Proposal to define data names for atomic analysis information

[Brian McMahon]

The discussion on GitHub is nice, and an appropriate location for
refining the details (e.g. distinguishing between isotopes, valence
states etc.)

As Peter M-R responded, the second alternative seems the preferable
approach as it makes explicit the specific parameters important for
each different technique. As Matthew Rowles points out in the GitHub
discussion, each individual technique may have looped parameters,
and so is going to be characterised by a distinct category.

By eye, it's "obvious" that the _atom_analytical.technique_type
value of "XRF" is intended as a pointer into the category
ATOM_ANALYTICAL_XRF that includes

_atom_analytical_XRF.mass_loss_percent    12.4

because of that shared occurrence of the string "XRF". But strictly,
category and data names have no intrinsic semantic meaning. Is there
a formal mechanism in the DDL to allow the value of a data item to be
understood as a pointer to a specific category, and if not, does
there need to be?

It's possible that there doesn't need to be, since in the full example 
as worked out on GitHub, the links between the categories are followed
through the *.id and *.meas_id codes:

loop_
_atom_analytical.atom_type
_atom_analytical.meas_id # <- point to atom_analytical_source.id
_atom_analytical.chemical_species
_atom_analytical.analytical_mass_percent
_atom_analytical.chemical_species_mass_percent
Si  a SiO2   ?     22.7
Al  a Al2O3  ?     27.4
Ti  b TiO2   ?      2.7
Si  c  .      10.5  .
Si  d Si     11.7  11.7

loop_
_atom_analytical_source.id
_atom_analytical_source.technique
a  XRF
b  XRF
c  ICP
d  EDS

loop_
_atom_analytical_XRF.meas_id # <- point to _atom_analytical_source.id
_atom_analytical_XRF.mass_loss_percent
_atom_analytical_XRF.ignition_temperature
a 12.4 1000
b 13.5 1100

Arguably the middle loop is redundant, and the use of (say) XRF is
deduced from the fact that you have ended up in a category that will
be defined as applicable only for XRF measurements; but in practice
I assume that having a synoptic overview of the different techniques
used would be welcomed by most users.

Brian

On 04/10/2022 02:43, James H via coreDMG wrote:
> Dear Core CIF dictionary maintenance group:
> 
> A proposal has been developed by some powder people to include results 
> of sample analysis for atomic content in CIF files. It seems to me that 
> this is more general than just powder, so I have transferred to proposal 
> to the CIF core dictionary issues list. Please read through 
> https://github.com/COMCIFS/cif_core/issues/304 
> <https://github.com/COMCIFS/cif_core/issues/304> and add your comments 
> there or here. For reference, the final comment on that issue, which 
> gives the flavour of the proposal, is reproduced below.
> 
> best wishes,
> James.
> =================================
> 
> Given the desire to allow general details of techniques to be included, 
> we will need one or more separate categories. One alternative is to 
> bundle all details of techniques into a general purpose category, in the 
> example below it is |ATOM_ANALYTICAL_TECHNIQUE|
> 
> Here is an example of how this would appear in the CIF file (adapted 
> from above):
> 
> |data_block1 loop_ _atom_analytical.id <http://atom_analytical.id> 
> _atom_analytical.atom_type _atom_analytical.chemical_species 
> _atom_analytical.analytical_mass_percent 
> _atom_analytical.chemical_species_mass_percent 
> _atom_analytical.technique_id #<- refers to an 
> _atom_analytical_technique.id <http://atom_analytical_technique.id> 1 Si 
> SiO2 ? 22.7 XRF 2 Al Al2O3 ? 27.4 XRF 3 Ti TiO2 ? 2.7 XRF 4 Si . 10.5 . 
> ICP 5 Si Si 11.7 11.7 EDS loop_ _atom_analytical_technique.id 
> <http://atom_analytical_technique.id> #<- this could be a run id if more 
> than one performed _atom_analytical_technique.type #XRF/ICP/EDS etc. 
> _atom_analytical_technique.special_details XRF XRF ; The loss on 
> ignition at 1000 °C was 12.4 wt% ; #... |
> 
> The other alternative, and the one most conducive to expansion in the 
> future, is to define categories for each analytical technique. These can 
> remain largely empty until others want to fill them in. So the above 
> would become:
> 
> |loop_ _atom_analytical.id <http://atom_analytical.id> 
> _atom_analytical.atom_type _atom_analytical.chemical_species 
> _atom_analytical.analytical_mass_percent 
> _atom_analytical.chemical_species_mass_percent 
> _atom_analytical.technique_type 1 Si SiO2 ? 22.7 XRF 2 Al Al2O3 ? 27.4 
> XRF 3 Ti TiO2 ? 2.7 XRF 4 Si . 10.5 . ICP 5 Si Si 11.7 11.7 EDS 
> _atom_analytical_XRF.mass_loss_percent 12.4 
> _atom_analytical_XRF.ignition_temperature 1000 |
> 
> Of these I strongly prefer the second as it ensures that the minimum 
> amount of information is hidden in machine-opaque text.
> 
> -- 
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
> 
> _______________________________________________
> coreDMG mailing list
> coreDMG at iucr.org
> http://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg