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Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5
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From: Martin R. <mar...@gm...> - 2017-11-29 09:31:58
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Hi Adam, I am using 1.5, which I thought was the latest (according to https://cclib.github.io/how_to_install.html) The source code of the newest release of cclib (version 1.5) is distributed as: - A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz Where can the even newer versions be found? Best, Martin On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...> wrote: > Are you using 1.5? Or one of the newer releases like 1.5.2? If you're > still having problems with the latest release, are you able to share your > file for some debugging? > > On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...> > wrote: > >> Hi cclib-lovers, >> >> I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities >> with the basic parsing. Maybe this has been explained somewhere, and if so >> I apologize. I have been unable to find an answer on my own, and hope you >> can help. I'm running a Linux environment with Python 3.6 (I used to run >> 2.7.5 so that might have affected things as well). >> >> from cclib.parser import ccopen >> >> seem to have been replaced by >> >> from cclib.io import ccopen >> >> >> so the basic guide shown https://cclib.github.io/methods.html doesn't >> seem to be right anymore. >> >> >> ccopen doesn't seem to function as it used to. >> >> data = ccopen("file.out") results in the following error: >> >> >> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py", >> line 190, in ccopen >> >> inputfile.seek(0, 0) >> >> AttributeError: 'FileInput' object has no attribute 'seek' >> >> This led me to use the (new?) functions: >> >> from cclib.parser import Gaussian ORCA >> >> >> when calling >> >> data = ORCA("inputfile.out") >> >> >> This seems to work, albeit sometimes with the following omnious error >> messages: >> >> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed >> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8]) >> >> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute >> should not exist yet. There is a problem in the parser. >> >> >> when instead calling >> >> data = Gaussian("file.out") >> >> >> it proceeds to crash at the next line, which is >> >> data = data.parse() >> >> >> Traceback (most recent call last): >> >> File "./script.py", line 87, in <module> >> >> data = data.parse() >> >> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site- >> packages/cclib/parser/logfileparser.py", line 301, in parse >> >> self.extract(inputfile, line) >> >> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site- >> packages/cclib/parser/gaussianparser.py", line 163, in extract >> >> line = inputfile.next() >> >> AttributeError: 'FileInput' object has no attribute 'next' >> >> >> So, to sum up, my questions are: >> >> >> 1. Can cclib no longer automatically determine which output it is trying >> to parse (ccopen could do this, and there was nothing fancy with the output >> files I tried)? >> >> >> 2. Do the the errors shown for the ORCA parser imply a real problem >> >> >> 3. How do I get the Gaussian parser to run? >> >> >> Many thanks, >> >> >> Martin >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >> _________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> > |
