Hello everyone!
I have the question related to preparing of crystal structure for atomistic simulation.
I need 3*3*3 translated unit cell that opposite faces complement each other in.
I use experimental structure of crystal for starting. But after unit cell translation I have got big cell that opposite faces superimpose on one another and not complement each other (yellow border).
So I need to delete excessive atoms. But I don't know how I can check that my "manual cutting" is perfect? (i.e. the best way to do it) I'm afraid that my eyes can deceive me.
May be you have such experience and know how to make some additional objective examination?
Thank you for any answer!
Dear, I'm not quite understanding what you want to do.
But I reminder that the "excessive atoms" in your pic is not excessive.
The "excessive atom" is due to the 3-d periodic boundary shown by visulaization software. If you do a bulk state calculation, no atoms are needed to deleted.
Mr. Wang Jinkai, thank you for the answer!
I want to do the modeling of interaction of ions with the crystal surface in the water solution. So I need models of crystals with different thickness for each dimension to make different surfaces (i.e. gradual dissolution or sedimentation of new ion layer: the layer lesser than length of cell).
Now my preparation methodology is translate CIF file unit cell to 3*3*3 cell, remove some layers of atoms and then convert it to xyz file.
You said that "no atoms are needed to deleted". Did you mean that there are alternative ways to prepare crystal structure?
Thanking you in anticipation!
If I remember correctly ASE (Atomistic simulation Environment) offered a way to prepare surfaces with an arbitrary number of layers and supercell. Then you were allowed to add the amount of vacuum you needed. It also did allow for cutting along certain Miller indexes (If I am not mistaken) to produce the wanted surface. However, I admittedly never worked on similar problems.
Regards,
Roberto
hi, Vitalii S. Frolov
What i mean "no atoms need to delete" is the response to your first question about the 'yellow atom'.
If you wanna a surface, your propose is simple and correct. You can create 001, 010, and 100 surface by deleting atoms in corresponding directions, respectively.
ASE metioned by Roberto D'Agosta will create complex surface as you will , but ASE needs some python skills.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Materials Science
- Materials
- Inorganic Materials
- Ceramics
- Glass