The wrong space group type given by spglib. #514

hongyi-zhao · 2024-07-28T15:36:17Z

hongyi-zhao
Jul 28, 2024

Dear spglib Development Team,

I try to obtain the space group type by spglib using a cif file as shown below:

import numpy as np
import spglib
from CifFile import ReadCif
import re

def parse_float_with_uncertainty(value):
    """Parse a string with a floating point number and uncertainty."""
    match = re.match(r'^(-?\d+\.?\d*)(\(\d+\))?$', value)
    if match:
        return float(match.group(1))
    else:
        raise ValueError(f"Unable to parse value: {value}")

def get_element(atom_type):
    """Extract the element symbol from an atom type string."""
    return re.match(r'^([A-Z][a-z]?)', atom_type).group(1)

def parse_cif_with_pycifrw(filename):
    """Parse CIF file using PyCifRW and return cell parameters and atom data."""
    cif = ReadCif(filename)
    data = cif[cif.keys()[0]]  # Assume single data block

    # Extract cell parameters
    a = parse_float_with_uncertainty(data['_cell_length_a'])
    b = parse_float_with_uncertainty(data['_cell_length_b'])
    c = parse_float_with_uncertainty(data['_cell_length_c'])
    alpha = np.radians(parse_float_with_uncertainty(data['_cell_angle_alpha']))
    beta = np.radians(parse_float_with_uncertainty(data['_cell_angle_beta']))
    gamma = np.radians(parse_float_with_uncertainty(data['_cell_angle_gamma']))

    # Calculate cell matrix
    v = np.sqrt(1 - np.cos(alpha)**2 - np.cos(beta)**2 - np.cos(gamma)**2 + 2*np.cos(alpha)*np.cos(beta)*np.cos(gamma))
    cell = np.array([
        [a, 0, 0],
        [b*np.cos(gamma), b*np.sin(gamma), 0],
        [c*np.cos(beta), c*(np.cos(alpha)-np.cos(beta)*np.cos(gamma))/(np.sin(gamma)), c*v/np.sin(gamma)]
    ])

    # Extract atom positions
    x = data['_atom_site_fract_x']
    y = data['_atom_site_fract_y']
    z = data['_atom_site_fract_z']
    positions = np.array([[parse_float_with_uncertainty(xi), 
                           parse_float_with_uncertainty(yi), 
                           parse_float_with_uncertainty(zi)] for xi, yi, zi in zip(x, y, z)])

    # Extract atom types and convert to numbers
    atom_types = data['_atom_site_type_symbol']
    type_to_number = {'H': 1, 'He': 2, 'Li': 3, 'Be': 4, 'B': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'Ne': 10,
                      'Na': 11, 'Mg': 12, 'Al': 13, 'Si': 14, 'P': 15, 'S': 16, 'Cl': 17, 'Ar': 18, 'K': 19, 'Ca': 20,
                      'Sc': 21, 'Ti': 22, 'V': 23, 'Cr': 24, 'Mn': 25, 'Fe': 26, 'Co': 27, 'Ni': 28, 'Cu': 29, 'Zn': 30}
    numbers = [type_to_number[get_element(atom)] for atom in atom_types]

    return cell, positions, numbers

def analyze_space_group(filename):
    """Analyze space group with different tolerances."""
    try:
        cell, positions, numbers = parse_cif_with_pycifrw(filename)
    except Exception as e:
        print(f"Error parsing CIF file: {filename}")
        print(f"Exception: {e}")
        return

    tolerances = [1e-1, 1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7]

    print(f"Analysis for file: {filename}")
    print(f"Cell parameters:\n{cell}")
    print(f"Number of atoms: {len(positions)}")
    print(f"Atom types: {set(numbers)}")
    
    for tol in tolerances:
        spacegroup = spglib.get_spacegroup((cell, positions, numbers), symprec=tol)
        print(f"Tolerance {tol:.1e}: {spacegroup}")

if __name__ == "__main__":
    cif_file = "ICSD_CollCode262928.cif"
    analyze_space_group(cif_file)

After running the above script, I obtained the following results:

Analysis for file: ICSD_CollCode262928.cif
Cell parameters:
[[ 3.37170000e+00  0.00000000e+00  0.00000000e+00]
 [-1.68585000e+00  2.91997785e+00  0.00000000e+00]
 [ 3.29766767e-16  5.71172795e-16  5.38550000e+00]]
Number of atoms: 2
Atom types: {8, 25}
Tolerance 1.0e-01: P6mm (183)
Tolerance 1.0e-02: P6mm (183)
Tolerance 1.0e-03: P6mm (183)
Tolerance 1.0e-04: P6mm (183)
Tolerance 1.0e-05: P6mm (183)
Tolerance 1.0e-06: P6mm (183)
Tolerance 1.0e-07: P6mm (183)

These results show that spglib consistently determines the space group as P6mm (183) across all tested symmetry tolerances, which differs from P6_3mc (186) given in the cif file.

I'm very puzzled by the wrong results given by spglib. Any hints/comments will be appreciated.

ICSD_CollCode262928.cif.zip

See here for the related discussion.

Regards,
Zhao

hongyi-zhao · 2024-07-28T15:50:19Z

hongyi-zhao
Jul 28, 2024
Author

On the other hand, I also tried to use ase and pymatgen to do the same thing as follows:

Using ase:

In [15]: import numpy as np
    ...: from ase.io import read
    ...: from ase.spacegroup import get_spacegroup
    ...: 
    ...: def analyze_space_group_ase(filename):
    ...:     """Analyze space group using ASE with different tolerances."""
    ...:     # Read the CIF file
    ...:     atoms = read(filename)
    ...: 
    ...:     # Define tolerances to test
    ...:     tolerances = [1e-1, 1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7]
    ...: 
    ...:     print(f"Analysis for file: {filename}")
    ...:     print(f"Cell parameters:\n{atoms.cell}")
    ...:     print(f"Number of atoms: {len(atoms)}")
    ...:     print(f"Atom types: {set(atoms.get_chemical_symbols())}")
    ...: 
    ...:     for tol in tolerances:
    ...:         spacegroup = get_spacegroup(atoms, symprec=tol)
    ...:         print(f"Tolerance {tol:.1e}: {spacegroup.symbol} ({spacegroup.no})")
    ...: 
    ...: if __name__ == "__main__":
    ...:     cif_file = "ICSD_CollCode262928.cif"
    ...:     analyze_space_group_ase(cif_file)
    ...: 
Analysis for file: ICSD_CollCode262928.cif
Cell parameters:
Cell([[3.3717, 0.0, 0.0], [-1.6858499999999994, 2.9199778539399923, 0.0], [0.0, 0.0, 5.3855]])
Number of atoms: 4
Atom types: {'Mn', 'O'}
Tolerance 1.0e-01: P 63 m c (186)
Tolerance 1.0e-02: P 63 m c (186)
Tolerance 1.0e-03: P 63 m c (186)
Tolerance 1.0e-04: P 63 m c (186)
Tolerance 1.0e-05: C m c 21 (36)
Tolerance 1.0e-06: C m c 21 (36)
Tolerance 1.0e-07: C m c 21 (36)

About this problem, I've posted here for further discussion.

Using pymatgen:

In [16]: from pymatgen.core import Structure
    ...: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
    ...: 
    ...: def analyze_space_group_pymatgen(filename):
    ...:     """Analyze space group using pymatgen with different tolerances."""
    ...:     # Read the CIF file
    ...:     structure = Structure.from_file(filename)
    ...: 
    ...:     # Define tolerances to test
    ...:     tolerances = [1e-1, 1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7]
    ...: 
    ...:     print(f"Analysis for file: {filename}")
    ...:     print(f"Lattice parameters: {structure.lattice.abc}")
    ...:     print(f"Lattice angles: {structure.lattice.angles}")
    ...:     print(f"Number of sites: {len(structure)}")
    ...:     print(f"Element types: {set(structure.species)}")
    ...: 
    ...:     for tol in tolerances:
    ...:         analyzer = SpacegroupAnalyzer(structure, symprec=tol)
    ...:         spacegroup = analyzer.get_space_group_symbol()
    ...:         spacegroup_number = analyzer.get_space_group_number()
    ...:         print(f"Tolerance {tol:.1e}: {spacegroup} ({spacegroup_number})")
    ...: 
    ...:     # Additional analysis
    ...:     print("\nDetailed symmetry analysis:")
    ...:     analyzer = SpacegroupAnalyzer(structure)
    ...:     print(f"Refined structure:\n{analyzer.get_refined_structure()}")
    ...:     print(f"Symmetry dataset:\n{analyzer.get_symmetry_dataset()}")
    ...: 
    ...: if __name__ == "__main__":
    ...:     cif_file = "ICSD_CollCode262928.cif"
    ...:     analyze_space_group_pymatgen(cif_file)
    ...: 
/home/werner/Public/repo/github.com/materialsproject/pymatgen.git/src/pymatgen/io/cif.py:1285: UserWarning: Issues encountered while parsing CIF: 4 fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
Analysis for file: ICSD_CollCode262928.cif
Lattice parameters: (3.3717, 3.3717, 5.3855)
Lattice angles: (90.0, 90.0, 119.99999999999999)
Number of sites: 4
Element types: {Species O2-, Species Mn2+}
Tolerance 1.0e-01: P6_3mc (186)
Tolerance 1.0e-02: P6_3mc (186)
Tolerance 1.0e-03: P6_3mc (186)
Tolerance 1.0e-04: P6_3mc (186)
Tolerance 1.0e-05: P6_3mc (186)
Tolerance 1.0e-06: P6_3mc (186)
Tolerance 1.0e-07: P6_3mc (186)

Detailed symmetry analysis:
Refined structure:
Full Formula (Mn2 O2)
Reduced Formula: MnO
abc   :   3.371700   3.371700   5.385500
angles:  90.000000  90.000000 120.000000
pbc   :       True       True       True
Sites (4)
  #  SP           a         b        c
---  ----  --------  --------  -------
  0  Mn2+  0.666667  0.333333  0.51096
  1  Mn2+  0.333333  0.666667  0.01096
  2  O2-   0.666667  0.333333  0.87547
  3  O2-   0.333333  0.666667  0.37547
Symmetry dataset:
SpglibDataset(number=186, hall_number=480, international='P6_3mc', hall='P 6c -2c', choice='', transformation_matrix=array([[1.00000000e+00, 5.55111512e-17, 0.00000000e+00],
       [0.00000000e+00, 1.00000000e+00, 0.00000000e+00],
       [0.00000000e+00, 6.16297582e-33, 1.00000000e+00]]), origin_shift=array([1.11022302e-16, 1.11022302e-16, 0.00000000e+00]), rotations=array([[[ 1,  0,  0],
        [ 0,  1,  0],
        [ 0,  0,  1]],

       [[ 1, -1,  0],
        [ 1,  0,  0],
        [ 0,  0,  1]],

       [[ 0, -1,  0],
        [ 1, -1,  0],
        [ 0,  0,  1]],

       [[-1,  0,  0],
        [ 0, -1,  0],
        [ 0,  0,  1]],

       [[-1,  1,  0],
        [-1,  0,  0],
        [ 0,  0,  1]],

       [[ 0,  1,  0],
        [-1,  1,  0],
        [ 0,  0,  1]],

       [[ 0,  1,  0],
        [ 1,  0,  0],
        [ 0,  0,  1]],

       [[ 1,  0,  0],
        [ 1, -1,  0],
        [ 0,  0,  1]],

       [[ 1, -1,  0],
        [ 0, -1,  0],
        [ 0,  0,  1]],

       [[ 0, -1,  0],
        [-1,  0,  0],
        [ 0,  0,  1]],

       [[-1,  0,  0],
        [-1,  1,  0],
        [ 0,  0,  1]],

       [[-1,  1,  0],
        [ 0,  1,  0],
        [ 0,  0,  1]]], dtype=int32), translations=array([[ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00],
       [-1.11022302e-16,  0.00000000e+00,  5.00000000e-01],
       [-2.22044605e-16, -1.11022302e-16, -6.84227766e-49],
       [-2.22044605e-16, -2.22044605e-16,  5.00000000e-01],
       [-1.11022302e-16, -2.22044605e-16, -1.36845553e-48],
       [-6.16297582e-33, -1.11022302e-16,  5.00000000e-01],
       [ 0.00000000e+00,  0.00000000e+00,  5.00000000e-01],
       [-6.16297582e-33, -1.11022302e-16, -6.84227766e-49],
       [-1.11022302e-16, -2.22044605e-16,  5.00000000e-01],
       [-2.22044605e-16, -2.22044605e-16, -1.36845553e-48],
       [-2.22044605e-16, -1.11022302e-16,  5.00000000e-01],
       [-1.11022302e-16,  0.00000000e+00,  0.00000000e+00]]), wyckoffs=['b', 'b', 'b', 'b'], site_symmetry_symbols=['3m.', '3m.', '3m.', '3m.'], crystallographic_orbits=array([0, 0, 2, 2], dtype=int32), equivalent_atoms=array([0, 0, 2, 2], dtype=int32), primitive_lattice=array([[ 3.37170000e+00,  0.00000000e+00,  2.06457081e-16],
       [-1.68585000e+00,  2.91997785e+00,  2.06457081e-16],
       [ 0.00000000e+00,  0.00000000e+00,  5.38550000e+00]]), mapping_to_primitive=array([0, 1, 2, 3], dtype=int32), std_lattice=array([[ 3.3717    ,  0.        ,  0.        ],
       [-1.68585   ,  2.91997785,  0.        ],
       [ 0.        ,  0.        ,  5.3855    ]]), std_positions=array([[0.66666667, 0.33333333, 0.51096   ],
       [0.33333333, 0.66666667, 0.01096   ],
       [0.66666667, 0.33333333, 0.87547   ],
       [0.33333333, 0.66666667, 0.37547   ]]), std_types=array([1, 1, 2, 2], dtype=int32), std_rotation_matrix=array([[ 1.00000000e+00,  0.00000000e+00,  6.12323400e-17],
       [-6.49415036e-33,  1.00000000e+00,  1.06057524e-16],
       [-6.12323400e-17, -1.06057524e-16,  1.00000000e+00]]), std_mapping_to_primitive=array([0, 1, 2, 3], dtype=int32), pointgroup='6mm')

As you can see, under different tolerances, only pymatgen gave all the correct results. I don't know why this happened.

0 replies

atztogo · 2024-07-29T00:50:40Z

atztogo
Jul 29, 2024
Maintainer

I think this is not (yet) a question about spglib. We will be able to answer only the questions whose crystal structures are provided in the format given here https://spglib.readthedocs.io/en/stable/python-interface.html#crystal-structure-cell.

0 replies

hongyi-zhao · 2024-07-29T01:59:39Z

hongyi-zhao
Jul 29, 2024
Author

Thank you for your tip. Now it gives the correct result as shown below:

import numpy as np
import spglib

# Lattice parameters
a = 3.3717
c = 5.3855

# Lattice matrix
lattice = [
    [a, 0, 0],
    [-a/2, a*np.sqrt(3)/2, 0],
    [0, 0, c]
]

# Atomic positions (fractional coordinates)
positions = [
    [2/3, 1/3, 0.51096],
    [1/3, 2/3, 0.01096],
    [2/3, 1/3, 0.87547],
    [1/3, 2/3, 0.37547]
]

# Atomic numbers (25 for Mn, 8 for O)
numbers = [25, 25, 8, 8]

# Create the cell tuple
cell = (lattice, positions, numbers)

def get_spacegroup(cell, symprec):
    dataset = spglib.get_symmetry_dataset(cell, symprec=symprec)
    if dataset is not None:
        return dataset.number, dataset.international
    return None, None

# Try different symprec values
print("Space group determination for different symprec values:")
for symprec in [1e-1, 1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-8]:
    sg_number, sg_symbol = get_spacegroup(cell, symprec)
    print(f"symprec = {symprec:.1e}: Space group {sg_number} ({sg_symbol})")

# Attempt to standardize the cell
print("\nAttempting to standardize the cell:")
try:
    cell_std = spglib.standardize_cell(cell, to_primitive=False, no_idealize=True)
    sg_number, sg_symbol = get_spacegroup(cell_std, symprec=1e-5)
    print(f"Standardized cell: Space group {sg_number} ({sg_symbol})")
except Exception as e:
    print(f"Error in standardizing cell: {e}")

The result of the above code:

Space group determination for different symprec values:
symprec = 1.0e-01: Space group 186 (P6_3mc)
symprec = 1.0e-02: Space group 186 (P6_3mc)
symprec = 1.0e-03: Space group 186 (P6_3mc)
symprec = 1.0e-04: Space group 186 (P6_3mc)
symprec = 1.0e-05: Space group 186 (P6_3mc)
symprec = 1.0e-06: Space group 186 (P6_3mc)
symprec = 1.0e-07: Space group 186 (P6_3mc)
symprec = 1.0e-08: Space group 186 (P6_3mc)

Attempting to standardize the cell:
Standardized cell: Space group 186 (P6_3mc)

1 reply

hongyi-zhao Aug 8, 2024
Author

See materialsproject/pymatgen#3963 for the related discussion.

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