Mismatch between CifParser parsed coordinates and coordinates in the CIF file

[JuJueTanWan]

Python version

Python 3.9.21

Pymatgen version

2024.8.9

Operating system version

CentOS 7.9

Current behavior

Hello, I encountered an issue when using pymatgen's CifParser to parse a .cif file. Specifically, I noticed that the fractional coordinates of some atoms (X and Y) parsed by CifParser do not match the original fractional coordinates in the CIF file. Below are the details of my observation.

Here is the content of the c2db-2832-WSe2-_shixc2db-2696-MoS2-_shi_1.cif file I am using:
W W0 1 0.66666667 0.33333333 0.31812705 1
Se Se1 1 0.33333333 0.66666667 0.26186394 1
Se Se2 1 0.33333333 0.66666667 0.37439016 1
Mo Mo3 1 1.00000000 1.00000000 0.55060730 1
S S4 1 0.66666666 1.33333334 0.49811805 1
S S5 1 0.66666666 1.33333334 0.60309655 1

Here is the code I used to parse the CIF file:
from pymatgen.io.cif import CifParser

cif_file = "c2db-2832-WSe2-_shixc2db-2696-MoS2-_shi_1.cif "
parser = CifParser(cif_file)
structure = parser.get_structures(primitive=False)[0]

for site in structure.sites:
specie = site.specie
original_frac_coords = site._frac_coords
print(f"{specie}: {original_frac_coords}")

The output from the code is as follows:
Mo: [0.33333334 0.66666667 0.5506073 ]
W: [0.66666667 0.33333333 0.31812705]
Se: [0.33333333 0.66666667 0.26186394]
Se: [0.33333333 0.66666667 0.37439016]
S: [0. 0. 0.49811805]
S: [0. 0. 0.60309655]

The Z coordinates for all atoms are correct.
The X and Y coordinates for W and Se atoms match the values in the CIF file, but the X and Y coordinates for Mo and S atoms are incorrect:
Mo's original fractional coordinates in the CIF file are [1.00000000, 1.00000000, 0.55060730], but CifParser outputs [0.33333334, 0.66666667, 0.55060730].
S's original fractional coordinates in the CIF file are [0.66666666, 1.33333334, 0.49811805], but CifParser outputs [0.0, 0.0, 0.49811805].

Expected Behavior

Why does CifParser parse some fractional coordinates (X and Y) as values that do not match the original CIF file?
Is there a way to avoid this normalization or mapping behavior and directly retrieve the fractional coordinates as they are in the CIF file?
Any clarification or guidance on this behavior would be greatly appreciated. Thank you!

Minimal example

No response

Relevant files to reproduce this bug

No response

[DanielYang59]

@JuJueTanWan Hi thanks for reporting this issue. While I'm happy to look into this issue, is it possible for you to provide the complete CIF file (looks like the provided is a snippet of it) for me to recreate this issue (GitHub doesn't support uploading cif files directly, but you could add a .txt extension as it's a text file anyway)?

[JuJueTanWan]

Hi,

Thank you for your prompt response and for your willingness to look into this issue. I've renamed the CIF file and processing script with a .txt extension as you suggested. Please find the updated files attached.

Thanks again for your help, and I look forward to your feedback!

c2db-2832-WSe2-_shixc2db-2696-MoS2-_shi_0.txt
insert_atom_M_TM_X.txt

[JuJueTanWan]

Hi, Thank you for your prompt response and for your willingness to look into this issue. I've renamed the CIF file and processing script with a .txt extension as you suggested. Please find the updated files attached. Thanks again for your help, and I look forward to your feedback! xudonghuichem97 ***@***.*** ---- Replied Message ---- FromHaoyu (Daniel) ***@***.***>Date1/13/2025 ***@***.***>***@***.***>, ***@***.***>SubjectRe: [materialsproject/pymatgen] Mismatch between CifParser parsed coordinates and coordinates in the CIF file (Issue #4250) @JuJueTanWan Hi thanks for reporting this issue. While I'm happy to look into this issue, is it possible for you to provide the complete CIF file (looks like the provided is a snippet of it) for me to recreate this issue (GitHub doesn't support uploading cif files directly, but you could add a .txt extension as it's a text file anyway)? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***> # generated using pymatgen data_MoW(SeS)2 _symmetry_space_group_name_H-M 'P 1' _cell_length_a 3.33061866 _cell_length_b 3.33061866 _cell_length_c 29.90433353 _cell_angle_alpha 90.00000000 _cell_angle_beta 90.00000000 _cell_angle_gamma 120.00000000 _symmetry_Int_Tables_number 1 _chemical_formula_structural MoW(SeS)2 _chemical_formula_sum 'Mo1 W1 Se2 S2' _cell_volume 287.28607864 _cell_formula_units_Z 1 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 'x, y, z' loop_ _atom_site_type_symbol _atom_site_label _atom_site_symmetry_multiplicity _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy W W0 1 0.66666667 0.33333333 0.31812705 1 Se Se1 1 0.33333333 0.66666667 0.26186394 1 Se Se2 1 0.33333333 0.66666667 0.37439016 1 Mo Mo3 1 1.00000000 1.00000000 0.55060730 1 S S4 1 0.66666666 1.33333334 0.49811805 1 S S5 1 0.66666666 1.33333334 0.60309655 1 #!/usr/bin/env python3 import os import shutil import warnings from pymatgen.io.vasp import Poscar from pymatgen.io.cif import CifParser, CifWriter from pymatgen.core.structure import Structure warnings.filterwarnings("ignore", category=FutureWarning) warnings.filterwarnings("ignore", category=UserWarning) def insert_atom_M_TM_X(cif_file, atom_type, output_file, suppress_warnings=True): """ The file's comments are the same as insert_atom_X_TM_V.py, which you can refer to if necessary! """ parser = CifParser(cif_file) structure = parser.parse_structures(primitive=True)[0] sulfur_atoms = [] metal_atoms = [] for site in structure: if site.species_string in ["S", "Se", "Te"]: sulfur_atoms.append(site) else: metal_atoms.append(site) z_coords_metal = [] for site in metal_atoms: z_coords_metal.append(site.frac_coords[2]) z_min_metal = min(z_coords_metal) z_max_metal = max(z_coords_metal) z_middle = (z_min_metal + z_max_metal) / 2.0 top_layer_metal = [] for site in metal_atoms: if site.frac_coords[2] > z_middle: top_layer_metal.append(site) if not top_layer_metal: raise ValueError(f"Cannot distinguish the top metal atoms, please check the input structure.") selected_site = top_layer_metal[0] x = selected_site.frac_coords[0] y = selected_site.frac_coords[1] structure.append(atom_type, [x, y, z_middle]) writer = CifWriter(structure) writer.write_file(output_file) if __name__ == "__main__": input_cif = "c2db-2832-WSe2-_shixc2db-2696-MoS2-_shi_0" metals = ["Cu"] for metal in metals: insert_atom_M_TM_X(input_cif, metal, f"{metal}.cif")

[DanielYang59]

@JuJueTanWan Thanks for sending through the file and code snippet. However I cannot recreate the issue (I didn't look into the custom insert_atom_M_TM_X code but I'm not seeing any issue with the CifParser).

---

from pymatgen.io.cif import CifParser


cif_file = "test_cif.cif"
parser = CifParser(cif_file)
structure = parser.parse_structures(primitive=False)[0]

for site in structure.sites:
    print(f"{site.specie}: {site.frac_coords}")

I got:

Mo: [0.        0.        0.5506073]
W: [0.66666667 0.33333333 0.31812705]
Se: [0.33333333 0.66666667 0.26186394]
Se: [0.33333333 0.66666667 0.37439016]
S: [0.66666667 0.33333334 0.49811805]
S: [0.66666667 0.33333334 0.60309655]

The cif file:

  W  W0  1  0.66666667  0.33333333  0.31812705  1
  Se  Se1  1  0.33333333  0.66666667  0.26186394  1
  Se  Se2  1  0.33333333  0.66666667  0.37439016  1
  Mo  Mo3  1  1.00000000  1.00000000  0.55060730  1
  S  S4  1  0.66666666  1.33333334  0.49811805  1
  S  S5  1  0.66666666  1.33333334  0.60309655  1

[QuantumChemist]

It seems to me that the cell's space group allows for different definitions/orientations in space, and therefore, the parser changes the coordinates. The cells might be equal, just facing another direction.

[shyuep]

By default, CifParser performs a primitive cell reduction since this is generally desired for calculations. If you prefer not to, you can always specify primitive=False as an arg to get_structures. Otherwise, users generally should use Structure.from_file, which works more in the way that the data is returned unmodified.