Hello fellow researchers,
I want to use quartz crystal along with some other systems for MD simulation but I really want a Tetragonal system (alpha = beta = gamma = 90 degree). Quartz has gamma = 120 degree which makes it difficult to use it in my system. Also it is quite slow in a simulation to have a non orthogonal system. I know people used to cut it such a way so that the periodicity is maintained and also stoichiometry is balanced. Is there any tool to do this easily? Any help is very much appreciated. Thank you.
Mohammad
There are various polymorphs of quartz, but you can't get them by cutting. Here is a reference to polymorphs including tetragonal variations. http://www.minerals.net/Quartz_polymorphs.aspx
I don't think that you are talking about "tetragonal" but about orthogonal. Anyway, whether you prefer the use of an orthogonal volume, you need to transform the crystallographic coordinates into a Cartesian. What you need is a translation lattice which describes your crystal symmetry by an orthogonal unit cell. This is best done by subgroup transitions. In your case (trigonal quartz) you have to go to monoclinic since in 32 there are no 2 diads perpendicular to each other. Below all atoms of the unit cell are listed as relative as well as Cartesinn coordinates. Attached is the *.cel file (PowderCell) describing the asymmetric unit and the unit cell dimension.
No name crystal coordinates Cartesian coordinates
x y z x y z
------------------------------------------------------------------
1 Si 0.0000 0.4704 0.0000 -4.2539 -0.1454 -2.7020
2 Si 0.2352 0.7648 0.3334 -2.2529 1.3007 -0.9003
3 O 0.2068 0.0608 0.4524 -2.4945 -2.1574 -0.2572
4 O 0.3662 0.7798 0.1191 -1.1384 1.3744 -2.0586
5 O 0.4270 0.1594 0.7857 -0.6211 -1.6730 1.5441
6 Si 0.7648 0.7648 0.6666 2.2529 1.3007 0.9003
7 O 0.7932 0.0608 0.5476 2.4945 -2.1573 0.2572
8 O 0.6338 0.7798 0.8809 1.1384 1.3744 2.0586
9 O 0.5730 0.1594 0.2143 0.6210 -1.6730 -1.5441
10 Si 0.5000 0.9704 0.0000 0.0000 2.3106 -2.7020
11 Si 0.7352 0.2648 0.3334 2.0010 -1.1553 -0.9003
12 O 0.7068 0.5608 0.4524 1.7594 0.2986 -0.2572
13 O 0.8662 0.2798 0.1191 3.1155 -1.0816 -2.0586
14 O 0.9270 0.6594 0.7857 3.6329 0.7830 1.5441
15 Si 0.2648 0.2648 0.6666 -2.0010 -1.1553 0.9003
16 O 0.2932 0.5608 0.5476 -1.7594 0.2987 0.2572
17 O 0.1338 0.2798 0.8809 -3.1156 -1.0816 2.0586
18 O 0.0730 0.6594 0.2143 -3.6329 0.7830 -1.5441
Thank you for your answer. Yes, I actually need an orthogonal unit cell with the symmetry maintained. Can you send me an xyz file instead of this format? Or a cif file should be also OK. What are the last two col in this file? Which are the fractional coordinates? And also can you let me know how you converted to orthogonal from the original trigonal format? Is there any tools for it or do you need to write your own script for that? Thank you again for your help.
Regards,
Mohammad
The columns are No of atom, element, x,y,z (frac. coord.), x,y,z (in Angstroem).
About which columns you are talking?
The transformation rules from fractional coordinates into Cartesian coordinates you will find in many books. These are fundamental crystallographic rules. I am using PowderCell but it is not made for export of data. The given list of coordinates is a part of the software which enables a copy of all generated and displayed atomic positions. At least the selected volume is translation-symmetric so that you can shift them and generate a clearly bigger cell. The question is, how many atoms do you need? PowderCell is limited, e.g. 1000 atoms, since it has been written in a time where memory was still limited in computers or not accessable by the operation system.
Thanks for the information. Let me see if I can play with PowderCell a little bit and do what you just mentioned. Appreciate your help a lot.
On Bilbao Crystallographic server (http://www.cryst.ehu.es/) you will find a lot of useful tools for your problems :-)
I thought you were looking for the actual material and didn't realize at first you were looking to do a simulation.
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