Re: [cclib-users] problem parsing GAMESS output

[Martin R. <mar...@gm...>]

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
> > -----------
>
>
> >
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>
> --
> written by Karol M. Langner
> Mon Sep 15 17:05:04 EDT 2014
>