The strange result of `SurfaceGenerator` for MoS2.

[hongyi-zhao]

The code snippet is as follows:

# Import the SurfaceGenerator class
from OgreInterface.generate import SurfaceGenerator

# Create a surface generator instance from a CIF file
subs = SurfaceGenerator.from_file(
    "MoS2_mp-1434.cif",
    miller_index=[0, 0, 1],  # Specify the Miller index for the surface
    layers=1,                # Number of layers in the generated surface
    vacuum=15                # Vacuum spacing around the surface
    # refine_structure=False  # Don't refine the initial structure; uncomment if needed
)

# Print the number of generated surfaces
print(len(subs))

# Select the first generated surface
sub = subs._slabs[0]

# Remove layers from the selected surface
# sub.remove_layers(num_layers=3, top=True)  # Remove 3 layers from the bottom side

# Write the modified surface to a file with the `c`-axis orthogonal to the `ab` plane
sub.write_file("POSCAR", orthogonal=True)

The result is as follows:

The top structure looks like the Mo and S atoms are far apart in some positions, which is weird. All the files mentioned above have been attached.

MoS2-Ogre.zip

Regards,
Zhao