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cif_twinning.dic
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##############################################################################
# #
# CIF Twinning Definitions #
# #
# This dictionary contains names and definitions of twinning data items #
# recognized 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 1.0
_dictionary_update 2014-02-14
_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 wording of some definitions, corrected syntax errors,
added _twin_refln_include_status,
removed '_mandatory yes' from _twin_refln_index_
Rearranged the order of items in some examples to put the
list reference first.
2013-11-13 IDB: Following comments from Tony Linden and George Sheldrick
an alternative version of twin_refln is proposed.
If this is adopted _twin_contribution would be dropped.
2013-12-04 IDB: The alternative twin_refln is adopted and
twin_contribution is deleted.
2012-12-04 Minor spelling corrections,removal of old twin_contribution
material and example clarification added. VGY
2012-12-05 IDB: Made changes in the description of the example
under the twin category to reflect the deletion
of the twin_contribution category.
Removed '_twin_contribution_individual_id' from
_link_list_child in the definition of _twin_individual_id.
Modified the description of the twin_refln category
to reflect the merging of twin_contribution with twin_refln.
Added r to enumeration list of _twin_refln_include_status.
2014-02-14 BMcM and NJA: minor editing for clean release version
;
###############
## 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_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
1 2 1 -1 32 40.17 55.86 7.39 o
2 1 0 1 -32 125.83 145.63 9.36 o
2 2 1 0 32 125.83 145.63 9.36 o
3 1 1 1 -32 10.33 30.89 7.39 o
3 2 1 1 32 10.33 30.89 7.39 o
4 1 -3 2 -32 28.26 26.84 9.47 o
4 2 2 -3 32 28.26 26.84 9.47 o
5 1 -2 2 -32 4.31 13.21 9.78 o
5 2 2 -2 32 4.31 13.21 9.78 o
6 1 -1 2 -32 10.71 17.48 9.88 o
6 2 2 -1 32 10.71 17.48 9.88 o
7 1 0 2 -32 13.94 37.66 10.51 o
7 2 2 0 32 13.94 37.66 10.51 o
8 1 1 2 -32 58.60 75.41 9.88 o
8 2 2 1 32 58.60 75.41 9.88 o
9 1 -2 3 -32 27.75 41.40 8.01 o
9 2 3 -2 32 27.75 41.40 8.01 o
10 1 -1 3 -32 59.22 65.53 8.11 o
10 2 3 -1 32 59.22 65.53 8.11 o
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_example_detail
;
The twinning example presented here 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 International Tables for Crystallography
(2005), Vol. A].
The TWIN_REFLN loop gives the properties of each diffraction peak
(identified by _twin_refln_datum_id) which is indexed
to both the twin individuals.
In each of the loops shown in this example the first items on a line
are the list reference. While the list reference must be present
in every loop, it is not necessary that it should be declared as the
first item in the loop.
;
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 will be triperiodic.
Reference: Donnay, G. & Donnay, J. D. H. (1974). Can. Mineral. 12, 422-425.
;
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_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
_list_link_child
'_twin_refln_individual_id'
_definition
;
The unique identifier 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 (2004), 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 (h k l )
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.
The calculated structure factor for each twin contribution can also
be given.
;
loop_ _example
_example_detail
# - Example 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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_meas
_twin_refln_F_squared_sigma
_twin_refln_include_status
1 1 1 0 0 1.03 0.18 o
1 3 1 0 0 1.03 0.18 o
2 1 2 0 0 1290.01 55.59 o
2 3 2 0 0 1290.01 55.59 o
3 1 3 0 0 2.59 0.42 o
3 3 3 0 0 2.59 0.42 o
4 1 4 0 0 30.98 1.47 o
4 3 4 0 0 30.98 1.47 o
5 1 5 0 0 1.97 0.96 o
5 3 5 0 0 1.97 0.96 o
6 1 6 0 0 1.55 1.14 o
6 2 6 1 2 1.55 1.14 o
6 3 6 0 0 1.55 1.14 o
6 4 6 1 2 1.55 1.14 o
7 1 -6 1 0 0.47 1.06 o
7 2 6 2 2 0.47 1.06 o
;
#---------------------------------------------------------------------
# Description of Example 1
;
This partial listing describes seven observed diffraction peaks
in a four-individual twin by non-merohedry. The reference individual
is 1. Reflections from the other three individuals 2, 3 and 4 are
present only if these cannot be experimentally separated from the
reference individual.
;
# ---- Example 2 ------------------------------------------------------
;
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
625 2 3 -6 1 204.45 204.38 4.48 o
626 1 3 -6 -3 240.97 241.19 3.75 o
626 2 -3 6 3 240.97 241.19 3.75 o
627 1 3 6 3 288.54 281.53 4.31 o
627 2 -3 -6 -3 288.54 281.53 4.31 o
628 1 -5 -6 -3 179.56 176.35 5.36 o
628 2 -3 6 5 179.56 176.35 5.36 o
629 1 5 6 3 235.04 238.84 4.06 o
629 2 -5 -6 -3 235.04 238.84 4.06 o
;
# --------------------------------------------------------------------
;
This example is taken from Colombo Young & Gladfelter
[Inorg. Chem. (2000), 39, 4621-4624].
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 it is clear that datums 620-624 do not contain
overlapping reflections, whereas datums 625-629 contain contributions
from both twins.
;
data_twin_refln_datum_id
_name '_twin_refln_datum_id'
_category twin_refln
_type char
_list yes
_list_mandatory yes
_definition
;
This item serves to identify an observed diffraction peak.
It may include contributions from one or more twin components
and so may appear more than once in the list.
The values of _twin_refln_F_squared_calc and
_twin_refln_F_squared_meas indexed by
_twin_refln_datum_id include the contributions from all the twins.
The diffraction peak is indexed by
_twin_refln_index_h, *_k and *_l referred to the cell of
the twin component identified by _twin_refln_individual_id.
The list reference includes both _twin_refln_datum_id and
_twin_refln_individual_id. The combination of these two items
may only appear once in a list.
;
data_twin_refln_F_squared_calc
_name '_twin_refln_F_squared_calc'
_category twin_refln
_type numb
_list yes
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_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 as follows:
_twin_refln_F_squared_calc = osf * Sum (mf * _refln_F_squared_calc)
where osf is the overall scale factor,
mf is the mass fraction,
and the sum is taken over all the twin components that contribute
to this diffraction peak.
Reference: Pratt, C. S., Coyle, B. A. & Ibers, J. A. (1971).
J. Chem. Soc. A, pp. 2146-2151.
;
data_twin_refln_F_squared_calc_individual
_name '_twin_refln_F_squared_calc_individual'
_category twin_refln
_type numb
_list yes
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_id'
_definition
;
Contribution of the twin identified by _twin_refln_individual_id
to _twin_refln_F_squared_calc.
_twin_refln_F_squared_calc_individual = osf * mf * _refln_F_squared_calc
where osf is the overall scale factor, mf is the mass factor.
For X-ray diffraction the units are electrons squared.
;
data_twin_refln_F_squared_meas
_name '_twin_refln_F_squared_meas'
_category twin_refln
_type numb
_list yes
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_id'
_definition
;
The observed value F^2^ of the peak referenced by
_twin_refln_datum_id. This is typically the observed peak
intensity after Lorentz and polarization corrections.
;
data_twin_refln_F_squared_sigma
_name '_twin_refln_F_squared_sigma'
_category twin_refln
_type numb
_list yes
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_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
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_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'
r 'removed from the refinement for other reasons'
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
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_id'
_definition
;
Miller indices of a reflection from the twin component
labelled by _twin_refln_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_mandatory yes
_list_link_parent '_twin_individual_id'
loop_
_list_reference '_twin_refln_datum_id' '_twin_refln_individual_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.
The list reference includes both _twin_refln_datum_id and
_twin_refln_individual_id. The combination of these two items
may only appear once in a list.
;