The header is standard for DDLm dictionaries.
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# #
# SYMMETRY CIF DICTIONARY #
# #
# Converted from DDL2 to DDLm 12 Jun 2014 #
# Updated by J Hester July 2016 #
# #
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data_CIF_SYM
_dictionary.title CIF_SYM
_dictionary.class Instance
_dictionary.version 2.0.01
_dictionary.date 2016-xx-xx
_dictionary.uri www.iucr.org/cif/dic/cif_sym.dic
_dictionary.ddl_conformance 3.11.09
_dictionary.namespace CifSym
_description.text
;
The CIF_SYM dictionary expands the core dictionary symmetry definitions to
allow tabulation of space group relationships and presentation of structural
data in alternative space groups or space group settings.
;
#==============================================================================
The head category (which acts as the parent of all categories in the
dictionary) imports the core dictionary in Full mode, which means
that the categories in the core dictionary are reparented to the
symmetry dictionary, and that the symmetry dictionary definitions
replace any identical definitions in the core dictionary.
save_SYMMETRY
_definition.id SYMMETRY
_definition.scope Category
_definition.class Head
_definition.update 2014-06-12
_description.text
;
The parent category of all other categories.
;
_name.category_id CIF_SYM
_name.object_id SYMMETRY
_include.get {["file":cif_core.dic "save":CORE_CIF "mode":Full]}
save_
#-------------------------------------------------------------------------------
We define a category that other categories can have child keys of; if this category has multiple rows, then the other categories can have multiple values of the child key and thereby contain information for more than one space group. By adding a child key of this category to other categories, we signal that datanames in those other categories depend on knowledge of the space group in order to be correctly interpreted.
Note that, in the particular case of SPACE_GROUP, the SPACE_GROUP
category itself could become the ‘Hub’ category. The only changes to
this example would be the removal of the SPACE_GROUP_HUB category
and the parent of all child keys (the one specified in
_name.linked_item_id) being changed to the SPACE_GROUP key. The
separate hub category has been left in this example to demonstrate how
the system works for concepts that have no existing category in the
dictionary.
save_SPACE_GROUP_HUB
_definition.id SPACE_GROUP_HUB
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
This category must be present in order to loop items from the
SPACE_GROUP category. Categories that need to reference a
particular space group provide a child key of this category's
key.
;
_name.category_id SYMMETRY
_name.object_id SPACE_GROUP_HUB
_category.key_id '_space_group_hub.id'
loop_
_category_key.name '_space_group_hub.id'
save_
save_space_group_hub.id
_definition.id '_space_group_hub.id'
_definition.update 2016-xx-xx
_description.text
;
This is a unique identifier for items in the space_group_hub category.
Categories that depend upon particular values in the SPACE_GROUP
category should include a child key of this dataname
;
The following definitions replace those found in the core
dictionary. SPACE_GROUP is redefined to be a Loop category and a
child key of space_group_hub is added to the list of keys and a
definition provided.
save_SPACE_GROUP
_definition.id SPACE_GROUP
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
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 number as listed in
International Tables for Crystallography Volume A, or by their
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 Volume 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. A
Hermann-Mauguin symbol contains information on the choice of
the basis, but not on the choice of origin.
Ref: International Tables for Crystallography (2002). Volume A,
Space-group symmetry, edited by Th. Hahn, 5th ed.
Dordrecht: Kluwer Academic Publishers.
;
_name.category_id SYMMETRY
_name.object_id SPACE_GROUP
_category.key_id '_space_group.id'
loop_
_category_key.name '_space_group.id'
save_space_group.id
_definition.id '_space_group.id'
_description.text
;
This item uniquely identifies an entry in the space_group table.
It must be one of the values provided in space_group_hub.id
;
_name.category_id space_group
_name.object_id id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
These datanames come from the old symCIF dictionary. They were not included in the core dictionary as they make no sense in the context of a single space group.
save_space_group.reference_setting
_definition.id '_space_group.reference_setting'
_definition.update 2014-06-12
_description.text
;
The reference setting of a given space group is the setting
chosen by the International Union of Crystallography as a
unique setting to which other settings can be referred
using the transformation matrix column pair given in
_space_group.transform_Pp_abc and _space_group.transform_Qq_xyz.
The settings are given in the enumeration list in the form
'_space_group.IT_number:_space_group.name_Hall'. The
space-group number defines the space-group type and the
Hall symbol specifies the symmetry generators referred to
the reference coordinate system.
The 230 reference settings chosen are identical to the settings
listed in International Tables for Crystallography Volume A
(2002). For the space groups where more than one setting is
given in International Tables, the following choices have
been made.
For monoclinic space groups: unique axis b and cell choice 1.
For space groups with two origins: origin choice 2 (origin at
inversion centre, indicated by adding :2 to the Hermann-Mauguin
symbol in the enumeration list).
For rhombohedral space groups: hexagonal axes (indicated by
adding :h to the Hermann-Mauguin symbol in the enumeration list).
Based on the symmetry table of R. W. Grosse-Kunstleve, ETH,
Zurich.
The enumeration list may be extracted from the dictionary
and stored as a separate CIF that can be referred to as
required.
In the enumeration list, each reference setting is identified
by Schoenflies symbol and by the Hermann-Mauguin symbol,
augmented by :2 or :h suffixes as described above.
Ref: International Tables for Crystallography (2002). Volume A,
Space-group symmetry, edited by Th. Hahn, 5th ed.
Dordrecht: Kluwer Academic Publishers.
Grosse-Kunstleve, R. W. (2001). Xtal System of
Crystallographic Programs, System Documentation.
http://xtal.crystal.uwa.edu.au/man/xtal3.7-228.html
(or follow links to Docs->Space-Group Symbols from
http://xtal.sourceforge.net).
;
_name.category_id space_group
_name.object_id reference_setting
_type.purpose State
_type.source assigned
_type.container Single
_type.contents Code
_import.get [{"file":'templ_enum.cif',"save":'ref_set'}]
save_
save_space_group.transform_Pp_abc
_definition.id '_space_group.transform_Pp_abc'
_definition.update 2014-06-12
_description.text
;
This item specifies the transformation (P,p) of the basis
vectors from the setting used in the CIF (a,b,c) to the
reference setting given in _space_group.reference_setting
(a',b',c'). The value is given in Jones-Faithful notation
corresponding to the rotational matrix P combined with the
origin shift vector p in the expression:
(a',b',c') = (a,b,c)P + p.
P is a post-multiplication matrix of a row (a,b,c) of column
vectors. It is related to the inverse transformation (Q,q) by:
P = Q^-1^
p = Pq = -(Q^-1^)q.
These transformations are applied as follows:
atomic coordinates (x',y',z') = Q(x,y,z) + q
Miller indices (h',k',l') = (h,k,l)P
symmetry operations W' = (Q,q)W(P,p)
basis vectors (a',b',c') = (a,b,c)P + p
This item is given as a character string involving the
characters a, b and c with commas separating the expressions
for the a', b' and c' vectors. The numeric values may be
given as integers, fractions or real numbers. Multiplication
is implicit, division must be explicit. White space within
the string is optional.
;
_name.category_id space_group
_name.object_id transform_Pp_abc
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
'R3:r to R3:h' '-b+c, a+c, -a+b+c'
'Pnnn:1 to Pnnn:2' 'a-1/4, b-1/4, c-1/4'
'Bbab:1 to Ccca:2' 'b-1/2, c-1/2, a-1/2'
save_
save_space_group.transform_Qq_xyz
_definition.id '_space_group.transform_Qq_xyz'
_definition.update 2014-06-12
_description.text
;
This item specifies the transformation (Q,q) of the atomic
coordinates from the setting used in the CIF [(x,y,z) referred
to the basis vectors (a,b,c)] to the reference setting given in
_space_group.reference_setting [(x',y',z') referred to the
basis vectors (a',b',c')].
The value given in Jones-Faithful notation corresponds to the
rotational matrix Q combined with the origin shift vector q in
the expression:
(x',y',z') = Q(x,y,z) + q.
Q is a pre-multiplication matrix of the column vector (x,y,z).
It is related to the inverse transformation (P,p) by:
P = Q^-1^
p = Pq = -(Q^-1^)q,
where the P and Q transformations are applied as follows:
atomic coordinates (x',y',z') = Q(x,y,z) + q
Miller indices (h',k',l') = (h,k,l)P
symmetry operations W' = (Q,q)W(P,p)
basis vectors (a',b',c') = (a,b,c)P + p
This item is given as a character string involving the
characters x, y and z with commas separating the expressions
for the x', y' and z' components. The numeric values may be
given as integers, fractions or real numbers. Multiplication
is implicit, division must be explicit. White space within
the string is optional.
;
_name.category_id space_group
_name.object_id transform_Qq_xyz
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
'R3:r to R3:h' '-x/3+2y/3-z/3, -2x/3+y/3+z/3, x/3+y/3+z/3'
'Pnnn:1 to Pnnn:2' 'x+1/4,y+1/4,z+1/4'
'Bbab:1 to Ccca:2' 'z+1/2,x+1/2,y+1/2'
save_
#-------------------------------------------------------------------------------
The SPACE_GROUP_SYMOP and SPACE_GROUP_WYCKOFF definitions have an
extra key added pointing to the SPACE_GROUP_HUB definition.
save_SPACE_GROUP_SYMOP
_definition.id SPACE_GROUP_SYMOP
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
Contains information about the symmetry operations of the
space group.
;
_name.category_id SYMMETRY
_name.object_id SPACE_GROUP_SYMOP
# _category.key_id '_space_group_symop.id'
loop_
_category_key.name '_space_group_symop.id' '_space_group_symop.sg_id'
save_
save_space_group_symop.sg_id
_definition.id '_space_group_symop.sg_id'
_definition.update 2016-xx-xx
_description.text
;
The hub identifier for the space group containing this symmetry operator.
;
_name.category_id space_group_symop
_name.object_id sg_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
#-------------------------------------------------------------------------------
save_SPACE_GROUP_WYCKOFF
_definition.id SPACE_GROUP_WYCKOFF
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
Contains information about Wyckoff positions of a space group.
Only one site can be given for each special position but the
remainder can be generated by applying the symmetry operations
stored in _space_group_symop.operation_xyz.
;
_name.category_id SYMMETRY
_name.object_id SPACE_GROUP_WYCKOFF
# _category.key_id '_space_group_Wyckoff.id'
loop_
_category_key.name '_space_group_Wyckoff.id' '_space_group_Wyckoff.sg_id'
save_
save_space_group_Wyckoff.sg_id
_definition.id '_space_group_Wyckoff.sg_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the Wyckoff position
to be identified with a particular space group.
;
_name.category_id space_group_Wyckoff
_name.object_id sg_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
The following categories are changed to ‘Loop’ categories and/or supplied
with an extra child key of the SPACE_GROUP_HUB category. This allows
them to indicate which space group the dataname values are to be interpreted
relative to.
How do we determine if a category requires a key from a newly-looped category?
Mathematically, our category datanames are functions from the keys to the dataname values. If absence of the key would make it impossible to assign a unique value to even one dataname (ontologically, i.e. according to our understanding of the scientific discipline) then the key is required.
save_REFLN
_definition.id REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
The CATEGORY of data items used to describe the reflection data
used in the refinement of a crystallographic structure model.
;
_name.category_id DIFFRACTION
_name.object_id REFLN
#_category.key_id '_refln.key'
loop_
_category_key.name
'_refln.index_h'
'_refln.index_k'
'_refln.index_l'
'_refln.sg_id'
save_
save_refln.sg_id
_definition.id '_refln.sg_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the reflection
to be explicitly associated with a particular space group.
;
_name.category_id refln
_name.object_id sg_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
Strictly speaking, a unique atomic site cannot be associated with an atom label, so it would appear that there is no functional relationship between the label and the fractional coordinates in even the cif core dictionary. In fact, the fractional coordinates when combined with the symmetry operators yield a unique set of coordinates (the orbit). So the fractional coordinates are used as proxies for an orbit, however, this is only possible if the symmetry operators are known - thus the need to explicitly specify the space group if there is more than one.
save_ATOM_SITE
_definition.id ATOM_SITE
_definition.scope Category
_definition.class Loop
_definition.update 2016-07-25
_description.text
;
The CATEGORY of data items used to describe atom site information
used in crystallographic structure studies.
;
_name.category_id ATOM
_name.object_id ATOM_SITE
_category.key_id '_atom_site.key'
loop_
_category_key.name
'_atom_site.label'
'_atom_site.sgt_id'
save_
save_atom_site.sgt_id
_definition.id '_atom_site.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the atom site
to be explicitly associated with a particular space group.
;
_name.category_id atom_site
_name.object_id sgt_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
ATOM_SITE_ANISO is a child loop category of ATOM_SITE. Therefore, it must
also contain a child key of each atom_site key. By extension of the
original DDLm rule, the parent-child relationship means that only those
combinations of key values that are present in the parent may be present
in the child.
save_ATOM_SITE_ANISO
_definition.id ATOM_SITE_ANISO
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe the anisotropic
thermal parameters of the atomic sites in a crystal structure.
;
_name.category_id ATOM_SITE
_name.object_id ATOM_SITE_ANISO
loop_
_category_key.name
'_atom_site_aniso.label'
'_atom_site_aniso.sgt_id'
save_
save_atom_site_aniso.sgt_id
_definition.id '_atom_site_aniso.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the atom site
to be explicitly associated with a particular space group.
;
_name.category_id atom_site_aniso
_name.object_id sgt_id
_name.linked_item_id '_atom_site.sgt_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
The addition of an explicit space group hub id flows through to any
categories that work with the atom site list. As a unique atom can
appear more than once (once for each space group) other categories in
turn must provide the space group hub id in order to reference a
particular atom site row, so must have a child key of space group hub
as one of their keys. In particular, model_site must do this, and
then all of the geom categories that access model_site do the same
in turn.
The dREL category method has been omitted for brevity.
save_MODEL_SITE
_definition.id MODEL_SITE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe atomic sites and
connections in the proposed atomic model.
;
_name.category_id MODEL
_name.object_id MODEL_SITE
_category.key_id '_model_site.key'
loop_
_category_key.name
'_model_site.label'
'_model_site.symop'
'_model_site.sgt_id'
save_
save_model_site.sgt_id
_definition.id '_model_site.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the model site
to be explicitly associated with a particular space group.
;
_name.category_id model_site
_name.object_id sgt_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
Only a definition for GEOM_ANGLE is provided in this example, as
the construction of the remaining categories would be identical.
save_GEOM_ANGLE
_definition.id GEOM_ANGLE
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
The CATEGORY of data items used to specify the geometry angles in the
structural model as derived from the atomic sites.
;
_name.category_id GEOM
_name.object_id GEOM_ANGLE
loop_
_category_key.name
'_geom_angle.sgt_id'
'_geom_angle.atom_site_label_1'
'_geom_angle.atom_site_label_2'
'_geom_angle.atom_site_label_3'
'_geom_angle.site_symmetry_1'
'_geom_angle.site_symmetry_2'
'_geom_angle.site_symmetry_3'
save_
save_geom_angle.sgt_id
_definition.id '_geom_angle.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the model site
to be explicitly associated with a particular space group.
;
_name.category_id geom_angle
_name.object_id sgt_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
Note that the original draft cif core dictionary had all CELL_* categories as
children of the CELL category. It is proposed to move all the datanames back
into the CELL_ category in the core dictionary.
CELL_MEASUREMENT remains as separate category, which is also provided with
a space group hub child key to indicate which space group the reflection
indices are relative to.
save_CELL
_definition.id CELL
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
The CATEGORY of data items used to describe the parameters of
the crystal unit cell and their measurement.
;
_name.category_id EXPTL
_name.object_id CELL
_category_key.name
'_cell.sgt_id'
save_
save_cell.sgt_id
_definition.id '_cell.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the model site
to be explicitly associated with a particular space group.
;
_name.category_id cell
_name.object_id sgt_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
As the reflection hkl may depend on the space group chosen, we must also add
a link in cell_measurement_refln
save_CELL_MEASUREMENT_REFLN
_definition.id CELL_MEASUREMENT_REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2016-xx-xx
_description.text
;
The CATEGORY of data items used to describe the reflection data
used in the measurement of the crystal unit cell.
;
_name.category_id EXPTL
_name.object_id CELL_MEASUREMENT_REFLN
loop_
_category_key.name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l'
'_cell_measurement_refln.sgt_id'
save_
save_cell_measurement_refln.sgt_id
_definition.id '_cell_measurement_refln.sgt_id'
_definition.update 2016-xx-xx
_description.text
;
A child of _space_group_hub.id allowing the model site
to be explicitly associated with a particular space group.
;
_name.category_id cell_measurement_refln
_name.object_id sgt_id
_name.linked_item_id '_space_group_hub.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Text
save_
Note exptl_crystal.F_000: number of electrons in the unit cell. This
does depend on the unit cell chosen, unlike the other exptl_crystal
items, so would entail exptl_crystal having an sgt_id value.
Further categories requiring the addition of an extra space group key
dataname are atom_sites_cartn_transform,
atom_sites_fract_transform, exptl_crystal_face. These have been
omitted as they are identical in approach to the above categories
and involve no new ideas.