From 96f2e7a1ae231066555ba3a0a5da2f054151fe60 Mon Sep 17 00:00:00 2001 From: rowlesmr Date: Sun, 18 Jun 2023 20:35:39 +0800 Subject: [PATCH 1/7] replace PD_AMORPHOUS with PD_AMORPHOUS_PEAK --- cif_pow.dic | 232 +++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 192 insertions(+), 40 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index ef5adb0..c3718f2 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -46,91 +46,225 @@ 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). + + 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 instansiated 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 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' 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 Single - _type.contents Code + _type.container List + _type.dimension '[]' + _type.contents Text save_ -save_pd_amorphous.peak_overall_id +save_pd_amorphous_peak.id - _definition.id '_pd_amorphous.peak_overall_id' - _definition.update 2023-04-13 + _definition.id '_pd_amorphous_peak.id' + _definition.update 2023-06-18 _description.text ; - A code linking to general information about peak description and - determination for the amorphous phase peaks. + An arbitrary code to identify each peak in an amorphous phase. ; - _name.category_id pd_amorphous - _name.object_id peak_overall_id - _name.linked_item_id '_pd_peak_overall.id' - _type.purpose Link + _name.category_id pd_amorphous_peak + _name.object_id id + _type.purpose Key _type.source Assigned _type.container Single + _type.contents Word + +save_ + +save_pd_amorphous_peak.intensity + + _definition.id '_pd_amorphous_peak.intensity' + _definition.update 2023-06-18 + _description.text +; + Relative integrated area for the peak. This value must be obeyed by any + peaks used in an 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_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 + 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 Text + +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 @@ -140,6 +274,24 @@ save_pd_amorphous.phase_id save_ +save_pd_amorphous_peak.special_details + + _definition.id 'save_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. +; + _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 From 005553155cdb9f560de3d3dc588e828c9c219b85 Mon Sep 17 00:00:00 2001 From: rowlesmr Date: Sun, 18 Jun 2023 20:52:24 +0800 Subject: [PATCH 2/7] add an example --- cif_pow.dic | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/cif_pow.dic b/cif_pow.dic index c3718f2..5295fda 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -89,6 +89,28 @@ save_PD_AMORPHOUS_PEAK '_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 + _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.d_spacing From cb73dd4828790bf0da8d1b8973f6d2ac5248ad84 Mon Sep 17 00:00:00 2001 From: rowlesmr Date: Sun, 18 Jun 2023 21:02:26 +0800 Subject: [PATCH 3/7] update update dates and changes. --- cif_pow.dic | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 5295fda..02db87d 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -14,7 +14,7 @@ data_CIF_POW _dictionary.title CIF_POW _dictionary.class Instance _dictionary.version 2.5.0 - _dictionary.date 2023-06-13 + _dictionary.date 2023-06-18 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/Powder_Dictionary/master/cif_pow.dic _dictionary.ddl_conformance 3.11.10 @@ -298,7 +298,7 @@ save_ save_pd_amorphous_peak.special_details - _definition.id 'save_pd_amorphous_peak.special_details' + _definition.id '_pd_amorphous_peak.special_details' _definition.update 2023-06-18 _description.text ; @@ -12734,7 +12734,7 @@ save_ Deprecated _pd_refln.wavelength_id after consultation with PDDMG. ; - 2.5.0 2023-06-13 + 2.5.0 2023-06-18 ; ## Retain above version number and increment date until final ## release @@ -12786,8 +12786,6 @@ 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. @@ -12863,4 +12861,6 @@ save_ Converted all 'Array' and 'Matrix'-type data items to be 'List', except _pd_pref_orient_march_dollase.hkl. + + Created PD_AMORPHOUS_PEAK. ; From 46bd2aa62e12c9705471067d3e9475d675951b2c Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 23 Apr 2025 12:52:39 +0800 Subject: [PATCH 4/7] speeling Co-authored-by: Antanas Vaitkus --- cif_pow.dic | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index 72c6949..1f66df7 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -70,7 +70,7 @@ save_PD_AMORPHOUS_PEAK To maintain complete generality, amorphous peak positions are given only in terms of d spacing, and peak intensities as relative intensities. These are - then instansiated in a specific diffractogram by related data items in + 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 From 2c15e9e128be3d4ab96ce5a21dcd32ec13fbe0b4 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 23 Apr 2025 12:52:57 +0800 Subject: [PATCH 5/7] grammer Co-authored-by: Antanas Vaitkus --- cif_pow.dic | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index 1f66df7..b96f729 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -197,7 +197,7 @@ save_pd_amorphous_peak.intensity _description.text ; Relative integrated area for the peak. This value must be obeyed by any - peaks used in an diffractogram which are assigned to peaks in this phase. + 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 From b38dc016232e73ce4a41ba0ebe3c3399ee8bc870 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 23 Apr 2025 12:53:33 +0800 Subject: [PATCH 6/7] Fix type.contents Co-authored-by: Antanas Vaitkus --- cif_pow.dic | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index b96f729..63d57f9 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -274,7 +274,8 @@ save_pd_amorphous_peak.peak_overall_ids _type.source Assigned _type.container List _type.dimension '[]' - _type.contents Text + _type.contents ByReference + _type.contents_referenced_id '_pd_peak_overall.id' save_ From 363dc0997dce5e055b379b727c012c692b6b313f Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 23 Apr 2025 12:55:09 +0800 Subject: [PATCH 7/7] peak ids in this dictionary seem to be of the Code content type so maybe it would make sense to change this to Code as well --- cif_pow.dic | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index 63d57f9..2c501e8 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -186,7 +186,7 @@ save_pd_amorphous_peak.id _type.purpose Key _type.source Assigned _type.container Single - _type.contents Word + _type.contents Code save_