I made a 15x15x15 Armstrong unit cell with 64 Al atoms (copy pasted a selection of 8). What you see now is the result after “Wrap Atoms to Unit cell”: I tried to find a way to spread out the Al atoms more evenly across the unit cell that would not involve calculating the coordinates of all 64 and manually changing the xyz file, but did not find much.
Let’s start from the beginning. What are you trying to do? Do you want to place 64 Al atoms in a big unit cell but with equal spacing? Or do you want a 15 Å x 15 Å x 15 Å unit cell filled in with all the atoms? Or something else.
Hello @ghutchis, thank you for your response!
I am trying to place 64 Al atoms in a big unit cell with equal spacing, and the measurements I tried seemed appropriate. Thank you!
It looks like you’re already using an Avogadro2 nightly?
My suggestion would be to open the aluminum unit cell, create a supercell that would have the number of atoms you want (e.g., 2x2x2) - I didn’t do the math, so that may not be the right size:
Then you want to scale it up to 15 Å on a side (e.g., volume of 3375 Å^3) - and make sure to check the “transform atoms” (e.g., re-scale the atom positions rather than just add a bunch of empty space)
Hello and thanks again for your help! Yes, I am on Avogadro2 nightly!
How would I go about the first step? ("My suggestion would be to open the aluminum unit cell, create a supercell that would have the number of atoms you want (e.g., 2x2x2)). I checked out this guide but I do not have a starting template like they do (Super Cell Builder - Avogadro). I added a unit cell with initial tentative dimensions (e.g. 15x15x15), as the guide says that I need a crystal surface before using the Supercell builder. Thank you!
Go to File ⇒ Import ⇒ Crystal and select aluminum.
Go to Crystal => Space Group => Fill Unit Cell (this will shortly be un-necessary)
Okay… how many atoms are there in the unit cell?
There are 8 corner atoms, each 1/8 in the cell
There are 6 face-centered atoms, each 1/2 in the cell
So that’s 4 atoms per unit cell. You wanted 64 atoms. So that’s 4^3 atoms. If we double along the a-axis, we get 8 atoms. If we double that along the b-axis (i.e., 2x2x1 super-cell) we get 16 atoms. And if we double along the c-axis, we get 32 atoms.
So it’s a little tricky to get 64 Al atoms in a cube. Let’s go with a 2x2x3 super cell, which at least gives us the 64 atoms you want.
I’m not sure how you’d want to handle that - do you absolutely need a cube?
Hello Geoff, thank you so so much for your patient guidance and help! No, I do not specifically need a cube and your instructions worked great for me. Thanks and have a great day!
This is the final image for anyone visiting the forum in the future:
