[cclib-users] Problem with the parser when going from 1.3 --> 1.5

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

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seem to have been replaced by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