Error: Type is not JSON serializable when Exporting POSCAR Structure to JSON #4460
Description
Python version
Python 3.12.0
Pymatgen version
2025.6.14
Operating system version
Mac Os
Current behavior
Attempting to export a Structure object initialized from a POSCAR file containing site_properties["selective_dynamics"] to JSON format using to(filename="structure.json", fmt="json") results in a Error: Type is not JSON serializable: numpy.ndarray. The error message indicates that numpy.ndarray objects within the site_properties are not JSON serializable.
Expected Behavior
The Structure object should be successfully serialized to JSON format.
Minimal example
import json
import numpy as np
from pymatgen.io.vasp import Poscar
from pymatgen.core.structure import Structure
# Create a mock structure with selective_dynamics
structure = Structure(
lattice=[[10, 0, 0], [0, 10, 0], [0, 0, 10]],
species=["H", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
site_properties={"selective_dynamics": [[True, True, True], [False, False, False]]}
)
# Create a POSCAR object from the structure
poscar1 = Poscar(structure)
# write poscar to file
poscar1.write_file("test.poscar")
# read poscar from file
poscar = Poscar.from_file("test.poscar")
# Attempt to export the POSCAR structure to JSON
try:
poscar.structure.to(filename="structure.json", fmt="json")
except TypeError as e:
print(f"Error: {e}")Relevant files to reproduce this bug
test.poscar is created by the minimal example itself.