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[Jmol-developers] [ jmol-Feature Requests-2791729 ] Wien2k + vibrations
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From: SourceForge.net <no...@so...> - 2009-05-16 17:03:59
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Feature Requests item #2791729, was opened at 2009-05-14 09:14 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2791729&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Laurence Marks (ldm001) Assigned to: Nobody/Anonymous (nobody) Summary: Wien2k + vibrations Initial Comment: Can you please provide a reader for Wien2k DFT files www.wien2k.at (I can provide format info etc). Also, can you provide information on how to input vibrational modes; I am writing an interface for these so can produce a file in the "appropriate" format, if someone tells me what! ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2009-05-16 12:03 Message: Checking files further. In my opinion.... Pyrope.struct says ang, but it is not. I hope you hand-coded that in just as a test; Jmol can't be expected to read "unit=ang" as BOHR. B Lattice looks good to me. NdZrO.struct looks good -- F lattice SrTiO3t.struct looks good -- I lattice TiO.struct looks good - Hall symbol: -F 4 2 3 Ti2O3.struct looks good -- same as AM model FeF2.struct looks good -- CXY Olivine, Andalusite SrTiO3 all look fine. hydroxy.struct -- no good. Exactly what are the lattice shifts for "CXZ"? Are you sure this is the structure? The symmetry? I guess we are missing something with the CXZ lattice. You will need, of course, to check all these yourself, but they appear "reasonable" to me, except ofr hydroxy.struct. I'd like to see an image created from another program and a list of all actual operators and ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-16 00:29 Message: One last upload for the evening. Here I think I have correctly interpreted Wien2k User Manual Table 4.4: P --> SHELX P B --> SHELX I CXY --> SHELX C CXZ --> SHELX B CYZ --> SHELX A R --> SHELX R I guess that makes reasonable sense ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-15 18:33 Message: OK, I think we are there. The Jar file, again, is in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm for examples. Thank you very much, Laurence, for getting me going on this. Turns out there was a bug that only applied to SHELX files, which also require lattice elaboration. The missing atoms are now there. Again, Jmol by default honors the symmetry operators in the file and does not presume packing is desired. You will probably want the PACKED keyword: load TiO.struct PACKED like that, or the -1 option if more than one unit cell is indicated: load Ti2O3.struct {444 666 -1} I am eager for you to test this extensively and let me know how it goes. Also, for the record, the way Jmol applies lattices is by converting the lattice information to specific Hall notations: final static String[] latticeTranslationData = { "\0", "unknown", "" ,"P", "primitive", "" ,"I", "body-centered", " 1n" ,"R", "rhombohedral", " 1r 1r" ,"F", "face-centered", " 1ab 1bc 1ac" ,"A", "A-centered", " 1bc" ,"B", "B-centered", " 1ac" ,"C", "C-centered", " 1ab" ,"S", "rhombohedral(S)", " 1s 1s" ,"T", "rhombohedral(T)", " 1t 1t" }; This is in symmetry.HallInfo.java. Jmol can read Hall notation directly and translate that to exactly the rotations necessary to complete the symmetry. Note that since Jmol can also apply symmetry expressed in the LOAD command to override what is in the file, one can do some very interesting things, like only apply a portion of the full symmetry. So please check this out with all available lattice types. Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-15 12:01 Message: Right, the Jar file is in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip I just uploaded a revision - still not quite right, because I'm missing a few atoms, but the PACKED option is much better. You will always want it, I think: load TiO.struct PACKED like that, or load TiO.struct {444 666 -1} which packs a larger set of unit cells. There is still a bug, but I'm out of time today. Bob ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-15 10:46 Message: Sorry, but I'm stuck testing and cannot get anywhere. It looks like the latest binary is 7.35 and the Wien2k is in 7.36. I downloaded 7.36 but it looks like it needs to be build (no jmol.jar), and I'm not familiar with this. In my cygwin environment I have gcj and jikes.... ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-15 09:12 Message: You are moving way too fast for me; I have not had a chance to install the version yet! Please give me a few days. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-15 08:42 Message: Laurence, I'd like to move this discussion to the Jmol user list. There are many options for Jmol loading. Take a look at http://chemapps.stolaf.edu/jmol/docs under LOAD and consider the options there for crystal structures. One option is, as you suggest, to fold back atoms into the unit cell. But there are lots of situations (whole small molecules, for instance) where that is not desired. People have come up with a variety of ways to work with this. One simple way to get all the atoms, and duplicates for atoms with positions on faces, is to generate a 3x3x3 cube and look only at the center cube: load xxxxx {3 3 3} center cell=666 unitcell offset {1 1 1} display cell=666 This is probably the best way to go, because it adds the duplication of points at 0 and 1, which otherwise might be missed. Please use that method and then let me know if atoms are still missing. They should not be. Bob ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-15 08:35 Message: Another, trickier (general) bug; the minimizer function assumes that the structure is an isolated cell and ignores the translational symmetry. Probably less than simple to fix. ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-15 08:19 Message: Two comments: a) There is a glitch in what atoms are shown. For instance, for Andalusite {111} and Olivine {111} atoms are shown for z > 1 or < 0; they should have been translated back into the unit cell. This is a clear example of what I mentioned in my previous email and looks like it is for the c-axis only. b) I'm told (by someone else who is testing the code) that the Bravais lattices are not being recognized. To clarify, Wien2k is using the (fairly standard) convention of only showing the symmetry operations without the Bravais symmetry. Therefore for a F cell for each of the symmetry operations in the file, the additional translations (0,1/2,1/2); (1/2,0,1/2); (1/2,1/2,0) need to be included. I've added a simple TiO fcc cell so this can be checked. (It might be bug a), I have not checked myself.) ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-15 07:18 Message: I assume that this version is in the latest SVN (which I can figure out how to download) -- please confirm; I'll test it and have some of my students (and a few others) test it as well. I meant something different with spacefilling. All the bulk structures I attached are dense, so have no voids but it looked like there were some in the displays (there were small so it was hard to see). It may be that some symmetry operations+translations are missing. This is a bit tricky because algorithmically it's not a question of a limited loop over the initial positions, but one needs to use a larger loop over translations and test if the final atoms fall within the bounds. This may be too obscure, it's early in the morning. To be 100% clear, to get a cell between -1 and +1 you don't want (in Fortran, I'm C/Java challenged) DO IX=-1,1 DO ISYM=1,NSYM X=... ... ENDDO ENDO But instead a loop like DO IX=-2,2 DO ISYM=1,NSYM XTMP=... IF (XTMP.GE.-1).and.(XTMP.LE.1)then X=XTMP ... ENDIF ENDDO ENDDO ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 21:53 Message: Laurence, You can set the spacefill radius to anything you want. If the charges are not present, then the radii will not be representative of metal and oxide ions. The easiest way to rectify this is to set the charges, then specify spacefill ionic: For example: {_Al}.charge = 3; {_Ti}.charge = 3; {_Si}.charge = 4; {_O}.charge = -2; {_Mg}.charge = 2; {_Ca}.charge = 2; {_Na}.charge = 1; {_K}.charge = 2; select *; spacefill ionic; OK, so at this point I need you to field test this with a bunch of different structures and symmetries. If you haven't used Jmol much, you are in for a treat. There are lots and lots of interesting renderings you can do based on symmetry and space groups, including planes based on Miller indices. I particularly like planes such as: isosurface hkl {1 1 0} map molecular Bob ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 18:23 Message: Yup, it looks right. There is a bit of an issue with space-filling "nicely" and also for Andalusite and Olivine both of which should be almost the same as the AM cif structure. (The lattice parameters and atomic positions may be a few percent different, I cannot remember if I DFT optimized these structures or not.) ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 18:12 Message: OK, I can verify that the AM cif structure and the Wien2k structure are identical. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 18:04 Message: (for a comparison of Ti2O3 from the American Mineralogist database and your struct file, see the uploaded wien-test.png ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 18:03 Message: Success! Since the symmetry definitions are in terms of the primitive cell, I needed to stay with that. So all I am doing is converting the hex cell dimensions to rhombohedral. This certainly provides the correct structure in the case of Ti2O3. See now http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar Maybe still some atoms missing? -- oh, maybe those MULT ones? ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 17:49 Message: p55 of http://www.wien2k.at/reg_user/textbooks/usersguide.pdf has the specific matrices to use to convert both directions. I may have sent an older version earlier, and they don't look like what either of us had. I would assume that this pdf is correct. ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 17:28 Message: I've uploaded all the types I have and will upload a simpler CXY in a few moments; I don't have an example CYZ file and have asked for one, but people in Europe may already be asleep. I'm less than 90% confident of the transformation and I may have given you wrong information earlier. I did a test for the matrix I gave you, taken from some rarely used contributed code, and I'm less than confident that it's right. I've asked for clarification on this as well since I don't want to steer you hopelessly wrong. In terms of units, checking again unit=bohr or unit=BOHR or nothing are all BOHR unit=ang or unit=ANG for Angstroms Pyrope is a B lattice ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 17:04 Message: how do I convert a b c alpha beta gamma (hex) to a b c alpha beta gamma (rhom)? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 16:57 Message: So those coordinates are opposite mine, but that's a minor detail. If the symmetry elements are in the R lattice, then what I need to do is convert the h cell to an r cell and stick with the coord and symmetries there. I will try that.... ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 16:54 Message: You are ahead of me. To convert from the Wien2k units (which are in the rhombohedral cell) to the hexagonal cell the matrix I found in the code is ah = -ar * 2/3 + br * 2/3 + cr * 2/3 bh = -ar * 1/3 - br * 1/3 + cr * 2/3 ch = ar * 1/3 + br * 1/3 + cf * 1/3 (ah, bh, ch) would be in the full hexagonal cell; (ar, br, cr) are what is listed in the struct file. I am pretty sure that the symmetry operations will be in terms of the R-lattice (not the H-lattice). I've uploaded some more file examples. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 16:43 Message: OK, what I believe should be true is this: float a = parseFloat(line.substring(12,22)); float b = parseFloat(line.substring(25,35)); float c = parseFloat(line.substring(38,48)); if (isrhombohedral) { float ar = a; float br = b; float cr = c; a = ar * 2 / 3 - br * 1 / 3 - cr * 1 / 3; b = ar * 1 / 3 + br * 1 / 3 - cr * 2 / 3; c = ar * 1 / 3 + br * 1 / 3 + cr * 1 / 3; } That's from http://homepage2.nifty.com/a-m/bandmemo/node1.html#SECTION00012500000000000000 Is that correct? Now, the next question is this: Are the symmetry operations expressed in terms of the hexagonal lattice or the rhombohedral lattice? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 16:32 Message: nope, too crypic. I need clear specifications for how to transform the a b c coordinates in the file to a'b'c' cooresponding to the indicated unit cell. ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 16:26 Message: Web source: http://www.wien2k.at/reg_user/textbooks/usersguide.pdf I've attached Ti2O3.struct converted to a standard cif Hunting a bit more, I think Angstroms have vanished from all the cases, so please assume that everything is in BOHR (even if that key is not there) and just ignore the units. I'll put some additional cases in shortly (alas, it deletes the message if not sent). ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 16:14 Message: Oh, just saw that latest comment --- ANG like that, in caps? unit=ANG or unit=ang right now I see unit=bohr not unit=BOHR OK, I'll try fixing the coordinate values for R. Some examples of the F, B, I, C$$ cells would be helpful. So you mean the symmetry operations are not complete? Really? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 16:11 Message: I could use a bit more information -- web source for that PDF guide? -- check of the Ti2O3 structure. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 15:09 Message: OK, check out http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar contains the files. I think there is a problem with Ti2O3.struct -- it doesn't say BOHR, but it looks like Bohr, and I'm not convinced the rhombahedral cell is loading properly. I might need some help with that. But please check all of them to see if they are loading properly. Bob Hanson ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 13:27 Message: Nobody was ldm001 (different computer, forgot to login). ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2009-05-14 13:26 Message: Yes, units=Bohr means atomic units or Bohr's, conversion a0=0.529177E0. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 13:11 Message: When it says units=Bohr, that does mean this unit cell is in Bohr? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 13:10 Message: Looks reasonable. The files you have provided should provide plenty of examples. Jmol should be able to read the unit cell and symmetries and derive all additional atoms from just the first atom in the set. This will be a good test, of course, since the additional atom positions are also given. I'll give it a try. ---------------------------------------------------------------------- Comment By: Laurence Marks (ldm001) Date: 2009-05-14 10:23 Message: I've attached some examples, as well as the relevant part of the documentation. Fairly self evident and the Space Group numbers/names are normally correct although it is more robust to use the symmetry. Are all the atoms needed (as against the symmetry reduced set)? It is simpler to use the reduced set although I can also do the full set. Also, does Jmol understand about "F", "B", "I" cells etc to know that these operations are implied or will it need more information? (For assorted reasons A, B, or C centered cells are coded differently in Wien2k.) ---------------------------------------------------------------------- Comment By: Jonathan Gutow (gutow) Date: 2009-05-14 10:15 Message: As there is money being collected for distribution of Wien2k, I suggest that the Wien2k project should put some programmer time into developing the file reader if they want Jmol to read their files. Jonathan ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-05-14 09:47 Message: please attach a few file examples. Vibrational modes are read along with file data, so if your file format included vibrational mode information then that could be automatically incorporated. If your vibrational information must be separate, then I recommend the extended XYZ format. This is simply: # of atoms comment line [atom line] [atom line] [atom line] [atom line] ... where the atom line is simply: element x y z vibx viby vibz For example: 3 CoolMolecules Vibration Generator O 0 0 0 0 0.005799922848714869 0 H 0.7698177590299584 -0.5480927092035551 0 0.06516975737819754 -0.04639938278971895 0 H -0.7698177590299585 -0.548092709203555 0 -0.06516975737819754 -0.04639938278971894 0 For multiple modes, you just string as many of those together as you want: 3 CoolMolecules Vibration Generator mode 1 O 0 0 0 0 0.005799922848714869 0 H 0.7698177590299584 -0.5480927092035551 0 0.06516975737819754 -0.04639938278971895 0 H -0.7698177590299585 -0.548092709203555 0 -0.06516975737819754 -0.04639938278971894 0 3 CoolMolecules Vibration Generator mode 2 O 0 0 0 0 0.005799922848714869 0 H 0.7698177590299584 -0.5480927092035551 0 0.06516975737819754 -0.04639938278971895 0 H -0.7698177590299585 -0.548092709203555 0 -0.06516975737819754 -0.04639938278971894 0 3 CoolMolecules Vibration Generator mode 3 O 0 0 0 0 0.005799922848714869 0 H 0.7698177590299584 -0.5480927092035551 0 0.06516975737819754 -0.04639938278971895 0 H -0.7698177590299585 -0.548092709203555 0 -0.06516975737819754 -0.04639938278971894 0 And if you want to include charge, you can do that between z and vibx: element x y z charge vibx viby vibz ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2791729&group_id=23629 |