Need data name to act as the original meaning of `_pd_phase_id`

[rowlesmr]

From the end of https://github.com/COMCIFS/Powder_Dictionary/pull/39#issuecomment-1371739998

In the original pdCIF dictionary (or at least the one converted to DDLm), PD_PHASE was a Loop category, and _pd_phase_id served only to link between _pd_phase_block_id and _refln_phase_id. See also description in §3.3.6.1 in Vol. G.

We no longer have that ability to use a short, block-level identifier.

I think we make something like _pd_phase.short_id and _pd_diffractogram.short_id, which have block-scope (ie not necessarily globally unique, only locally) to link between things like _pd_refln.phase_id, _pd_pref_orient_March_Dollase.diffractogram_id, etc. so that we don't have to have huge, UUID-like values everywhere.

For example involving phase id, from the CIF1.1 version of things, you would do:

#/#CIF_1.1
data_xye_files\576460-mac-001_reb_0003.xye_0

_pd_block_id                    xye_files\576460-mac-001_reb_0003.xye_0

loop_
_pd_phase_id  # this data item acts only as a link between _pd_refln_phase_id and _pd_phase_block_id
_pd_phase_block_id
_pd_phase_mass_%
1   ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE   72.11
2   SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE 27.89

loop_
_refln_index_h
_refln_index_k
_refln_index_l
_pd_refln_phase_id
_refln_d_spacing
0    0   12 1    1.082702
1    0  -14 1    0.905365
2    2    0 2    1.920168
3    1    1 2    1.637525
#...

 loop_
_pd_meas_2theta_scan
_pd_proc_intensity_total
_pd_calc_intensity_total
_pd_proc_intensity_bkg_calc
5.001    43.364    25.994    25.991 
5.004    38.007    26.200    26.200 
5.007    38.318    26.404    26.403 
#...

With the current dictionary, you would have to do:

#/#CIF_2.0
data_xye_files\576460-mac-001_reb_0003.xye_0

_pd_diffractogram.id                    xye_files\576460-mac-001_reb_0003.xye_0

loop_
_pd_phase_mass.phase_id
_pd_phase_mass.percent
ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE   72.11
SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE 27.89

loop_
_refln.index_h
_refln.index_k
_refln.index_l
_pd_refln.phase_id
_refln.d_spacing
0    0   12 ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE       1.082702
1    0  -14 ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE       0.905365
2    2    0 SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE     1.920168
3    1    1 SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE     1.637525
#...

 loop_
_pd_meas.2theta_scan
_pd_proc.intensity_total
_pd_calc.intensity_total
_pd_proc.intensity_bkg_calc
5.001    43.364    25.994    25.991 
5.004    38.007    26.200    26.200 
5.007    38.318    26.404    26.403 
#...

which is not very pretty.

[rowlesmr]

ignore this comment - I forgot you can't loop items from different categories

Could something like this work?

• create new data item: _pd_phase_block.short_id - PD_PHASE_BLOCK is described as "A table of phases relevant to the current data block.". It is a Loop category. Its value would be a code.
• loop _pd_phase_block.short_id with _pd_phase_block.phase_id to create a reference between a short id and a full id
• redefine _pd_refln.phase_id to link with _pd_phase_block.short_id. (maybe even rename to _pd_refln.short_id, although that might be a little too far)

#/#CIF_2.0
data_xye_files\576460-mac-001_reb_0003.xye_0

_pd_diffractogram.id                    xye_files\576460-mac-001_reb_0003.xye_0

loop_
_pd_phase_block.short_id
_pd_phase_block.phase_id
_pd_phase_mass.percent
1   ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE   72.11
2   SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE 27.89

loop_
_refln.index_h
_refln.index_k
_refln.index_l
_pd_refln.phase_id
_refln.d_spacing
0    0   12 1 1.082702
1    0  -14 1 0.905365
2    2    0 2 1.920168
3    1    1 2 1.637525
#...

 loop_
_pd_meas.2theta_scan
_pd_proc.intensity_total
_pd_calc.intensity_total
_pd_proc.intensity_bkg_calc
5.001    43.364    25.994    25.991 
5.004    38.007    26.200    26.200 
5.007    38.318    26.404    26.403 
#...

[rowlesmr]

A bit more of a radical idea: revert PD_PHASE_BLOCK and PD_BLOCK_DIFFRACTOGRAM to just deal with block id values; nothing at all to do with the new phase and diffractogram_id. Create PD_PHASE_LIST and PD_DIFFRACTOGRAM_LIST to deal with cases when we need to loop phase and diffractogram ids.

Both would be Loop categories. Both would have two data items.

• PD_PHASE_LIST. Loop keyed on _pd_phase_list.id
  • _pd_phase_list.id. Acts as the Key for the category. Is an arbitrary code identifying a _pd_phase.id *.
  • _pd_phase_list.phase_id. Acts as Link back to _pd_phase.id (which should be unique in the entire world).
• PD_DIFFRACTOGRAM_LIST. Loop keyed on _pd_diffractogram_list.id
  • _pd_diffractogram_list.id. Acts as the Key for the category. Is an arbitrary code identifying a _pd_diffractogram.id *.
  • _pd_diffractogram_list.diffractogram_id. Acts as Link back to _pd_diffractogram.id (which should be unique in the entire world).

In this world, the new data item _pd_refln.phase_list_id would be linked to _pd_phase_list.id, and _pd_refln.phase_list_id would be aliased with _pd_refln_phase_id, and become a category key for REFLN, instead of _pd_refln.phase_id (which gets deprecated).

Furthermore, categories that have _categoryname.phase_id and/or _categoryname.diffractogram_id will also get _categoryname.phase_list_id and/or _categoryname.diffractogram_list_id to be able to take advantage of this.

#/#CIF_2.0
data_xye_files\576460-mac-001_reb_0003.xye_0

_pd_diffractogram.id                    xye_files\576460-mac-001_reb_0003.xye_0

loop_
_pd_phase_list.id
_pd_phase_list.phase_id
1   ALUMINA_A_BIG_LONG_STRING_THAT_IS_GLOBALLY_UNIQUE
2   SILICON_ANOTHER_STRING_THAT_IS_SUPPOSED_TO_BE_ALONE

loop_
_pd_phase_mass.phase_list_id
_pd_phase_mass.percent
1   72.11
2   27.89

loop_
_refln.index_h
_refln.index_k
_refln.index_l
_pd_refln.phase_list_id
_refln.d_spacing
0    0   12 1 1.082702
1    0  -14 1 0.905365
2    2    0 2 1.920168
3    1    1 2 1.637525
#...

 loop_
_pd_meas.2theta_scan
_pd_proc.intensity_total
_pd_calc.intensity_total
_pd_proc.intensity_bkg_calc
5.001    43.364    25.994    25.991 
5.004    38.007    26.200    26.200 
5.007    38.318    26.404    26.403 
#...

* Do these arbitrary codes need to be unique within the entire container, or just in the block?

[rowlesmr]

This has wandered a bit off course. I'll try again.

[jamesrhester]

OK, interesting ideas. Note in your initial example that if each data block contains only a single phase, then the long complicated phase id is only provided once in the file, and all other values are then obtained from that value, so I don't see long complicated names as being an issue. I think we can simply instruct the pdCIF creator to ensure that all phase_id values will be unique within the data set.

[rowlesmr]

if each data block contains only a single phase, then the long complicated phase id is only provided once in the file, and all other values are then obtained from that value

? I don't understand how this works? How can you refer to other things without their (long) key?

data_phase1
_pd_phase.id   PHASE_ONE_ID
# phase 1 information goes here

data_phase2
_pd_phase.id   PHASE_TWO_ID
# phase 2 information goes here

data_diffpat1
_pd_diffractogram.id   DIFFPATT_WITH_PHASE_1

loop_
_pd_phase_mass.phase_id  # what else goes here but a _pd_phase.id?
_pd_phase_mass.percent
PHASE_ONE_ID   72.11  # I don't know, the rest is amorphous...

# other diffractogram info goes here

data_diffpat2
_pd_diffractogram.id   DIFFPATT_WITH_PHASE_2

loop_
_pd_phase_mass.phase_id  # what else goes here but a _pd_phase.id?
_pd_phase_mass.percent
PHASE_TWO_ID   37.33  # I don't know, the rest is amorphous...

# other diffractogram info goes here

[rowlesmr]

can we take this to #74? its a better version of the description of PD_PHASE_LIST and PD_DIFFRACTOGRAM_LIST.

[jamesrhester]

? I don't understand how this works? How can you refer to other things without their (long) key?

I misspoke, I meant provided once per data block, not per file. Let us move to #74