Tutorial 12

🧪 Tutorial 12: PyMatGen

The Python Materials Genomics (PyMatGen) toolkit is one of the most powerful Python libraries in computational materials science.

Developed as a core part of the Materials Project, PyMatGen helps you analyze, manipulate, and generate crystal structures, perform symmetry analysis, and more.

🔗 Official Website: https://pymatgen.org/
📹 YouTube Tutorials: Materials Virtual Lab

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🛠️ Installing PyMatGen

To install PyMatGen on your Mac or on the POWER cluster, activate your mamba environment and run:

mamba install pymatgen

⏳ Note: This may take a few minutes. PyMatGen has several dependencies.

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✅ Verifying Your Installation

Let's start with a quick check to see if PyMatGen works:

from pymatgen.symmetry.groups import SpaceGroup

symmetrynumber = 10

print(SpaceGroup.from_int_number(symmetrynumber).symbol)

This should print the Hermann–Mauguin symbol for space group #10.

Now, let’s extend that to print all 230 space group symbols:

from pymatgen.symmetry.groups import SpaceGroup

for sg_num in range(1, 231):
    sg = SpaceGroup.from_int_number(sg_num)
    print(sg)

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🔍 Comparing Crystal Structures

PyMatGen can also help you compare two structures, either fully or partially (e.g. ignoring atomic species).

Basic Structure Comparison

from pymatgen.core import Structure
from pymatgen.analysis.structure_matcher import StructureMatcher

structure1 = Structure.from_file("path/to/file/my_structure.cif")
structure2 = Structure.from_file("path/to/file/target_structure.cif")

matcher = StructureMatcher()
print(matcher.fit(structure1, structure2))  # Returns True or False

🛠️ You can tune the comparison with parameters like:

ltol       # Length tolerance (default: 0.2)
stol       # Site tolerance (default: 0.3)
angle_tol  # Angle tolerance in degrees (default: 5)

🧱 Framework Comparison

You can also compare structures ignoring the atom types, to see if they share the same framework (e.g. Si and C in diamond structure):

from pymatgen.core import Structure
from pymatgen.analysis.structure_matcher import StructureMatcher, FrameworkComparator

diamond = Structure.from_file("path/to/file/diamond.cif")
silicon = Structure.from_file("path/to/file/Si.cif")

matcher = StructureMatcher(comparator=FrameworkComparator())
print(matcher.fit(diamond, silicon))  # Should return True

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🎉 Success!

If you've reached this point:

✅ PyMatGen is installed and working
✅ You can analyze symmetry and compare structures
✅ You're ready for more advanced structure analysis!

👉 Continue to Tutorial 13 →