[CPMD-list] problems with point group recognition and symmetrisation of coordinates

[Juerg Hutter]

Hi

There are several possible sources of errors using the
point group molecule functionality.

- you need to position the molecule according the following
  rules

C   - Positioning of the molecule:
C            z-axis   is the principal axis
C            x-axis   is the two-fold axis
C            xz-plane is the sigma-v plane
C            xy-plane is the sigma-h or the Cs symmetry plane
C            origin   is the center of inversion

This means for example that for certain subgroups of Td
you have to rotate the molecule in the input.

- The parser has a rather strange format for the
  Schoenfliess symbols

  SYMBOL  NAXIS

  where SYMBOL is C,CNH,CS,CNV,S,D,DNH,DND,DN,T,TD,O,OH,I,IH
  and NAXIS the value of the principle axis N. Put NAXIS=0
  where there is no priciple axis.

It's still possible that there are some bugs for certain
point groups. I can't remember how seriously this was
checked at the time.

regards

Juerg


----------------------------------------------------------
Juerg Hutter                   Phone : ++41 1 635 4491
Physical Chemistry Institute   FAX   : ++41 1 635 6838
University of Zurich           E-mail: hutter at pci.unizh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
----------------------------------------------------------


On Wed, 17 Mar 2004, Christian Tuma wrote:

> Dear CPMD developers,
>
> using CPMD 3.7.2 (Linux-PC, Redhat 9.0, ifort 8.0, ATLAS 3.6.0) I encountered
> problems with the recognition of molecular point groups and subsequent
> symmetrisation of coordinates.
> For the case of the methane molecule (CH4, symmetry point group "Td") I used
> two different orientations of the molecule in a cartesian coordinate system.
> Depending on which orientation I have chosen, I got quite different results
> concerning the recognition of a number of subgroups of "Td" and "Td" itself:
>
> A) one C2-axis corresponds to the z-axis, and the x-axis is orthogonal to
>    a mirror plane
>
>    ...
>    &ATOMS
>    *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER
>     LMAX=P
>     1
>      0.0000    0.0000    0.0000
>    *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER
>     LMAX=S
>     4
>      0.0035   -0.8952    0.6336
>     -0.8988   -0.0005   -0.6284
>      0.0031    0.8958    0.6327
>      0.8920    0.0000   -0.6379
>    &END
>    ...
>
>    C2, C2v : recognition and symmetrisation ok
>    S4      : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE"
>    Td      : recognition ok, symmetrisation problems
>                             DELTA=0.01 : bonds far too short
>                             DELTA=0.1  : loss of 4 symmetry operations
>    D2d, D2 : not recognised
>
>
> B) all C2-axes correspond to cartesian axes
>
>    ...
>    &ATOMS
>    *TM/C_TM_PBE_pade_110 KLEINMAN-BYLANDER
>     LMAX=P
>     1
>      0.0000    0.0000    0.0000
>    *TM/H_TM_PBE_pade_070 KLEINMAN-BYLANDER
>     LMAX=S
>     4
>      0.6355   -0.6304    0.6336
>     -0.6352   -0.6359   -0.6286
>     -0.6312    0.6356    0.6327
>      0.6307    0.6308   -0.6379
>    &END
>    ...
>
>    C2, D2  : recognition and symmetrisation ok
>    C2v, Td : not recognised
>    S4      : recognition ok, symmetrisation problem "ATOMS ARE VERY CLOSE"
>    D2d     : recognition ok, symmetrisation problems (bonds far too short)
>
>
> The rest of the input was as follows (with different Schoenfliess symbols):
>
>    ! CH4
>    &CPMD
>     OPTIMIZE GEOMETRY
>     MAXSTEP
>      1
>     STRUCTURE BONDS ANGLES
>    &END
>    &SYSTEM
>     ANGSTROM
>     POINT GROUP MOLECULE DELTA=0.01
>     DND  2
>     sYMMETRIZE COORDINATES
>     SYMMETRY
>      0
>     CUTOFF
>      50
>     CELL
>      5.0 1.0 1.0 0.0 0.0 0.0
>    &END
>    &ATOMS
>    ...
>    &END
>    &DFT
>     NEWCODE
>     FUNCTIONAL PBE
>    &END
>
>
> These observations for (A) and (B) are somehow complementary, especially
> concerning the "D" point subgroups. That's why I think there is no way to
> put the CH4-molecule such that everything goes fine with all these symmetry
> point subgroups.
> So what's wrong? I took a look into the source code, but at some point I
> was unable to follow the programmers' ideas. My only vague idea is that
> the generation of the symmetry operators might not be sufficiently flexible,
> i.e. some of them could be excluded from each other. Do the CPMD developers
> know where the problem is hidden and how it can be fixed?
>
> Thanks a lot,
>
> Christian Tuma.
>
> PS: Another example for the failure in symmetry recognition is the case
>     of the staggered ethane molecule C2H6. Although being aligned along
>     the z-axis, CPMD doesn't recognise it as "D3d".
>
> --
> Christian Tuma             Humboldt-Universitaet Berlin
> ct at chemie.hu-berlin.de     Arbeitsgruppe Quantenchemie (Prof. Sauer)
> phone: +49-30-20937140     Brook-Taylor-Str. 2, 12489 Berlin, GERMANY
> fax:   +49-30-20937136     http://www.chemie.hu-berlin.de/ag_sauer
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