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I'm trying to model a 2D TMD (transition metal dichalcogenide) nanocrystal on a graphene substrate. I know how to generate 2D TMDs through the MX2 module, and I certainly know how to make graphene on ASE, but I am unsure how to stack the two together. Is there a specific module that could get the job done? The ASE documentation has not been too helpful.

Any help would be appreciated!

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To stack two 2D structures in ASE, a matching of the two unit cells is required. I will assume your graphene and TMD unit cells have the same $\alpha$, $\beta$, $\gamma$ lattice parameters but slightly different $a$ and $b$. The common choice is to use the larger unit cell as reference, and scale the atomic coordinates in the smaller unit cell to fit in the larger cell. The stacking can be done by ase.build.add_adsorbate, where you can play around the height parameter to adjust the relative position of the adsorbate in the z direction. This often results in a decent heterogeneous structure, but if you want to adjust the adsorbate in the x and y directions, the easiest way is to move the atoms in the ASE's GUI by pressing Ctrl+M.

Below is an example of stacking a 3-layer MoS$_2$ (larger cell) on top of a graphene monolayer (samller cell) in ASE:

from ase.build import graphene, mx2
from ase.build import add_adsorbate
from ase.visualize import view

# Build a graphene monolayer
atoms = graphene()

# Build a 3-layer MoS2 
MoS2 = mx2(formula='MoS2', kind='2H', a=3., thickness=3.19, vacuum=5.)
# Match the two unit cells in the z direction
atoms.cell[2] = MoS2.cell[2]

# Save the fractional coordinates of graphene
fracs = atoms.get_scaled_positions()
# Match the two unit cells in all directions
atoms.cell = MoS2.cell
# Scale the atomic coordinates of graphene
atoms.positions = fracs @ MoS2.cell

# Stack the two structures
add_adsorbate(atoms, adsorbate=MoS2, height=3.)
# Center the structure in the z direction
atoms.center(vacuum=5., axis=2)
# Visualize
view(atoms)

enter image description here

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