I am trying to optimize a copper supercell for the study of chalcones adsorption using Quantum ESPRESSO, however, the size of my supercell is large (>200 atoms) and QE can not handle it.
What is an alternative for it?
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It should be possible to use Quantum Espresso to handle more than 200 atoms.
I guess you are studying a surface, in that case, please note that in PW-based codes the vacuum makes your calculation more expensive since it is considered as if it was matter. For this reason, you can try to lower a little the vacuum (while always ensuring convergence). Always on the 2D case, you can try to use a Coulomb potential along the non-periodic directions to ease the convergence.
Lastly, if you are optimizing the cell and you need to study absorption, you can try to consider the optimization of only 1/2 layers on the surface while keeping frozen the bottom layers.
To finally answer your question, if you don't want to use Quantum Espresso, there are alternative PW codes (such as Abinit, VASP) and localized basis sets that would ease the fact that you are dealing with vacuum (such as Siesta).