Martin, one problem is that we don't seem to have any Molden sample files.
Could you please send me a variety of those that we can put on the site and
use for testing? The one below is a good start. I have a feeling the Molden
reader was never tested. It's really very very basic. Let's get it upgraded
if you are interested in using it.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip for the
initial fix.
Thanks,
Bob
On Tue, Feb 15, 2011 at 3:27 AM, Martin Kleinschmidt <
[email protected]> wrote:
> Hi,
>
> I think the molden.input interface is broken:
> When I load a molden.input file, the element types are all set to "Xx".
> The element symbol is assigned to the name of the atom correctly, but
> not to the element symbol.
>
> I had a workaround I could use: in jmol version 12.0.12 I have always
> done
>
> {atomName==h}.elemno=1
> {atomName==c}.elemno=6
> {atomName==n}.elemno=7
> {atomName==o}.elemno=8
> connect
>
> as the first commands, which correctly sets the element symbol from the
> name. But this workaroud does not work in 12.0.31 any longer (just
> nothing happens).
>
> oh - just found version 12.0.32 and this bug has been fixed already -
> your release cycle is really fast!
>
> I think the molden.input bug is a missing line in
> org/jmol/adapter/readers/quantum/MoldenReader.java:
>
> diff MoldenReader.java MoldenReader.java_2
> 78a79
> > atom.elementNumber = parseInt(tokens[2]);
>
>
> martin
>
> an example molden.input (just save as "molden.input" and load with
> "jmol.sh molden.input"):
>
> [Molden Format]
> [Atoms] AU
> c 1 6 0.00000000000000E+00 0.00000000000000E+00
> 0.00000000000000E+00
> c 2 6 0.26328251500000E+01 0.00000000000000E+00
> 0.00000000000000E+00
> c 3 6 0.39772391200000E+01 0.22811105800000E+01
> 0.00000000000000E+00
> c 4 6 0.26519736800000E+01 0.45664361600000E+01
> 0.00000000000000E+00
> c 5 6 0.14745780000000E-01 0.45672472200000E+01
> 0.00000000000000E+00
> c 6 6 -.13741491700000E+01 0.22901382700000E+01
> 0.00000000000000E+00
> c 7 6 -.41370281300000E+01 0.24102387600000E+01
> 0.00000000000000E+00
> c 8 6 -.57980578900000E+01 0.45340113000000E+00
> 0.00000000000000E+00
> c 9 6 -.85027705000000E+01 0.76075586000000E+00
> 0.00000000000000E+00
> c 10 6 -.10196831650000E+02 -.11774133800000E+01
> 0.00000000000000E+00
> c 11 6 -.12900696060000E+02 -.86303080000000E+00
> 0.00000000000000E+00
> c 12 6 -.14571246840000E+02 -.28115301000000E+01
> 0.00000000000000E+00
> c 13 6 -.17333660500000E+02 -.26726812700000E+01
> 0.00000000000000E+00
> c 14 6 -.18740348020000E+02 -.49389005200000E+01
> 0.00000000000000E+00
> c 15 6 -.21377539240000E+02 -.49160299400000E+01
> 0.00000000000000E+00
> c 16 6 -.22684232800000E+02 -.26200968300000E+01
> 0.00000000000000E+00
> c 17 6 -.21322141770000E+02 -.34933793000000E+00
> 0.00000000000000E+00
> c 18 6 -.18689594250000E+02 -.37210918000000E+00
> 0.00000000000000E+00
> h 19 1 -.10051886900000E+01 -.18035060800000E+01
> 0.00000000000000E+00
> h 20 1 0.36532777600000E+01 -.17972248600000E+01
> 0.00000000000000E+00
> h 21 1 0.60429937300000E+01 0.22719550500000E+01
> 0.00000000000000E+00
> h 22 1 0.36783039200000E+01 0.63599709300000E+01
> 0.00000000000000E+00
> h 23 1 -.10092967500000E+01 0.63634849400000E+01
> 0.00000000000000E+00
> h 24 1 -.49257092200000E+01 0.43275567500000E+01
> 0.00000000000000E+00
> h 25 1 -.50934513000000E+01 -.14952112900000E+01
> 0.00000000000000E+00
> h 26 1 -.92238891900000E+01 0.27060380500000E+01
> 0.00000000000000E+00
> h 27 1 -.94775235800000E+01 -.31232437200000E+01
> 0.00000000000000E+00
> h 28 1 -.13598215560000E+02 0.10880548600000E+01
> 0.00000000000000E+00
> h 29 1 -.13793650630000E+02 -.47333728800000E+01
> 0.00000000000000E+00
> h 30 1 -.17731902770000E+02 -.67439111500000E+01
> 0.00000000000000E+00
> h 31 1 -.22418985300000E+02 -.67008250700000E+01
> 0.00000000000000E+00
> h 32 1 -.24749834960000E+02 -.25940339500000E+01
> 0.00000000000000E+00
> h 33 1 -.22328960290000E+02 0.14555422200000E+01
> 0.00000000000000E+00
> h 34 1 -.17670679770000E+02 0.14236591300000E+01
> 0.00000000000000E+00
>
>
>
> ------------------------------------------------------------------------------
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Northfield, MN 55057
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------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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