Use this Skill for materials science with pymatgen: crystal structure manipulation, Materials Project API queries (bandgap, DOS, formation energy), phase diagrams, and symmetry analysis.
Instrucciones de origen · Vista previa de solo lectura
name
pymatgen-materials
description
Use this Skill for materials science with pymatgen: crystal structure manipulation, Materials Project API queries (bandgap, DOS, formation energy), phase diagrams, and symmetry analysis.
TL;DR — Manipulate crystal structures, query the Materials Project database for
band gaps, DOS, and formation energies, construct phase diagrams, and perform
space group symmetry analysis with pymatgen.
When to Use
Use this Skill when you need to:
Load and manipulate crystal structures from CIF, POSCAR (VASP), or XYZ files
Query Materials Project for DFT-computed properties: band gap, DOS, formation energy,
stability (e_above_hull)
Construct binary or ternary phase diagrams and identify stable phases
Perform symmetry analysis: detect space group, find equivalent sites, get conventional cell
Build supercells, substitute atoms, or apply structure transformations
Visualize electronic band structure and density of states (DOS)
Calculate Pourbaix diagrams for electrochemical stability
Task
Key pymatgen Class
Crystal structure
Structure, Lattice
File I/O
CifParser, Poscar, XYZ
API query
MPRester (mp-api)
Phase diagram
PhaseDiagram, PDPlotter
Symmetry
SpacegroupAnalyzer
Band structure
BSPlotter
Pourbaix
PourbaixDiagram
Background & Key Concepts
The Structure Object
Structure is the central pymatgen object. It contains:
Lattice: three lattice vectors defining the unit cell
Species: list of element symbols or Species with oxidation states
frac_coords: fractional coordinates of all sites
Materials Project API
The Materials Project (https://materialsproject.org) provides DFT-computed properties
for ~150,000 inorganic compounds. Access requires a free API key. The new API uses
mp-api package with MPRester.
# Get your API key at https://materialsproject.org/apiexport MP_API_KEY="<paste-your-key>"
Phase Diagrams
A phase diagram maps thermodynamic stability in composition space. The PhaseDiagram
class constructs the convex hull of formation energies. Points on the hull are stable;
e_above_hull measures distance to the hull in eV/atom.
Symmetry Analysis
SpacegroupAnalyzer uses spglib to detect the space group, find the conventional
cell, primitive cell, and symmetry operations. Essential for comparing structures and
setting up DFT calculations.
import os
from mp_api.client import MPRester
defquery_material_properties(
formula_or_mpid: str,
api_key: str = None,
) -> list:
"""
Query the Materials Project for key properties of a compound.
Args:
formula_or_mpid: Chemical formula (e.g., 'TiO2') or mp-id (e.g., 'mp-2657').
api_key: Materials Project API key. Falls back to MP_API_KEY env var.
Returns:
List of dicts with material_id, formula, bandgap, formation_energy,
e_above_hull, and crystal_system for each matching entry.
"""
api_key = api_key or os.getenv("MP_API_KEY")
ifnot api_key:
raise ValueError("Set MP_API_KEY environment variable:\n export MP_API_KEY='<paste-your-key>'")
results = []
with MPRester(api_key) as mpr:
docs = mpr.materials.summary.search(
formula=formula_or_mpid,
fields=[
"material_id", "formula_pretty", "band_gap",
"formation_energy_per_atom", "e_above_hull",
"symmetry", "volume", "nsites",
],
)
for doc in docs:
results.append({
"material_id": doc.material_id,
"formula": doc.formula_pretty,
"band_gap_eV": doc.band_gap,
"formation_energy_eV_at": doc.formation_energy_per_atom,
"e_above_hull_eV_at": doc.e_above_hull,
"space_group": doc.symmetry.symbol if doc.symmetry elseNone,
"volume_A3": doc.volume,
"nsites": doc.nsites,
"is_stable": doc.e_above_hull < 0.025,
})
results.sort(key=lambda x: x["e_above_hull_eV_at"])
print(f"Found {len(results)} entries for '{formula_or_mpid}'")
return results
defget_dos_and_bandgap(
mp_id: str,
api_key: str = None,
output_plot: str = None,
) -> dict:
"""
Retrieve the electronic DOS and plot it for a given Materials Project entry.
Args:
mp_id: Materials Project ID (e.g., 'mp-2657' for TiO2 anatase).
api_key: API key; defaults to MP_API_KEY env var.
output_plot: If given, save the DOS plot as PNG.
Returns:
Dictionary with band_gap, cbm, vbm, and DOS data object.
"""
api_key = api_key or os.getenv("MP_API_KEY")
with MPRester(api_key) as mpr:
dos = mpr.get_dos_by_material_id(mp_id)
summary = mpr.materials.summary.get_data_by_id(
mp_id, fields=["band_gap", "cbm", "vbm", "is_gap_direct"]
)
if output_plot and dos isnotNone:
from pymatgen.electronic_structure.plotter import DosPlotter
plotter = DosPlotter()
plotter.add_dos("Total DOS", dos.get_dos())
ax = plotter.get_plot(xlim=(-5, 5))
ax.set_title(f"DOS for {mp_id}")
ax.figure.savefig(output_plot, dpi=150)
print(f"DOS plot saved to {output_plot}")
return {
"mp_id": mp_id,
"band_gap_eV": summary.band_gap,
"is_gap_direct": summary.is_gap_direct,
"dos_object": dos,
}
# Example usage (requires API key):# api_key = os.getenv("MP_API_KEY")# tio2_data = query_material_properties("TiO2", api_key)# for entry in tio2_data[:3]:# print(f"{entry['material_id']:12s} {entry['formula']:8s} "# f"Eg={entry['band_gap_eV']:.2f} eV "# f"Ef={entry['formation_energy_eV_at']:.3f} eV/at")
Advanced Usage
Phase Diagram Construction
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter, PDEntry
from pymatgen.core.composition import Composition
defbuild_phase_diagram_from_api(
elements: list,
api_key: str = None,
output_path: str = None,
) -> dict:
"""
Build a phase diagram for a set of elements using Materials Project data.
Args:
elements: List of element symbols, e.g. ['Li', 'Fe', 'O'].
api_key: MP API key; defaults to MP_API_KEY env var.
output_path: If given, save the diagram as PNG.
Returns:
Dictionary with PhaseDiagram object and list of stable entries.
"""
api_key = api_key or os.getenv("MP_API_KEY")
with MPRester(api_key) as mpr:
entries = mpr.get_entries_in_chemsys(elements)
print(f"Downloaded {len(entries)} entries for {'-'.join(elements)}")
pd = PhaseDiagram(entries)
stable = [e for e in pd.stable_entries]
print(f"Stable phases ({len(stable)}):")
for e insorted(stable, key=lambda x: x.composition.reduced_formula):
eabove = pd.get_e_above_hull(e)
print(f" {e.composition.reduced_formula:15s} Ef={e.energy_per_atom:.3f} eV/at "f"e_hull={eabove:.3f} eV/at")
if output_path:
plotter = PDPlotter(pd, show_unstable=0.1)
ax = plotter.get_plot()
ax.set_title(f"{'-'.join(elements)} Phase Diagram")
ax.figure.savefig(output_path, dpi=150, bbox_inches="tight")
print(f"Phase diagram saved to {output_path}")
return {"phase_diagram": pd, "stable_entries": stable}
# Example: Li-Fe-O phase diagram# api_key = os.getenv("MP_API_KEY")# pd_result = build_phase_diagram_from_api(["Li", "Fe", "O"], api_key,# output_path="/tmp/LiFeO_phase.png")defbuild_manual_phase_diagram(
compositions_energies: list,
output_path: str = None,
) -> PhaseDiagram:
"""
Build a phase diagram from manually supplied (composition, energy) pairs.
Useful for data from your own DFT calculations.
Args:
compositions_energies: List of (formula_str, total_energy_eV) tuples.
output_path: Save path for the plot.
Returns:
PhaseDiagram object.
"""
entries = []
for formula, energy in compositions_energies:
comp = Composition(formula)
entries.append(PDEntry(comp, energy))
pd = PhaseDiagram(entries)
if output_path:
plotter = PDPlotter(pd)
ax = plotter.get_plot()
ax.figure.savefig(output_path, dpi=150)
return pd
# Example: Cu-Zn binary system (representative DFT energies)
cu_zn_data = [
("Cu", -3.72 * 1),
("Zn", -1.25 * 1),
("CuZn", -4.80 * 2),
("Cu3Zn", -4.62 * 4),
("CuZn3", -4.09 * 4),
]
pd_cuzn = build_manual_phase_diagram(cu_zn_data, output_path="/tmp/CuZn_phase.png")
print(f"\nCu-Zn stable phases: "f"{[e.composition.reduced_formula for e in pd_cuzn.stable_entries]}")
Structure Transformations
from pymatgen.transformations.standard_transformations import (
SupercellTransformation,
SubstitutionTransformation,
)
defmake_supercell(structure: Structure, scaling_matrix) -> Structure:
"""
Create a supercell from a structure.
Args:
structure: pymatgen Structure.
scaling_matrix: 3x3 matrix or scalar. E.g., [[2,0,0],[0,2,0],[0,0,2]]
for a 2x2x2 supercell.
Returns:
Supercell Structure object.
"""
trans = SupercellTransformation(scaling_matrix)
supercell = trans.apply_transformation(structure)
print(f"Supercell: {supercell.formula}, {len(supercell)} sites")
return supercell
defsubstitute_atoms(
structure: Structure,
substitution_dict: dict,
) -> Structure:
"""
Substitute one element for another across all sites.
Args:
structure: pymatgen Structure.
substitution_dict: Mapping from original to new element, e.g. {'Na': 'K'}.
Returns:
New Structure with substitutions applied.
"""
trans = SubstitutionTransformation(substitution_dict)
new_struct = trans.apply_transformation(structure)
print(f"After substitution {substitution_dict}: {new_struct.formula}")
return new_struct
# Make a 2x2x2 NaCl supercell
nacl_super = make_supercell(nacl, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
# Substitute Na -> K (KCl structure)
kcl = substitute_atoms(nacl, {"Na": "K"})
print(f"KCl lattice parameter: {kcl.lattice.a:.3f} Ang")
Examples
Example 1 — CIF Load + Full Symmetry Analysis
import numpy as np
from pymatgen.core import Structure, Lattice
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.io.vasp import Poscar
defanalyze_structure_from_poscar_string(poscar_string: str) -> dict:
"""
Parse a POSCAR-format string, run symmetry analysis, and return results.
Args:
poscar_string: VASP POSCAR format crystal structure as a multiline string.
Returns:
Dictionary with formula, space group, lattice parameters, and volume.
"""import tempfile, os
with tempfile.NamedTemporaryFile(mode="w", suffix=".vasp", delete=False) as f:
f.write(poscar_string)
tmp_path = f.name
structure = Poscar.from_file(tmp_path).structure
os.unlink(tmp_path)
analyzer = SpacegroupAnalyzer(structure, symprec=0.05)
sg = analyzer.get_space_group_symbol()
sg_num = analyzer.get_space_group_number()
conventional = analyzer.get_conventional_standard_structure()
lat = structure.lattice
result = {
"formula": structure.formula,
"space_group": f"{sg} (#{sg_num})",
"a": lat.a, "b": lat.b, "c": lat.c,
"alpha": lat.alpha, "beta": lat.beta, "gamma": lat.gamma,
"volume_A3": lat.volume,
"nsites": len(structure),
"density_g_cm3": structure.density,
"conventional": conventional,
}
print(f"Formula: {result['formula']}")
print(f"Space group: {result['space_group']}")
print(f"a={lat.a:.3f} b={lat.b:.3f} c={lat.c:.3f} Ang")
print(f"Volume: {lat.volume:.2f} Ang^3")
print(f"Density: {structure.density:.3f} g/cm^3")
return result
# Example: TiO2 rutile (POSCAR format)
rutile_poscar = """\
TiO2 rutile
1.0
4.5937 0.0000 0.0000
0.0000 4.5937 0.0000
0.0000 0.0000 2.9587
Ti O
2 4
Direct
0.00000 0.00000 0.00000
0.50000 0.50000 0.50000
0.30530 0.30530 0.00000
0.69470 0.69470 0.00000
0.80470 0.19530 0.50000
0.19530 0.80470 0.50000
"""
rutile_info = analyze_structure_from_poscar_string(rutile_poscar)
Example 2 — Materials Project Band Gap Query and Visualization
import os
import pandas as pd
import matplotlib.pyplot as plt
defcompare_bandgaps_api(
formulas: list,
api_key: str = None,
output_path: str = "/tmp/bandgap_comparison.png",
) -> pd.DataFrame:
"""
Query Materials Project for the lowest-e_above_hull entry of each formula,
collect band gaps, and produce a bar chart.
Args:
formulas: List of chemical formulae, e.g. ['TiO2', 'ZnO', 'GaAs'].
api_key: MP API key; reads MP_API_KEY env var if not given.
output_path: Path to save the bar chart.
Returns:
DataFrame with formula, mp_id, band_gap_eV, space_group, e_above_hull.
"""
api_key = api_key or os.getenv("MP_API_KEY")
records = []
with MPRester(api_key) as mpr:
for formula in formulas:
docs = mpr.materials.summary.search(
formula=formula,
fields=["material_id", "formula_pretty", "band_gap",
"e_above_hull", "symmetry"],
sort_fields=["e_above_hull"],
)
if docs:
best = docs[0] # lowest e_above_hull
records.append({
"formula": best.formula_pretty,
"mp_id": best.material_id,
"band_gap_eV": best.band_gap,
"e_above_hull": best.e_above_hull,
"space_group": best.symmetry.symbol if best.symmetry else"?",
})
df = pd.DataFrame(records).sort_values("band_gap_eV")
# Plot
fig, ax = plt.subplots(figsize=(max(6, len(df) * 0.8), 4))
colors = ["#2196F3"if g > 0else"#F44336"for g in df["band_gap_eV"]]
bars = ax.bar(df["formula"], df["band_gap_eV"], color=colors, edgecolor="k", lw=0.5)
ax.axhline(0, color="k", lw=0.8)
ax.set_ylabel("Band gap (eV)")
ax.set_title("Band Gaps from Materials Project (lowest-hull entry)")
for bar, row inzip(bars, df.itertuples()):
h = bar.get_height()
ax.text(bar.get_x() + bar.get_width() / 2, h + 0.05,
f"{h:.2f}", ha="center", va="bottom", fontsize=8)
fig.tight_layout()
fig.savefig(output_path, dpi=150)
print(f"Band gap chart saved to {output_path}")
plt.show()
print(df.to_string(index=False))
return df
# Usage (requires MP_API_KEY):# df_bg = compare_bandgaps_api(# ["TiO2", "ZnO", "GaN", "Si", "Ge", "GaAs"],# output_path="/tmp/bandgap_comparison.png",# )
Example 3 — Binary Phase Diagram from Materials Project
import os
import matplotlib.pyplot as plt
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
defplot_binary_phase_diagram(
element_a: str,
element_b: str,
api_key: str = None,
show_unstable: float = 0.05,
output_path: str = None,
) -> dict:
"""
Retrieve entries from Materials Project and plot a binary phase diagram.
Args:
element_a: First element, e.g. 'Cu'.
element_b: Second element, e.g. 'Zn'.
api_key: MP API key.
show_unstable: Show entries up to this eV/atom above hull as unstable.
output_path: Save path for the plot.
Returns:
Dictionary with phase_diagram, n_stable, n_total.
"""
api_key = api_key or os.getenv("MP_API_KEY")
with MPRester(api_key) as mpr:
entries = mpr.get_entries_in_chemsys([element_a, element_b])
pd_obj = PhaseDiagram(entries)
stable = pd_obj.stable_entries
print(f"{element_a}-{element_b} system: {len(entries)} total, "f"{len(stable)} stable phases")
for e insorted(stable, key=lambda x: x.composition.get_atomic_fraction(element_a)):
print(f" {e.composition.reduced_formula:10s} "f"Ef = {pd_obj.get_form_energy_per_atom(e):.4f} eV/at")
if output_path:
plotter = PDPlotter(pd_obj, show_unstable=show_unstable, backend="matplotlib")
ax = plotter.get_plot(label_stable=True, label_unstable=False)
ax.set_title(f"{element_a}-{element_b} Phase Diagram (MP data)")
ax.figure.savefig(output_path, dpi=150, bbox_inches="tight")
print(f"Phase diagram saved to {output_path}")
return {
"phase_diagram": pd_obj,
"n_stable": len(stable),
"n_total": len(entries),
}
# Usage (requires MP_API_KEY):# result = plot_binary_phase_diagram(# "Cu", "Zn",# output_path="/tmp/CuZn_pd.png",# )
Troubleshooting
Error
Cause
Fix
APIError: 401 Unauthorized
Missing or invalid API key
Set export MP_API_KEY="<paste-your-key>" from materialsproject.org/api
CifParserError
Malformed or non-standard CIF
Try primitive=True; or repair with VESTA
Space group detected as P1
Loose tolerance
Decrease symprec in SpacegroupAnalyzer(struct, symprec=0.001)
CompositionError
Unknown element symbol
Check formula string; use standard IUPAC symbols
Phase diagram has only terminal phases
No intermediate compounds in DB
Check with mpr.get_entries_in_chemsys and print all formulas
e_above_hull is None
Entry not on the computed hull
Use pd_obj.get_e_above_hull(entry) after building PhaseDiagram
