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

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Alright, thanks Adam.

Then I am sorry to bother you with this request for clarification:

I was under the impression that cclib per default considers the last sets
of energies if there are multiple sepparate jobs in a file. For instance,
if several scf calculations have proceeded in a geometry optimization run,
that it is the last set that is parsed.

If inputfile is a file with several jobs in it, such as my N2 example, or
any general opt+freq run, and I write

data = ccopen(inputfile)

data = data.parse()

energies_alpha=data.moenergies[0]

Then the size of the array data.moenergies is one. There is only one set of
orbital energies, and those are the one of the last successful calculation,
no?

Thanks again,

Martin

On Tue, Dec 5, 2017 at 1:02 AM, Adam Tenderholt <ate...@gm...>
wrote:

> Hi Martin,
>
> Eric looked at your files, and says that there appear to be multiple jobs
> in a single file: https://github.com/cclib/cclib/issues/453. Generally,
> it's best to run things as separate jobs. Let us know if we're missing
> something, or if you have any other questions or problems.
>
> Best regards,
>
> Adam
>
>
> On Wed, Nov 29, 2017 at 6:57 AM Adam Tenderholt <ate...@gm...>
> wrote:
>
>> 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
>>>>>>    <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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>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>