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From: Pavel S. <pav...@gm...> - 2012-03-22 05:13:05
Attachments:
triazole_tddft_c1_b3lyp_631Gdp_sp.out
|
Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
version form svn and QMforge program. In console i got
[GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
MO section found but could not be parsed!
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
250, in fileOpen
File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
150, in open
File
"/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
line 221, in parse
File
"/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
line 720, in extract
self.logger.warning('MO section found but could not be parsed!')
File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
self._log(WARNING, msg, args, **kwargs)
File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
self.handle(record)
File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
self.callHandlers(record)
File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
hdlr.handle(record)
TypeError: QWidget.handle(): too many arguments
If i run this file with gamess us it goes withput problems. The problem
file for Firefly is attached.
Thank you.
Pavlo.
--
Pavlo V. Solntsev
pavlo.solntsev at gmail.com
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From: Noel O'B. <bao...@gm...> - 2012-03-22 10:44:37
|
Hello Pavel,
We have a policy of only fixing bugs for public domain log files. Are
you happy to place this log file in the public domain?
- Noel
On 22 March 2012 05:12, Pavel Solntsev <pav...@gm...> wrote:
> Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
> version form svn and QMforge program. In console i got
> [GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
> MO section found but could not be parsed!
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
> 250, in fileOpen
> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
> 150, in open
> File
> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
> line 221, in parse
> File
> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
> line 720, in extract
> self.logger.warning('MO section found but could not be parsed!')
> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
> self._log(WARNING, msg, args, **kwargs)
> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
> self.handle(record)
> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
> self.callHandlers(record)
> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
> hdlr.handle(record)
> TypeError: QWidget.handle(): too many arguments
>
> If i run this file with gamess us it goes withput problems. The problem
> file for Firefly is attached.
>
> Thank you.
>
> Pavlo.
>
>
>
> --
> Pavlo V. Solntsev
> pavlo.solntsev at gmail.com
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
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|
From: Pavel S. <pav...@gm...> - 2012-03-22 16:04:52
|
Yes. You can place this log file in the public domain
PS.
On 03/22/2012 05:44 AM, Noel O'Boyle wrote:
> Hello Pavel,
>
> We have a policy of only fixing bugs for public domain log files. Are
> you happy to place this log file in the public domain?
>
> - Noel
>
> On 22 March 2012 05:12, Pavel Solntsev <pav...@gm...> wrote:
>> Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
>> version form svn and QMforge program. In console i got
>> [GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
>> MO section found but could not be parsed!
>> Traceback (most recent call last):
>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>> 250, in fileOpen
>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>> 150, in open
>> File
>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>> line 221, in parse
>> File
>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
>> line 720, in extract
>> self.logger.warning('MO section found but could not be parsed!')
>> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
>> self._log(WARNING, msg, args, **kwargs)
>> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
>> self.handle(record)
>> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
>> self.callHandlers(record)
>> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
>> hdlr.handle(record)
>> TypeError: QWidget.handle(): too many arguments
>>
>> If i run this file with gamess us it goes withput problems. The problem
>> file for Firefly is attached.
>>
>> Thank you.
>>
>> Pavlo.
>>
>>
>>
>> --
>> Pavlo V. Solntsev
>> pavlo.solntsev at gmail.com
>>
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
--
Pavlo V. Solntsev
pavlo.solntsev at gmail.com
|
|
From: Adam T. <ate...@gm...> - 2012-03-22 17:15:30
|
Hi Pavel,
Thanks for bringing this problematic file to our attention. I believe
you've uncovered two bugs, one in cclib and one in QMForge. It looks
like the cclib bug has to do with handling the MO section of your
logfile, and hopefully is a relatively straight-forward fix. The bug
in QMForge is harder to address without knowing more about your
system, although I suspect it's a Qt API problem.
1) What version of QMForge are you using (2.1 or SVN)? From source?
2) What version of Qt4 and PyQt4 do you have installed?
3) Does QMForge crash, or does it not open the window showing
warnings/errors/info? (The first is a critical bug, the latter is
missing functionality).
Adam
On Thu, Mar 22, 2012 at 9:04 AM, Pavel Solntsev
<pav...@gm...> wrote:
> Yes. You can place this log file in the public domain
>
> PS.
>
>
>
> On 03/22/2012 05:44 AM, Noel O'Boyle wrote:
>> Hello Pavel,
>>
>> We have a policy of only fixing bugs for public domain log files. Are
>> you happy to place this log file in the public domain?
>>
>> - Noel
>>
>> On 22 March 2012 05:12, Pavel Solntsev <pav...@gm...> wrote:
>>> Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
>>> version form svn and QMforge program. In console i got
>>> [GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
>>> MO section found but could not be parsed!
>>> Traceback (most recent call last):
>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>> 250, in fileOpen
>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>> 150, in open
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>> line 221, in parse
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
>>> line 720, in extract
>>> self.logger.warning('MO section found but could not be parsed!')
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
>>> self._log(WARNING, msg, args, **kwargs)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
>>> self.handle(record)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
>>> self.callHandlers(record)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
>>> hdlr.handle(record)
>>> TypeError: QWidget.handle(): too many arguments
>>>
>>> If i run this file with gamess us it goes withput problems. The problem
>>> file for Firefly is attached.
>>>
>>> Thank you.
>>>
>>> Pavlo.
>>>
>>>
>>>
>>> --
>>> Pavlo V. Solntsev
>>> pavlo.solntsev at gmail.com
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>
>
>
> --
> Pavlo V. Solntsev
> pavlo.solntsev at gmail.com
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
|
|
From: Adam T. <ate...@gm...> - 2012-03-25 18:09:25
|
Hi Pavel,
I have fixed this bug in the svn trunk version of cclib. Please let me know if you'd prefer me to send you the updated source code.
Take care,
Adam
On Mar 22, 2012, at 9:04 AM, Pavel Solntsev wrote:
> Yes. You can place this log file in the public domain
>
> PS.
>
>
>
> On 03/22/2012 05:44 AM, Noel O'Boyle wrote:
>> Hello Pavel,
>>
>> We have a policy of only fixing bugs for public domain log files. Are
>> you happy to place this log file in the public domain?
>>
>> - Noel
>>
>> On 22 March 2012 05:12, Pavel Solntsev <pav...@gm...> wrote:
>>> Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
>>> version form svn and QMforge program. In console i got
>>> [GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
>>> MO section found but could not be parsed!
>>> Traceback (most recent call last):
>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>> 250, in fileOpen
>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>> 150, in open
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>> line 221, in parse
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
>>> line 720, in extract
>>> self.logger.warning('MO section found but could not be parsed!')
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
>>> self._log(WARNING, msg, args, **kwargs)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
>>> self.handle(record)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
>>> self.callHandlers(record)
>>> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
>>> hdlr.handle(record)
>>> TypeError: QWidget.handle(): too many arguments
>>>
>>> If i run this file with gamess us it goes withput problems. The problem
>>> file for Firefly is attached.
>>>
>>> Thank you.
>>>
>>> Pavlo.
>>>
>>>
>>>
>>> --
>>> Pavlo V. Solntsev
>>> pavlo.solntsev at gmail.com
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>
>
>
> --
> Pavlo V. Solntsev
> pavlo.solntsev at gmail.com
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
|
|
From: Adam T. <ate...@gm...> - 2012-04-01 17:53:01
|
Hi Pavlo,
Can you supply cclib with a public domain file that has this problem? We should have similar file in our regression tests.
Thanks,
Adam
On Apr 1, 2012, at 9:02 AM, Pavel Solntsev wrote:
> Dear Adam.
>
> I found another bug in cclib.
> If you have ECP job cclib doesn't extract correct number for HOMO orbitals.
> Firefly removes all core electrons and corresponding orbitals. All
> another orbitals are renumbered. After that number of the HOMO orbital
> will be lower by number of the core orbitals. I solved program by
> commenting couple lines in the gamessparser.py file. Now cclib works
> correctly with FF output files with and without ECP. I didn't check
> cclib with GAMESS US, but it looks like it should not be any problem.
>
> # line 857
> if line[1:28] == "NUMBER OF OCCUPIED ORBITALS" and not
> hasattr(self,'homos'):
> homos = [int(line.split()[-1])-1]
> line = inputfile.next()
> homos.append(int(line.split()[-1])-1)
> self.homos = numpy.array(homos, "i")
>
>
> All the best.
>
> Pavlo.
>
>
>
> On 03/28/2012 11:19 AM, Adam Tenderholt wrote:
>> Oops, one minor mistake in my email. You need to keep the following
>> line (since it does all the parsing magic):
>>
>> 150 data = parser.parse()
>>
>> Adam
>>
>>
>> On Wed, Mar 28, 2012 at 9:18 AM, Adam Tenderholt <ate...@gm...> wrote:
>>> Hi Pavel,
>>>
>>> Your error now looks like a problem with QMForge. For the windows and
>>> Mac version, I wanted the cclib info/warning/errors to be displayed in
>>> a nice window after parsing the file. This, however, appears to be
>>> broken due to Qt 4.8 (I think I wrote QMForge with Qt 4.4 or 4.5 in
>>> mind...it's been too long).
>>>
>>> The easiest fix that will get you up and running involves changing the
>>> source code of QMForge a bit. Edit qmforge.py, go to the open function
>>> (near line 126), and comment out (or remove) the following lines:
>>>
>>> 129 viewer = LogViewer(self)
>>>
>>> and
>>>
>>> 149 parser.logger.addHandler(viewer)
>>> 150 data = parser.parse()
>>> 151 warnings = viewer.ui.textEdit.toPlainText()
>>> 152 if len(warnings) > 0:
>>> 153 viewer.show()
>>>
>>> Let me know if this works for you. The info/warnings/errors from cclib
>>> should be printed in the console.
>>>
>>> Take care,
>>>
>>> Adam
>>>
>>>
>>> On Wed, Mar 28, 2012 at 7:34 AM, Pavel Solntsev
>>> <pav...@gm...> wrote:
>>>> Hi Adam.
>>>>
>>>> I checked another output file from Firefly with last version of the
>>>> cclib and also found some problems .
>>>> In terminal i can see:
>>>> $ qmforge
>>>> [GAMESS
>>>> /home/pavel/Documents/people/Lysenko/IC/ag2trz2/sp/ag2trz2_ci_sp_b3lyp.out
>>>> WARNING] Number of occupied orbitals not consistent. This is normal for
>>>> ECP and FMO jobs.
>>>> Traceback (most recent call last):
>>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>>> 250, in fileOpen
>>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>>> 150, in open
>>>> File
>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>>> line 221, in parse
>>>> self.extract(inputfile, line)
>>>> File
>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
>>>> line 877, in extract
>>>> self.logger.warning("Number of occupied orbitals not consistent.
>>>> This is normal for ECP and FMO jobs.")
>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
>>>> self._log(WARNING, msg, args, **kwargs)
>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
>>>> self.handle(record)
>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
>>>> self.callHandlers(record)
>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
>>>> hdlr.handle(record)
>>>> TypeError: QWidget.handle(): too many arguments
>>>> $
>>>>
>>>> My input file is normal single point run with ECP.
>>>> $CONTRL SCFTYP=RHF RUNTYP=energy
>>>> DFTTYP=B3LYP
>>>> MAXIT=100 inttyp=hondo icut=10 itol=30
>>>> ICHARG=2 MULT=1
>>>> ecp=read exetyp=run $END
>>>> $SYSTEM TIMLIM=9999999 mwords=40 $END
>>>> $BASIS extfil=.t. $END
>>>> $SCF DIRSCF=.TRUE. fdiff=.t. $END
>>>> $smp call64=.t. $end
>>>> $DATA
>>>> Ci
>>>>
>>>> coordinates
>>>>
>>>> $ecp
>>>> ......
>>>> $end
>>>>
>>>> Unfortunately i can't provide this file in the public domain, but i can
>>>> send it to you.
>>>>
>>>> Thank you very much for you help.
>>>>
>>>> PS.
>>>>
>>>>
>>>>
>>>>
>>>> On 03/25/2012 01:09 PM, Adam Tenderholt wrote:
>>>>> Hi Pavel,
>>>>>
>>>>> I have fixed this bug in the svn trunk version of cclib. Please let me know if you'd prefer me to send you the updated source code.
>>>>>
>>>>> Take care,
>>>>>
>>>>> Adam
>>>>>
>>>>>
>>>>> On Mar 22, 2012, at 9:04 AM, Pavel Solntsev wrote:
>>>>>
>>>>>> Yes. You can place this log file in the public domain
>>>>>>
>>>>>> PS.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 03/22/2012 05:44 AM, Noel O'Boyle wrote:
>>>>>>> Hello Pavel,
>>>>>>>
>>>>>>> We have a policy of only fixing bugs for public domain log files. Are
>>>>>>> you happy to place this log file in the public domain?
>>>>>>>
>>>>>>> - Noel
>>>>>>>
>>>>>>> On 22 March 2012 05:12, Pavel Solntsev <pav...@gm...> wrote:
>>>>>>>> Hi i have a file from Firefly ( pcgamess)i can't parse with cclib. I use
>>>>>>>> version form svn and QMforge program. In console i got
>>>>>>>> [GAMESS <path to my file>/triazole_tddft_c1_b3lyp_631Gdp_sp.out WARNING]
>>>>>>>> MO section found but could not be parsed!
>>>>>>>> Traceback (most recent call last):
>>>>>>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>>>>>>> 250, in fileOpen
>>>>>>>> File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", line
>>>>>>>> 150, in open
>>>>>>>> File
>>>>>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>>>>>>> line 221, in parse
>>>>>>>> File
>>>>>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py",
>>>>>>>> line 720, in extract
>>>>>>>> self.logger.warning('MO section found but could not be parsed!')
>>>>>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1144, in warning
>>>>>>>> self._log(WARNING, msg, args, **kwargs)
>>>>>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1250, in _log
>>>>>>>> self.handle(record)
>>>>>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1260, in handle
>>>>>>>> self.callHandlers(record)
>>>>>>>> File "/usr/lib/python2.7/logging/__init__.py", line 1300, in callHandlers
>>>>>>>> hdlr.handle(record)
>>>>>>>> TypeError: QWidget.handle(): too many arguments
>>>>>>>>
>>>>>>>> If i run this file with gamess us it goes withput problems. The problem
>>>>>>>> file for Firefly is attached.
>>>>>>>>
>>>>>>>> Thank you.
>>>>>>>>
>>>>>>>> Pavlo.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Pavlo V. Solntsev
>>>>>>>> pavlo.solntsev at gmail.com
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> This SF email is sponsosred by:
>>>>>>>> Try Windows Azure free for 90 days Click Here
>>>>>>>> http://p.sf.net/sfu/sfd2d-msazure
>>>>>>>> _______________________________________________
>>>>>>>> cclib-devel mailing list
>>>>>>>> ccl...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>>>>>>
>>>>>> --
>>>>>> Pavlo V. Solntsev
>>>>>> pavlo.solntsev at gmail.com
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF email is sponsosred by:
>>>>>> Try Windows Azure free for 90 days Click Here
>>>>>> http://p.sf.net/sfu/sfd2d-msazure
>>>>>> _______________________________________________
>>>>>> cclib-devel mailing list
>>>>>> ccl...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>>
>>>> --
>>>> Pavlo V. Solntsev
>>>> pavlo.solntsev at gmail.com
>>>>
>
>
> --
> Pavlo V. Solntsev
> pavlo.solntsev at gmail.com
>
|
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