Re: [cclib-users] problem parsing GAMESS output

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Nope that doesn't seem to work either. I'm still stuck with "1.2b". The
test all.py script now produces a different error (below).

:cclib-master martin$ sudo python setup.py install -f

running install

running build

running build_py

running build_scripts

running install_lib

copying build/lib/cclib/__init__.py ->
/Library/Python/2.7/site-packages/cclib

copying build/lib/cclib/bridge/__init__.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2biopython.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2openbabel.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2pyquante.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/method/__init__.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/calculationmethod.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/cda.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/cspa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/density.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/fragments.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/lpa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/mbo.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/mpa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/opa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/population.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/volume.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/parser/__init__.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/adfparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/ccopen.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/data.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gamessparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gamessukparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gaussianparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/jaguarparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/logfileparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/molproparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/nwchemparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/orcaparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/psiparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/qchemparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/utils.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/progress/__init__.py ->
/Library/Python/2.7/site-packages/cclib/progress

copying build/lib/cclib/progress/qt4progress.py ->
/Library/Python/2.7/site-packages/cclib/progress

copying build/lib/cclib/progress/textprogress.py ->
/Library/Python/2.7/site-packages/cclib/progress

byte-compiling /Library/Python/2.7/site-packages/cclib/__init__.py to
__init__.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/bridge/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2biopython.py to
cclib2biopython.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2openbabel.py to
cclib2openbabel.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2pyquante.py to
cclib2pyquante.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/method/calculationmethod.py to
calculationmethod.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/cda.py to
cda.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/cspa.py to
cspa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/density.py to
density.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/fragments.py
to fragments.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/lpa.py to
lpa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/mbo.py to
mbo.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/mpa.py to
mpa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/opa.py to
opa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/population.py
to population.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/volume.py to
volume.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/__init__.py
to __init__.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/adfparser.py
to adfparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/ccopen.py to
ccopen.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/data.py to
data.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gamessparser.py to
gamessparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gamessukparser.py to
gamessukparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gaussianparser.py to
gaussianparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/jaguarparser.py to
jaguarparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/logfileparser.py to
logfileparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/molproparser.py to
molproparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/nwchemparser.py to
nwchemparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/orcaparser.py
to orcaparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/psiparser.py
to psiparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/qchemparser.py to
qchemparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/utils.py to
utils.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/progress/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/progress/qt4progress.py to
qt4progress.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/progress/textprogress.py to
textprogress.pyc

running install_scripts

copying build/scripts-2.7/ccget -> /usr/local/bin

copying build/scripts-2.7/cda -> /usr/local/bin

changing mode of /usr/local/bin/ccget to 755

changing mode of /usr/local/bin/cda to 755

running install_egg_info

Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info

Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info

:cclib-master martin$ python

Python 2.7.5 (default, Mar  9 2014, 22:15:05)

[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import cclib

>>> cclib.__version__

'1.2b'

:cclib-master martin$ python test/testall.py

Traceback (most recent call last):

  File "test/testall.py", line 16, in <module>

    from cclib.parser import (ADF, GAMESS, GAMESSUK, Gaussian,

ImportError: cannot import name NWChem

On Tue, Sep 16, 2014 at 7:46 AM, Karol M. Langner <kar...@gm...>
wrote:

> I think you might be running in to the fact that Python does not overwrite
> files
> by default when it installs. But it will if you add the appropriate flag:
>
> sudo python set.py install -f
>
> Also, I'll be clear and point out that this fix is not in any release yet,
> and
> you will need to download the development source code. You can get it
> directly
> from the github repository or via this link:
> https://github.com/cclib/cclib/archive/master.zip
>
> Let us know if that helps,
> Karol
>
> On Sep 15 2014, Martin Rahm wrote:
> > I'm at a bit of a loss now, since I can't install the new version. I seem
> > stuck with the 1.2b version.
> >
> > $ sudo python setup.py build
> >
> > running build
> >
> > running build_py
> >
> > running build_scripts
> >
> > :cclib-1.2 martin$ sudo python setup.py install
> >
> > running install
> >
> > running build
> >
> > running build_py
> >
> > running build_scripts
> >
> > running install_lib
> >
> > running install_scripts
> >
> > changing mode of /usr/local/bin/ccget to 755
> >
> > changing mode of /usr/local/bin/cda to 755
> >
> > running install_egg_info
> >
> > Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> >
> > Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> >
> > :cclib-1.2 martin$ python
> >
> > Python 2.7.5 (default, Mar  9 2014, 22:15:05)
> >
> > [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
> >
> > Type "help", "copyright", "credits" or "license" for more information.
> >
> > >>> import cclib
> >
> > >>> cclib.__version__
> >
> > '1.2b'
> >
> > This has to the best of my knowledge always worked before. What am I
> > missing? Is it that Python is only 2.7.5?
> >
> > The test script returns the following:
> >
> > :test martin$ python testall.py
> >
> > Traceback (most recent call last):
> >
> >   File "testall.py", line 216, in <module>
> >
> >     tests = testall(chosen_parsers, chosen_modules)
> >
> >   File "testall.py", line 151, in testall
> >
> >     testdata = gettestdata(module)
> >
> >   File "testall.py", line 71, in gettestdata
> >
> >     lines = open(testdatadir+'/testdata').readlines()
> >
> > IOError: [Errno 2] No such file or directory:
> > '/Applications/cclib-1.2/test/testdata'
> >
> >
> > Thanks,
> >
> > Martin
> >
> > On Mon, Sep 15, 2014 at 5:05 PM, Karol M. Langner <
> kar...@gm...>
> > wrote:
> >
> > > Hi,
> > >
> > > This should be fixed in master now.
> > >
> > > Thanks for reporting,
> > > Karol
> > >
> > > On Sep 10 2014, Martin Rahm wrote:
> > > > Hi,
> > > >
> > > > I am trying a script that is working fine with both gaussian and orca
> > > > output. I wish to print out the alpha and beta orbital energies of
> the
> > > > nitrogen atom (here in the quartet ground state). The script prints
> out
> > > > beta instead of alpha, and then returns "IndexError: list index out
> of
> > > > range".
> > > >
> > > > I hope this is something stupefyingly simple, and would really
> appreciate
> > > > the help! The output file is attached if anyone would like to give
> it a
> > > > try.
> > > >
> > > > Many thanks,
> > > > Martin
> > > >
> > > > My script:
> > > > ---------------
> > > > from numpy import *
> > > > from cclib.parser import ccopen
> > > > import cclib
> > > > import sys
> > > >
> > > > inputfile = sys.argv
> > > > data = ccopen(inputfile)
> > > > data = data.parse()
> > > >
> > > > print "alpha:"
> > > > print data.moenergies[0]
> > > > print "beta:"
> > > > print data.moenergies[1]
> > > > print "done"
> > > > ------------
> > > >
> > > > My output:
> > > > --------------
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > atomcoords[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atomnos[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> gbasis[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> nbasis:
> > > 20
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> charge:
> > > 0
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> mult: 4
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> homos[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> natom: 1
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > scftargets[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > scfvalues[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > scfenergies[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > moenergies[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> mosyms[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> nmo: 20
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > mocoeffs[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atombasis[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > aonames[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > atomcharges: {}
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > coreelectrons[]
> > > > alpha:
> > > > [-423.94520709  -19.75274401    3.43679786    3.43679786
> 3.43679786
> > > >    15.00163627   15.19755824   15.19755824   15.19755824
>  59.89225728
> > > >    59.89225728   59.89225728   61.45146962   68.88017758
>  68.88017758
> > > >    68.88017758   68.88017758   68.88017758  162.94721266
> 976.48325392]
> > > > beta:
> > > > Traceback (most recent call last):
> > > >   File "./analyze.py", line 21, in <module>
> > > >     print data.moenergies[1]
> > > > IndexError: list index out of range
> > > > -----------
> > >
> > >
> > > >
> > >
> ------------------------------------------------------------------------------
> > > > Want excitement?
> > > > Manually upgrade your production database.
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> > > > Perforce version control. Predictably reliable.
> > > >
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> > >
> > > > _______________________________________________
> > > > cclib-users mailing list
> > > > ccl...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> > >
> > >
> > > --
> > > written by Karol M. Langner
> > > Mon Sep 15 17:05:04 EDT 2014
> > >
>
> --
> written by Karol M. Langner
> Tue Sep 16 07:42:17 EDT 2014
>