Pymatgen Analysis

Overview

Pymatgen analysis provides higher-level workflows for thermodynamics, reactions, structure comparison, surfaces, and property analyses. Use it once you have structures or entries ready.

Required Python Environment

Ensure pymatgen is installed in your Python environment:

pip install pymatgen
# or
conda install -c conda-forge pymatgen

Example usage pattern:

from pymatgen.analysis.phase_diagram import PhaseDiagram
# your code here

When to Use This Skill

• Phase diagrams, reactions, Pourbaix, and thermochemistry
• Structure matching, dimensionality, or local environments
• Surface/interface analysis or property analysis (diffraction, elasticity, magnetism)

Core Capabilities

1. Thermodynamics and Phase Stability

• Phase and chemical potential diagrams
• Reaction energies and Pourbaix analysis

2. Structure Analysis

• Structure matching and comparison
• Coordination environments (ChemEnv) and dimensionality

3. Surfaces and Properties

• Slabs, Wulff shapes, and interfaces
• Diffraction, elasticity, magnetism, and related utilities

Quick Workflow

1. Gather Structure/Molecule or Entry inputs.
2. Choose the analysis module (phase diagram, matcher, surface, etc.).
3. Run analysis and export plots or derived data.

Resources

scripts/

Executable examples in the scripts/ directory:

• 2013-01-01-Calculating_Reaction_Energies_with_the_Materials_API.py - Reaction energies using Materials Project data.
• 2013-01-01-Plotting_and_Analyzing_a_Phase_Diagram_using_the_Materials_API.py - Phase diagram plotting and analysis with MP data.
• 2017-04-03-Slab_generation_and_Wulff_shape.py - Slab generation and Wulff shape construction.
• 2017-12-15-Plotting_a_Pourbaix_Diagram.py - Pourbaix diagram plotting.
• 2018-01-01-ChemEnv_-_How_to_automatically_identify_coordination_environments_in_a_structure.py - Automatic coordination environment identification (ChemEnv).
• 2018-03-09-Computing_the_Reaction_Diagram_between_Two_Compounds.py - Reaction diagram between compounds.
• 2018-07-24-Adsorption_on_solid_surfaces.py - Adsorption analysis on solid surfaces.
• 2018-11-6-Dopant_suggestions_using_Pymatgen.py - Dopant suggestion workflows.
• 2019-03-11-Interface_Reactions.py - Interface reaction analysis.
• 2021-5-12-Explanation_of_Corrections.py - Energy correction explanations and usage.
• 2023-03-10-Plotting_a_Pourbaix_Diagram-new.py - Updated Pourbaix diagram plotting example.
• 2024-06-28-Charge_Density_Difference.py - Charge density difference analysis.

Note: Some scripts require Materials Project API access; set your API key before running.

references/

Detailed reference material (load as needed):

• references/analysis-workflows.md - Common analyses and examples
• references/docs/ - Local API docs for pymatgen.analysis