mat-phase-diagram

Phase Diagram Retrieval

Goal

Retrieve pre-computed phase diagrams from Materials Project to analyze thermodynamic stability, competing phases, and convex hull relationships. Phase diagrams are essential for understanding:

• Which compounds are stable at 0 K
• Energy above hull (formation energy distance to the convex hull)
• Competing phases that may form during synthesis
• Thermodynamic driving forces for phase transformations

Instructions

1. Basic Phase Diagram Retrieval

Retrieve a phase diagram for a chemical system:

# Env: base-agent
python .agents/skills/mat-phase-diagram/scripts/get_phase_diagram.py \
  --chemsys "Li-O" \
  --output li_o_phase_diagram.json

Output: JSON file containing the phase diagram data (entries, energies, hull)

2. Generate Phase Diagram Plot

Add --plot flag to create a visualization:

# Env: base-agent
python .agents/skills/mat-phase-diagram/scripts/get_phase_diagram.py \
  --chemsys "Li-O" \
  --output li_o_pd.json \
  --plot li_o_pd.png

Output: PNG plot showing the convex hull and stable/unstable phases

3. Use Different DFT Functional

By default, retrieves GGA+U phase diagrams. For R2SCAN data:

# Env: base-agent
python .agents/skills/mat-phase-diagram/scripts/get_phase_diagram.py \
  --chemsys "Li-Fe-P-O" \
  --thermo_type "R2SCAN" \
  --output lifepo4_r2scan_pd.json \
  --plot lifepo4_r2scan_pd.png

Thermo types:

• GGA_GGA+U (default): Standard PBE with U corrections
• R2SCAN: Meta-GGA functional (more accurate)
• GGA: Pure PBE without U corrections

Integration with Other Skills

With material-stability Skill

Use phase diagrams to visualize competing phases:

# 1. Get phase diagram
python .agents/skills/mat-phase-diagram/scripts/get_phase_diagram.py \
  --chemsys "Li-O" \
  --output li_o_pd.json \
  --plot li_o_pd.png

# 2. Check specific material's position on hull
python .agents/skills/mat-db-mp/scripts/query_mp.py \
  --formula "Li2O" \
  --properties energy_above_hull formation_energy_per_atom \
  --output li2o_stability.json

With MatterGen Fine-Tuning

Query stable structures from a chemical system for training data:

# 1. Visualize phase diagram to understand stable phases
python .agents/skills/mat-phase-diagram/scripts/get_phase_diagram.py \
  --chemsys "Li-S" \
  --output li_s_pd.json \
  --plot li_s_pd.png

# 2. Query all stable structures
python .agents/skills/mat-db-mp/scripts/query_mp.py \
  --chemsys "Li-S" \
  --e_above_hull_max 0.0 \
  --properties energy_above_hull formation_energy_per_atom \
  --output li_s_stable.json

Constraints

• API Key Required: Set MP_API_KEY environment variable
• Pre-Computed Only: Returns Materials Project's pre-computed phase diagrams. Cannot compute custom phase diagrams with user-provided energies.
• Chemical System Format: Use hyphen-separated elements (e.g., "Li-O", not "LiO" or "Li O")
• Availability: Not all chemical systems have pre-computed phase diagrams. Common systems (binary oxides, battery materials) are well-covered.
• Thermo Type Availability: R2SCAN phase diagrams are available for a subset of systems
• Environment: Requires base-agent conda environment
• Dependencies: mp-api, pymatgen, matplotlib (all installed in base-agent)

When to Use This vs. Calculate

Use MP Phase Diagrams (this skill) when:

• You need quick exploratory analysis
• You want DFT-quality phase diagrams without running calculations
• You're analyzing common chemical systems
• You need GGA+U or R2SCAN accuracy

Calculate Custom Phase Diagrams when:

• You have MLIP-relaxed structures not in MP
• You need to compare MLIP formation energies
• Your chemical system is not in MP
• You want to use specific MLIP models or DFT settings

For custom phase diagram construction, see material-stability skill which can build phase diagrams from user-provided energies.

Examples

See examples/ directory for:

• Li-O binary phase diagram retrieval and visualization
• Li-Fe-P-O quaternary phase diagram (LiFePO4 system)
• Integration with stability analysis workflow

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Author: Bowen Deng Contact: GitHub @learningmatter-mit