[Jmol-developers] [ jmol-Bugs-3413444 ] MOs not showing for molden file

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Bugs item #3413444, was opened at 2011-09-23 16:17
Message generated for change (Comment added) made by rkanters
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Category: Graphics
Group: None
Status: Open
Resolution: Fixed
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Bob Hanson (hansonr)
Summary: MOs not showing for molden file

Initial Comment:
Hi,

I just, after a long time, updated the Jmol source with the repository and for one reason or another a molden file that works properly (after forcing it to consider it as a molden file since the header has ' [Molden Format]' with Jmol Version: 12.0.49  2011-07-30 15:57, does not show the molecular orbitals. I traced the interpretation of the file and it seems to me that it still indeed reads the orbitals and all, but doesn't display them. A test with the Jmol-datafiles molden sample water_novib.molden show that for that one I am able to show orbitals, so I am completely confused here.

I was hoping to change
if (leader.startsWith(recordTag)) (line 452 in Resolver.java) to
if (leader.trim().startsWith(recordTag))
so that leading spaces in the header would get ignored (and hoping that that would not break any other readers).

I'll try to attach the gzipped archive of the file to this report.
Thanks,
René


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>Comment By: Rene Kanters (rkanters)
Date: 2011-09-24 15:02

Message:
Hi Bob,

The sample file I attached was for a multi-configuration calculation so
occupancy doesn't make much sense. Columbus just put 2's for every one of
them.
I just checked in a molden formatted file with the s, p and d orbitals for
an atom so one can see the order in which Jmol visualizes them.
The order according to the molden website
(http://www.cmbi.ru.nl/molden/molden_format.html) is 

The following order of D, F en G functions is expected:

   5D: D 0, D+1, D-1, D+2, D-2
   6D: xx, yy, zz, xy, xz, yz

   7F: F 0, F+1, F-1, F+2, F-2, F+3, F-3
  10F: xxx, yyy, zzz, xyy, xxy, xxz, xzz, yzz, yyz, xyz

   9G: G 0, G+1, G-1, G+2, G-2, G+3, G-3, G+4, G-4
  15G: xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy,
       xxyy xxzz yyzz xxyz yyxz zzxy

which, I think (not sure) is indeed what Jmol does. It really is up to the
computational package to indeed use that ordering as well :-).

Thanks,
René


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Comment By: Bob Hanson (hansonr)
Date: 2011-09-24 13:09

Message:
Rene, can you check on the order of coefficients for 5D and 7F for Molden?
Or at least confirm that various orbitals using those appear correctly.

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Comment By: Bob Hanson (hansonr)
Date: 2011-09-24 13:01

Message:
I've modified the Resolver and also enabled reading of the [5D] [7F]
records in MoldenReader. Although I think there may be a bug in Molden --
it's reporting all occupancies = 1. Why would that be? 

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