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nautolycus merged 2 commits into from
Mar 24, 2025
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Release version 1.0.0 #15

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7fbeeef
Release version 1.0.0
nautolycus Mar 24, 2025
d171d9f
Fixed Unicode characters in cif_ed.dic and date in draft_new_items.dic
nautolycus Mar 24, 2025
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -4,12 +4,12 @@ Data names for describing electron diffraction. These are presented here as a CI

This project is best seen as an opportunity to focus on the new items required in the context of electron crystallography, and to invite content review from the user community.

The first set of data definitions incorporated into the core CIF dictionary are those in **release 1.0.0** of 18 February 2025. Any definitions in cif_ed.dic with latest revision later than that date should be considered work in progress, and should not be used in production software.
The first set of data definitions incorporated into the core CIF dictionary are those in **release 1.0.0** of 24 March 2025. Any definitions in cif_ed.dic with latest revision later than that date should be considered work in progress, and should not be used in production software.


This GitHub project contains:

* cif_ed.dic : a draft electron diffraction dictionary. This is currently set up as a new extension dictionary, but if in the end only few new data names are needed, it may be incorporated into the core dictionary.
* cif_ed.dic : a draft electron diffraction dictionary. This was initially set up as a new extension dictionary, but because relatively few new data names are needed, many of which are of general relevance to diffraction experiments, its content has been incorporated into the core dictionary.
* draft_new_items.dic: a file containing additional definitions that are more likely to be incorporated in the future in the imgCIF dictionary
* docs : a folder containing supporting documentation.
* docs/ed.pdf : a PDF typeset representation of the draft dictionary to facilitate review by people unfamiliar with DDL formalism.
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67 changes: 8 additions & 59 deletions cif_ed.dic
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Expand Up @@ -12,8 +12,8 @@ data_CIF_ED

_dictionary.title CIF_ED
_dictionary.class Instance
_dictionary.version 1.0.1-dev
_dictionary.date 2025-02-19
_dictionary.version 1.0.0
_dictionary.date 2025-03-24
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/cif_ed/main/cif_ed.dic
_dictionary.ddl_conformance 4.2.0
Expand Down Expand Up @@ -142,30 +142,6 @@ save_computing.sample_tracking

save_

save_diffrn_detector.distance_sample

_definition.id '_diffrn_detector.distance_sample'
_definition.update 2024-07-26
_description.text
;
Mean distance in millimetres from the diffracting sample
to the detector. Appropriate for instrument geometries where
the detector is fixed or maintained at a constant distance
from the diffraction target. More general geometries and
provision for adjusting the instrument geometries between or
during scans are handled by the imgCIF dictionary.
;
_name.category_id diffrn_detector
_name.object_id distance_sample
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code millimetres

save_

save_diffrn.precession_semi_angle

_definition.id '_diffrn.precession_semi_angle'
Expand Down Expand Up @@ -205,26 +181,6 @@ save_diffrn.precession_semi_angle_su

save_

save_diffrn_detector.ed_calibration_constant

_definition.id '_diffrn_detector.ed_calibration_constant'
_definition.update 2024-07-15
_description.text
;
The electron diffraction camera constant calibration factor.
Ref: Millette, J. (1987). The Microscope, 35, 107-117.
;
_name.category_id diffrn_detector
_name.object_id ed_calibration_constant
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms_per_pixel

save_

save_diffrn_measurement.method_precession

_definition.id '_diffrn_measurement.method_precession'
Expand Down Expand Up @@ -361,8 +317,8 @@ save_diffrn_source.convergence_angle
;
The angle of convergence of the source beam (for example in
convergent-beam electron diffraction). The convergence angle
is the angular spread of the cone of illumination (i.e. 2\a,
where the semi-angle \a is measured from the axis defining the
is the angular spread of the cone of illumination (i.e. 2α,
where the semi-angle α is measured from the axis defining the
beam direction).
;
_name.category_id diffrn_source
Expand Down Expand Up @@ -777,12 +733,12 @@ save_refine_ls.sample_shape_expression
_type.contents Text
_description_example.case
;
F(\t) = 1 - ( 1 - \t^2^)^1/2^
F(𝜏) = 1 - ( 1 - 𝜏^2^)^1/2^
;
_description_example.detail
;
The cumulative distribution function in terms of the reduced thickness \t
of a sample treated as a cylinder. \t = t/t~m~, where t is the thickness
The cumulative distribution function in terms of the reduced thickness 𝜏
of a sample treated as a cylinder. 𝜏 = t/t~m~, where t is the thickness
at the point illuminated and t~m~ the maximum thickness of the cylinder
(i.e. its diameter).
;
Expand Down Expand Up @@ -844,7 +800,7 @@ save_
Initial draft of new or revised (from coreCIF) data definitions
following nanED round robin project. (B. McMahon)
;
1.0.0 2025-02-18
1.0.0 2025-03-24
;
Initial release version of this dictionary cif_ed.dic for electron
diffraction, developed by the NanED standards committee and with
Expand All @@ -856,11 +812,4 @@ save_
core CIF or other relevant COMCIFS-managed CIF dictionaries. Some
of the definitions in this dictionary may be copies of core
definitions with extended attributes.
;
1.0.1-dev 2025-02-19
;
# Please update the date above and describe the change below until
# ready for the next release

Initialised new development version.
;
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7 changes: 1 addition & 6 deletions docs/recommendations.md
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@@ -1,6 +1,6 @@
# Recommendations for reporting structures determined by 3D electron diffraction

### _Early draft for discussion_
### _Draft suggesting recommendations that might be added to Notes for Authors_

## Description of the experiment and crystal

Expand Down Expand Up @@ -104,7 +104,6 @@ _exptl_crystal.mosaic_method 'From rocking curve, width 0.00070'

(_b_)
```
_diffrn_detector.ed_calibration_constant 0.008259
_diffrn_source.convergence_angle 0.000
_diffrn_source.ed_diffracting_area_selection probe
_refine_ls.sample_thickness 0.014
Expand All @@ -116,10 +115,6 @@ _refine_ls.sample_shape_expression 'F(\t) = 1 - ( 1 - \t^2^)^1/2^'

The mosaicity (in degrees) and method of determination may be supplied. If known, the average mosaic block size in ångström units may also be given using `_exptl_crystal.mosaic_block_size`.

### `_diffrn_detector.ed_calibration_constant`

The calibration factor for the electron diffraction camera constant.

### `_diffrn_source.convergence_angle`
The angle of convergence of the beam may be given in degrees. Typically found in convergent-beam electron diffraction. Not necessary for parallel beams, though the given example describes a parallel beam with a quoted standard uncertainty.

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64 changes: 62 additions & 2 deletions draft_new_items.dic
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Expand Up @@ -9,7 +9,7 @@ data_DRAFT_NEW_ITEMS
_dictionary.title DRAFT_NEW_ITEMS
_dictionary.class Instance
_dictionary.version 0.0.10
_dictionary.date 2025-02-18
_dictionary.date 2025-03-24
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/cif_ed/1.0.0/draft_new_items.dic
_dictionary.ddl_conformance 4.2.0
Expand Down Expand Up @@ -52,6 +52,61 @@ save_DRAFT_NEW_ITEMS_HEAD

save_

save_diffrn_detector.distance_sample

_definition.id '_diffrn_detector.distance_sample'
_definition.update 2025-03-24
_description.text
;
THIS DEFINITION WAS ORIGINALLY SUGGESTED FOR cif_ed.dic BUT TRANSFERRED
HERE AS A PLACEHOLDER FOLLOWING QUERY FROM JAMES HESTER FOR CLARIFICATION
(https://github.com/COMCIFS/cif_core/pull/514). CURRENTLY RETAINED AS A
REMINDER BUT A BETTER TREATMENT OF INSTRUMENT GEOMETRY MAY BE PREFERRED.
IN ED THIS MAY BE AN 'EFFECTIVE' DISTANCE CONTROLLED BY MICROSCOPE OPTICS.

Mean distance in millimetres from the diffracting sample
to the detector. Appropriate for instrument geometries where
the detector is fixed or maintained at a constant distance
from the diffraction target. More general geometries and
provision for adjusting the instrument geometries between or
during scans are handled by the imgCIF dictionary.
;
_name.category_id diffrn_detector
_name.object_id distance_sample
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code millimetres

save_

save_diffrn_detector.ed_calibration_constant

_definition.id '_diffrn_detector.ed_calibration_constant'
_definition.update 2025-03-24
_description.text
;
THIS DEFINITION WAS ORIGINALLY SUGGESTED FOR cif_ed.dic BUT TRANSFERRED
HERE AS A PLACEHOLDER ALONGSIDE _diffrn_detector.distance_sample UNTIL
A BETTER REFERENCE IS FOUND OR MORE SPECIFIC INFORMATION IS GIVEN ABOUT
HOW THE INSTRUMENT IS CALIBRATED AND WHAT ITS EFFECT IS.

The electron diffraction camera constant calibration factor.
Ref: Millette, J. (1987). The Microscope, 35, 107-117.
;
_name.category_id diffrn_detector
_name.object_id ed_calibration_constant
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms_per_pixel

save_

save_diffrn_scan_frame.precession_angle

_definition.id '_diffrn_scan_frame.precession_angle'
Expand Down Expand Up @@ -134,7 +189,12 @@ save_
_dictionary_audit.date
_dictionary_audit.revision

0.0.10 2025-02-18
0.0.10 2025-03-24
;
Initial draft dictionary.

Includes candidate items for cif_ed.dic that were thought better
handled in a cif_img.dic context or else elaborated with more
precise definitions and indications where relevant only to
electron diffraction.
;
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