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

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

I don't know. Best to luck at the code. You may be able to rearrange the atoms.

- Noel

On 25 February 2013 23:27, Karol M. Langner <kar...@gm...> wrote:
> 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