Wrapping in unit cell - inorganic system, guess_bonds?

[mikiefromhell]

Hello everyone!

I am just getting started with MDA and I am getting a little confused about the connections between different classes. I am trying to wrap back in the unit cell only the Al atoms in a system with a layer of Al covered in CO2 gas. The Al atoms are the only thing that migrated during 2D-periodic DFT. Can anyone point out some glaring issues?

import MDAnalysis as mda
import MDAnalysis.transformations as trans
import numpy as np

# Load the trajectory
u = mda.Universe(r"[file path]",guess_bonds=True)

Al = u.select_atoms('name Al', periodic=True)

Al.unwrap(Al)

# Define a unit cell if not already present in the trajectory
# (Replace with actual dimensions if known)

Al_center = Al.center_of_mass(wrap=True)

unitcell_dims = np.array([10.88480, 10.88480, 32.65432])  # Example values in angstroms

box_center = np.sum(unitcell_dims,axis=0)/2
u.atoms.translate(box_center-Al_center)

# Apply transformations
transformations = [
    trans.wrap(u.atoms),  # Wrap atoms inside the unit cell
    trans.center_in_box(u.atoms, center='mass', wrap=True)  # Center system
]

u.trajectory.add_transformations(*transformations)

# Save the wrapped trajectory
with mda.Writer("wrapped_trajectory.xyz", multiframe=True) as W:
    for ts in u.trajectory:
        W.write(u.atoms)

[orbeckst]

Did you visualize your output trajectory?

Does the output agree with what you expect?

I am not 100% sure but possibly switch the order of the wrap and the center_in_box transformations. Also note that you're wrapping all atoms, not just Al.