Initial commit
This commit is contained in:
Zhongwei Li
233
skills/pymatgen/scripts/phase_diagram_generator.py
Normal file
233
skills/pymatgen/scripts/phase_diagram_generator.py
Normal file
@@ -0,0 +1,233 @@
|
||||
#!/usr/bin/env python3
|
||||
"""
|
||||
Phase diagram generator using Materials Project data.
|
||||
|
||||
This script generates phase diagrams for chemical systems using data from the
|
||||
Materials Project database via pymatgen's MPRester.
|
||||
|
||||
Usage:
|
||||
python phase_diagram_generator.py chemical_system [options]
|
||||
|
||||
Examples:
|
||||
python phase_diagram_generator.py Li-Fe-O
|
||||
python phase_diagram_generator.py Li-Fe-O --output li_fe_o_pd.png
|
||||
python phase_diagram_generator.py Fe-O --show
|
||||
python phase_diagram_generator.py Li-Fe-O --analyze "LiFeO2"
|
||||
"""
|
||||
|
||||
import argparse
|
||||
import os
|
||||
import sys
|
||||
from pathlib import Path
|
||||
|
||||
try:
|
||||
from pymatgen.core import Composition
|
||||
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
|
||||
except ImportError:
|
||||
print("Error: pymatgen is not installed. Install with: pip install pymatgen")
|
||||
sys.exit(1)
|
||||
|
||||
try:
|
||||
from mp_api.client import MPRester
|
||||
except ImportError:
|
||||
print("Error: mp-api is not installed. Install with: pip install mp-api")
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
def get_api_key() -> str:
|
||||
"""Get Materials Project API key from environment."""
|
||||
api_key = os.environ.get("MP_API_KEY")
|
||||
if not api_key:
|
||||
print("Error: MP_API_KEY environment variable not set.")
|
||||
print("Get your API key from https://next-gen.materialsproject.org/")
|
||||
print("Then set it with: export MP_API_KEY='your_key_here'")
|
||||
sys.exit(1)
|
||||
return api_key
|
||||
|
||||
|
||||
def generate_phase_diagram(chemsys: str, args):
|
||||
"""
|
||||
Generate and analyze phase diagram for a chemical system.
|
||||
|
||||
Args:
|
||||
chemsys: Chemical system (e.g., "Li-Fe-O")
|
||||
args: Command line arguments
|
||||
"""
|
||||
api_key = get_api_key()
|
||||
|
||||
print(f"\n{'='*60}")
|
||||
print(f"PHASE DIAGRAM: {chemsys}")
|
||||
print(f"{'='*60}\n")
|
||||
|
||||
# Get entries from Materials Project
|
||||
print("Fetching data from Materials Project...")
|
||||
with MPRester(api_key) as mpr:
|
||||
entries = mpr.get_entries_in_chemsys(chemsys)
|
||||
|
||||
print(f"✓ Retrieved {len(entries)} entries")
|
||||
|
||||
if len(entries) == 0:
|
||||
print(f"Error: No entries found for chemical system {chemsys}")
|
||||
sys.exit(1)
|
||||
|
||||
# Build phase diagram
|
||||
print("Building phase diagram...")
|
||||
pd = PhaseDiagram(entries)
|
||||
|
||||
# Get stable entries
|
||||
stable_entries = pd.stable_entries
|
||||
print(f"✓ Phase diagram constructed with {len(stable_entries)} stable phases")
|
||||
|
||||
# Print stable phases
|
||||
print("\n--- STABLE PHASES ---")
|
||||
for entry in stable_entries:
|
||||
formula = entry.composition.reduced_formula
|
||||
energy = entry.energy_per_atom
|
||||
print(f" {formula:<20} E = {energy:.4f} eV/atom")
|
||||
|
||||
# Analyze specific composition if requested
|
||||
if args.analyze:
|
||||
print(f"\n--- STABILITY ANALYSIS: {args.analyze} ---")
|
||||
try:
|
||||
comp = Composition(args.analyze)
|
||||
|
||||
# Find closest entry
|
||||
closest_entry = None
|
||||
min_distance = float('inf')
|
||||
|
||||
for entry in entries:
|
||||
if entry.composition.reduced_formula == comp.reduced_formula:
|
||||
closest_entry = entry
|
||||
break
|
||||
|
||||
if closest_entry:
|
||||
# Calculate energy above hull
|
||||
e_above_hull = pd.get_e_above_hull(closest_entry)
|
||||
print(f"Energy above hull: {e_above_hull:.4f} eV/atom")
|
||||
|
||||
if e_above_hull < 0.001:
|
||||
print(f"Status: STABLE (on convex hull)")
|
||||
elif e_above_hull < 0.05:
|
||||
print(f"Status: METASTABLE (nearly stable)")
|
||||
else:
|
||||
print(f"Status: UNSTABLE")
|
||||
|
||||
# Get decomposition
|
||||
decomp = pd.get_decomposition(comp)
|
||||
print(f"\nDecomposes to:")
|
||||
for entry, fraction in decomp.items():
|
||||
formula = entry.composition.reduced_formula
|
||||
print(f" {fraction:.3f} × {formula}")
|
||||
|
||||
# Get reaction energy
|
||||
rxn_energy = pd.get_equilibrium_reaction_energy(closest_entry)
|
||||
print(f"\nDecomposition energy: {rxn_energy:.4f} eV/atom")
|
||||
|
||||
else:
|
||||
print(f"No entry found for composition {args.analyze}")
|
||||
print("Checking stability of hypothetical composition...")
|
||||
|
||||
# Analyze hypothetical composition
|
||||
decomp = pd.get_decomposition(comp)
|
||||
print(f"\nWould decompose to:")
|
||||
for entry, fraction in decomp.items():
|
||||
formula = entry.composition.reduced_formula
|
||||
print(f" {fraction:.3f} × {formula}")
|
||||
|
||||
except Exception as e:
|
||||
print(f"Error analyzing composition: {e}")
|
||||
|
||||
# Get chemical potentials
|
||||
if args.chemical_potentials:
|
||||
print("\n--- CHEMICAL POTENTIALS ---")
|
||||
print("(at stability regions)")
|
||||
try:
|
||||
chempots = pd.get_all_chempots()
|
||||
for element, potentials in chempots.items():
|
||||
print(f"\n{element}:")
|
||||
for potential in potentials[:5]: # Show first 5
|
||||
print(f" {potential:.4f} eV")
|
||||
except Exception as e:
|
||||
print(f"Could not calculate chemical potentials: {e}")
|
||||
|
||||
# Plot phase diagram
|
||||
print("\n--- GENERATING PLOT ---")
|
||||
plotter = PDPlotter(pd, show_unstable=args.show_unstable)
|
||||
|
||||
if args.output:
|
||||
output_path = Path(args.output)
|
||||
plotter.write_image(str(output_path), image_format=output_path.suffix[1:])
|
||||
print(f"✓ Phase diagram saved to {output_path}")
|
||||
|
||||
if args.show:
|
||||
print("Opening interactive plot...")
|
||||
plotter.show()
|
||||
|
||||
print(f"\n{'='*60}\n")
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(
|
||||
description="Generate phase diagrams using Materials Project data",
|
||||
formatter_class=argparse.RawDescriptionHelpFormatter,
|
||||
epilog="""
|
||||
Requirements:
|
||||
- Materials Project API key (set MP_API_KEY environment variable)
|
||||
- mp-api package: pip install mp-api
|
||||
|
||||
Examples:
|
||||
%(prog)s Li-Fe-O
|
||||
%(prog)s Li-Fe-O --output li_fe_o_phase_diagram.png
|
||||
%(prog)s Fe-O --show --analyze "Fe2O3"
|
||||
%(prog)s Li-Fe-O --analyze "LiFeO2" --show-unstable
|
||||
"""
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"chemsys",
|
||||
help="Chemical system (e.g., Li-Fe-O, Fe-O)"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--output", "-o",
|
||||
help="Output file for phase diagram plot (PNG, PDF, SVG)"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--show", "-s",
|
||||
action="store_true",
|
||||
help="Show interactive plot"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--analyze", "-a",
|
||||
help="Analyze stability of specific composition (e.g., LiFeO2)"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--show-unstable",
|
||||
action="store_true",
|
||||
help="Include unstable phases in plot"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--chemical-potentials",
|
||||
action="store_true",
|
||||
help="Calculate chemical potentials"
|
||||
)
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
# Validate chemical system format
|
||||
elements = args.chemsys.split("-")
|
||||
if len(elements) < 2:
|
||||
print("Error: Chemical system must contain at least 2 elements")
|
||||
print("Example: Li-Fe-O")
|
||||
sys.exit(1)
|
||||
|
||||
# Generate phase diagram
|
||||
generate_phase_diagram(args.chemsys, args)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user