diff --git a/README.md b/README.md index 5da23fe..9e2e107 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/cif_ed.dic b/cif_ed.dic index 149c107..2a2167e 100644 --- a/cif_ed.dic +++ b/cif_ed.dic @@ -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 @@ -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' @@ -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' @@ -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 @@ -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). ; @@ -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 @@ -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. ; diff --git a/docs/ed.pdf b/docs/ed.pdf index 32f69a4..91daf1a 100644 Binary files a/docs/ed.pdf and b/docs/ed.pdf differ diff --git a/docs/recommendations.md b/docs/recommendations.md index 3fcdbae..0677b0b 100644 --- a/docs/recommendations.md +++ b/docs/recommendations.md @@ -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 @@ -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 @@ -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. diff --git a/draft_new_items.dic b/draft_new_items.dic index 663e0df..f00b8fb 100644 --- a/draft_new_items.dic +++ b/draft_new_items.dic @@ -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 @@ -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' @@ -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. ;