Unit 2.7 - The Software VESTA

[@פרופסוראור]

Danke danke danke danke! Alles ist sehr hillfreich! Danke für teilen deises Material mit uns!

[@MrFerroceno]

Danke schön! Dieses Tutorial ist prima! Es wird meinen Studenten sehr hilfreich sein. Grüsse aus Mexiko.

[@dagobertocardona6066]

Excellent tutorial, it has been very useful for me and my students, thank you very much

[@FrankHoffmann1000]

Thanks, Dago, for your kind words!

[@hanshaun1350]

However, the biggest issue is how you obtained that PDF file...! I would love to build a monoclinic BiVO4 unit cell but cannont find any data for this...

[@FrankHoffmann1000]

That's not that difficult: pubs.acs.org/doi/10.1021/cm5025074 or pubs.acs.org/doi/10.1021/cm0103390 Here the transformed cell into the standard setting C2/c: Lattice parameters a b c alpha beta gamma 7.25250 11.69000 5.09100 90.0000 134.1830 90.0000 Unit-cell volume = 309.524926 Å^3 Structure parameters x y z Occ. B Site Sym. 1 Bi Bi 0.00000 0.13000 0.25000 1.000 1.000 4e 2 V V 0.00000 0.63000 0.25000 1.000 1.000 4e 3 O O1 0.15000 0.29000 0.16000 1.000 1.000 8f 4 O O2 0.26000 0.05000 0.14000 1.000 1.000 8f best! Frank

[@joelaw999]

try materialsproject.org where u can find information for almost ALL known crystals

[@asedefp175]

Hello Frank, Thank you for sharing knowledge. How can I put the legend in vesta side by structure? Arafat

[@FrankHoffmann1000]

Unfortunately, that’s not possible with VESTA right now.

[@weichuanxu6461]

"Introduction" at 00:17 is misspelled.

[@FrankHoffmann1000]

Thanks for the hint. Yes, it was misspelled at the time we produced this screencast. The authors of the website of VESTA already recognized this and have corrected it: jp-minerals.org/vesta/en/ Best! Frank

[@weichuanxu6461]

You don't actually need to reply, but thanks. Really like your videos, and I used some concepts here in my comprehensive exam. Danke!

Thanks!

[@ammaralhelal5603]

hi i want to know more about this software... can i see the hydration shell of mineral ions such as Ca, Mg, and CO3 in aqueous solution.

[@FrankHoffmann1000]

Hi, no, VESTA is only able to visualize crystal structures, not liquid phases. best! Frank

[@ammaralhelal5603]

Frank Hoffmann thank you for your reply... so could you advice me which applications can describe the hydration shell... and is there any calculation methods to find number of water molecules around the ions?

[@FrankHoffmann1000]

Dear Ammar, the problem is in the first instance inferring the number and geometry of the water molecules, which are surrounding the cation in question in an aqueous solution; note, that this not a static structure. This is by far not a trivial task, and I am not aware which _method_ is able to give reliable results.... There is, I think, a bunch of publications out there, in which these questions are addressed; see for an arbitrary entry point: doi.org/10.1016/j.cplett.2005.04.062 Nevertheless, it is well known how the structure of the first "hydration shell" some of the most commons metal cations look like; Mg2+ is usually octahedrally surrounded by six waters and so on. I am sure, you will find some atomistic picture or even structure files out in the web (MOL, PDB or whatsoever atomic coordination format). best Frank

[@ammaralhelal5603]

Frank Hoffmann You are right ther are many publications about this phenomenon but what about adding some additive that may change the number of water molecules... as you mentioned Mg2+ has 6 molecules which may increase or decrease after treatment. The idea is what electrical conductivity will be? Because there is an inverse proportional relationship between the hydration shell and electrical conductivity... I tried to measure the EC after treatment but it is not easy due to high temperatures sensitivity... I’d like to share my conclusions with you to find a good understanding... Regards

[@NitinK6]

Can we calculate site degeneracy of vacancies using VESTA? If yes, can we do that for sites having multiple vacancies?

[@FrankHoffmann1000]

I am not sure, if I understand your question - the site _multiplicity_ is given, if you click on an atom/pseudoatom in the lower info panel.

[@smashgambits]

Would you know if it's possible to use VESTA to generate the distances between one atom and all the others (like, a radial distribution function)? For example, in a simple cubic crystal I know the nearest neighbor is 1a away, the next-nearest neighbor is sqrt(2)a, the next-next nearest neighbor is sqrt(3)a . . . I was recently calculating (by hand) the nearest-neighbor vs next-nearest neighbor distance for BCC (as a hand-wavy argument for why high temperature elements are often BCC), and it occurred to me that there must be a program out there which can just tell me ALL the neighbor distances for any given structure :)

[@FrankHoffmann1000]

No, VESTA can't calculate the RDF. But VMD, CrystalMaker and Diamond are are able to evaluate RDFs.

[@smashgambits]

@@FrankHoffmann1000 Thanks, I'll look into those!

[@mamourmamour4685]

Super vidéo, mais comment faire pour avoir les paramètres de maille, ou y'a t'il une base de données pour ces coordonnées pour chaque structure.

[@FrankHoffmann1000]

Dear Mamour SOCE, yes, there are a number of databases, where you can find those data, at least for minerals. Two very popular databases freely available on the internet are: www.webmineral.com/ and rruff.geo.arizona.edu/AMS/amcsd.php kind regards Frank

[@mamourmamour4685]

Merci pour ces infos, mais j'arrive toujours pas à trouver pour le CuInGaSe2 chalcopyrite ou même le Zinc blende. Je vais faire une petite recherche bibliographique et j’espère y arriver.

[@debbieobie9398]

hey

[@srikanthguntoju6232]

Hey great mate, I wanted to know... If I have a new material which was not reported earlier, how can I get atomic parameters? How can I use vesta for that?

[@FrankHoffmann1000]

See my answer to your question in unit 2.6. VESTA is only for visualization purposes, if and when you have these atomic parameters at hand.

[@pritirajput2054]

Hello sir, which software we used to measure the spin up and spin down states of any alloy ??

[@FrankHoffmann1000]

Sorry, you may use a software for a device that is able to measure spin densities / magnetic fields, but in the first instance you have to _measure_ them (for instance with EPR or a SQUID).

[@pritirajput2054]

Does VESTA is used to plot the graph between energy Vs DOS of any alloy??

[@FrankHoffmann1000]

I don't think so.

[@gunjanrajendraramteke1417]

please tell me sir if is it possible to get electrostatic potential in vesta? or which will be the best software for the visualization of electrostatic potential..

[@FrankHoffmann1000]

You cannot calculate the electrostatic potential with VESTA, but VESTA is able to visualize these kind of data, which were calculated by other software packages, like GAUSSIAN, GAMESS etc. For details, please refer to the manual of VESTA, from page 137 on: jp-minerals.org/vesta/archives/VESTA_Manual.pdf

[@narasimhanv2375]

Hii, When i give in the lattice parameters, it automatically changes back to 1A witout accepting the values, may I know why?

[@FrankHoffmann1000]

Hi! Please try to press the TAB key after inserting your specific value in order to jump to the next field; this should work.

[@narasimhanv2375]

Sill not working! i tried it in a different machine, it worked though, but not in mine!

[@FrankHoffmann1000]

Sorry don't know, why this is not working on your machine - do you have all read and write rights in the respective folders? Perhaps you can describe your problem in the VESTA forum.

[@narasimhanv2375]

Frank Hoffmann hey! thank you, I got it sorted out. was problem with the keyboard

[@xingliwang8741]

is it possible to crystal alloy with VESTA?

[@FrankHoffmann1000]

It is possible to visualize every compound that has a defined crystal structure; it is also possible to specify the occupancy for each atomic position, so in principle this is possible, yes. However, it is difficult to specify compounds which would be classified as solid solutions, in which the solute has no dictinct crystallographic position or is disordered. But substitution crystals, for instance brass, cam also be visualized with VESTA (or an equivalent software package, capable of display CIF files).

[@xingliwang8741]

many thanks

[@nidiaestherreinagonzalez452]

Thanks for your video is very good

[@joelaw999]

Hi Frank thx a lot ! do you have any idea how i can get the labels showed in the model? I tried objects->properties->atoms->labels but only got some commas instead of atom labels.

[@FrankHoffmann1000]

Hi Joe, only one idea: make sure that you actually have Labels specified - go to Edit - Edit Data - Structure Parameters - then choose an atomic entry. This has to have not only a Symbol, but also a Label. In this way you can name the atoms also "Frank" or "Joe" :-) Hope this helps! best Frank

[@joelaw999]

@@FrankHoffmann1000 just solved it, thx a lot for ur help sir!

[@xdxd525]

Can we show intercalation of ions inside crystal structure using VESTA? HOW?

[@FrankHoffmann1000]

Don't know what kind of system you are thinking about. If the ions are ordered and if you have any structural model that VESTA is able to read, then the answer is definitely yes. If you speak about one crystalline phase to which you want to add a non-crystalline guest phase, this should also be possible - please refer to the Manual, Chapter 7: jp-minerals.org/vesta/archives/VESTA_Manual.pdf

[@xdxd525]

@@FrankHoffmann1000 I am talking about structures having guest ions in intersticial sites of host crystal without affecting the crystal structure ( how to place guest ions in intersticial sites in them if they are not the part of host structure. simple as that.

[@xdxd525]

@@FrankHoffmann1000 btw I appreciate your efforts to reply each comment even after 3 years of posting video.

[@FrankHoffmann1000]

@@xdxd525 Of course, remove the symmetry from your phase, i.e. turn it into P1, and then you are free to add any ion at a place you like (via Edit Data, Structure parameters...).

[@ahmedismail8867]

Dear sir i found this video very informative. I want to draw crystal structure of NaVO3 oxide (pdf number 75-0716) i have information about space group unit cell dimensions but i dont know the atomic parameters. Thank you

[@FrankHoffmann1000]

You can download a ZIP file with both known structures of NaVO3 here: 1drv.ms/u/s!ArTbwWHXPrwekbwDPzEJIKdquwtuXg?e=zcylNq

[@najmulhasam]

how to be appear Oxygen atoms

[@FrankHoffmann1000]

Dear Najmul, sorry, I think I don't understand your question - they appear, if you transfer the parameters for the oxygen atoms into VESTA as shown in this video from minute 4:27 onwards. Have you tried to follow all the instructions given in the Video? best! Frank

[@najmulhasam]

Dear I am unable to draw the structure, If I send the required parameter, can you show me, how to draw the structure.

[@FrankHoffmann1000]

I am very sorry, but I think I will be unable to help you, if you don't explain in detail what kind of problems do you face - all the steps that have to be done in order to built such a crystal structure are explicitely shown in this video

[@najmulhasam]

Thank You Mr. Frank I have learnt to draw the structure with the help of your video, but I want to know, how to find out any kind of interactions within the molecule, like pi-pi stacking and hydrogen bonding.

[@FrankHoffmann1000]

Dear Najmul, great that this video was finally helpful. Concerning the analysis of structures in terms of interactions: This has to be done mainly manually, i.e. you have to figure out certain bond lengths, geometries and so on; ion that basis you have to conclude if and which certain interactions might be present or not. VESTA is not capable of an automated analysis. Mercury (from the CCDC) is able to display short-contacts and H-bonds, but not Pi-Pi interactions.. best regards Frank

[@Y2Ka966]

Thanks..very helpfull !