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Re: [cclib-devel] [cclib-users] Orca 2.9.0 error
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From: Karol M. L. <kar...@gm...> - 2013-02-25 23:25:03
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I agree, and I'll leave this one to you guys. Have you checked if perhaps this is caused by a change between ORCA versions? I'm not really up-to-date on it's output.
Karol
On Feb 25 2013, Noel O'Boyle wrote:
> I'm all for parsing it. Since this is fairly GaussSum-specific I'm
> happy to do it if you can make sure these files are public domain. In
> the meanwhile, you can point out to the user that he can comment out
> the offending code.
>
> On 25 February 2013 17:31, Adam Tenderholt <ate...@gm...> wrote:
> > CC: dev list
> >
> > Any thoughts on this? Should we try to parse the alternate SCF convergence
> > info, or just change the code so it doesn't raise an exception?
> >
> > Adam
> >
> > On Mon, Feb 25, 2013 at 3:14 AM, msmqbm <ms...@ci...> wrote:
> >>
> >> Dear Adam,
> >>
> >> Thanks for your message. The reason for that strange output is the
> >> NormalPrint keyword, it has nothing to do with the MRCI (you can delete that
> >> part). Here I attach an output with a DFT calculation and a normalPrint
> >> keyword, so that you can see the source of the problem.
> >> It's ok if you make this input or output public.
> >>
> >> It would be nice that, even if the parser cannot read the whole file, it
> >> didn't raise an exception, so that one could get at least the geometry, the
> >> number of atoms or the information it has read so far.
> >>
> >> Cheers,
> >>
> >>
> >> On 02/25/2013 01:24 AM, Adam Tenderholt wrote:
> >>
> >> Hi Melchor,
> >>
> >> Sorry for the delay. I've finally looked into your parse error. The
> >> problem is the output from the SCF convergence. For instance, it your file,
> >> it is:
> >>
> >> --------------
> >> SCF ITERATIONS
> >> --------------
> >> *** Starting incremental Fock matrix formation ***
> >>
> >> ----------------------------
> >> ! ITERATION 0 !
> >> ----------------------------
> >> Total Energy : -377.995940441385 Eh
> >> Energy Change : -377.995940441385 Eh
> >> MAX-DP : 0.104636203272
> >> RMS-DP : 0.004511416837
> >> Actual Damping : 0.7000
> >> Actual Level Shift : 0.2500 Eh
> >> Int. Num. El. : 43.99928165 (UP= 21.99964083 DN=
> >> 21.99964083)
> >> Exchange : -34.30375363
> >> Correlation : -2.02696332
> >>
> >>
> >> ----------------------------
> >> ! ITERATION 1 !
> >> ----------------------------
> >> Total Energy : -378.158637308210 Eh
> >> Energy Change : -0.162696866825 Eh
> >> MAX-DP : 0.056981704567
> >> RMS-DP : 0.002392614971
> >> Actual Damping : 0.7000
> >> Actual Level Shift : 0.2500 Eh
> >> Int. Num. El. : 43.99902992 (UP= 21.99951496 DN=
> >> 21.99951496)
> >> Exchange : -34.01830967
> >> Correlation : -2.01718102
> >>
> >> However, cclib is expecting the following:
> >>
> >> --------------
> >> SCF ITERATIONS
> >> --------------
> >> ITER Energy Delta-E Max-DP RMS-DP [F,P]
> >> Damp
> >> *** Starting incremental Fock matrix formation ***
> >> 0 -381.9867779344 0.000000000000 0.05707535 0.00425410 0.0807540
> >> 0.7000
> >> 1 -382.0079986969 -0.021220762511 0.02895905 0.00220039 0.0411442
> >> 0.7000
> >>
> >> I tried to make sense of your input file, but I don't have any experience
> >> with MRCI calculations with ORCA. Do you know if there was some option that
> >> caused the SCF convergence to be printed differently? Or is this how the
> >> convergence for all MRCI calculations is printed?
> >>
> >> Also, are you willing to place your logfile in the public domain? We would
> >> like to include it with our other regression files.
> >>
> >> Thanks,
> >>
> >> Adam
> >>
> >>
> >>
> >>
> >> On Thu, Feb 21, 2013 at 1:48 AM, msmqbm <ms...@ci...> wrote:
> >>>
> >>> Dear cclib developers,
> >>> When trying to parse an Orca 2.9.0 output file I get the following error:
> >>>
> >>> >>> import cclib
> >>> >>> f1= cclib.parser.ORCA("DAT6600.out")
> >>> >>> data1= f1.parse()
> >>> [ORCA DAT6600.out INFO] Creating attribute atomcoords[]
> >>> [ORCA DAT6600.out INFO] Creating attribute atomnos[]
> >>> [ORCA DAT6600.out INFO] Creating attribute natom: 9
> >>> [ORCA DAT6600.out INFO] Creating attribute nbasis: 90
> >>> [ORCA DAT6600.out INFO] Creating attribute charge: 0
> >>> [ORCA DAT6600.out INFO] Creating attribute mult: 1
> >>> [ORCA DAT6600.out INFO] Creating attribute scfvalues[]
> >>> Traceback (most recent call last):
> >>> File "<stdin>", line 1, in <module>
> >>> File "/usr/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
> >>> line 221, in parse
> >>> self.extract(inputfile, line)
> >>> File "/usr/lib/python2.7/dist-packages/cclib/parser/orcaparser.py",
> >>> line 90, in extract
> >>> assert line[1] == "Energy"
> >>> AssertionError
> >>>
> >>> I'm using cclib version 1.1 (the latest one). I attach the file
> >>> DAT6600.out.
> >>>
> >>> Is there a solution to this?
> >>>
> >>> Thanks in advance,
> >>>
> >>> --
> >>> Melchor Sánchez
> >>> PhD candidate
> >>> Institute of Advanced Chemistry of Catalonia
> >>> http://www.iqac.csic.es/qteor
> >>> IQAC - CSIC
> >>> Tel. +34 934006100 ext: 1307
> >>> Jordi Girona 18-26
> >>> 08034 Barcelona (Spain)
> >>>
> >>>
> >>>
> >>> ------------------------------------------------------------------------------
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> >>>
> >>
> >>
> >>
> >> --
> >> Melchor Sánchez
> >> PhD candidate
> >> Institute of Advanced Chemistry of Catalonia
> >> http://www.iqac.csic.es/qteor
> >> IQAC - CSIC
> >> Tel. +34 934006100 ext: 1307
> >> Jordi Girona 18-26
> >> 08034 Barcelona (Spain)
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_feb
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> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
> >
>
> ------------------------------------------------------------------------------
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> Download AppDynamics Lite for free today:
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--
written by Karol M. Langner
Tue Feb 26 00:22:12 CET 2013
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