# Jkitchin Skillz Pymatgen > Pymatgen Materials Analysis - Skill: `tomevault-io/jkitchin-skillz-pymatgen` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add tomevault-io/jkitchin-skillz-pymatgen` - Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/jkitchin-skillz-pymatgen/raw - Safety review: pending (external: skill-scanner PASS, skillspector CAUTION) - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - Author: tomevault-io (https://skillmd.com/u/tomevault-io) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/tomevault-io/jkitchin-skillz-pymatgen --- # Pymatgen Materials Analysis Systematic guidance for using pymatgen to analyze crystal structures, access materials databases, and interface with computational chemistry codes. ## Pymatgen Workflow ### 1. Identify Task Type **What do you want to do?** **Structure Creation/Loading:** - Create structure from scratch → `references/core-objects.md` - Read from file (CIF, POSCAR, XYZ) → `references/file-io.md` - Get from Materials Project → `references/materials-project.md` - Generate from symmetry → `references/structure-analysis.md` **Structure Analysis:** - Analyze symmetry/space groups → `references/structure-analysis.md` - Compare structures → `references/structure-analysis.md` - Calculate properties → `references/properties.md` - Visualize structures → `references/visualization.md` **Structure Manipulation:** - Create supercells/slabs → `references/transformations.md` - Substitute atoms → `references/transformations.md` - Apply symmetry operations → `references/transformations.md` - Interpolate for NEB → `references/transformations.md` **Materials Database:** - Query Materials Project → `references/materials-project.md` - Retrieve structures/properties → `references/materials-project.md` - Build phase diagrams → `references/phase-diagrams.md` **Electronic Structure:** - Parse band structures → `references/electronic-structure.md` - Plot DOS → `references/electronic-structure.md` - Analyze VASP outputs → `references/vasp-integration.md` **Input Generation:** - Create VASP inputs → `references/vasp-integration.md` - Generate Gaussian inputs → `references/file-io.md` - Set up calculations → `references/vasp-integration.md` ### 2. Core Pymatgen Workflow **Basic pattern:** ```python # 1. Import modules from pymatgen.core import Structure, Lattice, Element # 2. Load or create structure structure = Structure.from_file("POSCAR") # 3. Analyze or manipulate print(f"Formula: {structure.composition.reduced_formula}") print(f"Space group: {structure.get_space_group_info()}") # 4. Transform if needed supercell = structure * (2, 2, 1) # 2x2x1 supercell # 5. Write output supercell.to(filename="POSCAR_supercell") ``` ## Quick Reference - Common Tasks **Load structure:** `Structure.from_file("file.cif")` - Auto-detects format **Create structure:** See `references/core-objects.md` for Element, Lattice, Structure creation **Analyze symmetry:** `SpacegroupAnalyzer(struct).get_space_group_symbol()` **Make supercell:** `structure * (2, 2, 1)` or use transformations **Query MP:** `MPRester(key).get_structure_by_material_id("mp-149")` **Generate VASP:** `MPRelaxSet(struct).write_input("dir")` **Plot bands/DOS:** See `references/electronic-structure.md` Detailed examples for all tasks in reference files. ## Task Routing ### Core Objects and Creation **Route to:** `references/core-objects.md` **When:** - Creating structures from scratch - Understanding Element, Site, Structure classes - Working with Lattice objects - Creating molecules - Composition analysis **Key classes:** - Element, Species - Lattice - Site, PeriodicSite - Structure, Molecule - Composition ### File Input/Output **Route to:** `references/file-io.md` **When:** - Reading CIF, POSCAR, XYZ files - Writing structures to files - Format conversion - Parsing calculation outputs - Working with multiple formats **Supported formats:** - CIF (Crystallographic Information File) - POSCAR/CONTCAR (VASP) - XYZ (molecular coordinates) - JSON (serialization) - Many computational chemistry codes ### Structure Analysis **Route to:** `references/structure-analysis.md` **When:** - Finding space groups - Symmetry operations - Comparing structures - Getting primitive/conventional cells - Neighbor analysis **Key tools:** - SpacegroupAnalyzer - StructureMatcher - VoronoiAnalysis - Distance calculations ### Structure Transformations **Route to:** `references/transformations.md` **When:** - Creating supercells - Making slabs/surfaces - Substituting elements - Perturbing structures - High-throughput workflows **Key modules:** - pymatgen.transformations.standard_transformations - pymatgen.transformations.advanced_transformations - pymatgen.alchemy ### Materials Project API **Route to:** `references/materials-project.md` **When:** - Querying materials database - Getting structures by formula - Retrieving calculated properties - Accessing experimental data - Building chemical systems **Key class:** - MPRester for API access - Requires API key from materialsproject.org ### Phase Diagrams **Route to:** `references/phase-diagrams.md` **When:** - Constructing phase diagrams - Analyzing stability - Finding decomposition products - Pourbaix diagrams - Grand potential diagrams **Key classes:** - PhaseDiagram - PhaseDiagramError (for stability analysis) - PourbaixDiagram ### Electronic Structure **Route to:** `references/electronic-structure.md` **When:** - Analyzing band structures - Plotting DOS - Finding band gaps - Analyzing orbital contributions - Electronic property calculations **Key modules:** - pymatgen.electronic_structure.bandstructure - pymatgen.electronic_structure.dos - pymatgen.electronic_structure.plotter ### VASP Integration **Route to:** `references/vasp-integration.md` **When:** - Generating VASP inputs - Parsing VASP outputs - Creating input sets - High-throughput VASP - Custom INCAR settings **Key classes:** - MPRelaxSet, MPStaticSet, etc. - Vasprun, Outcar parsers - Poscar, Incar classes ## Common Patterns **Pattern 1: Structure Analysis** - Load → Analyze composition/symmetry → Get primitive/conventional - See `examples/structure_analysis.py` for complete workflow **Pattern 2: Materials Project to Calculation** - Query MP → Get structure → Generate VASP inputs → Customize settings - See `examples/mp_to_vasp.py` **Pattern 3: High-Throughput Substitution** - Load base structure → Apply transformations → Write outputs - See `examples/substitution_study.py` **Pattern 4: Electronic Structure Analysis** - Parse vasprun.xml → Extract band structure/DOS → Plot and analyze - See `examples/band_structure.py` All patterns detailed in `examples/` directory with complete code. ## Installation and Setup ### Install Pymatgen ```bash pip install pymatgen # Or with optional dependencies pip install pymatgen[all] ``` ### Configure Materials Project API ```bash # Register at materialsproject.org to get API key pmg config --add PMG_MAPI_KEY your_api_key_here ``` ### Set VASP Pseudopotential Path ```bash pmg config --add PMG_VASP_PSP_DIR /path/to/vasp/potentials ``` ### Configuration File Located at `~/.pmgrc.yaml`: ```yaml PMG_MAPI_KEY: your_api_key_here PMG_VASP_PSP_DIR: /path/to/vasp/potentials PMG_DEFAULT_FUNCTIONAL: PBE ``` ## Common Issues and Solutions ### Issue: Structure not defined **Problem:** `NameError: name 'Structure' is not defined` **Solution:** ```python from pymatgen.core import Structure ``` ### Issue: API key not working **Problem:** MPRester returns authentication error **Solution:** 1. Get API key from materialsproject.org (free account) 2. Configure: `pmg config --add PMG_MAPI_KEY your_key` 3. Or pass directly: `MPRester("your_key")` ### Issue: POTCAR generation fails **Problem:** Cannot write POTCAR files **Solution:** 1. Set PSP directory: `pmg config --add PMG_VASP_PSP_DIR /path` 2. Ensure VASP pseudopotentials are properly installed 3. Check directory structure matches expected format ### Issue: Import errors for optional dependencies **Problem:** `ImportError` for plotting or specialized modules **Solution:** ```bash pip install pymatgen[all] # Install all optional dependencies # Or specific ones: pip install matplotlib # For plotting pip install scipy # For analysis tools ``` ## Best Practices ### Object-Oriented Approach - Use Structure/Molecule objects, not raw coordinates - Leverage built-in methods (composition, symmetry, etc.) - Chain operations for clarity ### Serialization - Use `as_dict()` / `from_dict()` for persistence - Prefer JSON over pickle for code evolution - Use MontyEncoder/MontyDecoder for complex objects ### Transformations - Use Transformation classes for reproducibility - TransformedStructure tracks history - Alchemy framework for high-throughput ### Input Sets - Use MPRelaxSet, MPStaticSet for standard calculations - Customize by modifying Incar after creation - Use InputGenerator for custom workflows ### Materials Project - Use context manager: `with MPRester(...) as mpr:` - Batch queries when possible - Cache results to avoid repeated API calls ## Examples Directory See `examples/` for complete workflows: - `structure_analysis.py` - Comprehensive structure analysis - `mp_query.py` - Materials Project queries - `phase_diagram.py` - Phase diagram construction - `band_structure.py` - Electronic structure analysis - `vasp_workflow.py` - VASP calculation setup - `substitution_study.py` - High-throughput substitutions ## Reference Documentation - `references/core-objects.md` - Element, Structure, Lattice, Composition - `references/file-io.md` - Reading/writing all file formats - `references/structure-analysis.md` - Symmetry, comparison, neighbors - `references/transformations.md` - Supercells, substitutions, perturbations - `references/materials-project.md` - API usage and queries - `references/phase-diagrams.md` - Phase diagram construction - `references/electronic-structure.md` - Band structures and DOS - `references/vasp-integration.md` - VASP input/output handling - `references/properties.md` - Calculated properties - `references/visualization.md` - Structure visualization ## External Resources - **Official docs:** https://pymatgen.org/ - **Materials Project:** https://materialsproject.org/ - **GitHub:** https://github.com/materialsproject/pymatgen - **Forum:** https://matsci.org/pymatgen --- > Converted and distributed by [TomeVault](https://tomevault.io/claim/jkitchin) — claim your Tome and manage your conversions.