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COMCIFS / Powder_Dictionary

CIF definitions for powder diffraction
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how to reference other phases/diffractograms? #163

Open rowlesmr opened 1 year ago

rowlesmr commented 1 year ago

This was raised in the third dot point of @vaitkus https://github.com/COMCIFS/Powder_Dictionary/pull/161#issuecomment-1606398139

What is the correct way to define a data item that is used to point to another place which contains the information you're after?

In the example below, there is a diffractogram with _pd_diffractogram.id having the value of DIFFRACTOGRAM_0020. It was quantified by the external method using the information contained in the PD_QPA_EXTERNAL_STD category data items (ie the K factor and standard MAC) associated with the key _pd_qpa_external_std.diffractogram_id which has the value SRM676A.

I've currently indicated that by having _pd_qpa_external_std.diffractogram_id SRM676A given inside the block containing DIFFRACTOGRAM_0020. The definition of _pd_qpa_external_std.diffractogram_id is below.

save_pd_qpa_external_std.diffractogram_id

    _definition.id                '_pd_qpa_external_std.diffractogram_id'
    _definition.update            2023-01-15
    _description.text
;
    The diffractogram (see _pd_diffractogram.id) which is being used to
    calculate the diffractometer constant.
;
    _name.category_id             pd_qpa_external_std
    _name.object_id               diffractogram_id
    _name.linked_item_id          '_pd_diffractogram.id'
    _type.purpose                 Link
    _type.source                  Related
    _type.container               Single
    _type.contents                Text

save_

Is this the correct way to do it, or should there be another data item used to point? Something like

save_pd_qpa_external_std.ref_diffractogram_id

    _definition.id                '_pd_qpa_external_std.ref_diffractogram_id'
    _definition.update            2023-06-26
    _description.text
;
    The diffractogram from which the diffractometer constant was calculated.
;
    _name.category_id             pd_qpa_external_std
    _name.object_id               ref_diffractogram_id
    _type.purpose                 Encode
    _type.source                  Related
    _type.container               Single
    _type.contents                Text

save_

where it isn't linked, but does Encode a diffractometer_id in order to find all the information?

#\#CIF_2.0

####### Begin common information    #######
data_global
_diffrn_radiation_wavelength.value   1.7889847
####### End common information  #######

####### Begin powder diffraction data   #######
data_DIFFRACTOGRAM_0020
_pd_diffractogram.id    DIFFRACTOGRAM_0020

loop_
_pd_phase_mass.phase_id
_pd_phase_mass.percent
Goethite_0020   70.6(2)
Hematite_0020   8.11(17)
Quartz_0020     6.48(6)
Kaolinite_0020  1.88(18)
Nacrite_0020    1.21(12)
Anatase_0020    0.35(3)
Rutile_0020     0.44(4)
#amor 10.9(4)

_pd_qpa_external_std.diffractogram_id   SRM676A
_pd_char.mass_atten_coef_mu_calc        4.52708878
_pd_qpa_overall.method                  external_standard

loop_
    _pd_data.point_id
    _pd_meas.2theta_scan
    _pd_meas.counts_total
    _pd_calc.intensity_total
    _pd_proc.intensity_bkg_calc
1   5.007880    737 805.948339  805.681930  
#...
5713    95.008094   77  76.586601   63.972674
####### End powder diffraction data #######

####### Begin External Standard information #######
data_STD_Aluminium_oxide_alpha
_pd_phase.id    STD_Aluminium_oxide_alpha
#...

data_SRM676A
_pd_diffractogram.id    SRM676A

loop_
    _pd_phase_mass.phase_id
    _pd_phase_mass.percent
    _pd_phase_mass.percent_su
STD_Aluminium_oxide_alpha   99.02   1.11

_pd_qpa_external_std.k_factor           321.82
_pd_char.mass_atten_coef_mu_calc        4.87922752
_pd_qpa_overall.method                  external_standard
##
# _pd_qpa_external_std.diffractogram_id gets the value "SRM676A"
# solely due to the fact that _pd_diffractogram.id exists in this
# block, and has the value "SRM676A"
##

loop_
    _pd_data.point_id
    _pd_meas.2theta_scan
    _pd_meas.counts_total
    _pd_calc.intensity_total
    _pd_proc.intensity_bkg_calc
191 8.001585    66  62.572173   62.572174
#...
5713    95.008094   26  25.050297   23.441636
####### End External Standard information   #######

####### Begin powder crystal structures #######
data_Goethite_0020
_pd_phase.id    Goethite_0020
#...
data_Hematite_0020
_pd_phase.id    Hematite_0020
#...
data_Quartz_0020
_pd_phase.id    Quartz_0020
#...
data_Kaolinite_0020
_pd_phase.id    Kaolinite_0020
#...
data_Nacrite_0020
_pd_phase.id    Nacrite_0020
#...
data_Anatase_0020
_pd_phase.id    Anatase_0020
#...
data_Rutile_0020
_pd_phase.id    Rutile_0020
#...
####### End powder crystal structures   #######
jamesrhester commented 1 year ago

What is the correct way to define a data item that is used to point to another place which contains the information you're after?

The first thing to do is to not think in terms of "pointing" to a "place" that "contains" something. Instead, you are simply "identifying" something - a diffractogram, or a phase, or an instrument, etc. So your first definition (the current one) seems correct to me.

The example also seems correct to me. It is a little strange to think that _pd_qpa_external_std.diffractogram_id has the value SRM676A, but I guess it makes sense to say that it is also calibrating itself, as well as being used by other diffractograms. 

# _pd_qpa_external_std.diffractogram_id gets the value "SRM676A"
# solely due to the fact that _pd_diffractogram.id exists in this
# block, and has the value "SRM676A"
rowlesmr commented 1 year ago

It is a little strange to think that _pd_qpa_external_std.diffractogram_id has the value SRM676A

To my mind, the SRM676A diffractogram owns the calibration value, and all other places are merely borrowing it.

Now that I think about it, as you need to collect the unknown data under identical circumstances, isn't the calibration owned by the diffrn.id? And then you need a seperate (hypothetical) _pd_diffrn.spec_id to identify each specimen for each diffraction experiment?

.

I don't know if I'm breaking out of my baliwick, but I'm trying to think up how to make a collection of powder CIF blocks into a single set of database tables, rather than a separate set for each block, and so I need to be able to uniquely identify things.

jamesrhester commented 1 year ago

I think PD_DIFFRACTOGRAM just needs a pointer to _diffrn.id, and then we have identified the conditions under which a diffractogram was measured. Sort of puzzled we don't have that yet, unless there's an indirect link.

Anyway, with that in place, SRM676A has a well-defined _diffrn.id, as do all other diffractograms, and they may differ slightly. A validation routine can decide if the variance is acceptable.

Not sure about the spec_id suggestion. The DIFFRN category does have a pointer to _exptl_crystal.id, which makes the particular crystal a part of the diffraction conditions, so by analogy spec_id has a place there as well. But spec_id is already pointed to by PD_DIFFRACTOGRAM so is already taken care of, I think.