Hello dear professors and researchers
How can I do the DFT simulation of nanoparticles on the WIEN2K or quantum espresso?
I can't create the vacuum between the cells.
And if there are any alternatives to these two software, please mention them.
What do you mean by the "cant create vacuum" part? You're adding vacuum to your simulation cell and the code is giving issues, or you don't know how to add the vacuum?
An easy way to not have to play with the cell parameters manually is to use the atomic simulation environment. Just load in your structure, and use the center function to pad the cell with the desired vacuum in Angstroms.
To create the vaccum lattice constant along one direction must be chosen in such a way that other layers do not interact with each other. For example to create monolayer graphene we increase the distance between two graphene layers in such a way that they don't interact with each other.
For nanomaterials, you have to create the vacuum along 2 axis. In this way you can proceed.
thank you for your answers
Mr. Robert Stanton I mean I tried to increase the cell parameters but the problem is that the atoms in my cell are moving away from each other (the structure is disappearing)
Should I increase the cell parameters in the gen structure section or in another section?
Hi Hamza, sounds like you might have your atomic structure input in fractional coordinates? When you increase cell parameters in that case you'll see exactly what you're describing, where the atoms move away from one another. If they're in fractional coordinates you can just convert those to angstroms, and then specify that in the atomic positions section. Then when you expand lattice vectors, you will get a larger cell, but the atomic positions relative to one another will remain the same.
Hello Mr. Stanton
Yes exactly, I entered the fractional coordinates, because in Wien2k the positions are put in fractions, I think there is no possibility to put them in angstroms. I will try with quantum espresso and see what I get.
Thank you very much sir for your time and your explanations.
Sir, please, I have another question.
Do you know how to optimize a monoclinic structure in wien2k. I used "VARY A, B, C and Gamma (4D-case) (monoclinic lattice)" but I can't find the curve (energy v.s volume)
Hi Hamza, yes you'd have to convert them to cartesian coordinates. I usually just use the atomic simulation environment (ASE is a python package you can simply install with pip/conda) to convert between the two, though you can find visualizers which might have a feature to do this. Here's a rough outline of what you'd need to do (this assumes your input file/structure file have the cell information within them, else you'll have to set the cell/pbc's manually'):
import ase.io
from ase.visualize import view
atoms = ase.io.read('your input')
view(atoms) # check everything looks right, I've not used ASE to read wien2k struct files, but I know ASE should be able to handle them
atoms.center(vacuum = desired vacuum in angstroms)
view(atoms) # check again the vacuum padding looks good
Then get your new cell parameters with:
atoms.cell
and get either the cartesian or scaled positions with:
atoms.get_positions()
atoms.get_scaled_positions()
and finally if desired save the new structure to a file in case you want to make any modifications or visualize in the future:
atoms.write('system.cif')
Hope that helps.
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