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pymatgen-analysis

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Mis à jour28 décembre 2025 à 12:56

Use for materials analysis tasks in pymatgen.analysis: phase/Pourbaix/chemical-potential diagrams, reactions, structure matching, surfaces/interfaces, local environments, diffraction, elasticity, magnetism, and related analyses.

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Hongyu-yu

Hongyu-yu/matsci-ai-skills

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Métiers associésSOC

Basé sur la classification professionnelle SOC

Scientifiques des donnéesProfessions informatiques et mathématiques·SOC 15-2051

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26 fichiers

SKILL.md

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name	pymatgen-analysis
description	Use for materials analysis tasks in pymatgen.analysis: phase/Pourbaix/chemical-potential diagrams, reactions, structure matching, surfaces/interfaces, local environments, diffraction, elasticity, magnetism, and related analyses.
metadata	{"short-description":"pymatgen analysis"}

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

Gather Structure/Molecule or Entry inputs.
Choose the analysis module (phase diagram, matcher, surface, etc.).
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

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name	pymatgen-analysis
description	Use for materials analysis tasks in pymatgen.analysis: phase/Pourbaix/chemical-potential diagrams, reactions, structure matching, surfaces/interfaces, local environments, diffraction, elasticity, magnetism, and related analyses.
metadata	{"short-description":"pymatgen analysis"}

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

Gather Structure/Molecule or Entry inputs.
Choose the analysis module (phase diagram, matcher, surface, etc.).
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