Re: [cclib-users] z-matrix in Gaussian

[Karol M. L. <kar...@gm...>]

BTW, Noel, is there a way to specify the atom order in OB for internal coordinates?

On Feb 19 2013, Noel O'Boyle wrote:
> (Nice use of OpenBabel :-)
> 
> Just to clarify, there is a difference between the z-matrix input
> format and the internal coordinate format used by Gaussian during
> geometry optimisations. The former is non-redundant while the latter
> is redundant ("redundant internal coordinates"). I'm not sure which
> you want.
> 
> - Noel
> 
> On 19 February 2013 22:02, Adam Tenderholt <ate...@gm...> wrote:
> > Hi Yaron,
> >
> > cclib doesn't directly support parsing internal coordinates. However, you
> > can use openbabel to save using an internal coordinate system:
> >
> >>>> from cclib.parser import ccopen
> >>>> import openbabel
> >>>> parser = ccopen("dvb_sp.log")
> >>>> data = parser.parse()
> >>>> from cclib.bridge import makeopenbabel
> >>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
> >>>> obconv = openbabel.OBConversion()
> >>>> obconv.SetInAndOutFormats("XYZ", "FH")
> >>>> obconv.WriteFile(mol, "test.fh")
> >
> > --
> > 20
> > C   1
> > C   1 1.421
> > C   2 1.402  1 120.857
> > C   3 1.422  2 121.354  1   0.0
> > C   4 1.421  3 117.789  2   0.0
> > H   2 1.098  1 119.765  3 180.0
> > H   3 1.099  2 119.629  1 180.0
> > H   5 1.098  4 119.765  3 180.0
> > C   4 1.498  3 119.172  2 180.0
> > C   9 1.344  4 126.593  3 180.0
> > H  10 1.096  9 122.647  4   0.0
> > H   9 1.100  4 114.434  3   0.0
> > H  10 1.096  9 121.228  4 180.0
> > C   1 1.498  2 123.039  3 180.0
> > H  14 1.100  1 114.434  2 180.0
> > C  14 1.344  1 126.593  2   0.0
> > H  16 1.096 14 122.647  1   0.0
> > H  16 1.096 14 121.228  1 180.0
> > C   5 1.402  4 120.857  3   0.0
> > H  19 1.099  5 119.629  4 180.0
> > --
> >
> > You may also want to see the list of formats supported by openbabel in case
> > you need something slightly different:
> > http://openbabel.org/docs/2.3.1/FileFormats/Overview.html
> >
> > Hope this helps,
> >
> > Adam
> >
> >
> >
> > On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky
> > <yar...@li...> wrote:
> >>
> >> Dear cclib community,
> >> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
> >> output file using cclib.
> >> I know that Gaussian do converts any internal or XYZ coordinates in the
> >> input to it's format so one can get internal coordinates from it, even if
> >> the input file was in cartesian coordinates.
> >> Can cclib output the internal coordinates?
> >>
> >> Thanks very much,
> >> Yaron
> >>
> >>
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-- 
written by Karol M. Langner
Tue Feb 26 00:27:13 CET 2013