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CIF core dictionary revisions List #5
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: CIF core dictionary revisions List #5
- From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
- Date: Wed, 22 Jan 2003 19:21:38 GMT
Dear Colleagues,
I enclose below the next list (#5) of changes and additions to the
core CIF dictionary for discussion and, if desired, approval. Syd Hall
circulated comments on thirteen of the items in list #4 and I repeat these
items here together with Syd's comments and my response (and
recommendation) so that they can be discussed further. The other items on
list #4 have been marked as approved since no one raised any objections to
them.
Apart from the 13 items below that have been held over from list #4, all
the relatively uncontroversial changes have now been approved and it is time
to move on to the more difficult items. The first of these concerns the
adoption of items from the newly approved symmetry dictionary to replace those
in the existing symmetry category.
Please read through this list carefully and share your comments with the
rest of the Core Dictionary Maintenance Group.
The deadline for comment is
########################
### 28 February 2003 ###
########################
If you have no comments, please indicate your approval (or otherwise) of the
proposed changes. Silence will be taken as approval, though a positive
affirmative vote is much preferred.
Please send your comments to the Core DMG list with the above subject
heading which you can most simply do by replying to this email.
Best wishes
David
*****************************************************
Dr.I.David Brown, Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************
LIST #5 OF THE CORE REVISION PROPOSALS CONTAINS THE FOLLOWING ITEMS. FULL
DETAILS GIVEN FOLLOWING THIS INDEX
# Items held over from list #4.
#
# EXPTL_CRYSTAL
# _exptl_crystal_colour (modification)
# _exptl_crystal_density_meas_gt
# _exptl_crystal_density_meas_lt
# _exptl_crystal_density_meas_temp_gt
# _exptl_crystal_density_meas_temp_lt
# _exptl_crystal_recrystallization
# REFINE
# _refine_ls_extinction_coef (replace?)
# _refine_ls_extinction_coef_Zach
# _refine_ls_extinction_coef_Becker-Coppens_1
# _refine_ls_extinction_coef_Becker-Coppens_2
# _refine_ls_extinction_BC_type
# _refine_ls_extinction_expression (replace?)
# _refine_ls_extinction_method (replace?)
#
# New items in this list. These are intended to replace the current _SYMMETRY
# items and are the marked with an asterisk * below. The full list of items
# defined in the Symmetry dictionary is given for information.
#
# SPACE_GROUP (General information on the space group)
# _Space_group_Bravais_type
# _Space_group_centring_type
# * _Space_group_crystal_system
# * _Space_group_id (Parent to various .sg_id's)
# _Space_group_Laue_class
# _Space_group_IT_coordinate_system_code
# * _Space_group_IT_number
# * _Space_group_name_Hall
# _Space_group_name_H-M_ref
# * _Space_group_name_H-M_alt
# _Space_group_name_H-M_alt_description
# _Space_group_name_H-M_full
# _Space_group_name_Schoenflies
# _Space_group_Patterson_name_H-M
# _Space_group_point_group_H-M
# _Space_group_reference_setting
# _Space_group_transform_Pp-abc
# _Space_group_transform_Qq_xyz
# SPACE_GROUP_SYMOP (Symmetry operators)
# * _space_group_symop_id (parent to various .symop_id's)
# _space_group_symop_generator_xyz
# _space_group_symop_operation_description
# * _space_group_symop_operation_xyz
# * _space_group_symop_sg_id
# SPACE_GROUP_WYCKOFF (Details of the Wyckoff positions)
# _space_group_wyckoff_coords_xyz
# _space_group_wyckoff_id (parent to various .wyckoff_id's to be
# defined)
# _space_group_wyckoff_letter
# _space_group_wyckoff_multiplicity
# _space_group_wyckoff_sg_id
# _space_group_wyckoff_site_symmetry
#
#################################################
#
# EXPTL_CRYSTAL
#
#################################################
data_exptl_crystal_colour
_name '_exptl_crystal_colour'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _example
dark_green
reddish_orange_metallic
_definition
; The colour of the crystal used in the experiment. The
following list of standardized names developed for the
International Center for Diffraction Data should be used.
Combinations of descriptors should be linked by an underscore.
The allowed colours are: colourless, white, black, gray, brown,
red, pink, orange, yellow, green, blue, violet.
Colours may be modified by using one of the prefixes: light,
dark, whitish, blackish, grayish, brownish,reddish, pinkish,
orangish, yellowish, greenish, bluish.
Intermediate hues may be indicated by linking two colours,
e.g. blue_green or bluish_green
Metallic colours are indicated by adding 'metallic' as a suffix,
e.g. reddish_orange_metallic for copper.
;
# COMMENT: This scheme is based on a scheme developed by the ICDD and
# recommended for use in the powder CIF. It is already being checked
# in submissions to Acta Cryst. It would be helpful to have it as part of the
# dictionary description, though it is difficult to define an enumeration list
# for the colours.
# STATUS: Open for discussion
#
# SUGGESTION from Syd Hall: Split into
# _exptl_crystal_appearance_colour_primary
# colourless, white, black, gray, brown,
# red, pink, orange, yellow, green, blue, violet.
# _exptl_crystal_appearance_colour_modifier
# light, dark, whitish, blackish, grayish, brownish, reddish,
# pinkish, orangish, yellowish, greenish, bluish.
# _exptl_crystal_appearance_lustre
# metallic, dull, clear
#
# RESPONSE: Syd's scheme would allow for enumeration lists and would avoid the
# problem of having to parse the value of this item. Unless there are
# objections, I recommend that we adopt Syd's suggestion.
data_exptl_crystal_density_meas_*
loop_ _name
'_exptl_crystal_density_meas_gt'
'_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_definition
; The lower (_*_gt) or upper limit (_*_lt) on the value of the
density measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
# COMMENT by Syd Hall:
# _exptl_crystal_density_meas_gt _lt
# I don't understand what thresholds "gt" and "lt" have to do with
# density measurements. Do you simply mean the upper and lower limits
# of a range of density measurements e.g. "high" and "low", or is it
# something else?
#
# RESPONSE: Normally a measured density would be a number with an experimental
# uncertainty. If the density were reported as lying between 2.5 and 3.5,
# _*_gt could be set to 2.5 and _*_lt to 3.5. To give the density as 3.0(5)
# implies that 3.0 is more likely than 2.5 or 3.5, which is not what was
# reported. In other cases the density might be reported as being greater
# than 1.0 because the sample sinks in water. In this case _*_gt would be set
# to 1.0. This, and the following item, were suggested by CCDC because the
# present set of items cannot be used to convey the imprecise information that
# sometimes appears in their records. I RECOMMEND that we approve these two
# items.
data_exptl_crystal_density_meas_temp_*
loop_
_name '_exptl_crystal_density_meas_temp_gt'
'_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail 'Kelvins'
_definition
; Temperature in kelvins above which (_*_gt) or below which
(_*_lt) _exptl_crystal_density_meas was determined.
;
# COMMENT: The above two items suggested by CCDC.
# STATUS: Open for discussion
#
# COMMENT by Syd Hall
# _exptl_crystal_density_meas_temp_gt _lt
# I really don't know what these temperatures mean!
#
# RESPONSE: See the comment above. The correct measurement temperature is not
# always given, but some information may be available.
data_exptl_crystal_recrystallization
_name '_exptl_crystal_recrystallization'
_category exptl_crystal
_type char
_example ?
_definition
; Describes the method used to recrystallize the sample
;
# COMMENT: Suggested by CCDC.
# STATUS: Open for discussion
#
# SUGGESTION by Syd Hall. The name should be
# _exptl_crystal_recrystallization_method
#
# RESPONSE: I RECOMMEND that we adopt Syd's suggestion.
#########################################
#
# REFINE category
#
#########################################
# The next five items relate to extinction and are an attempt to tighten up
# our definitions. The first item is the current definition which we may
# wish to replace or restrict.
#
# COMMENT from Syd Hall:
# _refine_ls_extinction_ etc.
#
# Please be careful with what you are advocating here... in my view it's
# moving the definitions away from the representation approach that will be
# most useful in the future. As above, enumeration is the key and what
# would be much better is to carefully enumerate _refine_ls_extinction_method
# to identify the widely used approaches. This simplifies both searching
# and validation... and future expansion for new methods.
#
# By the way, the reason for _refine_ls_extinction_expression is because
# there were a number of different "Zach" expressions in use by various
# packages at one stage... and it may well be still the case!
#
# RESPONSE: The present dictionary contains the three items
# _refine_ls_extinction_coef
# _refine_ls_extinction_expression
# _refine_ls_extinction_method
# Syd is suggesting that we provide _*_method with an enumeration list that
# covers the principal methods of correction. If it also covers the different
# expressions used to represent them then _*_expression would no longer be
# needed except for cases that were not covered in the enumeration list. In
# this way only a single _*_coef item would be needed and its meaning would be
# uniquely determined by the value of _*_method.
#
# The different possible values of _*_coef would all be syntactically
# equivalent, meaning that they could be read without knowing the value of
# _*_method, but _*_method would have to be consulted before a program would
# know how to use _*_coef. This should not cause a problem with the current
# dictionary languages, but might not work with the proposed 'methods'
# dictionaries (DDL3). Since we are still using DDL1, I recommend that we
# adopt Syd's proposal which is simpler and more elegant than the long list of
# changes I proposed below for _refine_ls_extinction_*. If we do adopt
# this route we will need an enumeration list for _*_method containing values
# such as the following.
# Zachariasen
# Becker-Coppens_1_Gaussian
# Becker-Coppens_1_Lorentzian
# Becker-Coppens_2_Gaussian
# Becker-Coppens_2_Lorentzian
# In each case a precise expression should be defined in the dictionary. Can
# anyone help in identifying what values should be included in this
# enumeration list and what expressions each of these values represents?
#
# I RECOMMEND that we adopt Syd's suggestion with the addition that the
# enumeration list imply the expression used (i.e. more than one enumeration
# may be needed for 'Zachariasen' if there are a number of different
# Zachariasen expressions in use).
#
###############################################################
# If Syd's recommendation is adopted, the rest of this section (the next 3
# pages) down to ####### END OF ITEMS FROM LIST #4 ####### can be ignored. I
# have kept them in this document so that you can compare Syd's suggestion to
# the more complex suggestion that I made earlier.
###############################################################
data_refine_ls_extinction_coef
_name '_refine_ls_extinction_coef'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine_ls_extinction_expression and
_refine_ls_extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value,
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
# COMMENT: This item is context sensitive in that it is necessary to know the
# _*_detail in order to interpret the coefficient. Since there is no
# enumeration list for _*_detail, machine interpretation is impossible. This
# item should be replaced for standard extinction methods by the following
# list of proposed items. Can we retain the above definition to cover cases
# where a non-standard extinction correction was performed, or should we
# retire this name and devise a new one? In any case we require a new
# definition.
# STATUS: open for comment
data_refine_ls_extinction_coef_*
loop_ _name '_refine_ls_extinction_coef_Zach'
'_refine_ls_extinction_coef_Becker-Coppens_1'
'_refine_ls_extinction_coef_Becker-Coppens_2'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the observed structure-factors.
For _refine_ls_extinction_coef_Zach (the Zachariasen, also known as
the Larson, method) the value given is the r* value,
For _refine_ls_extinction_coef_Becker-Coppens_1 (the Becker-Coppens
type 1 isotropic method) it is the 'g' value,
For _refine_ls_extinction_coef_Becker-Coppens_2 (Becker-Coppens type
2 isotropic method) it is the 'rho' value.
Note that the magnitude of these values is usually of the order of
10000.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; It is also
possible to use a mixture of types 1 and 2.
For the Becker-Coppens method it is necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' in
_refine_ls_extinction_B-C_type. If an anisotropic extinction
correction has been made the multiple coefficients cannot be
contained in *_extinction_coef_Becker-Coppens_* and they must be
listed in _refine_special_details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
# COMMENT: This is a new item which allows the specific extinction parameter
# to be given for each of the standard extinction corrections. Whichever item
# is given will identify the method used to determine the extinction so
# _*_expression and _*_method would not be needed.
# STATUS: Open for discussion.
data_refine_ls_extinction_BC_type
_name '_refine_ls_extinction_BC_type
_category refine_ls
_type char
loop_ _related_item
'_refine_ls_extinction_coef_Becker-Coppens_1'
'_refine_ls_extinction_coef_Becker-Coppens_2'
_related_function ?
loop_ _enumeration Gaussian
Lorentzian
_definition
; For the Becker-Coppens extinction correction, a statement is
needed of the function used to describe the mosaic spread.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-153.
;
# COMMENT: This is a new item is needed to complement the Becker-Coppens
# coefficients
# STATUS: Open for discussion
data_refine_ls_extinction_expression
_name '_refine_ls_extinction_expression'
_category refine
_type char
# _example
#; Larson, A. C. (1970). "Crystallographic Computing",
# edited by F. R. Ahmed. Eq. (22) p. 292.
# Copenhagen: Munksgaard.
#;
# A new example will be needed if the revised definition is adopted.
_definition
; A description or reference for the extinction correction equation
used to apply the data item _refine_ls_extinction_coef when this
is not one of the standard types defined under
_refine_ls_extinction_coef_*.
This information must be sufficient to reproduce the extinction
correction factors applied to the structure factors.
;
# COMMENT: This is an existing data item but its name suggests an algebraic
# expression while the example suggests that a reference is intended. I have
# changed the definition so maybe a different dataname is needed. It is not
# clear to me what the difference between _*_expression and _*_method was
# intended to be.
# STATUS: open for discussion.
data_refine_ls_extinction_method
_name '_refine_ls_extinction_method'
_category refine
_type char
# _enumeration_default 'Zachariasen'
# loop_ _example 'B-C type 2 Gaussian isotropic'
# 'none'
_definition
; A description of the extinction correction method applied with
the data item _refine_ls_extinction_coef when one of the standard
methods is not used.
# (The rest of this text should be deleted or transferred. The text above has
# been modified. The enumeration default should in any case be deleted. and
# a different example given.)
#
# This description should
# include information about the correction method, either
# 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
# referred to as the 'Larson' method even though it employs
# Zachariasen's formula.
#
# The Becker-Coppens procedure is referred to as 'type 1' when
# correcting secondary extinction dominated by the mosaic spread;
# as 'type 2' when secondary extinction is dominated by particle
# size and includes a primary extinction component; and as 'mixed'
# when there is a mixture of types 1 and 2.
#
# For the Becker-Coppens method it is also necessary to set the
# mosaic distribution as either 'Gaussian' or 'Lorentzian'; and
# the nature of the extinction as 'isotropic' or 'anisotropic'.
# Note that if either the 'mixed' or 'anisotropic' corrections
# are applied the multiple coefficients cannot be contained in
# *_extinction_coef and must be listed in _refine_special_details.
#
# Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
# 129-153.
# Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
# Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
#
# COMMENT: The default should be deleted since there should be no presumption
# about the method used. This proposal changes the meaning of this item in a
# significant way and perhaps a different dataname should be used.
# STATUS: Open for comment
#
######## END OF ITEMS FROM LIST #4 #################################
######## NEW ITEMS IN LIST #5 ######################################
#
# NEW PROPOSAL
#
# Recently COMCIFS approved the symmetry dictionary which was designed to
# provide a more complete and coherent list of symmetry items than is
# currently available in the core dictionary. While the current _symmetry_*
# items have proved satisfactory for reporting crystal structures, they are
# not suitable for further expansion of symmetry properties and in some cases,
# such as _symmetry_cell_setting, the names are quite misleading.
# The proposal is to replace the core items:
# _symmetry_cell_setting
# _symmetry_equiv_pos_as_xyz
# _symmetry_Int_Tables_number
# _symmetry_space_group_name_Hall
# _symmetry_space_group_name_H-M
# by some or all of the items in the list below.
#
# This list gives all the items and categories defined in the
# symmetry dictionary. Those marked with * are proposed for inclusion in the
# new version of the core dictionary. The definitions of the asterisked items
# are given in full in the list below.
# Definitions of the remaining items can be found in the full
# symmetry dictionary (written in DDL2) available on the IUCr web site.
#
#
# SPACE_GROUP (General information on the space group)
# _Space_group_Bravais_type
# _Space_group_centring_type
# * _Space_group_crystal_system
# * _Space_group_id (Parent to various .sg_id's)
# _Space_group_Laue_class
# _Space_group_IT_coordinate_system_code
# * _Space_group_IT_number
# * _Space_group_name_Hall
# _Space_group_name_H-M_ref
# * _Space_group_name_H-M_alt
# _Space_group_name_H-M_alt_description
# _Space_group_name_H-M_full
# _Space_group_name_Schoenflies
# _Space_group_Patterson_name_H-M
# _Space_group_point_group_H-M
# _Space_group_reference_setting
# _Space_group_transform_Pp-abc
# _Space_group_transform_Qq_xyz
# SPACE_GROUP_SYMOP (Symmetry operators)
# * _space_group_symop_id (parent to various .symop_id's)
# _space_group_symop_generator_xyz
# _space_group_symop_operation_description
# * _space_group_symop_operation_xyz
# * _space_group_symop_sg_id
# SPACE_GROUP_WYCKOFF (Details of the Wyckoff positions)
# _space_group_wyckoff_coords_xyz
# _space_group_wyckoff_id (parent to various .wyckoff_id's to be
# defined)
# _space_group_wyckoff_letter
# _space_group_wyckoff_multiplicity
# _space_group_wyckoff_sg_id
# _space_group_wyckoff_site_symmetry
#
################################################
#
# CATEGORY: SPACE_GROUP
#
################################################
data_SPACE_GROUP
_name space_group
_category category_overview
_type nul
_description
; Contains all the data items that refer to the space group as a
whole, such as its name, Laue group etc. It may be looped, for
example, in a list of space groups and their properties.
Space group types are identified by their International Tables
for Crystallography Vol A number or Schoenflies symbol.
Specific settings of the space groups can be identified by
their Hall symbol, by specifying their symmetry operations or
generators, or by giving the transformation that relates the
specific setting to the reference setting based on
International Tables for Crystallography Vol. A and stored in
this dictionary.
The commonly-used Hermann-Mauguin symbol determines the
space group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space group type. It contains
information on the choice of the basis, but not on the
choice of origin.
;
_example
;
_space_group_id 1
_space_group_name_H-M 'C 2/c'
_space_group_name_Schoenflies C2h.6
_space_group_IT_number 15
_space_group_name_Hall '-C 2yc'
_space_group_Bravais_type mS
_space_group_Laue_class 2/m
_space_group_crystal_system monoclinic
_space_group_centring_type C
_space_group_Patterson_name_H-M 'C 2/m'
;
data_space_group_crystal_system
_name '_space_group_crystal_system'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_description
; The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that crystals with the hR lattice type belong to the
trigonal system.
;
_type char
loop_
_enumeration
triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
_related_item '_symmetry_cell_setting'
_related_function replace
data_space_group_id
_name '_space_group_id'
_category space_group
_list yes
_list_mandatory yes
_description
; This is an identifier needed if _space_group_* items are looped.
;
_type char
loop_
_list_link_child
'_space_group_symop_sg_id'
'_space_group_Wyckoff_sg_id'
data_space_group_IT_number
_name '_space_group_IT_number'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_description
; The number as assigned in International Tables for
Crystallography Vol A, specifying the proper affine class (i.e.
the orientation preserving affine class) of space groups
(crystallographic space group type) to which the space group
belongs. This number defines the space group type but not
the coordinate system in which it is expressed.
;
_type numb
_enumeration_range 1:230
_related_item '_symmetry_Int_Tables_number'
_related_function replace
data_space_group_name_Hall
_name '_space_group_name_Hall'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
loop_
_example
_example_detail 'P 2c -2ac' 'Equivalent to Pca21'
'-I 4bd 2ab 3' 'Equivalent to Ia3d'
_description
; Space group symbol defined by Hall (Acta Cryst. (1981) A37,
517-525) (See also International Tables for Crystallography
Vol.B (1993) 1.4 Appendix B).
Each component of the space group name is separated by a
space or an underscore. The use of space is strongly
recommended. The underscore is only retained because it
was used in earlier archived files. It should not be
used in new CIFs.
_space_group_name_Hall uniquely defines the space group and
its reference to a particular coordinate system.
;
_type char
_related_item '_symmetry_space_group_name_Hall'
_related_function replace
data_space_group_name_H-M_alt
_name '_space_group_name_H-M_alt'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_type char
loop_
_example
_example_detail
;
loop_
_space_group_name_H-M_alt
_space_group_name_H-M_alt_description
'C m c m(b n n)' 'Extended Hermann-Mauguin symbol'
'C 2/c 2/m 21/m' 'Full unconventional Hermann-Mauguin symbol'
'A m a m' 'Hermann-Mauguin symbol corresponding to setting used'
;
'three examples for the space group number 63.'
_description
; *_name_H-M_alt allows for an alternative Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and should be described in the item
_space_group_name_H-M_alt_description. It may, for example, be
used to give one of the extended Hermann-Mauguin symbols given
in Table 4.3.1 of International Tables for Crystallography
Vol A (1995) or a full Hermann-Mauguin symbol for an
unconventional setting.
Each component of the space group name is separated by a
space or underscore. The use of space is strongly
recommended. The underscore is only retained because it
was used in earlier archived files. It should not be
used in new CIFs. Subscripts should appear
without special symbols. Bars should be given as negative
signs before the numbers to which they apply. The commonly
used Hermann-Mauguin symbol determines the space group type
uniquely but a given space group type may be described by
more than one Hermann-Mauguin symbol. The space group type
is best described using the *_IT_number or *_name_Schoenflies.
The Hermann-Mauguin symbol may contain information on the
choice of basis though not on the choice of origin. To
define the setting uniquely use *_name_Hall, list the
symmetry operations or generators, or give the transformation
that relates the setting to the reference setting defined
in this dictionary under *_reference_setting.
;
_related_item '_symmetry_space_group_name_H-M'
_related_function replacement
###########################################################
#
# SPACE GROUP SYMOP
#
###########################################################
data_SPACE_GROUP_SYMOP
_category category_overview
_type nul
_description
; Contains information about the symmetry operations of the
space group.
;
loop_
_example_detail
_example
;
The symmetry operations for the space group P21/c
;
; loop_
_space_group_symop_id
_space_group_symop_operation_xyz
_space_group_symop_operation_description
1 x,y,z 'identity mapping'
2 -x,-y,-z 'inversion'
3 -x,1/2+y,1/2-z '2-fold screw rotation with axis in (0,y,1/4)'
4 x,1/2-y,1/2+z 'c glide reflection through the plane (x,1/4,y)'
;
data_space_group_symop_id
_description
; An arbitrary identifier that uniquely labels each symmetry
operation in the list.
;
_type char
_name '_space_group_symop_id'
_category space_group_symop
_list yes
_list_mandatory yes
_related_item '_symmetry_equiv_pos_site_id'
_related_function replace
data_space_group_symop_operation_xyz
_name '_space_group_symop_operation_xyz'
_category space_group_symop
_list both
_list_mandatory no
_list_reference '_space_group_symop_id'
loop_
_example
_examples_detail
'x,1/2-y,1/2+z' 'c glide reflection through the plane (x,1/4,z)'
_description
; A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by the fractions, an equivalent position
X' is generated from a given position X by the equation:
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Section 5)
When a list of symmetry operations is given, it is assumed
that the list contains all the operations of the space
group (including the identity operation) as given by the
representatives of the general position in International
Tables for Crystallography Vol. A.
;
_type char
loop_
_related_item
_related_function
'_symmetry_equiv_pos_as_xyz' replace
'_space_group_symop_generator_xyz' alternate
_item_default_value 'x,y,z'
data_space_group_symop_sg_id
_name '_space_group_symop_sg_id'
_category space_group_symop
_list both
_list_mandatory no
_list_reference _space_group_symop_id
loop_
_example
_example_detail
? ?
_description
; A child of _space_group.id allowing the symmetry operation
to be identified with a particular space group.
;
_type numb
_list_link_parent '_space_group.id'
# COMMENT: See above. The _space_group items above have all been approved by
# COMCIFS. The only question we have to decide is which ones are to be included
# in the revised dictionary.
#
# STATUS: Open for discussion
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