cclib-devel

[cclib-devel] Gaussian: standard versus input orientation

[Adam T. <a-t...@st...>]

I've been adapting PyMOlyze to work with cclib, and I've encountered  
a slight problem with the Gaussian test file dvb_un_sp.out. I was  
hoping to be able to pull out the names of atoms from that file/ 
parser, but aonames isn't available after parse() is called. From  
what I can tell, the gaussian parser only looks for "Standard  
orientation" for geometry and atomnos info. Is there a reason "Input  
orientation" isn't used if other coordinate info isn't available?

Adam

Re: [cclib-devel] Gaussian: standard versus input orientation

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

You're right - input orientation should be used if nothing else is
available. The only thing to be careful is not to extract the same
information twice, e.g. for a single point calculation, there should only be
one geometry. After two steps in a geo-opt, there should be 3 geometries
(right? the starting, the 1st, the 2nd?). Also note that standard
orientation isn't available if you use 'NOSYM'.

Can you add a test for the SP unrestricted to ensure that atomnos exists and
has the right dimensions?

Regarding the release, I've overwhelmed with stuff at the moment, but I hope
to make a release at some point with the Changelog as we discussed.

On 19/09/06, Adam Tenderholt <a-t...@st...> wrote:
>
> I've been adapting PyMOlyze to work with cclib, and I've encountered
> a slight problem with the Gaussian test file dvb_un_sp.out. I was
> hoping to be able to pull out the names of atoms from that file/
> parser, but aonames isn't available after parse() is called. From
> what I can tell, the gaussian parser only looks for "Standard
> orientation" for geometry and atomnos info. Is there a reason "Input
> orientation" isn't used if other coordinate info isn't available?
>
> Adam
>
>
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Re: [cclib-devel] Gaussian: standard versus input orientation

[Adam T. <a-t...@st...>]

> Can you add a test for the SP unrestricted to ensure that atomnos  
> exists and has the right dimensions?

Done. Although right now, the unittest is using the dvb_un_sp_b.log  
file instead of dvb_un_sp.out which is the one missing the atomnos  
attribute. Should another group of tests be added (ie. Gaussian B),  
so that the parser is tested against both files?

> Regarding the release, I've overwhelmed with stuff at the moment,  
> but I hope to make a release at some point with the Changelog as we  
> discussed.

Completely understandable! Whenever it's released is fine by me...

Adam

Re: [cclib-devel] Gaussian: standard versus input orientation

[Adam T. <a-t...@st...>]

> Ah, okay, in that case it'd be great if you could add it also to  
> regression.py, which has what I think is a nice framework for  
> specifying tests for individual files. If you could take a look at  
> it, see if you can figure it out, and ask me any questions.
>
> There's some instructions on the wiki at:
>     http://cclib.sourceforge.net/wiki/index.php/Tests
>

Done, although right now, it's just checking for the presence of  
atomnos and not that it has the correct size.

Adam

Re: [cclib-devel] Gaussian: standard versus input orientation

[Adam T. <a-t...@st...>]

Added a fix so that input orientation is used if standard orientation  
isn't found. Info's in the svn log. Also, updated regression.py so  
that it checks for the right dimensions of atomcoords.

Adam

Re: [cclib-devel] Gaussian: standard versus input orientation

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

I've updated regression.py with a slightly more, um, useful docstring.
:-) Funny thing is, I got very confused because the docstring of the
following unittest seemed almost identical, apart from the
Irishisms...:-)

def testGaussian_basicGaussian03_dvb_un_sp_out(logfile):
    """
    This file had no atomcoords at all at all, due to only having an Input
    Orientation section and no Standard Orientation.
    """
    assert len(logfile.atomnos) == 20
    assert logfile.atomcoords.shape == (1,20,3)

def testGaussian_Gaussian03_Mo4OSibdt2_opt_log(logfile):
    """
    This file had no atomcoords as it did not contain any
    "Input orientation" sections, only "Standard orientation" sections
    """
    assert hasattr(logfile,"atomcoords")


On 11/10/06, Adam Tenderholt <a-t...@st...> wrote:
> Added a fix so that input orientation is used if standard orientation
> isn't found. Info's in the svn log. Also, updated regression.py so
> that it checks for the right dimensions of atomcoords.
>
> Adam
>
>