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

[Noel O'B. <bao...@gm...>]

(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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>
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