I am trying to compare different planes of two different crystals to see the misfit (for an epitaxy process). There might be different programs out there that can do this, I began with VESTA (mainly because it is free), I was able to plot (100) of two crystals together relatively easy (please see attached picture). However I was not able to only show plane of atoms on (110) direction, I already posted in VESTA user group in hope for some help. Does anyone know whether VESTA is capable of this?---to only show plane of atoms on (110) plane, or, is there another program can do this sort of plotting? --- free program if possible!
Vesta can do this, you generate an overlarge cell and then crop it by selecting cutoff planes. it's all done by clicking the "Boundary" button (or Boundary under Objects menu).
1. Generate a fairly large cell by selecting xmin-xmax etc. as suitable numbers.
2. Click "New" in the "Cutoff planes" section and put 1 1 0 as miller indices. Click Apply.
3. Put in another new cutoff plane and select it as -1 -1 0 and click apply.
4. Adjust the "Distance from origin" of your two planes to get the slab as thick as you like.
Try Diamond from Crystal Impact.
http://crystalimpact.com/
It is commersial, but they have a demo-version.
Vesta can do this, you generate an overlarge cell and then crop it by selecting cutoff planes. it's all done by clicking the "Boundary" button (or Boundary under Objects menu).
1. Generate a fairly large cell by selecting xmin-xmax etc. as suitable numbers.
2. Click "New" in the "Cutoff planes" section and put 1 1 0 as miller indices. Click Apply.
3. Put in another new cutoff plane and select it as -1 -1 0 and click apply.
4. Adjust the "Distance from origin" of your two planes to get the slab as thick as you like.
After you have your first plane (or "phase" as Vesta calls them), to fix two different phases and align them, you need to open Edit - Edit Data - Phase and then import coordinates for your second plane from some file. You then get two phases, and almost everywhere you go in the program from this point, you need to choose which phase you want your changes to apply to.
To cut out a plane, just do like above, but selecting phase 2. When you want to align them, you select phase two (say) in the list under Edit data-Phase and fill in the coordinates that you want to match, in this case you would typically say "place (0,0,0) of this layer at (x,y,z) of layer 1", where you have to fiddle around with x,y,z until you have the alignment you want. Note that the units of the x,y,z's are lattice coordinates of the unit cells of the two phases, respectively (I think, it has worked for me to think like that anyway). In my mac version of the program the cell is not updated properly until I go back and apply the "boundaries" of the phases again, but maybe you don't get that problem, I don't know.
A hint for best visualization is then that you choose the viewing angle "mathematically" by clicking the "orientation" button, rather than trying to rotate it to a good angle (you often see moiré patterns from misalignment better if you get it exact...).
Thanks again Torbjorn for the useful comment. After playing with it many hours, I finally decided to give up on this approach, it works great on {100} plane families, however when I tried to do {110} or {101} diagnol planes, new problem arises. If you see attached file, in order to see (110) plane, I have to extend the crystal this way, as a result there are lot of lattice cell above or below the plane of interest, therefore when I view from the top or bottom, I see some unwanted lattice cells, and those cells can not be cut using "cut plane", that feature only removes atoms, not unit cells. I hope you understand my problem. Anyways my new approach, is redesign new CIF files, to manually change plane (100) to that of (110), and to do it that way
Can't you just not show the unit cells? Properties -> General and then switch to "Do not show" for the unit cell.
Ah, I see. If I were you, I would try visualizing some bonds within the layers, that usually gives a rather clear moiré pattern. Otherwise, you seem to have a working solution there.
Ghazal: in case this is of any help --- I finally decided to change my approach after lot of attempt, my new method is to manually make a new crystal structure (.CIF file) with only one layer of atoms (like graphene) for different planes, and then just expand with that structure, and it worked out very well for me, my paper with that data is accepted and in press right now. Good luck.
Have you tried using Chimera?
https://www.cgl.ucsf.edu/chimera/download.html
It is quite easy to manipulate large amounts of atoms and selectively cut along a desired angle.
The latest version of CrystalMaker (10) allows you to create lattice planes and then slice the desired parts of the crystal so that you look directly at a certain plane of atoms. If the institution where you are is willing to invest into this software (it is not free for use), there are nice available features you can access.
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