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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