

Converta arquivos de estruturas cristalinas entre CIF, POSCAR, XYZ e outros formatos para diferentes códigos de simulação.

Analisar simetria cristalina

Determine grupos espaciais, operações de simetria e ambientes de coordenação a partir de arquivos de estrutura.

Tente Estes Prompts

Ler arquivo de estrutura 
Read the structure from file 'POSCAR' and show its composition, lattice parameters, and space group.
Converter formato 
Convert 'structure.cif' to POSCAR format and save as 'converted.POSCAR'.
Diagrama de fase 
Build a phase diagram for the Li-Fe-O system and identify stable compounds.
Materials Project 
Search the Materials Project for stable perovskite structures with band gap between 1.5 and 3.0 eV.

Melhores Práticas

  • Sempre use variáveis de ambiente (MP_API_KEY) para credenciais de API, nunca codifique chaves
  • Valide estruturas após a leitura para verificar átomos sobrepostos ou comprimentos de ligação irreais
  • Use SpacegroupAnalyzer para reduzir estruturas a células primitivas antes da análise

Evitar

  • Não codifique chaves de API em scripts - use variáveis de ambiente em vez disso
  • Não pule a análise de simetria ao comparar estruturas - diferentes grupos espaciais podem parecer semelhantes
  • Não presuma que a detecção automática de formato sempre funciona - especifique o formato quando não tiver certeza

Perguntas Frequentes

Quais formatos de arquivo o pymatgen suporta?
O Pymatgen suporta mais de 100 formatos, incluindo CIF, POSCAR, XYZ, PDB, JSON, YAML e entradas/saídas para VASP, Gaussian, Quantum ESPRESSO, LAMMPS e mais.
Como obtenho uma chave de API do Materials Project?
Crie uma conta em https://next-gen.materialsproject.org/ e gere uma chave de API no seu painel. Defina-a como a variável de ambiente MP_API_KEY.
O pymatgen pode analisar trajetórias de dinâmica molecular?
Sim, use Xdatcar para ler trajetórias de MD do VASP e DiffusionAnalyzer para calcular difusividade e condutividade a partir de dados de AIMD.
Como gero uma supercélula?
Use SupercellTransformation com uma matriz de escala, por exemplo: [[2,0,0],[0,2,0],[0,0,2]] para uma supercélula 2x2x2.
O pymatgen funciona com outros códigos de simulação?
Sim, o pymatgen integra-se ao VASP, Gaussian, Quantum ESPRESSO, LAMMPS, CP2K, ABINIT e pode converter para/de o formato ASE.
Como analiso ambientes de coordenação?
Use CrystalNN de pymatgen.analysis.local_env para casos gerais, ou VoronoiNN para identificação de vizinhos baseada em Voronoi.

Detalhes do Desenvolvedor

Licença

MIT license

Repositório

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pymatgen

Referência

main

Estrutura de arquivos

📁 references/

📄 analysis_modules.md

📄 core_classes.md

📄 io_formats.md

📄 materials_project_api.md

📄 transformations_workflows.md

📁 scripts/

📄 phase_diagram_generator.py

📄 structure_analyzer.py

📄 structure_converter.py

📄 SKILL.md