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From: Edward H. <hol...@ca...> - 2012-04-17 13:41:48
|
Hi All, I just added some stuff to the gaussian parser to collect themrochemistry data. I was realised i never got around the submitting the final patch for gaussian rigid scans so i have also included this. I have attached the patch file |
|
From: SourceForge.net <no...@so...> - 2012-04-16 16:15:32
|
Feature Requests item #3518357, was opened at 2012-04-15 23:11 Message generated for change (Comment added) made by atenderholt You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3518357&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: https://www.google.com/accounts () Assigned to: Nobody/Anonymous (nobody) Summary: ORCA support Initial Comment: Orca is a great and free to use program for computational chemistry. Supporting ORCA-output files would be nice. ---------------------------------------------------------------------- >Comment By: Adam Tenderholt (atenderholt) Date: 2012-04-16 09:15 Message: There is an ORCA branch in SVN, although it hasn't been tested with the newer versions of ORCA (i.e. 2.8 and 2.9). If you need help with getting or using the SVN version, please don't hesitate to ask. Adam ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3518357&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2012-04-16 06:11:08
|
Feature Requests item #3518357, was opened at 2012-04-15 23:11 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3518357&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: https://www.google.com/accounts () Assigned to: Nobody/Anonymous (nobody) Summary: ORCA support Initial Comment: Orca is a great and free to use program for computational chemistry. Supporting ORCA-output files would be nice. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3518357&group_id=161285 |
|
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
>
|
|
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...> - 2012-03-22 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: 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: 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
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> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
|
|
From: Pavel S. <pav...@gm...> - 2012-03-22 05:13:05
|
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
|
|
From: Karol M. L. <kar...@gm...> - 2012-03-06 19:56:58
|
Sounds good to me. - Karol On Feb 26 2012, Noel O'Boyle wrote: > Great idea. I've always found it a pain also. > > Maybe put the code as a function in logfileparser.py. And then just > call it with logfileparser.runmain(*argv). This will allow us to > easily add functionality in future if necessary. > > - Noel > > On 25 February 2012 22:51, Adam Tenderholt <ate...@gm...> wrote: > > Hi all, > > > > When testing recent changes to a parser, I've always wanted a way to just call 'python parser.py filename' to see if it works without resorting to another python script and/or installing and running ccget. I figured this could be handled in the main function, which I've modified for the gamessparser: > > > > -- > > if __name__ == "__main__": > > import doctest, gamessparser, sys > > if len(sys.argv) == 1: > > doctest.testmod(gamessparser, verbose=False) > > > > if len(sys.argv) >= 2: > > parser = gamessparser.GAMESS(sys.argv[1]) > > data = parser.parse() > > > > if len(sys.argv) > 2: > > for i in range(len(sys.argv[2:])): > > if hasattr(data, sys.argv[2 + i]): > > print getattr(data, sys.argv[2 + i]) > > -- > > > > Does this seem reasonable? Should it be added to the other parsers? > > > > Adam > > > > > > > > ------------------------------------------------------------------------------ > > Virtualization & Cloud Management Using Capacity Planning > > Cloud computing makes use of virtualization - but cloud computing > > also focuses on allowing computing to be delivered as a service. > > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > > _______________________________________________ > > cclib-devel mailing list > > ccl...@li... > > https://lists.sourceforge.net/lists/listinfo/cclib-devel > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel -- written by Karol Langner Tue Mar 6 20:56:16 CET 2012 |
|
From: Noel O'B. <bao...@gm...> - 2012-02-26 16:08:25
|
Great idea. I've always found it a pain also. Maybe put the code as a function in logfileparser.py. And then just call it with logfileparser.runmain(*argv). This will allow us to easily add functionality in future if necessary. - Noel On 25 February 2012 22:51, Adam Tenderholt <ate...@gm...> wrote: > Hi all, > > When testing recent changes to a parser, I've always wanted a way to just call 'python parser.py filename' to see if it works without resorting to another python script and/or installing and running ccget. I figured this could be handled in the main function, which I've modified for the gamessparser: > > -- > if __name__ == "__main__": > import doctest, gamessparser, sys > if len(sys.argv) == 1: > doctest.testmod(gamessparser, verbose=False) > > if len(sys.argv) >= 2: > parser = gamessparser.GAMESS(sys.argv[1]) > data = parser.parse() > > if len(sys.argv) > 2: > for i in range(len(sys.argv[2:])): > if hasattr(data, sys.argv[2 + i]): > print getattr(data, sys.argv[2 + i]) > -- > > Does this seem reasonable? Should it be added to the other parsers? > > Adam > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel |
|
From: Adam T. <ate...@gm...> - 2012-02-25 22:51:54
|
Hi all,
When testing recent changes to a parser, I've always wanted a way to just call 'python parser.py filename' to see if it works without resorting to another python script and/or installing and running ccget. I figured this could be handled in the main function, which I've modified for the gamessparser:
--
if __name__ == "__main__":
import doctest, gamessparser, sys
if len(sys.argv) == 1:
doctest.testmod(gamessparser, verbose=False)
if len(sys.argv) >= 2:
parser = gamessparser.GAMESS(sys.argv[1])
data = parser.parse()
if len(sys.argv) > 2:
for i in range(len(sys.argv[2:])):
if hasattr(data, sys.argv[2 + i]):
print getattr(data, sys.argv[2 + i])
--
Does this seem reasonable? Should it be added to the other parsers?
Adam
|
|
From: SourceForge.net <no...@so...> - 2012-02-10 14:20:36
|
Feature Requests item #3485907, was opened at 2012-02-08 16:20 Message generated for change (Settings changed) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Python 3 Port Initial Comment: Since numpy is ported to Python 3, it would be nice to see the Python 3 version of cclib. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2012-02-10 06:20 Message: You didn't leave your name or email so you probably will never read this. In any case, let me say that we already have ported cclib to Python 3. If you are familiar with svn, it's on the Python3 branch (see http://cclib.svn.sourceforge.net/viewvc/cclib/branches/). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2012-02-10 14:20:06
|
Feature Requests item #3485907, was opened at 2012-02-08 16:20 Message generated for change (Comment added) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Python 3 Port Initial Comment: Since numpy is ported to Python 3, it would be nice to see the Python 3 version of cclib. ---------------------------------------------------------------------- >Comment By: Noel O'Boyle (baoilleach) Date: 2012-02-10 06:20 Message: You didn't leave your name or email so you probably will never read this. In any case, let me say that we already have ported cclib to Python 3. If you are familiar with svn, it's on the Python3 branch (see http://cclib.svn.sourceforge.net/viewvc/cclib/branches/). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2012-02-09 00:20:55
|
Feature Requests item #3485907, was opened at 2012-02-08 16:20 Message generated for change (Tracker Item Submitted) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Python 3 Port Initial Comment: Since numpy is ported to Python 3, it would be nice to see the Python 3 version of cclib. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3485907&group_id=161285 |
|
From: Edward H. <hol...@ca...> - 2012-01-24 10:40:54
|
Hi Adam, 1) Yes, this is an over sight on my behalf, i can easily add this. 2) AS you mention this is some what complicated. The for rigid scan case the calculation is basically a series of single point energies, and cclib correctly collects these coordinates in the atom coords section. For this case i suggest we copy the atomcoords array to a scancoords array for clarity and completeness. The situation for a relaxed scan is much more complicated. Gaussian outputs the geometries as values for a z-matrix. While it is fairly simple to extract these values converting them into xyz coordinates this would require parsing the input z matrix and converting the z-matrix with open babel (i guess) As the scan is now a series of optimisations cclib does not correctly collect all geometries as the parser halts after the first optimisation has completed. I think the best solution for the relaxed scan problem is to avoid converting the z-mat and extent the code that searches for geometries to look for more than 1 optimisation step in scan jobs. My reasoning for choosing this option is that it avoids additional dependancies (open babel) and the coded would also be useful for other jobs that are expected to be a series of optimisations (IRC jobs for example). I'll probably have some time over the next weekend to work on this code. Yours Ed Holland On 21 Jan 2012, at 18:06, Adam Tenderholt wrote: > Hi Ed, > > Thanks for the patch. Your changes look pretty straight-forward. A > couple of questions: > > 1) Do you think the names of the variables should also be stored? This > would probably be important if it's a multi-dimensional scan. > 2) Do you have interest in trying to parse the final xyz coordinates > at each point? If I remember correctly, this is somewhat complicated > but something that cclib should probably handle. > > Thanks again, > > Adam > > > On Wed, Jan 18, 2012 at 7:14 AM, Edward Holland <hol...@ca...> wrote: >> helps if i attach the file!! >> >> >> >> On 18 Jan 2012, at 15:13, Edward Holland wrote: >> >>> Hi All, >>> >>> I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch. >>> >>> I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time. >>> >>> Yours >>> >>> Ed Holland >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> |
|
From: Adam T. <ate...@gm...> - 2012-01-21 18:06:20
|
Hi Ed, Thanks for the patch. Your changes look pretty straight-forward. A couple of questions: 1) Do you think the names of the variables should also be stored? This would probably be important if it's a multi-dimensional scan. 2) Do you have interest in trying to parse the final xyz coordinates at each point? If I remember correctly, this is somewhat complicated but something that cclib should probably handle. Thanks again, Adam On Wed, Jan 18, 2012 at 7:14 AM, Edward Holland <hol...@ca...> wrote: > helps if i attach the file!! > > > > On 18 Jan 2012, at 15:13, Edward Holland wrote: > >> Hi All, >> >> I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch. >> >> I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time. >> >> Yours >> >> Ed Holland > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
|
From: SourceForge.net <no...@so...> - 2012-01-19 14:49:38
|
Bugs item #3476063, was opened at 2012-01-19 06:23 Message generated for change (Comment added) made by langner You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Karol Langner (langner) Assigned to: Karol Langner (langner) Summary: Failed hessian parsing for newer GAMESS-US Initial Comment: Chengju Wang reported this on the cclib-users list. ---------------------------------------------------------------------- >Comment By: Karol Langner (langner) Date: 2012-01-19 06:49 Message: Fixed with commit r951. The log file now parses. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2012-01-19 14:23:31
|
Bugs item #3476063, was opened at 2012-01-19 06:23 Message generated for change (Tracker Item Submitted) made by langner You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Karol Langner (langner) Assigned to: Karol Langner (langner) Summary: Failed hessian parsing for newer GAMESS-US Initial Comment: Chengju Wang reported this on the cclib-users list. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285 |
|
From: Edward H. <hol...@ca...> - 2012-01-18 15:14:33
|
helps if i attach the file!! |
|
From: Edward H. <hol...@ca...> - 2012-01-18 15:13:37
|
Hi All, I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch. I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time. Yours Ed Holland |
|
From: Adam T. <ate...@gm...> - 2012-01-16 06:20:41
|
Any thoughts? It's a bit hard since we don't have the actual logfile.
Adam
Begin forwarded message:
> From: Chengju Wang <fra...@gm...>
> Date: January 12, 2012 11:20:05 PM PST
> To: Adam Tenderholt <ate...@gm...>
> Cc: ccl...@li...
> Subject: Re: [cclib-users] cclib.method
>
> Hi, Adam and other folks.
>
> Attached please find the requested file, which was given by
> "
> >>> f=open("aonames.txt",'w')
> >>> import pickle
> >>> pickle.dump(ps.aonames,f)
> >>> f.close()
> "
> following the previous email.
>
> By tail this file, one will get
> " tail aonames.txt
> p3711
> aS'H40_S'
> p3712
> aS'H40_X'
> p3713
> aS'H40_Y'
> p3714
> aS'H40_Z'
> p3715
> a."
>
> This file is incomplete. I think this is problem but I don't how to solve it. :P
>
> thanks for your attention.
>
> Best.
>
> Chengju
>
> On Wed, Jan 4, 2012 at 3:24 PM, Adam Tenderholt <ate...@gm...> wrote:
> Hi Chengju,
>
> Sorry for the late reply. Your error is a bit odd, and I'm not sure
> where the code is failing. Can you send us the aonames parsed by
> cclib? If that's not available, send fonames.
>
> Cheers,
>
> Adam
>
>
> On Thu, Dec 29, 2011 at 9:30 PM, Chengju Wang
> <fra...@gm...> wrote:
> > Dear all.
> >
> > I hope someone here can help me to analysis my GAMESS log file. Thank you.
> >
> > I tried to use cclib to extract the pdos, but have met with the following
> > problem.
> >
> > >>> from cclib.parser import GAMESS
> > >>> from cclib.method import CSPA
> > >>> s=GAMESS("test.log")
> > >>> ps=s.parse()
> > [GAMESS test.log INFO] Creating attribute atomcoords[]
> > [GAMESS test.log INFO] Creating attribute atomnos[]
> > [GAMESS test.log INFO] Creating attribute gbasis[]
> > [GAMESS test.log INFO] Creating attribute nbasis: 2343
> > [GAMESS test.log INFO] Creating attribute charge: 0
> > [GAMESS test.log INFO] Creating attribute mult: 1
> > [GAMESS test.log INFO] Creating attribute homos[]
> > [GAMESS test.log INFO] Creating attribute natom: 340
> > [GAMESS test.log INFO] Creating attribute aooverlaps[]
> > [GAMESS test.log INFO] Creating attribute scftargets[]
> > [GAMESS test.log INFO] Creating attribute scfvalues[]
> > [GAMESS test.log INFO] Creating attribute scfenergies[]
> > [GAMESS test.log INFO] Creating attribute moenergies[]
> > [GAMESS test.log INFO] Creating attribute mosyms[]
> > [GAMESS test.log INFO] Creating attribute nmo: 2343
> > [GAMESS test.log INFO] Creating attribute mocoeffs[]
> > [GAMESS test.log INFO] Creating attribute atombasis[]
> > [GAMESS test.log INFO] Creating attribute aonames[]
> > [GAMESS test.log INFO] Creating attribute coreelectrons[]
> > >>> m=CSPA(ps)
> > >>>>>> len(m.fragresults[0])
> > 2343
> > >>> len(m.fragresults[0][0])
> > 204
> >
> > Why is it not 340 here?
> >
> >
> > Sorry, the log file is too big to be attached.
> >
> >
> > My input key words:
> >
> > $CONTRL SCFTYP=RHF RUNTYP=ENERGY MAXIT=60 MULT=1 $END
> > $CONTRL MOLPLT=.TRUE. PLTORB=.TRUE. NPRINT=3 $END
> > $SYSTEM TIMLIM=525600 MWORDS=9000 $END
> > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
> > $SCF DIRSCF=.TRUE. $END
> > $STATPT OPTTOL=0.0001 NSTEP=2000 $END
> > $DATA
> >
> > There is no such problem found for my testing runs on smaller systems
> > (~100), i.e.: len(m.fragresults[0][0] always equals to natom.
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> > infrastructure or vast IT resources to deliver seamless, secure access to
> > virtual desktops. With this all-in-one solution, easily deploy virtual
> > desktops for less than the cost of PCs and save 60% on VDI infrastructure
> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
>
|
|
From: Edward H. <hol...@ca...> - 2011-12-19 18:22:09
|
Hi,
One second thoughts it probably makes more sense to use an array of rank 1 to store energies and an array of rank n (where n is the number of variables scanned) to store the scan parameters. Not only does this fit better with the rest of cclib but it also makes for nicer code!
***************************************************************************************
#!/software/languages/python/2.5.2/gnu-4.2.4/bin/python
import sys
filename = sys.argv[1]
scanEng = []
scanParm = []
try:
inputfile = open(filename, "r")
except:
print ("file cannot be opened")
for line in inputfile:
if "Summary of the potential surface scan:" in line:
colmNames = inputfile.next()
hyphens = inputfile.next()
line = inputfile.next()
while line != hyphens:
broken = line.split()
scanEng.append(broken[-1])
scanParm.append(broken[1:-1])
line = inputfile.next()
print scaneng, scanparm
***************************************************************************************
Yours
Ed
On 19 Dec 2011, at 16:27, Edward Holland wrote:
> Hi Karol,
>
> I think there must have been a problem with the attachments i sent. For ease i'll just include the relevant sections for each case.
>
> The most simple case in the rigid scan.
>
> *****************Rigid scan section from gaussian output file**********************
> Summary of the potential surface scan:
> N A SCF
> ---- --------- -----------
> 1 109.0000 -76.43373
> 2 119.0000 -76.43011
> 3 129.0000 -76.42311
> 4 139.0000 -76.41398
> 5 149.0000 -76.40420
> 6 159.0000 -76.39541
> 7 169.0000 -76.38916
> 8 179.0000 -76.38664
> 9 189.0000 -76.38833
> 10 199.0000 -76.39391
> 11 209.0000 -76.40231
> ---- --------- -----------
> ***************************************************************************************
>
> This is the most simple example as it only varies one value. More complex scans have additional columns like A.
>
> I think this can be parsed fairly simply using code such as (this code will handle an arbitrary number of columns like A)
>
> ***************************************************************************************
> #!/software/languages/python/2.5.2/gnu-4.2.4/bin/python
>
> import sys
>
> filename = sys.argv[1]
> scanres = []
>
> try:
> inputfile = open(filename, "r")
> except:
> print ("file cannot be opened")
>
> for line in inputfile:
> if "Summary of the potential surface scan:" in line:
> colmNames = inputfile.next()
> hyphens = inputfile.next()
>
> line = inputfile.next()
> while line != hyphens:
> broken = line.split()
> broken[1],broken[-1] = broken[-1],broken[1]
> scanres.append( (broken[1], tuple(broken[2:])) )
> line = inputfile.next()
>
> for res in scanres:
> print res[0] + '\t',
> for parm in res[1]:
> print parm+ '\t',
> print
> ***************************************************************************************
>
> I haven't written a patch for cclib to do similar as i thought it worthwhile to discuss the data structure used to hold this data. A list of tuples containing a float and a tuple doesn't seem like the most elegant solution!
>
> The other type of scan is the relaxed scan.
>
> *****************Relaxed scan section from gaussian output file**********************
> Summary of Optimized Potential Surface Scan
> 1 2 3 4 5
> EIGENVALUES -- -76.43381 -76.43364 -76.43343 -76.43318 -76.43289
> R1 0.96360 0.96297 0.96250 0.96204 0.96157
> R2 0.96360 0.96297 0.96250 0.96204 0.96157
> A1 109.00000 110.00000 111.00000 112.00000 113.00000
> 6 7 8 9 10
> EIGENVALUES -- -76.43256 -76.43219 -76.43178 -76.43134 -76.43086
> R1 0.96112 0.96067 0.96022 0.95978 0.95934
> R2 0.96112 0.96067 0.96022 0.95978 0.95934
> A1 114.00000 115.00000 116.00000 117.00000 118.00000
> 11
> EIGENVALUES -- -76.43035
> R1 0.95891
> R2 0.95891
> A1 119.00000
> ***************************************************************************************
>
> As you can see this case will be much more complicated to parse as gaussian outputs the optimised geometries as a series of z matrix variables.
>
> My thoughts regarding this is to to cheat somewhat. Instead of trying to convert the z-matrix we could search through the structures already found by cclib to find optimised structures.
> This is a very "hacky" way to solve this problem and i would be interested to know if you can think of a better way of doing this.
>
> Yours
>
> Ed
>
>
> On 15 Dec 2011, at 19:28, Karol M. Langner wrote:
>
>> Hi Ed,
>>
>> Sorry for not answering sooner, I was bogged down with work.
>>
>> On Nov 07 2011, Edward Holland wrote:
>>> I managed to run two fairly simple, and representative jobs over the weekend. They aren't very interesting jobs but the correctly illustrate the type of data that will need to be parsed.
>>> The key parts are headed with "Summary of Optimized Potential Surface Scan" or "Summary of the potential surface scan".
>>> as you will be able to see the non optimised jobs will be much simpler to parse as there is no need to store a complete set of geometry data for each step.
>>> One complicated i can see if translating the z matrix variables given by the output into xyz coordinates as normally expected within cclib.
>>
>> So, could you provide the output file(s) you would liked parsed for this? With something to work, it oculd be easy to implement what you want.
>>
>>> Another idea i've had is a boolean that stores if a output file has terminated at an expected point, or been cut short.
>>> I suspect this would be useful for people hoping to make their job submission scripts more intelligent.
>>
>> I'm afraid I don't understand this idea, and you need to explain in more detail what you mean.
>>
>> Best regards,
>> Karol
>>
>>> On 3 Nov 2011, at 13:08, Noel O'Boyle wrote:
>>>
>>>> Hi Ed,
>>>>
>>>> Sounds like an interesting project.
>>>>
>>>> Regarding the scans, your're right - currently we don't support this.
>>>> Can you provide an example? (Preferably a small test case.) Then we'll
>>>> be able to discuss this a bit more.
>>>>
>>>> - Noel
>>>>
>>>> On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote:
>>>>> Hi all,
>>>>>
>>>>> I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way!
>>>>>
>>>>> Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least.
>>>>>
>>>>> Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about.
>>
>> --
>> written by Karol M. Langner
>> Thu Dec 15 20:24:17 CET 2011
>
|
|
From: Edward H. <hol...@ca...> - 2011-12-19 16:52:24
|
Hi Karol,
I think there must have been a problem with the attachments i sent. For ease i'll just include the relevant sections for each case.
The most simple case in the rigid scan.
*****************Rigid scan section from gaussian output file**********************
Summary of the potential surface scan:
N A SCF
---- --------- -----------
1 109.0000 -76.43373
2 119.0000 -76.43011
3 129.0000 -76.42311
4 139.0000 -76.41398
5 149.0000 -76.40420
6 159.0000 -76.39541
7 169.0000 -76.38916
8 179.0000 -76.38664
9 189.0000 -76.38833
10 199.0000 -76.39391
11 209.0000 -76.40231
---- --------- -----------
***************************************************************************************
This is the most simple example as it only varies one value. More complex scans have additional columns like A.
I think this can be parsed fairly simply using code such as (this code will handle an arbitrary number of columns like A)
***************************************************************************************
#!/software/languages/python/2.5.2/gnu-4.2.4/bin/python
import sys
filename = sys.argv[1]
scanres = []
try:
inputfile = open(filename, "r")
except:
print ("file cannot be opened")
for line in inputfile:
if "Summary of the potential surface scan:" in line:
colmNames = inputfile.next()
hyphens = inputfile.next()
line = inputfile.next()
while line != hyphens:
broken = line.split()
broken[1],broken[-1] = broken[-1],broken[1]
scanres.append( (broken[1], tuple(broken[2:])) )
line = inputfile.next()
for res in scanres:
print res[0] + '\t',
for parm in res[1]:
print parm+ '\t',
print
***************************************************************************************
I haven't written a patch for cclib to do similar as i thought it worthwhile to discuss the data structure used to hold this data. A list of tuples containing a float and a tuple doesn't seem like the most elegant solution!
The other type of scan is the relaxed scan.
*****************Relaxed scan section from gaussian output file**********************
Summary of Optimized Potential Surface Scan
1 2 3 4 5
EIGENVALUES -- -76.43381 -76.43364 -76.43343 -76.43318 -76.43289
R1 0.96360 0.96297 0.96250 0.96204 0.96157
R2 0.96360 0.96297 0.96250 0.96204 0.96157
A1 109.00000 110.00000 111.00000 112.00000 113.00000
6 7 8 9 10
EIGENVALUES -- -76.43256 -76.43219 -76.43178 -76.43134 -76.43086
R1 0.96112 0.96067 0.96022 0.95978 0.95934
R2 0.96112 0.96067 0.96022 0.95978 0.95934
A1 114.00000 115.00000 116.00000 117.00000 118.00000
11
EIGENVALUES -- -76.43035
R1 0.95891
R2 0.95891
A1 119.00000
***************************************************************************************
As you can see this case will be much more complicated to parse as gaussian outputs the optimised geometries as a series of z matrix variables.
My thoughts regarding this is to to cheat somewhat. Instead of trying to convert the z-matrix we could search through the structures already found by cclib to find optimised structures.
This is a very "hacky" way to solve this problem and i would be interested to know if you can think of a better way of doing this.
Yours
Ed
On 15 Dec 2011, at 19:28, Karol M. Langner wrote:
> Hi Ed,
>
> Sorry for not answering sooner, I was bogged down with work.
>
> On Nov 07 2011, Edward Holland wrote:
>> I managed to run two fairly simple, and representative jobs over the weekend. They aren't very interesting jobs but the correctly illustrate the type of data that will need to be parsed.
>> The key parts are headed with "Summary of Optimized Potential Surface Scan" or "Summary of the potential surface scan".
>> as you will be able to see the non optimised jobs will be much simpler to parse as there is no need to store a complete set of geometry data for each step.
>> One complicated i can see if translating the z matrix variables given by the output into xyz coordinates as normally expected within cclib.
>
> So, could you provide the output file(s) you would liked parsed for this? With something to work, it oculd be easy to implement what you want.
>
>> Another idea i've had is a boolean that stores if a output file has terminated at an expected point, or been cut short.
>> I suspect this would be useful for people hoping to make their job submission scripts more intelligent.
>
> I'm afraid I don't understand this idea, and you need to explain in more detail what you mean.
>
> Best regards,
> Karol
>
>> On 3 Nov 2011, at 13:08, Noel O'Boyle wrote:
>>
>>> Hi Ed,
>>>
>>> Sounds like an interesting project.
>>>
>>> Regarding the scans, your're right - currently we don't support this.
>>> Can you provide an example? (Preferably a small test case.) Then we'll
>>> be able to discuss this a bit more.
>>>
>>> - Noel
>>>
>>> On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote:
>>>> Hi all,
>>>>
>>>> I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way!
>>>>
>>>> Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least.
>>>>
>>>> Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about.
>
> --
> written by Karol M. Langner
> Thu Dec 15 20:24:17 CET 2011
|
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