pymatgen

from pymatgen.core import Structure, Lattice
 
# Read structure from file (automatic format detection)
struct = Structure.from_file("POSCAR")
 
# Create structure from scratch
lattice = Lattice.cubic(3.84)
struct = Structure(lattice, ["Si", "Si"], [[0,0,0], [0.25,0.25,0.25]])
 
# Write to different format
struct.to(filename="structure.cif")
 
# Basic properties
print(f"Formula: {struct.composition.reduced_formula}")
print(f"Space group: {struct.get_space_group_info()}")
print(f"Density: {struct.density:.2f} g/cm³")

# Set up API key
export MP_API_KEY="your_api_key_here"

from mp_api.client import MPRester
 
with MPRester() as mpr:
    # Get structure by material ID
    struct = mpr.get_structure_by_material_id("mp-149")
 
    # Search for materials
    materials = mpr.materials.summary.search(
        formula="Fe2O3",
        energy_above_hull=(0, 0.05)
    )

# Automatic format detection
struct = Structure.from_file("structure.cif")
struct = Structure.from_file("POSCAR")
mol = Molecule.from_file("molecule.xyz")

from pymatgen.core import Structure, Lattice
 
# Using lattice parameters
lattice = Lattice.from_parameters(a=3.84, b=3.84, c=3.84,
                                  alpha=120, beta=90, gamma=60)
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
struct = Structure(lattice, ["Si", "Si"], coords)
 
# From space group
struct = Structure.from_spacegroup(
    "Fm-3m",
    Lattice.cubic(3.5),
    ["Si"],
    [[0, 0, 0]]
)

from pymatgen.transformations.standard_transformations import (
    SupercellTransformation,
    SubstitutionTransformation,
    PrimitiveCellTransformation
)
 
# Create supercell
trans = SupercellTransformation([[2,0,0],[0,2,0],[0,0,2]])
supercell = trans.apply_transformation(struct)
 
# Substitute elements
trans = SubstitutionTransformation({"Fe": "Mn"})
new_struct = trans.apply_transformation(struct)
 
# Get primitive cell
trans = PrimitiveCellTransformation()
primitive = trans.apply_transformation(struct)

# Read any format
struct = Structure.from_file("input_file")
 
# Write to any format
struct.to(filename="output.cif")
struct.to(filename="POSCAR")
struct.to(filename="output.xyz")

# Single file conversion
python scripts/structure_converter.py POSCAR structure.cif
 
# Batch conversion
python scripts/structure_converter.py *.cif --output-dir ./poscar_files --format poscar

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
sga = SpacegroupAnalyzer(struct)
 
# Get space group information
print(f"Space group: {sga.get_space_group_symbol()}")
print(f"Number: {sga.get_space_group_number()}")
print(f"Crystal system: {sga.get_crystal_system()}")
 
# Get conventional/primitive cells
conventional = sga.get_conventional_standard_structure()
primitive = sga.get_primitive_standard_structure()

from pymatgen.analysis.local_env import CrystalNN
 
cnn = CrystalNN()
neighbors = cnn.get_nn_info(struct, n=0)  # Neighbors of site 0
 
print(f"Coordination number: {len(neighbors)}")
for neighbor in neighbors:
    site = struct[neighbor['site_index']]
    print(f"  {site.species_string} at {neighbor['weight']:.3f} Å")

# Comprehensive analysis
python scripts/structure_analyzer.py POSCAR --symmetry --neighbors
 
# Export results
python scripts/structure_analyzer.py structure.cif --symmetry --export json

from mp_api.client import MPRester
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
 
# Get entries from Materials Project
with MPRester() as mpr:
    entries = mpr.get_entries_in_chemsys("Li-Fe-O")
 
# Build phase diagram
pd = PhaseDiagram(entries)
 
# Check stability
from pymatgen.core import Composition
comp = Composition("LiFeO2")
 
# Find entry for composition
for entry in entries:
    if entry.composition.reduced_formula == comp.reduced_formula:
        e_above_hull = pd.get_e_above_hull(entry)
        print(f"Energy above hull: {e_above_hull:.4f} eV/atom")
 
        if e_above_hull > 0.001:
            # Get decomposition
            decomp = pd.get_decomposition(comp)
            print("Decomposes to:", decomp)
 
# Plot
plotter = PDPlotter(pd)
plotter.show()

# Generate phase diagram
python scripts/phase_diagram_generator.py Li-Fe-O --output li_fe_o.png
 
# Analyze specific composition
python scripts/phase_diagram_generator.py Li-Fe-O --analyze "LiFeO2" --show

from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
 
# Read from VASP calculation
vasprun = Vasprun("vasprun.xml")
bs = vasprun.get_band_structure()
 
# Analyze
band_gap = bs.get_band_gap()
print(f"Band gap: {band_gap['energy']:.3f} eV")
print(f"Direct: {band_gap['direct']}")
print(f"Is metal: {bs.is_metal()}")
 
# Plot
plotter = BSPlotter(bs)
plotter.save_plot("band_structure.png")

from pymatgen.electronic_structure.plotter import DosPlotter
 
dos = vasprun.complete_dos
 
# Get element-projected DOS
element_dos = dos.get_element_dos()
for element, element_dos_obj in element_dos.items():
    print(f"{element}: {element_dos_obj.get_gap():.3f} eV")
 
# Plot
plotter = DosPlotter()
plotter.add_dos("Total DOS", dos)
plotter.show()

from pymatgen.core.surface import SlabGenerator
 
# Generate slabs for specific Miller index
slabgen = SlabGenerator(
    struct,
    miller_index=(1, 1, 1),
    min_slab_size=10.0,      # Å
    min_vacuum_size=10.0,    # Å
    center_slab=True
)
 
slabs = slabgen.get_slabs()
 
# Write slabs
for i, slab in enumerate(slabs):
    slab.to(filename=f"slab_{i}.cif")

from pymatgen.analysis.wulff import WulffShape
 
# Define surface energies
surface_energies = {
    (1, 0, 0): 1.0,
    (1, 1, 0): 1.1,
    (1, 1, 1): 0.9,
}
 
wulff = WulffShape(struct.lattice, surface_energies)
print(f"Surface area: {wulff.surface_area:.2f} Ų")
print(f"Volume: {wulff.volume:.2f} ų")
 
wulff.show()

from pymatgen.analysis.adsorption import AdsorbateSiteFinder
from pymatgen.core import Molecule
 
asf = AdsorbateSiteFinder(slab)
 
# Find sites
ads_sites = asf.find_adsorption_sites()
print(f"On-top sites: {len(ads_sites['ontop'])}")
print(f"Bridge sites: {len(ads_sites['bridge'])}")
print(f"Hollow sites: {len(ads_sites['hollow'])}")
 
# Add adsorbate
adsorbate = Molecule("O", [[0, 0, 0]])
ads_struct = asf.add_adsorbate(adsorbate, ads_sites["ontop"][0])

from mp_api.client import MPRester
 
with MPRester() as mpr:
    # Search by formula
    materials = mpr.materials.summary.search(formula="Fe2O3")
 
    # Search by chemical system
    materials = mpr.materials.summary.search(chemsys="Li-Fe-O")
 
    # Filter by properties
    materials = mpr.materials.summary.search(
        chemsys="Li-Fe-O",
        energy_above_hull=(0, 0.05),  # Stable/metastable
        band_gap=(1.0, 3.0)            # Semiconducting
    )
 
    # Get structure
    struct = mpr.get_structure_by_material_id("mp-149")
 
    # Get band structure
    bs = mpr.get_bandstructure_by_material_id("mp-149")
 
    # Get entries for phase diagram
    entries = mpr.get_entries_in_chemsys("Li-Fe-O")

from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPNonSCFSet
 
# Relaxation
relax = MPRelaxSet(struct)
relax.write_input("./relax_calc")
 
# Static calculation
static = MPStaticSet(struct)
static.write_input("./static_calc")
 
# Band structure (non-self-consistent)
nscf = MPNonSCFSet(struct, mode="line")
nscf.write_input("./bandstructure_calc")
 
# Custom parameters
custom = MPRelaxSet(struct, user_incar_settings={"ENCUT": 600})
custom.write_input("./custom_calc")

# Gaussian
from pymatgen.io.gaussian import GaussianInput
 
gin = GaussianInput(
    mol,
    functional="B3LYP",
    basis_set="6-31G(d)",
    route_parameters={"Opt": None}
)
gin.write_file("input.gjf")
 
# Quantum ESPRESSO
from pymatgen.io.pwscf import PWInput
 
pwin = PWInput(struct, control={"calculation": "scf"})
pwin.write_file("pw.in")

from pymatgen.analysis.diffraction.xrd import XRDCalculator
 
xrd = XRDCalculator()
pattern = xrd.get_pattern(struct)
 
# Get peaks
for peak in pattern.hkls:
    print(f"2θ = {peak['2theta']:.2f}°, hkl = {peak['hkl']}")
 
pattern.plot()

from pymatgen.analysis.elasticity import ElasticTensor
 
# From elastic tensor matrix
elastic_tensor = ElasticTensor.from_voigt(matrix)
 
print(f"Bulk modulus: {elastic_tensor.k_voigt:.1f} GPa")
print(f"Shear modulus: {elastic_tensor.g_voigt:.1f} GPa")
print(f"Young's modulus: {elastic_tensor.y_mod:.1f} GPa")

from pymatgen.transformations.advanced_transformations import MagOrderingTransformation
 
# Enumerate magnetic orderings
trans = MagOrderingTransformation({"Fe": 5.0})
mag_structs = trans.apply_transformation(struct, return_ranked_list=True)
 
# Get lowest energy magnetic structure
lowest_energy_struct = mag_structs[0]['structure']

from pymatgen.transformations.standard_transformations import SubstitutionTransformation
from pymatgen.io.vasp.sets import MPRelaxSet
 
# Generate doped structures
base_struct = Structure.from_file("POSCAR")
dopants = ["Mn", "Co", "Ni", "Cu"]
 
for dopant in dopants:
    trans = SubstitutionTransformation({"Fe": dopant})
    doped_struct = trans.apply_transformation(base_struct)
 
    # Generate VASP inputs
    vasp_input = MPRelaxSet(doped_struct)
    vasp_input.write_input(f"./calcs/Fe_{dopant}")

# 1. Relaxation
relax = MPRelaxSet(struct)
relax.write_input("./1_relax")
 
# 2. Static (after relaxation)
relaxed = Structure.from_file("1_relax/CONTCAR")
static = MPStaticSet(relaxed)
static.write_input("./2_static")
 
# 3. Band structure (non-self-consistent)
nscf = MPNonSCFSet(relaxed, mode="line")
nscf.write_input("./3_bandstructure")
 
# 4. Analysis
from pymatgen.io.vasp import Vasprun
vasprun = Vasprun("3_bandstructure/vasprun.xml")
bs = vasprun.get_band_structure()
bs.get_band_gap()

# 1. Get bulk energy
bulk_vasprun = Vasprun("bulk/vasprun.xml")
bulk_E_per_atom = bulk_vasprun.final_energy / len(bulk)
 
# 2. Generate and calculate slabs
slabgen = SlabGenerator(bulk, (1,1,1), 10, 15)
slab = slabgen.get_slabs()[0]
 
MPRelaxSet(slab).write_input("./slab_calc")
 
# 3. Calculate surface energy (after calculation)
slab_vasprun = Vasprun("slab_calc/vasprun.xml")
E_surf = (slab_vasprun.final_energy - len(slab) * bulk_E_per_atom) / (2 * slab.surface_area)
E_surf *= 16.021766  # Convert eV/Ų to J/m²

uv pip install pymatgen[analysis,vis]

export MP_API_KEY="your_key_here"

# Try explicit format specification
struct = Structure.from_file("file.txt", fmt="cif")

# Increase tolerance
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
sga = SpacegroupAnalyzer(struct, symprec=0.1)