I attach a CML file for Si/diamond that *does* work with JMOL. I did lots of trial and error and have found several inconsistencies between the CML reference and what works in Jmol. I raise these issues here not to in any way diminish the excellent behavior of the Jmol application (and the CDK library!), but in the hope that I can help fix these problems.
1. The CML reference I found (http://www.xml-cml.org/dtdschema/cmlCore/HTMLDOCS/) says that <crystal> records need to have a,b,c,alpha,beta, and gamma values specified as <scalar> fields. By looking at the estron.cml file in the samples directory, which does load properly, it seems that the lattice needs to be loaded as a matrix, e.g.
<crystal>
<floatArray convention="PMP" title="a" >10.200 0 0</floatArray>
<floatArray convention="PMP" title="b" >0 10.200 0</floatArray>
<floatArray convention="PMP" title="c" >0 0 10.200</floatArray>
</crystal>
I have no idea what convention="PMP" does, but it appears to be necessary.
2. The CML reference also states that atoms may be described using xFrac="0.25" yFrac="0.25" zfrac="0.25" descriptions rather than the corresponding x3,y3,z3 specifications. I have not found that fractional coordinates work. Oddly enough, I also haven't been able to get xyz3="0.0 0.0 0.0" type modifiers of atoms to work either.
3. <bond> tags don't seem to work for crystals.
Once again, I'm grateful that an application with the ease of use and power of Jmol exists. I'd be glad to look into these bugs (I should probably join the Jmol-developers email list), but there may be already people who can track this problem down in less time.
I attach a working Si/diamond structure.
Rick Muller [EMAIL PROTECTED]
si_diamond.cml
Description: Binary data
