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Draft CIF twin dictionary for approval
- To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
- Subject: Draft CIF twin dictionary for approval
- From: David Brown <idbrown@mcmaster.ca>
- Date: Mon, 30 Sep 2013 11:48:28 -0400
|
Dear Colleagues, After many years of gestation, a draft CIF dictionary of items for describing twinning in crystals is now available. It is attached to this email which is being circulated to the core CIF Dictionary Management Group for your approval, this being the final step in the formal COMCIFS approval process. If you are receiving this message you are invited to review the attached draft and either indicate your approval, or draw attention to potential problems, by replying to the core DMG list at coredmg@iucr.org. When approved the twinning dictionary will become an addendum to the coreCIF dictionary. The draft is open for review for six weeks ending on 11 November 2013. If you have not replied by then, it will be assumed that you approve of the attached document as circulated. If any questions are raised we will try if possible to resolve them within the review period. The dictionary is also available at the URL https://github.com/jamesrhester/twinning-dic I look forward to receiving your response. David Brown Chair of the core CIF Dictionary Management Group |
############################################################################## # # # CIF Twinning Definitions # # # # This dictionary contains draft names and definitions of twinning data items# # recognised by the International Union of Crystallography for the exchange # # of data between laboratories and submissions to journals and databases. # # # # The STAR/DDL dictionary to which this dictionary conforms # # is available as the file "ddl_core.dic" # # located at URL ftp://ftp.iucr.org/pub/cifdics/ddl_core_1.4.1.dic # # # ############################################################################## data_on_this_dictionary _dictionary_name cif_twinning.dic _dictionary_version 0.6 _dictionary_update 2013-09-13 _dictionary_history ; 2012-07-25 Created from Victor Young's draft text. JRH 2012-08-20 Added category definitions and corrected _list for _twin_lattice_type. JRH 2012-08-21 cosmetic changes such as arranging the items alphabetically and added queries for VY. I.D.Brown 2012-08-28 Inserted changes from V. Young as per I.D. Brown's comments; removed _example_detail for twin category; corrected _list_reference for _refln_ category; added explanation for _refln_F_squared_ . JRH 2012-08-31 Added _twin_special_details with example from VY. JRH 2013-01-17 Corrected equation defining F_calc. JRH 2013-01-18 Moved _refln_ items into separate _twin_refln category and rewrote definitions for clarity. 2013-03-13 Added missing _twin_refln_index_ . JRH 2013-03-25 IDB: Added enumeration range to _twin_individual__mass_fraction_refined and rewrote the definition Rewrote the definition of _twin_individual_twin_matrix Raised queries about what the _twin_refln category is actually recording. 2013-05-09 JRH: corrected _twin_refln_F_calc equation; added _list_reference to _twin_refln_h,k,l definition; fiddled with _twin_individual_twin_id definition text 2013-06-26 JRH,VY: added further example to TWIN category 2013-06-26 some syntax and formatting errors corrected (BM) 2013-06-27 IDB Changed _twin_refln_observed_status to _twin_refln_include_status Added the twin_contibution category Reworked the twin_refln category to change the list reference to _twin_refln_datum_id (name changed from _*_datum_index Made some improvements to the definitions. Converted space group symbols to CIF conventions Arranged items in alphabetic order to conform to other dictonaries. 2013-07-11 JRH edited examples to reflect proposed changes from IDB 2013-07-29 VGY modified examples to comply with IDB's suggested changes (see below). These are within comments, but not yet integrated into the text of the document. Added nmt for non-merohedral twin into data_twin_lattice_type. Somehow this was removed. 2013-08-16 VGY made corrections as directed by JH in examples 2 and 3. Removed work for these examples from commented text and integrated into document. Updated example 1 to include explicit _twin_contribution items for individual 2. 2013-09-02 JRH edited in latest examples from VGY after email discussion 2013-09-03 JRH: move lattice_twin_type into twin_individual category; add 'ref' lattice twin type. Changed _twin_contribution_twin_id to _twin_contribution_individual_id 2013-09-03 VGY: improve example to include single-contributor reflections coming from different individuals. 2013-09-13 IDB: Changed _refln_twin to _twin_refln, improved the wording of some definitions, corrected syntax errors, added _twin_refln_include_status, removed '_mandatory yes' from _twin_refn_index_ Rearranged the order of items in some examples to put the list reference first. ; ############### ## TWIN ## ############### data_twin_[] _name '_twin_[]' _category category_overview _type null _definition ; Data items in the TWIN category record general details about the nature of the twinning in the sample. Terminology for twin dataname definitions was taken directly from: "International Union of Crystallography Commission on Mathematical and Theoretical Crystallography Research themes: Crystal twinning" by Massimo Nespolo, February 3, 2009. http://www.crystallography.fr/mathcryst/twins.htm . ; _example # ----------------------------------------------------------------------------- ; _twin_formation_mechanism gt _twin_dimensionality triperiodic _twin_morphology polysynthetic _twin_special_details ; This is an example of a twin in space group P 32 by the 2 x,x,0 twin operation. ; loop_ _twin_individual_id _twin_individual_mass_fraction_refined _twin_individual_twin_lattice_type _twin_individual_twin_matrix_11 _twin_individual_twin_matrix_12 _twin_individual_twin_matrix_13 _twin_individual_twin_matrix_21 _twin_individual_twin_matrix_22 _twin_individual_twin_matrix_23 _twin_individual_twin_matrix_31 _twin_individual_twin_matrix_32 _twin_individual_twin_matrix_33 1 0.545(2) ref 1 0 0 0 1 0 0 0 1 2 0.455(2) mt_II 0 1 0 1 0 0 0 0 -1 loop_ _twin_contribution_individual_id _twin_contribution_index_h _twin_contribution_index_k _twin_contribution_index_l _twin_contribution_datum_id 1 -1 1 -32 1 2 1 -1 32 1 1 0 1 -32 2 2 1 0 32 2 1 1 1 -32 3 2 1 1 32 3 1 -3 2 -32 4 2 2 -3 32 4 1 -2 2 -32 5 2 2 -2 32 5 1 -1 2 -32 6 2 2 -1 32 6 1 0 2 -32 7 2 2 0 32 7 1 1 2 -32 8 2 2 1 32 8 1 -2 3 -32 9 2 3 -2 32 9 1 -1 3 -32 10 2 3 -1 32 10 loop_ _twin_refln_datum_id _twin_refln_individual_id _twin_refln_index_h _twin_refln_index_k _twin_refln_index_l _twin_refln_F_squared_calc _twin_refln_F_squared_meas _twin_refln_F_squared_sigma _twin_refln_include_status 1 1 -1 1 -32 40.17 55.86 7.39 o 2 1 0 1 -32 125.83 145.63 9.36 o 3 1 1 1 -32 10.33 30.89 7.39 o 4 1 -3 2 -32 28.26 26.84 9.47 o 5 1 -2 2 -32 4.31 13.21 9.78 o 6 1 -1 2 -32 10.71 17.48 9.88 o 7 1 0 2 -32 13.94 37.66 10.51 o 8 1 1 2 -32 58.60 75.41 9.88 o 9 1 -2 3 -32 27.75 41.40 8.01 o 10 1 -1 3 -32 59.22 65.53 8.11 o ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _example_detail ; The twinning example presented above shows twinning by merohedry for a trigonal crystal system. The simulated space group is P 32 2 1, but the true space group is P 32. The twin operation chosen is 2: x,x,0 in P 32 2 1 corresponding to operation (by rows) 0, 1, 0 / 1, 0, 0 / 0, 0, -1 (see table 11.2.2.1 of Internation Tables for Crystallography Vol A). The twin_contribution loop shows which reflection from which twin contributes to the diffraction peak identified by _twin_contribution_datum_id. The twin_refln loop gives the properties of each diffraction peak (identified by _twin_refln_datum_id) which is indexed to one of the twin individuals. Because this is an example of merohedral twinning, all the diffraction peaks can be indexed to the reference twin (_twin_refln_individual_id = 1). In cases of non-merohdral twinning some diffraction peaks would have to be indexed to different twin individuals. In each of the loops shown in this example the first item(s) on a line is(are) the list reference. While the list reference must be present in every loop, it may be placed at any point on the line. ; data_twin_dimensionality _name '_twin_dimensionality' _category twin _type char _list no loop_ _enumeration _enumeration_detail triperiodic 'common lattice in three dimensions' diperiodic 'common lattice in two dimensions' monoperiodic 'common lattice in one dimension' _definition ; The degree of overlap between the twin lattices. Most Twin Lattice Symmetry (TLS) and Twin Lattice Quasi-Symmetry (TLQS) twins as defined by Donnay and Donnay (1974, Can. Mineral. 12, 422-425) will be triperiodic. ; data_twin_formation_mechanism _name '_twin_formation_mechanism' _category twin _type char _list no loop_ _enumeration _enumeration_detail gt 'growth twin formed during crystal growth'' tt 'transformation twin formed during phase transition' mt 'mechanical twin formed as a result of mechanical action' _definition ; A description of the method of twin formation. ; data_twin_morphology _name '_twin_morphology' _category twin _type char _list no loop_ _enumeration _enumeration_detail contact 'separated by a surface' penetration 'sharing a volume' simple 'individuals are not repeated' polysynthetic 'individuals repeat in approximately linear arrangement' cyclic 'individuals repeat in closed edifice' _definition ; The physical relationship of the different twins to one another. ; data_twin_special_details _name '_twin_special_details' _category twin _type char _list no _example ; Individuals 3 and 4 arise from form (I) following an enantiotropic phase transition by sudden cooling in a cryostat to 173K. ; _definition ; Information about twinning in the sample not contained in other data items. ; ####################### ## TWIN_CONTRIBUTION ## ####################### data_twin_contribution_[] _name '_twin_contribution_[]' _category category_overview _type null _definition ; Items in the twin_contribution category identify the datum_id of the observed diffraction peak to which the reflection defined by _twin_contribution_index_h, k and l and _twin_contribution_individual_id contributes. ; _example ; loop_ _twin_contribution_individual_id _twin_contribution_index_h _twin_contribution_index_k _twin_contribution_index_l _twin_contribution_datum_id 3 1 0 0 1 1 1 0 0 1 3 2 0 0 2 1 2 0 0 2 3 3 0 0 3 1 3 0 0 3 3 4 0 0 4 1 4 0 0 4 3 5 0 0 5 1 5 0 0 5 4 6 1 2 6 3 6 0 0 6 2 6 1 2 6 1 6 0 0 6 2 6 2 2 7 1 -6 1 0 7 ; _example_detail ; This listing corresponds to seven observed diffraction spots from a simple four-component twin by non-merohedry. The corresponding F^2 data is presented in the _twin_refln example. ; data_twin_contribution_datum_id _name '_twin_contribution_datum_id' _category twin_contribution _type char _list yes loop_ _list_reference '_twin_contribution_individual_id' '_twin_contribution_index_h' '_twin_contribution_index_k' '_twin_contribution_index_l' _definition ; Each observed diffraction peak is assigned a unique _*_datum_id. The observed structure factor of this diffraction peak may contain contributions from more than one twin. These contributions are identified by the Miller indices of the reflection from the twin identified by _*_individual_id. ; data_twin_contribution_index_ loop_ _name '_twin_contribution_index_h' '_twin_contribution_index_k' '_twin_contribution_index_l' _category twin_contribution _type numb _list yes _list_mandatory yes loop_ _list_reference '_twin_contribution_individual_id' '_twin_contribution_index_h' '_twin_contribution_index_k' '_twin_contribution_index_l' _definition ; Miller indices of a reflection from a the twin identified by _*_individual_id. The values of the Miller indices must correspond to the cell defined in the cell category combined with the transformation matrix for the twin individual identified by _twin_contribution_individual_id. Together with _twin_contribution_individual_id it creates a unique list_reference for items in the this list. ; data_twin_contribution_individual_id _name '_twin_contribution_individual_id' _category twin_contribution _type char _list yes _list_link_parent '_twin_individual_id' _list_mandatory yes loop_ _list_reference '_twin_contribution_individual_id' '_twin_contribution_index_h' '_twin_contribution_index_k' '_twin_contribution_index_l' _definition ; The unique identifier for the twin individual. The identifier must match a _twin_individual_id in the twin_individual category. Together with _twin_contribution_index_h, *_k, *_l it creates a unique list_reference for items in the this list. ; ########################## ## TWIN_INDIVIDUAL ## ########################## data_twin_individual_[] _name '_twin_individual_[]' _category category_overview _type null _definition ; Data items in the twin_individual category describe properties of each twinned individual, and the symmetry relationships between the individuals. ; data_twin_individual_id _name '_twin_individual_id' _category twin_individual _type char _list yes _list_mandatory yes loop_ _list_link_child '_twin_contrbution_individual_id' '_twin_refln_individual_id' _definition ; The unique idenifier for this twin individual. The twin for which _twin_individual_twin_matrix is the identity matrix is called the reference twin. It is recommended that the reference twin be labelled '1'. ; data_twin_individual_mass_fraction_refined _name '_twin_individual_mass_fraction_refined' _category twin_individual _type numb _type_conditions esd _list yes _list_reference '_twin_individual_id' _enumeration_range 0:1.0 _definition ; The refined mass fraction of this twin individual; the sum of all mass fractions must equal unity within the limits of experimental uncertainty. ; data_twin_individual_twin_lattice_type _name '_twin_individual_twin_lattice_type' _category twin _type char _list yes loop_ _enumeration _enumeration_detail ref 'reference twin' mt_I 'merohedral class I (simple inversion)' mt_II 'merohedral class II (mirror or twofold)' mt_I+II 'class I and II simultaneously present' rmt 'reticular merohedral' pmt 'pseudo-merohedral' rpmt 'reticular pseudo-merohedral' nmt 'non-merohedral' _definition ; Identification of the symmetry relationships between the twin lattices as described in International Tables for Crystallography Vol C, Chapter 1.3. The twin with the identity matrix should be denoted as 'ref'. ; data_twin_individual_twin_matrix loop_ _name '_twin_individual_twin_matrix_11' '_twin_individual_twin_matrix_12' '_twin_individual_twin_matrix_13' '_twin_individual_twin_matrix_21' '_twin_individual_twin_matrix_22' '_twin_individual_twin_matrix_23' '_twin_individual_twin_matrix_31' '_twin_individual_twin_matrix_32' '_twin_individual_twin_matrix_33' _category 'twin_individual' _type numb _list yes _list_reference '_twin_individual_id' _definition ; Elements of the matrix U that multiplies the Miller indices h,k,l of the reference twin to give the Miller indices h',k',l', of the twin specified by _twin_individual_id [h'k'l'] = U.[hkl] It follows that the reference twin must have U = I, the identity matrix. ; ################ ## twin_refln ## ################ data_twin_refln_[] _name '_twin_refln_[]' _category category_overview _type null _definition ; Items in the twin_refln category tabulate the calculated values of F^2 for each peak observed in the diffraction pattern, together with the measured value of F^2. The calculated F^2 for an observed peak is a weighted sum of the contribution of all the twin components. ; loop_ _example _example_detail # - Example 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _twin_contribution_individual_id _twin_contribution_index_h _twin_contribution_index_k _twin_contribution_index_l _twin_contribution_datum_id 1 1 0 0 1 3 1 0 0 1 1 2 0 0 2 3 2 0 0 2 1 3 0 0 3 3 3 0 0 3 1 4 0 0 4 3 4 0 0 4 1 5 0 0 5 3 5 0 0 5 4 6 1 2 6 3 6 0 0 6 2 6 1 2 6 1 6 0 0 6 1 -6 1 0 7 2 6 2 2 7 loop_ _twin_refln_datum_id _twin_refln_index_h _twin_refln_index_k _twin_refln_index_l _twin_refln_F_squared_calc _twin_refln_F_squared_meas _twin_refln_F_squared_sigma _twin_refln_include_status _twin_refln_individual_id 1 1 0 0 0.47 1.03 0.18 o 1 2 2 0 0 1300.45 1290.01 55.59 o 1 3 3 0 0 2.34 2.59 0.42 o 1 4 4 0 0 32.45 30.98 1.47 o 1 5 5 0 0 2.19 1.97 0.96 o 1 6 6 0 0 0.95 1.55 1.14 o 1 7 -6 1 0 0.08 0.47 1.06 o 1 ; #--------------------------------------------------------------------- # Description of Example 1 ; This listing describes seven observed diffraction peaks corresponding to the diffraction peaks listed in the _twin_contributions_ example. ; # ---- Example 2 ------------------------------------------------------ ; loop_ _twin_contribution_individual_id _twin_contribution_index_h _twin_contribution_index_k _twin_contribution_index_l _twin_contribution_datum_id 1 1 -6 -3 620 1 -1 6 3 621 2 -1 6 3 622 1 -1 -6 -3 623 2 -1 -6 -3 624 1 1 6 3 625 2 3 -6 1 625 2 -3 6 3 626 1 3 -6 -3 626 1 3 6 3 627 2 -3 -6 -3 627 2 -3 6 5 628 1 -5 -6 -3 628 2 -5 -6 -3 629 1 5 6 3 629 loop_ _twin_refln_datum_id _twin_refln_individual_id _twin_refln_index_h _twin_refln_index_k _twin_refln_index_l _twin_refln_F_squared_calc _twin_refln_F_squared_meas _twin_refln_F_squared_sigma _twin_refln_include_status 620 1 1 -6 -3 200.22 207.88 3.35 o 621 1 -1 6 3 225.34 224.15 3.62 o 622 2 -1 6 3 184.64 196.34 3.95 o 623 1 -1 -6 -3 173.28 181.13 3.06 o 624 2 -1 -6 -3 143.40 152.05 2.78 o 625 1 1 6 3 204.45 204.38 4.48 o 626 1 3 -6 -3 240.97 241.19 3.75 o 627 1 3 6 3 288.54 281.53 4.31 o 628 1 -5 -6 -3 179.56 176.35 5.36 o 629 1 5 6 3 235.04 238.84 4.06 o ; # -------------------------------------------------------------------- ; This example is taken from Colombo, et. al, (2000) Inorg. Chem. 39, 4621. Two structures of nitronium tetranitratogallate are reported as a result of an enantiotropic phase transition. The higher temperature phase is in the tetragonal space group I-4, while the lower temperature phase is a twin by non-merohedry in space group I2. The individuals are enantiomorphic as a result of the phase transition. In the listing below it is clear that datums 620 - 624 do not contain overlapping reflections, whereas datums 624 - 629 contain overlapping reflections. ; data_twin_refln_datum_id _name '_twin_refln_datum_id' _category twin_refln _type char _list yes _list_mandatory yes _definition ; _twin_refln_datum_id is the list reference and serves to identify an observed diffraction peak that may include contributions from one or more twin components. The observed and calculated structure factors indexed by _twin_refln_datum_id include the contributions from all the twins. The diffraction peak is optionally indexed by _twin_refln_index_h, _*_k and _*_l for the this reflection contributed by the twin component given by_twin_refln_individual_id. Only one such indexing is allowed, the choice of which to include is arbitrary. Each value of _twin_refln_datum_id may only appear once in the list. ; data_twin_refln_F_squared_calc _name '_twin_refln_F_squared_calc' _category twin_refln _type numb _list yes _list_reference '_refl_twin_datum_id' _definition ; Calculated value for the overall squared structure factors (in electrons squared for X-ray diffraction) arising from all the twin contributions to the peak defined by _twin_refln_datum_id. The total contribution from all twins to a single observed reflection is modelled according to the method of Pratt, Coyle and Ibers (1971, J. Chem. Soc. A, 2146) as follows: _twin_refln_F_squared_calc = = osf*Sum{mass_fraction*_refln_F_squared_calc} Where osf is the overall scale factor and the sum is taken over all the twin components that contribute to this diffraction peak. ; data_twin_refln_F_squared_meas _name '_twin_refln_F_squared_meas' _category twin_refln _type numb _list yes _list_reference '_refl_twin_datum_id' _definition ; The obsderved value F^2 of the peak referenced by _twin_refln_datum_id. This is typically the observed peak intensity after Lorenz and polarisation corrections. ; data_twin_refln_F_squared_sigma _name '_twin_refln_F_squared_sigma' _category twin_refln _type numb _list yes _list_reference '_refl_twin_datum_id' _definition ; Standard uncertainty of _twin_refln_F_squared_meas ; data_twin_refln_include_status _name '_twin_refln_include_status' _category twin_refln _type char _list yes _list_reference '_refl_twin_datum_id' loop_ _enumeration _enumeration_detail o ; (lower-case letter o for 'observed') satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low exceeds _reflns_threshold_expression ; < ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low does not exceed _reflns_threshold_expression ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine_ls_d_res_high' l 'does not satisfy _refine_ls_d_res_low' _enumeration_default o _definition ; A symbol indicating how the reflection is treated during refinement. ; data_twin_refln_index_ loop_ _name '_twin_refln_index_h' '_twin_refln_index_k' '_twin_refln_index_l' _category twin_refln _type numb _list yes _list_reference '_refl_twin_datum_id' _definition ; Miller indices of a reflection from the twin component labelled by _refl_twin_individual_id. The values of the Miller indices must correspond to the cell defined for this twin component. ; data_twin_refln_individual_id _name '_twin_refln_individual_id' _category twin_refln _type char _list yes _list_link_parent '_twin_individual_id' _list_reference '_refl_twin_datum_id' _definition ; The unique identifier of the twin individual whose Miller indices are given in _twin_refln_index_. The ID must match a _twin_individual_id in the twin_individual category. ;
begin:vcard fn:I.David Brown n:Brown;I.David org:McMaster University;Brockhouse Institute for Materials Research adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada email;internet:idbrown@mcmaster.ca title:Professor Emeritus tel;work:+905 525 9140 x 24710 tel;fax:+905 521 2773 version:2.1 end:vcard
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