Yes. But here's what I see in the Java console:
SmarterJmolAdapter:The Resolver thinks:Cml
SmarterJmolAdapter:readAtomSetCollection
SmarterJmolAdapter:readAtomSetCollectionSax
SmarterJmolAdapter:Using JAXP/SAX XML parser.
SmarterJmolAdapter:incomplete/unrecognized unitcell
Sample data file is ci6455_i_symm.cml
I believe the implementation is pretty minimal:
1) The unit cell BOX can be displayed using
set showUnitCell true
2) fractional coordinates are not implemented yet in CmlReader.
3) your crystal structure format is not being read.
Fixing CmlReader would be a nice addition.
Rick Muller wrote:
Let me elaborate: by "not working" I mean that the unit cell and the
periodic images are not displayed.
On Apr 22, 2006, at 4:41 PM, Rick Muller wrote:
What is the status of viewing periodic systems (e.g.. systems with
unit cells) in Jmol? I thought this had been fixed before, but I'm
not finding that it works. For example, the following file doesn't
load the unit cell:
<?xml version="1.0" ?>
<cml title="crystal example">
<molecule id="Si">
<string title="COMMENT"></string>
<crystal>
<floatArray convention="PMP" title="a" >5.100 0 0</floatArray>
<floatArray convention="PMP" title="b" >0 5.100 0</floatArray>
<floatArray convention="PMP" title="c" >0 0 5.100</floatArray>
</crystal>
<atomArray>
<atom id="Si1" elementType="Si" x3="0.0" y3="0.0" z3="0.0"/>
<atom id="Si2" elementType="Si" x3="2.55" y3="2.55" z3="0.0"/>
<atom id="Si3" elementType="Si" x3="2.55" y3="0.0" z3="2.55"/>
<atom id="Si4" elementType="Si" x3="0.0" y3="2.55" z3="2.55"/>
<atom id="Si5" elementType="Si" x3="1.275" y3="1.275" z3="1.275"/>
<atom id="Si6" elementType="Si" x3="1.275" y3="3.825" z3="3.825"/>
<atom id="Si7" elementType="Si" x3="3.825" y3="1.275" z3="3.825"/>
<atom id="Si8" elementType="Si" x3="3.825" y3="3.825" z3="1.275"/>
</atomArray>
</molecule>
</cml>
I will gladly volunteer to work with the code to get this working,
if someone can bring me up to speed on what has been done and what
needs to be done.
Thanks,
Rick Muller
[EMAIL PROTECTED]
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Rick Muller
[EMAIL PROTECTED]
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
