Hi everyone! Actually I wish to study adsorption of various atoms/molecules on surfaces using CRYSTAL code (only)..but not able to understand and control the complete input for the same.
I mean various configurations.. distances.. relaxation of the structure.. etc.
Hope to get an assistance soon :-)
Thanks ..
Well that's a very broad question. A extremely brief summary of a possible workflow would be as follows:
1- Get the cif file of the solid's crystal structure, e.g. at http://www.crystallography.net/cod/
2- Create a CRYSTAL input to optimize the bulk structure and run it .
3- Take the optimized crystal structure and create a surface using the EXTERNAL and SLABCUT keywords. Particular attention should be paid to the thickness of the slab model and the supercell size in the periodical dimensions. Optimize the slab structure.
4- Using the resulting optimized slab as a base, add the atoms or molecules to be adsorbed using the ATOMINSE keyword. Optimize and calculate adsorption energy. Be mindful of the basis set superposition error.
And that's it. Depending on the system you may wish to study several different facets, adsorption modes, etc.
Finally, please note that the CRYSTAL developers have published a series of very good tutorials - including one on the modelling of surfaces: http://tutorials.crystalsolutions.eu/tutorial.html?td=surfaces&tf=surfaces_tut
Good luck!
Hello Mr. Mariano Curti
Thank you very much for your helpful response!
Yes, question is broad enough, since I do have confusions almost at every step :-)
So, just hope to get some insight through this discussion..
Like, optimization is fine, then for slabcut..
- Is it necessary to take at least one (several) irreducible unit (as we see in slabinfo). Can't I go with few layers only as per my convenience.
As the system under consideration is large and even an irreducible unit consists of 40 and more atoms!
-What should be the proper criterion in mind while deciding the coordinates of the adsorbed atom?
-After adsorption, again do we need to go with complete optimization?? cant we go with the partial one?? (few top layers only?)
Thanks
1- Depends on the system and the property of interest. See e.g. Article Surface structures and thermodynamics of low-index of rutile...
for an analysis on TiO2.If you are interested in adsorption and have a big unit cell, you may get away with just using a few layers. But in any case please note that this kind of calculation is always very demanding.
2- Depends on the chemistry of your system. For instance, in metal oxides the cations are usually assumed to act as Lewis acids, so the adsorption of a molecule that acts as a Lewis base will most likely involve such cations.
3- You may "freeze" the inner part of your surface using the bulk geometry, and leave it frozen after adsorption. Just make sure to subtract energy values under the same conditions.
I assume that by "spin calculations" you refer to "unrestricted (spin polarised) calculations".
It depends on your particular system. Do you have transition metals? Is the molecule to be adsorbed a radical? If the answer is yes to one of these questions, then most likely you will need to perform unrestricted calculations.
Sorry for the confusion - all unpaired electrons matter!
I'm confused though why the number of electrons "becomes odd" after adsorption. Are you maybe forgetting a proton?
I'm just trying to guess what the problem may be from the very limited information you give. If both the molecule to adsorb and the surface have an even number of electrons, then the complex should also have an even number of electrons.