From 3b0d6e8e7b693bcaf9a83cdb98813a0552de671d Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 5 Jul 2023 11:19:14 +0800 Subject: [PATCH 1/4] Alter CELL-related saveframes from Recorded to Derived (#441) Co-authored-by: James Hester --- cif_core.dic | 4 ++-- templ_attr.cif | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/cif_core.dic b/cif_core.dic index 878fbd3..b03acd3 100644 --- a/cif_core.dic +++ b/cif_core.dic @@ -10,7 +10,7 @@ data_CORE_DIC _dictionary.title CORE_DIC _dictionary.class Instance _dictionary.version 3.3.0 - _dictionary.date 2023-06-25 + _dictionary.date 2023-07-01 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic _dictionary.ddl_conformance 4.2.0 @@ -27542,7 +27542,7 @@ save_ Changed the purpose of the _diffrn_radiation_wavelength.id data item from 'Encode' to 'Key'. ; - 3.3.0 2023-06-25 + 3.3.0 2023-07-01 ; # Please update the date above and describe the change below until # ready for the next release diff --git a/templ_attr.cif b/templ_attr.cif index 0c88435..a2ce70e 100644 --- a/templ_attr.cif +++ b/templ_attr.cif @@ -218,13 +218,13 @@ save_index_limit_min save_cell_angle - _definition.update 2014-06-08 + _definition.update 2023-07-01 _description.text ; The angle between the bounding cell axes. ; _type.purpose Measurand - _type.source Recorded + _type.source Derived _type.container Single _type.contents Real _enumeration.range 0.0:180.0 @@ -240,7 +240,7 @@ save_cell_angle_su Standard uncertainty of the angle between the bounding cell axes. ; _type.purpose SU - _type.source Recorded + _type.source Related _type.container Single _type.contents Real _units.code degrees @@ -249,13 +249,13 @@ save_cell_angle_su save_cell_length - _definition.update 2014-06-08 + _definition.update 2023-07-01 _description.text ; The length of each cell axis. ; _type.purpose Measurand - _type.source Recorded + _type.source Derived _type.container Single _type.contents Real _enumeration.range 1.0: @@ -271,7 +271,7 @@ save_cell_length_su Standard uncertainty of the length of each cell axis. ; _type.purpose SU - _type.source Recorded + _type.source Related _type.container Single _type.contents Real _units.code angstroms From 81cd1d4b7e886485609d7ff34a98ec575fab607d Mon Sep 17 00:00:00 2001 From: vaitkus Date: Wed, 5 Jul 2023 15:12:45 +0300 Subject: [PATCH 2/4] Change parent category from ATOM_ANALYTICAL to ATOM. --- cif_core.dic | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cif_core.dic b/cif_core.dic index b03acd3..a5330d9 100644 --- a/cif_core.dic +++ b/cif_core.dic @@ -20115,7 +20115,7 @@ save_ATOM_ANALYTICAL_MASS_LOSS the purposes of determining elemental composition information for use in crystallographic structure studies. ; - _name.category_id ATOM_ANALYTICAL + _name.category_id ATOM _name.object_id ATOM_ANALYTICAL_MASS_LOSS _category_key.name '_atom_analytical_mass_loss.id' _description_example.case @@ -20311,7 +20311,7 @@ save_ATOM_ANALYTICAL_SOURCE of elemental composition information used in crystallographic structure studies. ; - _name.category_id ATOM_ANALYTICAL + _name.category_id ATOM _name.object_id ATOM_ANALYTICAL_SOURCE _category_key.name '_atom_analytical_source.id' _description_example.case From a8b8cb04e1bb231b0b4d054e7f300ec9937d581a Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Thu, 6 Jul 2023 10:33:07 +0800 Subject: [PATCH 3/4] Create `ATOM_SCAT_VERSUS_STOL` category (#371) * revert _atom_type_scat.versus_stol_list to DDL1-type definition * add `ATOM_SCAT_VERSUS_STOL` * Express stol in definitions using proper unicode symbols. * Change parent category from ATOM_TYPE to ATOM. * Deprecate the _atom_type_scat.versus_stol_list data item. --------- Co-authored-by: Antanas Vaitkus --- cif_core.dic | 162 +++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 150 insertions(+), 12 deletions(-) diff --git a/cif_core.dic b/cif_core.dic index a5330d9..61d4982 100644 --- a/cif_core.dic +++ b/cif_core.dic @@ -10,7 +10,7 @@ data_CORE_DIC _dictionary.title CORE_DIC _dictionary.class Instance _dictionary.version 3.3.0 - _dictionary.date 2023-07-01 + _dictionary.date 2023-07-05 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic _dictionary.ddl_conformance 4.2.0 @@ -20438,6 +20438,129 @@ save_atom_analytical_source.technique save_ +save_ATOM_SCAT_VERSUS_STOL + + _definition.id ATOM_SCAT_VERSUS_STOL + _definition.scope Category + _definition.class Loop + _definition.update 2023-07-05 + _description.text +; + The CATEGORY of data items used to list atomic scattering factor values for + use in crystallographic structure studies. +; + _name.category_id ATOM + _name.object_id ATOM_SCAT_VERSUS_STOL + + loop_ + _category_key.name + '_atom_scat_versus_stol.atom_type' + '_atom_scat_versus_stol.stol_value' + + _description_example.case +; + loop_ + _atom_scat_versus_stol.atom_type + _atom_scat_versus_stol.stol_value + _atom_scat_versus_stol.scat_value + Ac 0.00 89.00000 + Ac 0.01 88.91457 + Ac 0.02 88.66288 + #... + Ac 4.00 8.24987 + Ac 5.00 5.98858 + Ac 6.00 4.90623 + O 0.00 8.00000 + O 0.01 7.99171 + O 0.02 7.96693 + #... + O 4.00 0.13431 + O 5.00 0.06740 + O 6.00 0.03670 +; + _description_example.detail +; + A listing of the scattering factors for Ac and O in the range + (0, 6.00) reciprocal angstroms. +; +save_ + +save_atom_scat_versus_stol.atom_type + + _definition.id '_atom_scat_versus_stol.atom_type' + _definition.update 2023-07-05 + _description.text +; + The identity of the atom specie(s) representing this atom type. + See _atom_type.symbol for further details. +; + _name.category_id atom_scat_versus_stol + _name.object_id atom_type + _name.linked_item_id '_atom_type.symbol' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Word + +save_ + +save_atom_scat_versus_stol.scat_value + + _definition.id '_atom_scat_versus_stol.scat_value' + _definition.update 2023-07-05 + _description.text +; + The value of the scattering factor of a particular atom type at a particular + stol value. +; + _name.category_id atom_scat_versus_stol + _name.object_id scat_value + _type.purpose Measurand + _type.source Assigned + _type.container Single + _type.contents Real + _units.code electrons + +save_ + +save_atom_scat_versus_stol.scat_value_su + + _definition.id '_atom_scat_versus_stol.scat_value_su' + _definition.update 2023-07-05 + _description.text +; + Standard uncertainty of _atom_scat_versus_stol.scat_value. +; + _name.category_id atom_scat_versus_stol + _name.object_id scat_value_su + _name.linked_item_id '_atom_scat_versus_stol.scat_value' + _units.code electrons + + _import.get [{'file':templ_attr.cif 'save':general_su}] + +save_ + +save_atom_scat_versus_stol.stol_value + + _definition.id '_atom_scat_versus_stol.stol_value' + _definition.update 2023-07-05 + _description.text +; + The value of sin(θ)/λ (sin theta over lambda, stol) to which the + accompanying atom symbol and scattering factor value correspond to. + + A regularly spaced grid is strongly recommended. +; + _name.category_id atom_scat_versus_stol + _name.object_id stol_value + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _units.code reciprocal_angstroms + +save_ + save_ATOM_SITE _definition.id ATOM_SITE @@ -25100,26 +25223,34 @@ save_atom_type_scat.versus_stol_list _definition.id '_atom_type_scat.versus_stol_list' + loop_ + _definition_replaced.id + _definition_replaced.by + 1 '_atom_scat_versus_stol.atom_type' + 2 '_atom_scat_versus_stol.stol_value' + 3 '_atom_scat_versus_stol.scat_value' + loop_ _alias.definition_id '_atom_type_scat_versus_stol_list' '_atom_type.scat_versus_stol_list' - _definition.update 2013-04-17 + _definition.update 2023-07-05 _description.text ; - List of scattering factors as a function of sin(θ)/λ. - List has the form [[ ] [ ] ....] in increments of 0.01, increasing from 0.0. + Deprecated. Data items from the ATOM_SCAT_VERSUS_STOL category should be + used instead of this item. + + A table of scattering factors as a function of sin(θ)/λ (sin theta over + lambda, stol). This table should be well-commented to indicate the items + present. Regularly formatted lists are strongly recommended. ; _name.category_id atom_type_scat _name.object_id versus_stol_list - _type.purpose Number - _type.source Assigned - _type.container Array - _type.dimension '[]' - _type.contents Real - _units.code none + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text save_ @@ -27542,7 +27673,7 @@ save_ Changed the purpose of the _diffrn_radiation_wavelength.id data item from 'Encode' to 'Key'. ; - 3.3.0 2023-07-01 + 3.3.0 2023-07-05 ; # Please update the date above and describe the change below until # ready for the next release @@ -27577,4 +27708,11 @@ save_ Redefined _exptl_absorpt.coefficient_mu as a derived measurand item. Added the _exptl_absorpt.coefficient_mu_su data item. + + Reverted _atom_type_scat.versus_stol_list to a text-type to regain + compatibility with DDL1 dictionary. + + Added ATOM_SCAT_VERSUS_STOL to allow for the explicit listing of + scattering factor values with respect to sin theta over lambda. + Deprecated the _atom_type_scat.versus_stol_list data item. ; From eb0726f0f8ac0bb09e3513269b7fdf6df5dec867 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Thu, 6 Jul 2023 17:11:04 +0800 Subject: [PATCH 4/4] adding beta ADPS (#356) * removed save_aniso_betaIJ2 * added "betaani" option to _atom_site.adp_type * Augment _atom_site_aniso.matrix_beta dREL with _atom_site.tensor_beta * make _atom_site.tensor_beta an alias of _atom_site_aniso.matrix_beta I've also altered dREL that calls _atom_site.tensor_beta. * Declare _atom_site.tensor_beta_{su} as an alias of _atom_site_aniso.matrix_beta_{su}. * Enhance description of _atom_site_aniso.matrix_beta Co-authored-by: Antanas Vaitkus Co-authored-by: James Hester --- cif_core.dic | 345 +++++++++++++++++++++++++++++++++++++------------ templ_attr.cif | 105 ++++++++++----- 2 files changed, 338 insertions(+), 112 deletions(-) diff --git a/cif_core.dic b/cif_core.dic index 61d4982..3c86fb4 100644 --- a/cif_core.dic +++ b/cif_core.dic @@ -6230,7 +6230,7 @@ save_refln.f_complex Loop s as space_group_symop { - t = Exp(-h * s.R * a.tensor_beta * s.RT * h) + t = Exp(-h * s.R * a.matrix_beta * s.RT * h) fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T))) } } @@ -14167,7 +14167,7 @@ save_model_site.adp_matrix_beta a = atom_site[m.label] s = space_group_symop[SymKey(m.symop)] - _model_site.ADP_matrix_beta = s.R * a.tensor_beta * s.RT + _model_site.ADP_matrix_beta = s.R * a.matrix_beta * s.RT ; save_ @@ -20670,6 +20670,7 @@ save_atom_site.adp_type Bani 'Anisotropic Bij.' Biso 'Isotropic B.' Bovl 'Overall B.' + betaani 'Anisotropic betaij.' save_ @@ -21672,87 +21673,6 @@ save_atom_site.site_symmetry_order save_ -save_atom_site.tensor_beta - - _definition.id '_atom_site.tensor_beta' - _definition.update 2021-09-24 - _description.text -; - The symmetric anisotropic atomic displacement tensor beta[I,J] - appears in a structure factor expression as: - - t = exp - [ β11 h h + ............ 2 β23 k l ] - - It is related to the ADP matrices U(IJ) and B(IJ) as follows: - - t = exp - 2π^2^ ( U11 h h a* a* + ...... 2 U23 k l b* c* ) - t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* ) -; - _name.category_id atom_site - _name.object_id tensor_beta - _type.purpose Measurand - _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' - _type.contents Real - _units.code none - _method.purpose Evaluation - _method.expression -; - With a as atom_site - - label = a.label - - If (a.ADP_type == 'Uani') { - Loop b as atom_site_aniso { - If(label == b.label) { - - UIJ = b.matrix_U - Break - } } } - - Else If (a.ADP_type == 'Bani') { - Loop b as atom_site_aniso { - If(label == b.label) { - - UIJ = b.matrix_B / (8 * Pi**2) - Break - } } } - - Else { - If (a.ADP_type == 'Uiso') U = a.U_iso_or_equiv - Else U = a.B_iso_or_equiv / (8 * Pi**2) - - UIJ = U * _cell.convert_Uiso_to_Uij - } - - CUB = _cell.convert_Uij_to_betaij - - _atom_site.tensor_beta = CUB * UIJ * CUB -; - -save_ - -save_atom_site.tensor_beta_su - - _definition.id '_atom_site.tensor_beta_su' - _definition.update 2021-09-23 - _description.text -; - Standard uncertainty of _atom_site.tensor_beta. -; - _name.category_id atom_site - _name.object_id tensor_beta_su - _name.linked_item_id '_atom_site.tensor_beta' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' - _type.contents Real - _units.code none - -save_ - save_atom_site.type_symbol _definition.id '_atom_site.type_symbol' @@ -22141,6 +22061,150 @@ save_atom_site_aniso.b_33_su save_ +save_atom_site_aniso.beta_11 + + _definition.id '_atom_site_aniso.beta_11' + _alias.definition_id '_atom_site_aniso_beta_11' + _name.category_id atom_site_aniso + _name.object_id beta_11 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_11_su + + _definition.id '_atom_site_aniso.beta_11_su' + _alias.definition_id '_atom_site_aniso_beta_11_su' + _name.category_id atom_site_aniso + _name.object_id beta_11_su + _name.linked_item_id '_atom_site_aniso.beta_11' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + +save_atom_site_aniso.beta_12 + + _definition.id '_atom_site_aniso.beta_12' + _alias.definition_id '_atom_site_aniso_beta_12' + _name.category_id atom_site_aniso + _name.object_id beta_12 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_12_su + + _definition.id '_atom_site_aniso.beta_12_su' + _alias.definition_id '_atom_site_aniso_beta_12_su' + _name.category_id atom_site_aniso + _name.object_id beta_12_su + _name.linked_item_id '_atom_site_aniso.beta_12' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + +save_atom_site_aniso.beta_13 + + _definition.id '_atom_site_aniso.beta_13' + _alias.definition_id '_atom_site_aniso_beta_13' + _name.category_id atom_site_aniso + _name.object_id beta_13 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_13_su + + _definition.id '_atom_site_aniso.beta_13_su' + _alias.definition_id '_atom_site_aniso_beta_13_su' + _name.category_id atom_site_aniso + _name.object_id beta_13_su + _name.linked_item_id '_atom_site_aniso.beta_13' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + +save_atom_site_aniso.beta_22 + + _definition.id '_atom_site_aniso.beta_22' + _alias.definition_id '_atom_site_aniso_beta_22' + _name.category_id atom_site_aniso + _name.object_id beta_22 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_22_su + + _definition.id '_atom_site_aniso.beta_22_su' + _alias.definition_id '_atom_site_aniso_beta_22_su' + _name.category_id atom_site_aniso + _name.object_id beta_22_su + _name.linked_item_id '_atom_site_aniso.beta_22' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + +save_atom_site_aniso.beta_23 + + _definition.id '_atom_site_aniso.beta_23' + _alias.definition_id '_atom_site_aniso_beta_23' + _name.category_id atom_site_aniso + _name.object_id beta_23 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_23_su + + _definition.id '_atom_site_aniso.beta_23_su' + _alias.definition_id '_atom_site_aniso_beta_23_su' + _name.category_id atom_site_aniso + _name.object_id beta_23_su + _name.linked_item_id '_atom_site_aniso.beta_23' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + +save_atom_site_aniso.beta_33 + + _definition.id '_atom_site_aniso.beta_33' + _alias.definition_id '_atom_site_aniso_beta_33' + _name.category_id atom_site_aniso + _name.object_id beta_33 + + _import.get [{'file':templ_attr.cif 'save':aniso_betaij}] + +save_ + +save_atom_site_aniso.beta_33_su + + _definition.id '_atom_site_aniso.beta_33_su' + _alias.definition_id '_atom_site_aniso_beta_33_su' + _name.category_id atom_site_aniso + _name.object_id beta_33_su + _name.linked_item_id '_atom_site_aniso.beta_33' + + _import.get + [{'file':templ_attr.cif 'save':aniso_betaij_su}] + +save_ + save_atom_site_aniso.label _definition.id '_atom_site_aniso.label' @@ -22216,6 +22280,117 @@ save_atom_site_aniso.matrix_b_su save_ +save_atom_site_aniso.matrix_beta + + _definition.id '_atom_site_aniso.matrix_beta' + _alias.definition_id '_atom_site.tensor_beta' + _definition.update 2023-06-16 + _description.text +; + The symmetric anisotropic atomic displacement parameter (ADP) matrix, β, + which appears in a structure factor expression. + + The contribution of the ADPs to the calculation of the structure factor is + given as: + + T = exp(-1 * Sum(Sum(β^ij^ * h~i~ * h~j~, j=1:3), i=1:3)) + + where β^ij^ are the matrix elements, and h~m~ are the Miller indices. + + The ADP matrix β, is related to the ADP matrices U and B, as follows: + + |a~1~* 0 0 | |t^11^ t^12^ t^13^| |a~1~* 0 0 | + β = C * | 0 a~2~* 0 | * |t^12^ t^22^ t^23^| * | 0 a~2~* 0 | + | 0 0 a~3~*| |t^13^ t^23^ t^33^| | 0 0 a~3~*| + + where C is a constant (2 * π^2^ for U, and 0.25 for B), a~i~* is the + length of the respective reciprocal unit cell vector, and t represents + the individual anisotropic values, U^ij^ or B^ij^. +; + _name.category_id atom_site_aniso + _name.object_id matrix_beta + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code none + _method.purpose Evaluation + _method.expression +; + With a as atom_site_aniso + + label = a.label + + If (a.ADP_type == 'betaani') + { + a.matrix_beta = [[ a.beta_11, a.beta_12, a.beta_13 ], + [ a.beta_12, a.beta_22, a.beta_23 ], + [ a.beta_13, a.beta_23, a.beta_33 ]] + } + Else + { + If (a.ADP_type == 'Uani') + { + UIJ = b.matrix_U + } + Else If (a.ADP_type == 'Bani') + { + UIJ = b.matrix_B / (8 * Pi**2) + } + Else { + If (a.ADP_type == 'Uiso') + { + Loop b as atom_site + { + If(label == b.label) + { + U = b.U_iso_or_equiv + Break + } + } + } + Else If (a.ADP_type == 'Biso') + { + Loop b as atom_site + { + If(label == b.label) + { + U = b.B_iso_or_equiv / (8 * Pi**2) + Break + } + } + } + UIJ = U * _cell.convert_Uiso_to_Uij + } + CUB = _cell.convert_Uij_to_betaij + a.matrix_beta = CUB * UIJ * CUB + } +; + +save_ + +save_atom_site_aniso.matrix_beta_su + + _definition.id '_atom_site_aniso.matrix_beta_su' + _alias.definition_id '_atom_site.tensor_beta_su' + _definition.update 2023-02-15 + _description.text +; + Standard uncertainty of _atom_site_aniso.matrix_beta. +; + _name.category_id atom_site_aniso + _name.object_id matrix_beta_su + _name.linked_item_id '_atom_site_aniso.matrix_beta' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code none + +save_ + save_atom_site_aniso.matrix_u _definition.id '_atom_site_aniso.matrix_U' @@ -27709,6 +27884,10 @@ save_ Redefined _exptl_absorpt.coefficient_mu as a derived measurand item. Added the _exptl_absorpt.coefficient_mu_su data item. + Renamed _atom_site.tensor_beta to _atom_site_aniso.matrix_beta and + updated the associated dREL evaluation methods. The old data name was + retained as an alias. Added the _atom_site_aniso.beta_* data items. + Reverted _atom_type_scat.versus_stol_list to a text-type to regain compatibility with DDL1 dictionary. diff --git a/templ_attr.cif b/templ_attr.cif index a2ce70e..ece30f4 100644 --- a/templ_attr.cif +++ b/templ_attr.cif @@ -554,21 +554,26 @@ save_ save_aniso_bij - _definition.update 2013-03-08 + _definition.update 2023-02-16 _description.text ; - These are the standard anisotropic atomic displacement components - in angstroms squared which appear in the structure factor term: + These are the standard anisotropic atomic displacement components, in + angstroms squared, which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths + The unique elements of the real symmetric matrix are entered by row. - The IUCr Commission on Nomenclature recommends against the use - of B for reporting atomic displacement parameters. U, being - directly proportional to B, is preferred. + The IUCr Commission on Nomenclature recommends against the use of B for + reporting atomic displacement parameters. U, being directly proportional + to B, is preferred [1]. + + Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1]. + + [1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781. ; _type.purpose Measurand _type.source Derived @@ -578,55 +583,92 @@ save_aniso_bij save_ -save_aniso_bij2 +save_aniso_bij_su - _definition.update 2014-06-12 + _definition.update 2021-03-18 _description.text ; - The [I][J] tdf elements define the overall anisotropic - displacement model if one was refined for this structure. + These are the standard uncertainty values (SU) for the standard + form of the B^ij^ anisotropic atomic displacement components (see + aniso_BIJ). Because these values are TYPE measurand, the su values + may in practice be auto generated as part of the B^ij^ calculation. ; - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _units.code angstrom_squared + _type.purpose SU + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstrom_squared save_ -save_aniso_bij_su +save_aniso_betaij - _definition.update 2021-03-18 + _definition.update 2023-02-16 + _description.text +; + These are the standard unitless anisotropic atomic displacement components + which appear in the structure factor term: + + T = exp{-1 sum~i~ [ sum~j~ (β^ij^ h~i~ h~j~) ] } + + h = the Miller indices + + The unique elements of the real symmetric matrix are entered by row. + + The IUCr Commission on Nomenclature recommends against the use + of β for reporting atomic displacement parameters; U is preferred [1]. + + Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1]. + + [1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code none + save_ + + +save_aniso_betaij_su + + _definition.update 2023-02-15 _description.text ; These are the standard uncertainty values (SU) for the standard - form of the Bij anisotropic atomic displacement components (see - _aniso_BIJ). Because these values are TYPE measurand, the su values - may in practice be auto generated as part of the Bij calculation. + form of the β^ij^ anisotropic atomic displacement components (see + aniso_betaIJ). Because these values are TYPE measurand, the su values + may in practice be auto generated as part of the β^ij^ calculation. ; _type.purpose SU _type.source Derived _type.container Single _type.contents Real - _units.code angstrom_squared + _units.code none save_ save_aniso_uij - _definition.update 2013-03-08 + _definition.update 2023-02-16 _description.text ; - These are the standard anisotropic atomic displacement - components in angstroms squared which appear in the - structure factor term: + These are the standard anisotropic atomic displacement components, in + angstroms squared, which appear in the structure factor term: - T = exp{-2π^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } + T = exp{ -2π^2^ sum~i~ [ sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. + + The IUCr Commission on Nomenclature recommends the use of U for reporting + atomic displacement parameters [1]. + + Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1]. + + [1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781. ; _type.purpose Measurand _type.source Derived @@ -642,9 +684,9 @@ save_aniso_uij_su _description.text ; These are the standard uncertainty values (SU) for the standard - form of the Uij anisotropic atomic displacement components (see - _aniso_UIJ). Because these values are TYPE measurand, the su values - may in practice be auto generated as part of the Uij calculation. + form of the U^ij^ anisotropic atomic displacement components (see + aniso_UIJ). Because these values are TYPE measurand, the su values + may in practice be auto generated as part of the U^ij^ calculation. ; _type.purpose SU _type.source Derived @@ -989,4 +1031,9 @@ save_display_colour Updated descriptions of cromer_mann_coeff and hi_ang_fox_coeffs. Added the default value of '1_555' to the 'site_symmetry' save frame. + + Added descriptions for aniso_betaIJ, and aniso_betaIJ_su. + Updated descriptions of aniso_BIJ and aniso_UIJ. + + Removed the 'aniso_bij2' save frame. ;