Bugs item #3563670, was opened at 2012-08-31 02:30
Message generated for change (Tracker Item Submitted) made by vliegeois
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Category: File Translation
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Vincent LIEGEOIS (vliegeois)
Assigned to: Nobody/Anonymous (nobody)
Summary: Error reading gaussian g09 file
Initial Comment:
Hi
I have found that i have some problem converting gaussian file using: babel
-ig09 ok.log -oxyz test.xyz.
Sometimes, it does not work with openbabel 2.3.1 (and i also think with 2.3.0)
while it was working perfectly well with 2.2.3.
I was able to isolate the smallest piece of gaussian log file that works with
open babel 2.3.1 (as well as with 2.2.3):
Entering Gaussian System, Link
0=/cluster/apps/gaussian/09_A02-vl1/serial/x86_64-Linux/pgi/11.3-64/g09/g09
#
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 7 0 -0.477749 1.577049 -1.113058
2 7 0 0.477755 1.577016 1.113106
3 6 0 -2.682077 -0.519929 1.073098
---------------------------------------------------------------------
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 7 0 -10.477749 11.577049 -11.113058
2 7 0 0.477755 1.577016 1.113106
3 6 0 -12.682077 -0.519929 1.073098
For both version, it is the standard orientation geometry that is output. This
is all perfectly fine.
I have notice that since version 2.3.1 (and i guess also 2.3.0), two elements
are needed for the file to be correctly read:
1) The second line with: " # " indicating the route section in gaussian
2) Both the Input and standard orientation
These two facts were not needed in version 2.2.3
For instance, the following file was read without problem in 2.2.3 but not in
2.3.1:
Entering Gaussian System, Link
0=/cluster/apps/gaussian/09_A02-vl1/serial/x86_64-Linux/pgi/11.3-64/g09/g09
#
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 7 0 -0.477749 1.577049 -1.113058
2 7 0 0.477755 1.577016 1.113106
3 6 0 -2.682077 -0.519929 1.073098
---------------------------------------------------------------------
THIS IS A PROBLEM since when using the option NoSymm (noymmetry) in Gaussian,
the standard orientation does not exist and we should therefore read the input
orientation.
Is there a reason why you changed the behavior of the parser from 2.2.3 to
2.3.1?
Is it possible to fix that?
Best regards
Vincent LIEGEOIS
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