Dear JMol users,
I am presently trying to use JMol to plot the molecular orbitals that are
printed in a gaussian09 log file, using the pop=full keyword.
Nevertheless it seems that JMol has some problem to read the log file, which is
a basic Ru complex (the N3 complex), in the reading routine of the molecular
orbitals. It seems in particular that JMol has problems reading the format of
the MO of gaussian if it contains D functions. Indeed, the MO input looks like
Eigenvalues -- -88.79541 -88.79533 -19.20017 -19.20001 -19.19976
1 1 Ru 1S -0.00003 -0.00004 0.00016 0.00016 0.00018
2 2S 0.00008 0.00008 0.00007 0.00006 0.00006
3 3S -0.00154 -0.00152 0.00016 0.00036 0.00023
4 4PX 0.00005 -0.00005 -0.00003 0.00002 0.00003
5 4PY -0.00006 0.00006 0.00002 -0.00004 0.00001
6 4PZ 0.00008 0.00008 0.00002 0.00003 0.00001
7 5PX 0.00106 -0.00109 -0.00043 -0.00014 -0.00051
8 5PY -0.00069 0.00076 -0.00046 0.00004 -0.00059
9 5PZ 0.00095 0.00088 -0.00044 -0.00017 0.00040
10 6PX -0.00008 0.00008 0.00003 0.00030 0.00025
11 6PY 0.00041 -0.00044 0.00022 0.00001 0.00019
12 6PZ -0.00039 -0.00035 0.00017 0.00010 -0.00009
13 7D 0 -0.00001 -0.00001 -0.00001 0.00000 -0.00002
and the console message:
Error reading Gaussian file Molecular Orbitals at line: 13 7D 0
-0.00001 -0.00001 -0.00001 0.00000 -0.00002
And the reading bugs on all the "D 0" lines. Replacing the white space with a
+ makes JMol to run ok, so this looks like a bug of reading that will happen as
soon as we will have D functions ? Did anyone already encountered this
problem, and would have any idea whether I'm facing some localized bug, or if
it is something common in the present version of JMol ?
Another problem comes afterwards, if I replace these white space by "+", I can
read the MOs, but when I plot them using the command console (with mo=1 for
instance), nothing is displayed, only the molecular structure, but no MOs at
all, and at that moment the error console does not print any error message...
I know that it is possible to circumvene this problem by reading MO directly
through cube files, but so far, I am just able to read cubes containing one MO
only. So if I want to plot several MOs (to describe an electronic excitation
for instance) I need one cube file per MO, while one cube file could contain
all the needed MOs in theory. I was hoping to find a more flexible way to plot
MOs through the log file, as it is supposed to be used finally inside a wiki
page.
If anybody has a suggestion on the best and easiest way to generate my MOs
plots with JMol, I would greatly appreciate any help !
Thanks a lot in advance for any suggestion or help
Regards
M. Guillaume
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