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

[Adam T. <ate...@gm...>]

Yes, keep us posted if the new version works for you. Also, I think we push
releases to PyPI so you should be able to install easily with pip.


On Wed, Nov 29, 2017 at 1:40 AM Martin Rahm <mar...@gm...> wrote:

> 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 seem to have been replaced by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
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>
>>
>