[cclib-devel] [ cclib-Bugs-2904432 ] Assertion error trying to parse this gaussian log

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Bugs item #2904432, was opened at 2009-11-26 10:25
Message generated for change (Settings changed) made by baoilleach
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Category: Parsers
Group: None
>Status: Closed
Resolution: Works For Me
Priority: 5
Private: No
Submitted By: xaverxn (xaverxn)
Assigned to: Nobody/Anonymous (nobody)
Summary: Assertion error trying to parse this gaussian log

Initial Comment:
Hi,
I guess this is a bug. Trying to ccopen() this gaussian log gives me:

>>> import cclib
>>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log')
>>> data=myfile.parse()
[Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2
[Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5
[Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[]
[Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31
[Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse
    self.extract(inputfile, line)
  File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract
    assert self.natom == natom
AssertionError

As for the basis, this was a ub3lyp/gen job with a mixed basis set:

(...)

C H O 0
6-31G(d,p)
****
Fe 0
tzv
****

(...)

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Comment By: xaverxn (xaverxn)
Date: 2009-12-04 16:44

Message:
With the current trunk (rev. 826), this works for me, too, so I guess
you're right. Thanks.

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Comment By: Noel O'Boyle (baoilleach)
Date: 2009-12-01 10:14

Message:
This works for me with the cclib development code, so it must have been
fixed in the meanwhile. We will try to get out a cclib version before
Christmas (!) or early in the new year.

Marking as pending

- Noel

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Comment By: xaverxn (xaverxn)
Date: 2009-11-27 12:32

Message:
I hereby place the uploaded file g03_test_complete.log.tar.bz2 in the
public domain.

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Comment By: Noel O'Boyle (baoilleach)
Date: 2009-11-27 11:16

Message:
(Tried to respond earlier but SF was messed up)

We only fix bugs for public domain log files, so can you confirm (or
deny!) that you place this log file in the public domain?

- Noel

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Comment By: xaverxn (xaverxn)
Date: 2009-11-26 10:27

Message:
Forgot to say:
cclib-0.91
Python 2.5.2 (r252:60911, Jan  4 2009, 21:59:32)
[GCC 4.3.2] on linux2

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