Unit 2.7b - Crystal Shapes with VESTA

[@xoanxil]

Thanks for the video. I am not a crystal expert so, I apologyze if my question is very basic. I don´t know where can I find the values you are writting for the shapes. I am taking now from the Powder diffraction Pattern but I get a long list of values ther and I dont know how to filter them or how import them directly into crystal shape window. Thanks in advance for you help!

[@FrankHoffmann1000]

Dear Xoán-Xil López, thanks for your message and sorry for the late answer (busy days these days...). Usually you will get these values of the _visible_ faces (which are only some, or a very few, of all the possible lattice planes) from either a single-crystal X-ray analysis and/or by visible inspection. This means that you have to determine the faces that were developed during the growth of the crystal. But you can't do this by powder diffraction. A procedure to derive the 'names' of the planes that have been developed is described here: www.tulane.edu/~sanelson/eens211/axial_ratios_paramaters_miller_indices.htm Hope this clarifies things a little bit. best Frank

[@xoanxil]

Thank you so much for your answer @@FrankHoffmann1000. As I told you I am not an expert on Crystolaography. I am working on an artistic project based on liquid crystals representation and I would like to get the shape of the .cif files I have downloaded from COD database. I will go deeper on this article, thanks for sharing. But in short... Is it really possible to get the "Miller indices" and the "Distance from origin" having only the .cif file and using VESTA? Thanks again and sorry for these newbie questions.

[@FrankHoffmann1000]

No worries about asking newbie questions. No, in principle the CIF file contains _no_ information about the external, visible crystal shape (also called the habit)! With the structural information you can only say which crystal shapes can be potentially developed (roughly: the symmetry of outer shape is related to the space group and crystal system). Take rock salt, NaCl, which has always a cubic crystal structure. However, the individual shapes of the salt grains do not have to look like cubes. They can also be developed as octahedra! For pyrite (also cubic) more than 60 different external shapes have been found, although the (inner crystal) structure is, of course, always identical.

[@xoanxil]

Thank you very much for clarify this @@FrankHoffmann1000 . I will research more...

[@ShubhamSharma-bf2ws]

Hi Frank Could you please tell me whether we draw structures with forbidden symmetry using Vesta or not?

[@FrankHoffmann1000]

Hi Shubham, this isn't possible. VESTA allows only to build crystal structures according to one of the 230 space group types.

[@ShubhamSharma-bf2ws]

@@FrankHoffmann1000 Okay Frank, thanks for information.

[@maivuong7447]

Hello Frank, I followed the tutorial but I did not get the same result. I did not see the crystal planes after ticking "show crystal shape", and my unit cell of Chalcanthite disappeared after I tick "custom color". Do you suggest any solution? Thanks a lot for these videos

[@FrankHoffmann1000]

Hello Mai - Don't know what the reason might be... I just followed myself the tutorial again and had no problem. Make sure the faces are specified as follows: Faces of crystal shape ( h k l) d (Å) area (Å^2) ( 1 0 0) 5.67 255.267 ( -1 0 0) 5.67 255.267 ( 0 1 0) 5.72658 252.745 ( 0 -1 0) 5.72658 252.745 ( 0 0 1) 10.4196 138.907 ( 0 0 -1) 10.4196 138.907 Best wishes

[@abhishekkumbhar6118]

Hello Frank, I am not able to see the crystal shape. I followed steps 1. edit > edit data > crystal shape 2. gave 3xd with miller indices 1 1 1 3. checked the 'show shapes' and 'custom color' box I tried changing color, checking unchecking box but I did not succeed to see the crystal shape. Thank you.

[@FrankHoffmann1000]

Hi Abhishek, You must specify at least 6 faces, otherwise no closed form is created. If you have entered the (111) face as the only face, this cannot work. My suggestion would therefore be that you first draw in the 6 faces as in the video and then additionally try out the (111)/(-1-1-1) surfaces - good luck! best regards Frank

[@FrankHoffmann1000]

PS: Correction: In principle, it is of course, also possible to create a closed form with only 4 faces, for instance, in the form of a tetrahedron. But the faces have to be located at their right places, i.e. must form intersecting lines with the other (sur)faces.

[@bobukuttan]

Dear Frank, I have another doubt. From were we can find the CIF files for other compounds? I am actually trying to get the files CIF files for the various polymorphs of Alumina (Al2O3). I would be really grateful if you could help me in this.

[@FrankHoffmann1000]

Dear Bobu Manuel, one of the best resources is the Crystallography Open Database (COD): www.crystallography.net/cod/index.php If you click on search on the left side in the menu, you can, for instance specify 1 to 8 elements; if you want to restrict the search on binary compounds, it is recommended to specify the number of distinct elements as min = 2 and max = 2, otherwise you will get a huge number of results... I've done a trial search with Al and O as elements, only binary compounds, and that yielded 56 results. best! Frank

[@bobukuttan]

Thanks Frank for the information. I am going through it

[@riskapuspita6886]

Hi Frank How to add more axis? For example, i want to make four axis --> a, b, c, d Thank u

[@FrankHoffmann1000]

Hi Riska, that's not possible. There are only three crystallographic directions. What would be the purpose of a fourth axis? best Frank

[@riskapuspita6886]

@@FrankHoffmann1000 I was read the book that mention about hexagonal has 4 axis, c is vertical axis and a,b,d are horizontal axis. That should be wrong. Than i watched your Unit 1.8 - The Seven Crystal Symmetry, now my mind is clear. Thank u Frank

[@FrankHoffmann1000]

I see - you are talking about a different basis, a different system of coordinates that is often used by physicists. That's not wrong in a strict sense, but the three vectors/directions in the plane are then no longer independent, they are redundant. Physicists find them useful for indexing planes in the hexagonal case, see for instance: kzbin.info/www/bejne/rHycYmaljNGSjqs best!

[@riskapuspita6886]

I took geology course. We learn about crystallography as the basic before learn about mineralogy. Your videos help me to understand more about crytallography. Thank u ! Best regard

[@iborge]

I've got a question: Why when you introduce the S atom, appears "two" S atoms in different positions? Thanks!

[@FrankHoffmann1000]

In the definition file of the atomic structure only the so-called asymmetric unit is specified, I.e. the set of atoms that generates the whole unit cell if you apply all symmetry operations of the respective space group. Here the space group is P-1, so we have an inversion center in the structure. If we now specify one of the S atoms the software applies automatically the symmetry operations of the space group and will place copies of the atoms at the appropriate locations: Here only one additional S atom is generated, namely at -x, -y, -z.

[@iborge]

Dear @@FrankHoffmann1000, Thanks for your kind and professional answer. You've a really nice channel.

[@notmuch21]

Hi, For the crystal shapes when you add the planes 100 , 010 and 001 should not the distance from origin equal to "a = 5.9953", "b = 6.1084" and "c = 10.7048" ? from where the values 5.67 A, 5.72A and 10.4196 A come up for a,b, ,c respectively, please? could you comment on this

[@FrankHoffmann1000]

Dear notmuch21, well, the d values and lattice parameters would be only equal if all angles were 90° (orthogonal) - here we have angles different to 90° so the d values are (a bit) smaller. For instance, if we look along the a axis (on the b,c-plane) the d(001) value (the distance between the planes parallel to the C face) is 10.4196 Å, while the lattice constant c amounts to 10.7048 Å. I created a PDF to illustrate this deviation, which you can find here: crystalsymmetry.files.wordpress.com/2016/09/lattice_paramters_and_d_values.pdf kind regards! Frank

[@notmuch21]

Dear Dr. Hoffmann, Thanks very much for the input, appreciate it.

[@deepakbellur9676]

@@FrankHoffmann1000 Thanks for the clear illustration.

[@FrankHoffmann1000]

@@deepakbellur9676 very welcome!

[@omermutasim1200]

How can i create supercell:sqrt(3) X sqrt(3) X 1 transformation to my unit cell using VESTA ?

[@FrankHoffmann1000]

Edit - Edit Data - Unit Cell.... Then choose "Transform..." and modify the transformation matrix according to your needs...

[@omermutasim1200]

Frank Hoffmann it only accept integer number , i am talking about square root of 3

[@FrankHoffmann1000]

@@omermutasim1200 I did read that you are talking about the sqrt of 3. But that doesn't matter. Your statement that only integers are allowed is not correct. For certain space groups you have to, of course, remove the symmetry before applying a transformation matrix.

[@omermutasim1200]

Frank Hoffmann I removed the symmetry, but also doesn’t work, it gives a large number of atoms compared with the unit cell !

[@FrankHoffmann1000]

@@omermutasim1200 What do you mean by "doesn't work"? Why don't you describe what you purpose is?

[@omermutasim1200]

I have a question: How to cut half of unit cell using vesta and then save it as VASP file? I’m asking because i’m reproducing DFT paper , and they only consider half unit cell of Ni5P4. Please help me When i tried” Transform unit cell” by setting c to 0.5 , then saved it , I found it saved the original number of atoms

[@FrankHoffmann1000]

Sorry, but I haven't worked with VASP yet and I know nothing about the format or the export function within VESTA. Try to ask you question in the VESTA forum: jp-minerals.org/vesta/en/forum.html

[@omermutasim1200]

Frank Hoffmann thanks a lot What about cutting the unit cell only ? How to do it

[@FrankHoffmann1000]

@@omermutasim1200 probably: Boundary... then specify z(max) = 0.5; I think the export function to VASP then only will take into account the remaining atoms; possibility No 2: delete all atoms with fractional coordinates larger than z = 0.5 ?

[@omermutasim1200]

Frank Hoffmann great, thanks

[@dhoonygo]

Hi, I did exactly what you told but it didn't work.. set crystal shape, check "show shapes"(It didn't show even gray colored plane), check "custom color"(no change) I found other solution to show (hkl) plane from "lattice planes" menu, but why didn't that work..? I use VESTA 3.4.0 the latest

[@FrankHoffmann1000]

Hi Donghoon, I don't know what's going wrong in your particular case. I've just downloaded the newest VESTA version (3.4.0) and have been able to create a crystal shape for Chalcanthite. - did you check that your form is closed (did you specify exactly 6 face with the given face symbols 100, -100, 010, 0-10, 001, and 00-1)? - did you check that for none of the faces the checkbox "Apply symmetry operation" was ticked? You can send me an email with your VESTA file, if you want, and I will have a look: [e-mail] best! Frank

[@dhoonygo]

Thank you for answering. During double checking, I found the problems! it wasn't big deal. Thanks again!! By the way, can I have one more question? I would like to know real time projection during dragging crystal structures. I can set view direction from Orientation menu, but also want to know real time projection vector and upward vector when spinning crystal structure. I guess there's a hint in Orientation matrix, but don't know exactly.. Is this possible? I need this function.

[@dhoonygo]

and from that projection view, can I calculate the projected distance between projected atoms?(not 3-dimensional distance) I've tried to find out, but only did I find calculating 3D distance...

[@FrankHoffmann1000]

Dear Donghoon, sorry, I don't know how to realize this function within VESTA or if VESTA is capable at all to calculate these desired distances. Furthermore, I am not sure, what you could mean by "projected distances between projected atoms".(?) best Frank

[@dhoonygo]

Sorry for my bad English! You know, we can see certain projections from "Orientation" menu. After setting this, we see atoms projected to certain direction. In this situation, I would like to measure the distance between atoms. For example, I can measure distance between atoms by clicking "Distance(d)" and indicating two atoms I want to measure. But the result is a distance in 3D space between atoms which equates to bond length. This is not what I want to do. I want to measure a distance between atoms projected on a same 2D plane(able to set this plane from "Orientation") in order to calculate a lattice misfit on interface between two different materials. Hope you understand.