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Replace PD_AMORPHOUS with PD_AMORPHOUS_PEAK #158

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Replace PD_AMORPHOUS with PD_AMORPHOUS_PEAK #158

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96f2e7a
replace PD_AMORPHOUS with PD_AMORPHOUS_PEAK
rowlesmr Jun 18, 2023
0055531
add an example
rowlesmr Jun 18, 2023
cb73dd4
update update dates and changes.
rowlesmr Jun 18, 2023
ac3a21f
Merge branch 'master' into AMORPHOUS_PEAK
rowlesmr Jun 25, 2023
46bd2aa
speeling
rowlesmr Apr 23, 2025
2c15e9e
grammer
rowlesmr Apr 23, 2025
b38dc01
Fix type.contents
rowlesmr Apr 23, 2025
363dc09
peak ids in this dictionary seem to be of the Code content type so ma…
rowlesmr Apr 23, 2025
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257 changes: 216 additions & 41 deletions cif_pow.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -46,91 +46,248 @@ save_PD_GROUP

save_

save_PD_AMORPHOUS
save_PD_AMORPHOUS_PEAK

_definition.id PD_AMORPHOUS
_definition.id PD_AMORPHOUS_PEAK
_definition.scope Category
_definition.class Loop
_definition.update 2023-01-08
_definition.update 2023-06-18
_description.text
;
This section contains information about peaks in an amorphous phase
This category contains information about peaks in an amorphous phase
extracted from the measured or, if present, the processed diffractogram.
Each peak in this table will have a unique label
(see _pd_amorphous.peak_id).
Each peak in will have a unique label (see _pd_amorphous.id).
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@vaitkus vaitkus Jul 10, 2025 •
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Is there a word missing after "in". Also, the _pd_amorphous.id does not seem to be defined anywhere.


In the context of this category, an "amorphous" phase is a phase which does
not have atomic coordinates. An amorphous phase may consist solely of peaks.
Additionally, it could have one or more unit cell parameters, it could have
a space group, it could have a unit cell mass. One or more of the peaks
could be associated with an indexed reflection.

See PD_PEAK for details on the specific peak parameters that may be
recorded. Each amorphous peak may or may not be associated with an indexed
reflection, and as such, an "amorphous" phase could represent a material
with an unknown crystal structure. Amorphous peaks do not correspond to
background, and should not be used as such.
recorded. Amorphous peaks do not correspond to background, and should not
be used as such. For such an application, see PD_BACKGROUND.

To maintain complete generality, amorphous peak positions are given only in
terms of d spacing, and peak intensities as relative intensities. These are
then instantiated in a specific diffractogram by related data items in
PD_PEAK.

The intensities given in this category must only be correct relative to each
other. In the most correct case, the intensities will represent structure
factor amplitudes, but this is not necessary
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Suggested change
factor amplitudes, but this is not necessary
factor amplitudes, but this is not necessary.


Note that peak positions are customarily determined from the processed
diffractogram, and thus corrections for position and intensity will have
been previously applied.
;
_name.category_id PD_GROUP
_name.object_id PD_AMORPHOUS
_name.object_id PD_AMORPHOUS_PEAK

loop_
_category_key.name
'_pd_amorphous.peak_id'
'_pd_amorphous.phase_id'
'_pd_amorphous_peak.id'
'_pd_amorphous_peak.phase_id'

_description_example.case
;
_pd_phase.id AMOR_PHASE

loop_
_pd_amorphous_peak.id
_pd_amorphous_peak.d_spacing
_pd_amorphous_peak.rel_intensity
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This data name does not seem to be defined.

_pd_amorphous_peak.peak_ids
_pd_amorphous_peak.diffractogram_ids
i 4.413 0.642 [ 1 a ] [ DIFFRACTOGRAM_A DIFFRACTOGRAM_B ]
ii 2.792 0.648 [ 2 b ] [ DIFFRACTOGRAM_A DIFFRACTOGRAM_B ]
iii 2.467 1 [ 3 c ] [ DIFFRACTOGRAM_A DIFFRACTOGRAM_B ]
;
_description_example.detail
;
This amorphous phase consists of three peaks. This phase has been used
in two diffractograms, DIFFRACTOGRAM_A and DIFFRACTOGRAM_B. To find the
exact peak position, width and intensity details, you must find the
peaks indexed with the given peak id and diffractogram id combinations.
;

save_

save_pd_amorphous.peak_id
save_pd_amorphous_peak.d_spacing

_definition.id '_pd_amorphous.peak_id'
_definition.update 2023-01-08
_definition.id '_pd_amorphous_peak.d_spacing'
_definition.update 2023-06-18
_description.text
;
An arbitrary code is assigned to each peak in an amorphous phase.
Peak position as a d-spacing in angstroms.
;
_name.category_id pd_amorphous_peak
_name.object_id d_spacing
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms

Used to link with _pd_peak.id. Each peak will have a unique code. In cases
where two peaks are severely overlapped, it may be desirable to list them as
a single peak.
save_

A peak ID must be included for every amorphous peak.
save_pd_amorphous_peak.d_spacing_su

_definition.id '_pd_amorphous_peak.d_spacing_su'
_definition.update 2023-06-18
_description.text
;
_name.category_id pd_amorphous
_name.object_id peak_id
_name.linked_item_id '_pd_peak.id'
_type.purpose Link
Standard uncertainty of _pd_amorphous_peak.d_spacing.
;
_name.category_id pd_amorphous_peak
_name.object_id d_spacing_su
_name.linked_item_id '_pd_amorphous_peak.d_spacing'
_units.code angstroms

_import.get [{'file':templ_attr.cif 'save':general_su}]

save_

save_pd_amorphous_peak.diffractogram_ids

_definition.id '_pd_amorphous_peak.diffractogram_ids'
_definition.update 2023-06-18
_description.text
;
List of diffractogram id values (_pd_diffractogram.id) associated with this
amorphous peak.

Must be give in the same order as _pd_amorphous_peak.peak_ids.
That is, the n^th^ value in _pd_amorphous_peak.peak_ids and the n^th^ value
in _pd_amorphous_peak.diffractogram_ids must correctly identify the peak
associated with this amorphous peak.
;
_name.category_id pd_amorphous_peak
_name.object_id diffractogram_ids
_type.purpose Encode
_type.source Assigned
_type.container List
_type.dimension '[]'
_type.contents Text

save_

save_pd_amorphous_peak.id

_definition.id '_pd_amorphous_peak.id'
_definition.update 2023-06-18
_description.text
;
An arbitrary code to identify each peak in an amorphous phase.
;
_name.category_id pd_amorphous_peak
_name.object_id id
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Code

save_

save_pd_amorphous.peak_overall_id
save_pd_amorphous_peak.intensity

_definition.id '_pd_amorphous.peak_overall_id'
_definition.update 2023-04-13
_definition.id '_pd_amorphous_peak.intensity'
_definition.update 2023-06-18
_description.text
;
A code linking to general information about peak description and
determination for the amorphous phase peaks.
Relative integrated area for the peak. This value must be obeyed by any
peaks used in a diffractogram which are assigned to peaks in this phase.

This value, when properly calibrated, will represent a structure factor
amplitude, but this is not necessary. It is necessary that the value given
here must be such that it must be scaled by Lorentz-Polarisation, and other
such scaling factors, in order to be applied to a diffractogram.

It is good practice to include SUs for these values.
;
_name.category_id pd_amorphous
_name.object_id peak_overall_id
_name.linked_item_id '_pd_peak_overall.id'
_type.purpose Link
_type.source Assigned
_name.category_id pd_amorphous_peak
_name.object_id intensity
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none

save_

save_pd_amorphous_peak.intensity_su

_definition.id '_pd_amorphous_peak.intensity_su'
_definition.update 2023-06-18
_description.text
;
Standard uncertainty of _pd_amorphous_peak.intensity.
;
_name.category_id pd_amorphous_peak
_name.object_id intensity_su
_name.linked_item_id '_pd_amorphous_peak.intensity'
_units.code none

_import.get [{'file':templ_attr.cif 'save':general_su}]

save_

save_pd_amorphous_peak.peak_ids

_definition.id '_pd_amorphous_peak.peak_ids'
_definition.update 2023-06-18
_description.text
;
List of peak id values (_pd_peak.id) associated with this amorphous peak.

Must be give in the same order as _pd_amorphous_peak.diffractogram_ids.
That is, the n^th^ value in _pd_amorphous_peak.peak_ids and the n^th^ value
in _pd_amorphous_peak.diffractogram_ids must correctly identify the peak
associated with this amorphous peak.
;
_name.category_id pd_amorphous_peak
_name.object_id peak_ids
_type.purpose Encode
_type.source Assigned
_type.container List
_type.dimension '[]'
_type.contents Code

save_

save_pd_amorphous.phase_id
save_pd_amorphous_peak.peak_overall_ids

_definition.id '_pd_amorphous.phase_id'
_definition.update 2023-01-08
_definition.id '_pd_amorphous_peak.peak_overall_ids'
_definition.update 2023-06-18
_description.text
;
List of peak_overall id values (_pd_peak_overall.id) associated with this
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Suggested change
List of peak_overall id values (_pd_peak_overall.id) associated with this
List of PD_PEAK_OVERALL id values (_pd_peak_overall.id) associated with this

amorphous peak.

Must be give in the same order as _pd_amorphous_peak.peak_ids.
;
_name.category_id pd_amorphous_peak
_name.object_id peak_overall_ids
_type.purpose Encode
_type.source Assigned
_type.container List
_type.dimension '[]'
_type.contents ByReference
_type.contents_referenced_id '_pd_peak_overall.id'

save_

save_pd_amorphous_peak.phase_id

_definition.id '_pd_amorphous_peak.phase_id'
_definition.update 2023-06-18
_description.text
;
The phase (see _pd_phase.id) to which the amorphous peak relates.
;
_name.category_id pd_amorphous
_name.category_id pd_amorphous_peak
_name.object_id phase_id
_name.linked_item_id '_pd_phase.id'
_type.purpose Link
Expand All @@ -140,6 +297,24 @@ save_pd_amorphous.phase_id

save_

save_pd_amorphous_peak.special_details

_definition.id '_pd_amorphous_peak.special_details'
_definition.update 2023-06-18
_description.text
;
Description of amorphous peak details that cannot otherwise be recorded
using other PD_AMORPHOUS data items.
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Suggested change
using other PD_AMORPHOUS data items.
using other PD_AMORPHOUS_PEAK data items.

;
_name.category_id pd_amorphous_peak
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text

save_

save_PD_BACKGROUND

_definition.id PD_BACKGROUND
Expand Down Expand Up @@ -12615,8 +12790,6 @@ save_
Update definitions of _pd_phase.name, _pd_qpa_ext_std.phase_name, and
_pd_qpa_int_std.phase_name to better represent their contents.

Created PD_AMORPHOUS.

Deprecate _pd_calib.std_internal_mass_percent and
_pd_calib.std_internal_mass_percent_su.

Expand Down Expand Up @@ -12693,6 +12866,8 @@ save_
Converted all 'Array' and 'Matrix'-type data items to be 'List', except
_pd_pref_orient_march_dollase.hkl.

Created PD_AMORPHOUS_PEAK.

Change units of _pd_calib_incident_intensity.incident_* to
counts_per_second and per_second.

Expand Down