[Kalzium] [Blue-obelisk] Spectrum-Data

[peter murray-rust]

At 18:50 05/05/2006, Carsten Niehaus wrote:
>Hi
>
>I converted data from NIST.gov to a selfmade xml-format. An example for Gold
>can be found here:
>
>http://physics.nist.gov/PhysRefData/Handbook/Tables/goldtable3_a.htm
>
>This is how my xml looks like
>
>     <element>
>         <number>57</number>
>         <spectra>
>             <spectrum intensity="300" wavelength="3574.43" aki="0.0"
>energy1="0.000" energy2="27968.54" electronconfig1="5d6s2"
>electronconfig2="4f5d(3D&deg;)6s" term1="2D" term2="&deg;" J1="3/2"
>J2="3/2" />
>             <spectrum intensity="300" wavelength="4060.33" aki="0.0"
>energy1="4121.572" energy2="28743.24" electronconfig1="5d2(3F)6s"
>electronconfig2="4f5d(3G&deg;)6s" term1="4F" term2="4G&deg;" J1="9/2"
>J2="11/2" />
>     </element>
>
>Of course, this can be improved (<element number="57"> is the most 
>obvious). I
>guess CML also does have some kind of spectrum-data-xml  [1], I even found an
>example file [2], but that format is... huge. Furhtermore, not all terms from
>NIST translate into that format.
>So I guess I will stick with my selfmade xml-format until somebody converts
>that to cml-xml and adds it to BlueObelisk :)

CML does not support electronic configurations. It is clearly 
something that will need to be addressed at some stage in the future. 
I am not expert enough to address it. Note that we *are* addressing 
basis sets and that gives some idea of the effort required.

CML supports the spectrum concept and can support continuous data 
(which can be large) and peak data which can be small. I am not clear 
exactly what is being supported here;
<spectrum>
   <peak xValue="wavelength="3574.43" yValue="300" xUnits="???" 
yUnits="???".../>
   <peak xValue="wavelength="4060.33" yValue="300" xUnits="???" 
yUnits="???".../>

but it is not clear whether this is a good way to go.

General comments:
* your concepts will need documenting.
* the format does not support units well
* microformats like "4f5d(3D&deg;)6s" mean that you have to create a 
parser to manage this. It looks rather messy at present.

Is this an effort to unify the whole of atomic spectroscopy? If so I 
think it will need refactoring if you want that community to accept 
it. If not, what is the limitation of the current approach and how do 
you expect it to be used?

P.



>Carsten
>
>[1] -- http://www.ch.ic.ac.uk/omf/cml/doc/examples/spectra.html
>[2] -- http://www.ch.ic.ac.uk/omf/cml/doc/examples/nmr.cml
>
>
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069