import os
import sys
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.io.cif import CifWriter, CifParser


infile = None
prec = 1.0e-3
pause = 0

argv = sys.argv
narg = len(argv)
if narg >= 2:
    infile = argv[1]
if narg >= 3:
    outfile = argv[2]
else:
    dir_path = os.path.dirname(infile)
    filebody, ext = os.path.splitext(infile)
    outfile = os.path.join(dir_path, f"{filebody}-symmetrized.cif")
if narg >= 4:
    prec = float(argv[3])
if narg >= 5:
    pause = int(argv[4])

print()
print(f"infile: {infile}")
print(f"outfile: {outfile}")
print(f"prec: {prec}")

struct = Structure.from_file(infile, primitive = False)
print()
print("input structure:")
print(struct)

symmetry_analyzer = SpacegroupAnalyzer(struct, symprec = prec) #, angle_tolerance = 5.0)
symmetrized_structure = symmetry_analyzer.get_symmetrized_structure()
print()
print("symmetrized_structure:")
print(symmetrized_structure)

print()
print(f"Save the symmetrized structure to [{outfile}]")
writer = CifWriter(symmetrized_structure, symprec = prec) #, angle_tolerance = 5.0)
writer.write_file(outfile)

if pause: input("\nPress ENTER to terminate>>\n")