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

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

Thanks for sharing the files. I've created an issue on Github:
https://github.com/cclib/cclib/issues/453.


On Wed, Nov 29, 2017 at 6:49 AM Martin Rahm <mar...@gm...> wrote:

> Hi Adam,
>
> I resolved most of my problems. A few peculiarities remain, likely minor:
>
> N2 with ORCA runs OK, but results in the following warnings (not seen in
> some other orca output):
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets attribute
> should not exist yet. There is a problem in the parser.
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets attribute
> should not exist yet. There is a problem in the parser.
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] Modes corresponding to
> rotations/translations may be non-zero.
>
>
> NCNO2 with ORCA runs OK, but results in the following warnings (not seen
> in some other orca output):
>
> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] Attribute
> atomnos changed value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>
> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] The geotargets
> attribute should not exist yet. There is a problem in the parser.
>
>
> I do not think these affect my script output, but would still like to know
> what they refer to.. Have you seen this before? The two output files are
> attached, along with the script (remove .txt and unzip).
>
> Thanks for the help, and, as always, for cclib.
>
>
> Best regards,
>
> Martin
>
> On Wed, Nov 29, 2017 at 3:40 PM, Adam Tenderholt <ate...@gm...>
> wrote:
>
>> 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
>>>>>>
>>>>>
>>>>
>>>
>