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pymatgen

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تحليل البنى البلورية باستخدام pymatgen

Auch verfügbar von: davila7

العمل مع البنى البلورية وبيانات المواد. تحويل صيغ الملفات، ورسم مخططات الطور، وتحليل التماثل، والوصول إلى قاعدة بيانات Materials Project لأبحاث علوم المواد الحاسوبية.

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Verwendung von "pymatgen". Read structure from POSCAR and show its properties

Erwartetes Ergebnis:

  • 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

Verwendung von "pymatgen". Convert CIF to POSCAR format

Erwartetes Ergebnis:

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

Verwendung von "pymatgen". Query Materials Project for perovskites

Erwartetes Ergebnis:

  • 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

Sicherheitsaudit

Sicher
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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⚡ Enthält Skripte (6)
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⚙️ Externe Befehle (447)
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🌐 Netzwerkzugriff (14)
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🔑 Umgebungsvariablen (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
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البحث عن المركبات المستقرة

بناء مخططات الطور وتحديد المواد المستقرة باستخدام بيانات من قاعدة بيانات Materials Project.

تحويل صيغ البنية

تحويل ملفات البنى البلورية بين CIF وPOSCAR وXYZ وصيغ أخرى لمحاكاة مختلفة.

تحليل تماثل البلورة

تحديد مجموعات الفراغات وعمليات التماثل والبيئات التناسلية من ملفات البنية.

Probiere diese Prompts

قراءة ملف البنية 
Read the structure from file 'POSCAR' and show its composition, lattice parameters, and space group.
تحويل الصيغة 
Convert 'structure.cif' to POSCAR format and save as 'converted.POSCAR'.
مخطط الطور 
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.

Bewährte Verfahren

  • استخدم دائمًا متغيرات البيئة (MP_API_KEY) لبيانات الاعتماد، ولا تُضمّن المفاتيح في الكود أبدًا
  • تحقق من البنى بعد قراءتها للتأكد من عدم وجود ذرات متداخله أو أطوال روابط غير واقعية
  • استخدم SpacegroupAnalyzer لتحويل البنى إلى خلايا بدائية قبل التحليل

Vermeiden

  • لا تُضمّن مفاتيح API في السكربتات - استخدم متغيرات البيئة بدلاً من ذلك
  • لا تتخطى تحليل التماثل عند مقارنة البنى - قد تبدو مجموعات الفراغات المختلفة متشابهة
  • لا تفترض أن الاكتشاف التلقائي للصيغة يعمل دائمًا - حدد الصيغة عند الشك

Häufig gestellte Fragen

ما صيغ الملفات التي يدعمها pymatgen؟
يدعم pymatgen أكثر من 100 صيغة بما في ذلك CIF وPOSCAR وXYZ وPDB وJSON وYAML ومدخلات/مخرجات لـ VASP وGaussian وQuantum ESPRESSO وLAMMPS وغيرها.
كيف أحصل على مفتاح Materials Project API؟
أنشئ حسابًا على https://next-gen.materialsproject.org/ وأنشئ مفتاح API من لوحة التحكم. اضبطه كمتغير البيئة MP_API_KEY.
هل يمكن لـ pymatgen تحليل مسارات الديناميكا الجزيئية؟
نعم، استخدم Xdatcar لقراءة مسارات VASP MD وDiffusionAnalyzer لحساب الانتشارية والتوصيلية من بيانات AIMD.
كيف أولد خلية خارقة؟
استخدم SupercellTransformation مع مصفوفة التحجيم، على سبيل المثال: [[2,0,0],[0,2,0],[0,0,2]] لخلية خارقة 2x2x2.
هل يعمل pymatgen مع برامج محاكاة أخرى؟
نعم، يتكامل pymatgen مع VASP وGaussian وQuantum ESPRESSO وLAMMPS وCP2K وABINIT ويمكن التحويل من وإلى صيغة ASE.
كيف أحلل البيئات التناسلية؟
استخدم CrystalNN من pymatgen.analysis.local_env للحالات العامة، أو VoronoiNN للبحث عن الجيران بطريقة Voronoi.

Entwicklerdetails

Lizenz

MIT license

Repository

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

Ref

main

Dateistruktur

📁 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