[Pw_forum] Confused about vibrational modes of isolated molecule from ph.x

Jin Zhang jin.zhang.pku at gmail.com
Mon Nov 20 13:27:55 CET 2006


No. I didn't relax the molecule. As a matter of fact, I got this structure
from want code's self test, and thought it was already relaxed-.-
I'll relax it later and see if good things happen.

Best,
-- 
Jin Zhang
Dep. of Physics,
Peking Univ.

On 11/20/06, degironc <degironc at sissa.it> wrote:
>
> did you relaxed the structure ?
> These are the forces I get with your input  [a typical threshold for a
> structural relaxation is
> forc_conv_thr  REAL ( default = 1.0D-3 ) ].
> stefano
>
>     Forces acting on atoms (Ry/au):
>
>      atom   1 type  2   force =    -0.06870568    0.00011605    0.00070580
>      atom   2 type  1   force =     0.00057171   -0.00133033    0.00026104
>      atom   3 type  2   force =    -0.03470840    0.06008037
> 0.00060235
>      atom   4 type  1   force =    -0.00200170   -0.00052894   -0.00023669
>      atom   5 type  2   force =     0.03477692    0.05989867   -0.00004091
>      atom   6 type  1   force =     0.00029793     0.00027534   -
> 0.00032982
>      atom   7 type  2   force =     0.06862846   -0.00002844   -0.00054894
>      atom   8 type  1   force =    -0.00256825    0.00128897   -0.00025706
>      atom   9 type  2   force =     0.03495275    -0.06050673   -
> 0.00040942
>      atom  10 type  1   force =    -0.00020204    0.00131722    0.00025463
>      atom  11 type  2   force =    -0.03450037   -0.05925204    0.00020053
>      atom  12 type  1   force =     0.00345864   -0.00133014   -0.00020152
>
>      Total force =     0.169286     Total SCF correction =     0.000107
>
> stefano
>
>
> Jin Zhang wrote:
>
> > Dear MMC,
> >
> > The supercell I used is a simple cubic one (let ibrav=8
> > celldim(1,2,3)=20bohr). Because the molecule is isolated, I think the
> > kpoint sampling should be irrelevant. And I used gamma point for the
> > calculation.
> >
> > I increased ecut to 25Ry, and celldim to 30bohr) the number of
> > negative modes increase by 9 (to 21modes)!
> > OMG, there must be sth wrong!
> > I'll attach my input and see if someone can give some comments.
> > !-----------------------omega-------------------
> >      omega( 1) =    -123.660534 [THz] =   -4124.898815 [cm-1]
> >      omega( 2) =    -122.070631 [THz] =   -4071.865015 [cm-1]
> >      omega( 3) =    -109.408034 [THz] =   -3649.483445 [cm-1]
> >      omega( 4) =    - 103.611190 [THz] =   -3456.120267 [cm-1]
> >      omega( 5) =    -100.288151 [THz] =   -3345.274863 [cm-1]
> >      omega( 6) =     -86.921490 [THz] =   -2899.408087 [cm-1]
> >      omega( 7) =     -86.648147 [THz] =   - 2890.290289 [cm-1]
> >      omega( 8) =     -78.536226 [THz] =   -2619.703943 [cm-1]
> >      omega( 9) =     -63.552993 [THz] =   -2119.913758 [cm-1]
> >      omega(10) =     -60.437624 [THz] =   -2015.995524 [cm-1]
> >      omega(11) =     - 59.290658 [THz] =   -1977.736621 [cm-1]
> >      omega(12) =     -59.022664 [THz] =   -1968.797246 [cm-1]
> >      omega(13) =     -58.953578 [THz] =   -1966.492750 [cm-1]
> >      omega(14) =     -46.326804 [THz] =   -1545.306104 [cm-1]
> >      omega(15) =     -31.263942 [THz] =   -1042.859776 [cm-1]
> >      omega(16) =     -31.093207 [THz] =   -1037.164629 [cm-1]
> >      omega(17) =     - 27.758798 [THz] =    -925.939988 [cm-1]
> >      omega(18) =     - 27.694407 [THz] =    -923.792135 [cm-1]
> >      omega(19) =     -24.097859 [THz] =    -803.823410 [cm-1]
> >      omega(20) =     -20.675736 [THz] =    - 689.672916 [cm-1]
> >      omega(21) =     -20.064562 [THz] =    -669.286187 [cm-1]
> >      omega(22) =      15.218497 [THz] =     507.637805 [cm-1]
> >      omega(23) =      16.277849 [THz] =     542.974191 [cm-1]
> >      omega(24) =      20.249558 [THz] =     675.457041 [cm-1]
> >      omega(25) =      21.320279 [THz] =     711.172668 [cm-1]
> >      omega(26) =      22.104349 [THz] =     737.326626 [cm-1]
> >      omega(27) =       23.427206 [THz] =     781.452687 [cm-1]
> >      omega(28) =      30.392570 [THz] =    1013.793763 [cm-1]
> >      omega(29) =      43.644315 [THz] =    1455.827328 [cm-1]
> >      omega(30) =      55.006552 [THz] =     1834.833267 [cm-1]
> >      omega(31) =      57.997854 [THz] =    1934.613035 [cm-1]
> >      omega(32) =      61.898591 [THz] =    2064.728462 [cm-1]
> >      omega(33) =      68.862483 [THz] =    2297.020463 [cm-1]
> >      omega(34) =      68.979827 [THz] =    2300.934652 [cm-1]
> >      omega(35) =      69.303015 [THz] =    2311.715098 [cm-1]
> >      omega(36) =      69.697807 [THz] =    2324.884051 [cm-1]
> >
> > On 11/19/06, *Miguel Martínez Canales* < wmbmacam at lg.ehu.es
> > <mailto:wmbmacam at lg.ehu.es>> wrote:
> >
> >     Hi Jin,
> >
> >     Jin Zhang escribió:
> >     > The thing I cannot understand is, there're 12 negative frequencies
> >     > existing. I know 3 of them are purely translational modes and
> >     another 3
> >     > are rotational ones. But what about the rest 6? I'm a little
> >     confused
> >     > and hopefully someone can help.
> >     >
> >     > The eigenvals are pasted below and thanks in advance!
> >     >
> >     > (the result may not be accurate due to a only-15Ry ecut I used,
> >     but it
> >     > should not give out qualitative different result)
> >
> >     For a start, I wouldn't think 15 rydbergs is enough. Have you
> >     tested the
> >     pseudopotentials for ecut convergence? 25 or 30 would probably be
> >     a better
> >     choice. Anyway, what you probably are missing most in your
> >     calculations is
> >     k-point sampling convergence. Translational and rotational
> >     frequencies are
> >     a bit too large. What happens if you increase your k-point grid?
> >     Anyway,
> >     don¡t forget to relax your molecule with the new parametres.
> >
> >     BTW: What kind of cell are you using? I've never done molecular
> >     normal mode
> >     calculations but I guess that in the case of bencene using an
> >     hexagonal
> >     supercell might make sense.
> >
> >     --
> >     ----------------------------------------
> >     Miguel Martínez Canales
> >         Dto. Física de la Materia Condensada
> >         UPV/EHU
> >         Facultad de Ciencia y Tecnología
> >         Apdo. 644
> >         48080 Bilbao (Spain)
> >     Fax:  +34 94 601 3500
> >     Tlf:  +34 94 601 5437
> >     ----------------------------------------
> >
> >       "The problem with Renault is that they dont have
> >       the skills to convince FIA that the mass damper
> >       is just a brake cooler."
> >
> >     Annonymous
> >
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> >
> >
> >
> >
> > --
> > Jin Zhang
> > Dep. of Physics,
> > Peking Univ.
>
>
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