#159 Wien2k + vibrations

closed
5
2009-05-20
2009-05-14
No

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!

Discussion

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  • Bob Hanson

    Bob Hanson - 2009-05-14

    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

     
  • Laurence Marks

    Laurence Marks - 2009-05-14
     
  • Laurence Marks

    Laurence Marks - 2009-05-14
     
  • Jonathan Gutow

    Jonathan Gutow - 2009-05-14

    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

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    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.)

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    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.

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    When it says units=Bohr, that does mean this unit cell is in Bohr?

     
  • Nobody/Anonymous

    Yes, units=Bohr means atomic units or Bohr's, conversion a0=0.529177E0.

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    Nobody was ldm001 (different computer, forgot to login).

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    I could use a bit more information

    -- web source for that PDF guide?
    -- check of the Ti2O3 structure.

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    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?

     
  • Laurence Marks

    Laurence Marks - 2009-05-14
     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    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).

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    I Lattice (Tetragonal SrTiO3)

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    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.

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    F Lattice

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    B Lattice

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    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?

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    CXY (beware spacegroup name inconsistency)

     
  • Laurence Marks

    Laurence Marks - 2009-05-14

    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.

     
  • Bob Hanson

    Bob Hanson - 2009-05-14

    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....

     
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