Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

[Martin R. <mar...@gm...>]

My bad, Google didn't show me https://github.com/cclib/cclib/releases at
first.

I will try, and get back to you.

You might want to update the other webpage though, and maybe remove the
older http://cclib.sourceforge.net/wiki/index.php/Main_Page

Thanks,
Martin

On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...> wrote:

> Hi Adam,
>
> I am using 1.5, which I thought was the latest (according to
> https://cclib.github.io/how_to_install.html)
>
> The source code of the newest release of cclib (version 1.5) is
> distributed as:
>
>    - A .tar.gz file: https://github.com/cclib/cclib/releases/download/
>    v1.5/cclib-1.5.post1.tar.gz
>
> Where can the even newer versions be found?
>
> Best,
> Martin
>
>
>
> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...>
> wrote:
>
>> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
>> still having problems with the latest release, are you able to share your
>> file for some debugging?
>>
>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> Hi cclib-lovers,
>>>
>>> I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities
>>> with the basic parsing. Maybe this has been explained somewhere, and if so
>>> I apologize. I have been unable to find an answer on my own, and hope you
>>> can help. I'm running a Linux environment with Python 3.6 (I used to run
>>> 2.7.5 so that might have affected things as well).
>>>
>>> from cclib.parser import ccopen
>>>
>>> seem to have been replaced by
>>>
>>> from cclib.io import ccopen
>>>
>>>
>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>> seem to be right anymore.
>>>
>>>
>>> ccopen doesn't seem to function as it used to.
>>>
>>> data = ccopen("file.out") results in the following error:
>>>
>>>
>>> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>> line 190, in ccopen
>>>
>>>     inputfile.seek(0, 0)
>>>
>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>
>>> This led me to use the (new?) functions:
>>>
>>> from cclib.parser import Gaussian ORCA
>>>
>>>
>>> when calling
>>>
>>> data = ORCA("inputfile.out")
>>>
>>>
>>> This seems to work, albeit sometimes with the following omnious error
>>> messages:
>>>
>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>
>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>> should not exist yet. There is a problem in the parser.
>>>
>>>
>>> when instead calling
>>>
>>> data = Gaussian("file.out")
>>>
>>>
>>> it proceeds to crash at the next line, which is
>>>
>>> data = data.parse()
>>>
>>>
>>> Traceback (most recent call last):
>>>
>>>   File "./script.py", line 87, in <module>
>>>
>>>     data = data.parse()
>>>
>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages
>>> /cclib/parser/logfileparser.py", line 301, in parse
>>>
>>>     self.extract(inputfile, line)
>>>
>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages
>>> /cclib/parser/gaussianparser.py", line 163, in extract
>>>
>>>     line = inputfile.next()
>>>
>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>
>>>
>>> So, to sum up, my questions are:
>>>
>>>
>>> 1.  Can cclib no longer automatically determine which output it is
>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>> output files I tried)?
>>>
>>>
>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>
>>>
>>> 3. How do I get the Gaussian parser to run?
>>>
>>>
>>> Many thanks,
>>>
>>>
>>> Martin
>>>
>>>
>>>
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>>
>