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Re: [cclib-users] problem parsing GAMESS output
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From: Karol M. L. <kar...@gm...> - 2014-09-16 11:52:00
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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. > > > When you want reliability, choose Perforce > > > 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 |
