Topology CIF dictionary for discussion and review
James Hester
jamesrhester at gmail.com
Tue Feb 27 05:11:26 GMT 2018
Dear COMCIFS,
Vladislav Blatov and Davide Proserpio have prepared a new CIF dictionary
for description of topology. I have reviewed the dictionary from a
technical standpoint and believe that it is now ready for the broader
community to review and comment. A easily-readable, auto-generated HTML
version of the dictionary is available at
http://comcifs.github.io/Topology.dic.html.
A 6-week period for review and comment now begins. If no substantive issues
remain after this period, the dictionary will become official. I urge you
to read the dictionary, and to encourage anyone you know that is interested
in crystal topology to read the HTML version and provide feedback, either
through a Github issue (https://github.com/COMCIFS/TopoCif/issues), or by
you forwarding an email from them to this list.
For the record, I have appended the text dictionary to this email. It can
also be viewed, along with a short history, at
https://github.com/COMCIFS/TopoCif/blob/master/Topology.dic
James.
--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
#\#CIF_2.0
#################################################################################
#
#
# Topology CIF
dictionary #
#
#
#################################################################################
data_TOPOLOGY_CIF
_dictionary.title TOPOLOGY_CIF
_dictionary.class Instance
_dictionary.version 0.4
_dictionary.ddl_conformance 3.13.1
_dictionary.date 2018-02-27
_description.text
;
The Topology CIF dictionary provides datanames for describing crystal
structure
topology. This is a DRAFT version and datanames in this dictionary
should not
be used until approval by COMCIFS.
;
save_TOPOLOGY
_definition.id TOPOLOGY
_definition.scope Category
_definition.class Head
_description.text
'This category is the parent of all
categories in the dictionary'
_name.object_id TOPOLOGY
_name.category_id TOPOLOGY_CIF
save_
save_topol
_definition.id topol
_name.category_id TOPOLOGY
_name.object_id topol
_definition.update 2018-01-30
_definition.scope Category
_definition.class Set
_description.text
;
The TOPOL category covers data on connectivity
between atoms and structural groups and the
related structural properties as calculated from
the ATOM, CELL and SYMMETRY data.
;
loop_
_description_example.detail
_description_example.case
;
Connectivity of the diamond crystal structure.
All atoms coincide with the nodes and all bonds coincide
with the edges, so the atomic network coincides with the
underlying net.
;
;
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/4-x,1/4-y,z
# Other symmetry elements skipped
13 -y,-x,-z
# Other symmetry elements skipped
192 3/4-z,1/2+y,1/4-x
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
C1 C 8 0.12500 0.12500 0.12500 1.0000
loop_
_topol_repres_node.label
_topol_repres_node.atom_label
C1 C1
loop_
_topol_link.node_label_1
_topol_link.node_label_2
_topol_link.site_symmetry_1
_topol_link.site_symmetry_2
_topol_link.distance
_topol_link.voronoi_solidangle
_topol_link.type
_topol_link.multiplicity
C1 C1 1_0_0_0 13_0_0_0 1.5446 22.04 v 16
_topol_repres.overall_topology_RCSR dia
;
;
Connectivity of an underlying net of the calcite
(CaCO3) crystal structure. The nodes of the underlying
net correspond to Ca atoms and carbonate (CO3) groups.
The underlying net has the NaCl (pcu-b in the RCSR
nomenclature) topology.
;
;
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -y,x-y,z
# Other symmetry elements elided
20 1/3+x-y,2/3-y,1/6-z
# Other symmetry elements elided
36 1/3-y,2/3-x,1/6+z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
C1 C 6 0.00000 0.00000 0.25000 1.0000
O1 O 18 0.25930 0.00000 0.25000 1.0000
Ca1 Ca 6 0.00000 0.00000 0.00000 1.0000
loop_
_topol_repres_node.label
_topol_repres_node.chemical_formula_sum
_topol_repres_node.fract_x
_topol_repres_node.fract_y
_topol_repres_node.fract_z
ZA1 Ca 0.00000 0.00000 0.25000
ZB1 CO3 0.00000 0.00000 0.00000
loop_
_topol_link.node_label_1
_topol_link.node_label_2
_topol_link.site_symmetry_1
_topol_link.site_symmetry_2
_topol_link.distance
_topol_link.type
_topol_link.multiplicity
ZA1 ZB1 1_0_0_0 20_-1_-1_0 3.2122 v 36
_topol_repres.overall_topology_RCSR pcu-b
;
;
Connectivity of an underlying net of the cuprite (Cu2O)
crystal structure. Oxygen atoms coincide with the nodes,
while copper atoms represent the edges. There are two
interpenetrating networks of the diamond topology.
;
;
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,1/2-y,z
# Symmetry elements elided
13 -y,-x,-z
# Symmetry elements elided
48 1/2-z,y,1/2-x
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
O1 O 2 0.25000 0.25000 0.25000 1.0000
Cu1 Cu 4 0.00000 0.00000 0.00000 1.0000
loop_
_topol_repres_node.label
_topol_repres_node.atom_label
Node1 O1
loop_
_topol_link.id
_topol_link.node_label_1
_topol_link.node_label_2
_topol_link.site_symmetry_1
_topol_link.site_symmetry_2
_topol_link.type
_topol_link.multiplicity
1 Node1 Node1 1_0_0_0 13_0_0_0 v 4
loop_
_topol_repres_edge.id
_topol_repres_edge.chemical_formula_sum
1 Cu1
_topol_repres.overall_topology_RCSR dia
_topol_repres_entangl.type interp
_topol_repres_entangl.interp_deg 2
_topol_repres_entangl.interp_class Ia
;
save_
save__topol.repres_occurrence_total
_definition.id '_topol.repres_occurrence_total'
_name.category_id topol
_name.object_id repres_occurrence_total
_definition.update 2018-02-13
_description.text
;
The total number of occurrences in literature and databases of the
underlying net topology at the time the data file was prepared.
;
_type.contents Count
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save__topol.special_details
_definition.id '_topol.special_details'
_name.category_id topol
_name.object_id special_details
_definition.update 2018-01-30
_description.text
;
The description of topological information not covered by the
existing data names in the topology categories.
;
_type.contents Text
_type.purpose Describe
_type.source Assigned
_type.container Single
save_
save_topol_link
_definition.id topol_link
_name.category_id TOPOLOGY
_name.object_id topol_link
_definition.update 2018-01-30
_definition.scope Category
_definition.class Loop
_description.text
;
The TOPOL_LINK category describes the crystal structure
connectivity and encodes the weighted colored labeled quotient
graph, from which the whole periodic net describing the
overall topology of the crystal structure can be restored.
The connections described in TOPOL_LINK may correspond to
any vectors in the structure, not just bonds or contacts. The
nodes that are linked are listed in TOPOL_REPRES_NODE.
;
loop_
_category_key.name
'_topol_link.id'
save_
save__topol_link.node_label_1
_definition.id '_topol_link.node_label_1'
_name.category_id topol_link
_name.object_id node_label_1
_definition.update 2018-01-30
_type.contents Code
_description.text
;
The labels of two nodes that form a link. These must match
nodes specified in topol_repres_node
;
_type.purpose Link
_type.source Related
_type.container Single
_name.linked_item_id '_topol_repres_node.label'
save_
save__topol_link.node_label_2
_definition.id '_topol_link.node_label_2'
_name.category_id topol_link
_name.object_id node_label_2
_definition.update 2018-01-30
_type.contents Code
_description.text
;
The labels of two nodes that form a link. These must match
nodes specified in topol_repres_node
;
_type.purpose Link
_type.source Related
_type.container Single
_name.linked_item_id '_topol_repres_node.label'
save_
save_topol_link.distance
_definition.id '_topol_link.distance'
_name.category_id topol_link
_name.object_id distance
_definition.update 2018-01-30
_description.text 'The link length in angstroms.'
_enumeration.range 0.:
_type.contents Real
_type.purpose Measurand
_type.source Derived
_type.container Single
_units.code angstroms
save_
save_topol_link.id
_definition.id '_topol_link.id'
_name.category_id topol_link
_name.object_id id
_definition.update 2018-01-30
_description.text 'The identifier of the link.'
_type.contents Code
_type.purpose Key
_type.source Assigned
_type.container Single
save_
save_topol_link.multiplicity
_definition.id '_topol_link.multiplicity'
_name.category_id topol_link
_name.object_id multiplicity
_definition.update 2018-01-30
_description.text 'The number of these links in the
unit cell.'
_enumeration.range 1:
_type.contents Integer
_type.purpose Number
_type.source Derived
_type.container Single
save_
save_topol_link.site_symmetry_1
_definition.id '_topol_link.site_symmetry_1'
_name.category_id topol_link
_name.object_id site_symmetry_1
_definition.update 2018-01-30
_type.contents Code
_description.text
;
The symmetry code of each node as the symmetry-equivalent
position number n and the cell translation number xyz. These
numbers are combined to form the code n_x_y_z. The character
string n_x_y_z is composed as follows: n refers to the symmetry
operation that is applied to the coordinates of the node. It
must match a number given in _space_group.symop_id. x, y and z
are the translations that are subsequently applied to the
symmetry-transformed coordinates to generate the node used in
calculating the link. x, y and z can be any integer values.
Note that this is a different convention to that used in the
core dictionary.
;
loop_
_description_example.case
21_1_1_0
_type.purpose Encode
_type.source Derived
_type.container Single
save_
save_topol_link.site_symmetry_2
_definition.id '_topol_link.site_symmetry_2'
_name.category_id topol_link
_name.object_id site_symmetry_2
_definition.update 2018-01-30
_type.contents Code
_description.text
;
The symmetry code of each node as the symmetry-equivalent
position number n and the cell translation number xyz. These
numbers are combined to form the code n_x_y_z. The character
string n_x_y_z is composed as follows: n refers to the symmetry
operation that is applied to the coordinates of the node. It
must match a number given in _space_group_symop_id. x, y and z
are the translations that are subsequently applied to the
symmetry-transformed coordinates to generate the node used in
calculating the link. x, y and z can be any integer values.
Note that this is a different convention to that used in the
core dictionary.
;
loop_
_description_example.case
21_1_1_0
_type.purpose Encode
_type.source Derived
_type.container Single
save_
save_topol_link.type
_definition.id '_topol_link.type'
_name.category_id topol_link
_name.object_id type
_definition.update 2018-02-06
_type.container Single
_type.purpose State
_description.text
;
The chemical bond type associated with the connection between the
two sites.
;
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
sg 'single bond'
db 'double bond'
tr 'triple bond'
qd 'quadruple bond'
ar 'aromatic bond'
dl 'delocalized double bond'
v 'valence bond'
pi 'pi bond'
hb 'hydrogen bond'
s 'specific bond'
hg 'halogen bond'
vw 'van der Waals contact'
no 'no bond'
ab 'any kind of bond (unspecified)'
_type.source Assigned
save_
save_topol_link.voronoi_solidangle
_definition.id '_topol_link.voronoi_solidangle'
_name.category_id topol_link
_name.object_id voronoi_solidangle
_definition.update 2018-02-06
_enumeration.range 1:50
_description.text
;
The solid angle fraction of the interatomic contact A-X, which is
the percentage of the sphere of unit radius cut by the pyramid with
the
basal face of the Voronoi polyhedron of A or X, the two atoms defining
the contact. The total solid angle (the whole sphere) is equal to 100.
The face used is that corresponding to the A-X interatomic contact.
;
_type.contents Real
_type.purpose Measurand
_type.source Derived
_type.container Single
_units.code none
save_
save_topol_repres
_definition.id topol_repres
_name.category_id TOPOLOGY
_name.object_id topol_repres
_definition.update 2018-01-30
_definition.scope Category
_definition.class Set
_description.text
;
The TOPOL_REPRES category describes a particular crystal
structure representation, which corresponds to the periodic
(underlying) net topology specified in the TOPOL_BOND
category. The underlying net is the net of centroids of
structural units. The edges of this net represent the links
between the units.
;
save_
save__topol_repres.genus
_definition.id '_topol_repres.genus'
_name.category_id topol_repres
_name.object_id genus
_definition.update 2018-02-06
_description.text
;
The genus of the underlying net, defined as the cyclomatic number of
its
own quotient graph: g = 1 + e - v, where e and v are the number of
edges and vertices in the quotient graph. The quotient graph is a
finite
graph that contains all of the information of the periodic net: the
vertices
of the graph are the vertices of a translational repeat unit and the
edges
are all the edges of the repeat unit. See O. Delgado_Friedrichs, M.
O'Keeffe
J. Sol. State Chem. 178 (2005) 2480-2485
;
_type.contents Index
_type.purpose Number
_type.source Derived
_type.container Single
save_
save__topol_repres.overall_topology
_definition.id '_topol_repres.overall_topology'
_name.category_id topol_repres
_name.object_id overall_topology
_definition.update 2018-01-30
_description.text
;
The overall topology symbol in an arbitrary form.
;
_type.contents Text
loop_
_description_example.case
'face-centered cubic topology'
_type.purpose Describe
_type.source Assigned
_type.container Single
save_
save__topol_repres.overall_topology_EPINET
_definition.id
'_topol_repres.overall_topology_EPINET'
_name.category_id topol_repres
_name.object_id overall_topology_EPINET
_definition.update 2018-01-30
_description.text
;
The identifier for the overall topology as listed
in the EPINET database at http://epinet.anu.edu.au
;
_type.contents Text
loop_
_description_example.case
sqc6
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres.overall_topology_RCSR
_definition.id
'_topol_repres.overall_topology_RCSR'
_name.category_id topol_repres
_name.object_id overall_topology_RCSR
_definition.update 2018-01-30
_description.text
;
The overall topology symbol according to the RCSR nomenclature
described
by O'Keeffe, M., Peskov, M.A., Ramsden S. J., Yaghi O.M. (2008) Acc.
Chem.
Res. 41, 1782-1789.
;
_type.contents Text
loop_
_description_example.case
dia
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres.overall_topology_SP
_definition.id '_topol_repres.overall_topology_SP'
_name.category_id topol_repres
_name.object_id overall_topology_SP
_definition.update 2018-01-30
_description.text
;
The overall topology symbol according to the nomenclature of
Fischer for sphere packings described in Koch, E., Fischer, W.
and Sowa, H. (2006) Acta Cryst. A62, 152-167.
;
_type.contents Text
loop_
_description_example.case
4/6/c1
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres.overall_topology_TOPOS
_definition.id
'_topol_repres.overall_topology_TOPOS'
_name.category_id topol_repres
_name.object_id overall_topology_TOPOS
_definition.update 2018-02-06
_description.text
;
The overall topology symbol according to the TOPOS nomenclature. TOPOS
symbols NDn are interpreted as follows: N is a sequence of degrees
(coordination numbers) of all independent nodes; D is one of the
letters
C (chain), L (layer) or T (three-periodic) designating the
dimensionality
of the net; and n enumerates non-isomorphic nets with a given ND
sequence.
For finite (molecular) graphs the symbols NMK-n are used, where k is
the
number of vertices (atoms) in the graph. See Alexandrov, E.V., Blatov,
V.A.,
Kochetkov, A.V. & Proserpio, D.M. (2011) CrystEngComm, 13, 3947-3958.
;
_type.contents Text
loop_
_description_example.case
'3,3,4T3'
_description_example.detail
;
The third three-periodic trinodal net with two 3-coordinated and one
4-coordinated independent nodes
;
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres.period
_definition.id '_topol_repres.period'
_name.category_id topol_repres
_name.object_id period
_definition.update 2018-01-30
_type.container Single
_type.purpose State
_description.text
;
Periodicity of the underlying net. The allowed data values
have the following meaning:
0 0-periodic (finite)
1 1-periodic (chain)
2 2-periodic (layer)
3 3-periodic (framework)
;
_type.contents Count
_enumeration.range 0:3
_type.source Derived
save_
save__topol_repres.td10
_definition.id '_topol_repres.td10'
_name.category_id topol_repres
_name.object_id td10
_definition.update 2018-01-30
_description.text
;
The topological density TD10 of the underlying net. This is the
cumulative
sum of the first ten shells of topological neighbours including the
central
atom. For structures with more than one kind of vertex in the
asymmetric
unit the value given is a weighted average over the vertices.
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save__topol_repres.total_point_symbol
_definition.id '_topol_repres.total_point_symbol'
_name.category_id topol_repres
_name.object_id total_point_symbol
_definition.update 2018-01-30
_description.text
;
The total point symbol of the underlying net. This value summarizes
all the
point symbols for the non-equivalent nodes with their stoichiometric
coefficients.
;
_type.contents Text
loop_
_description_example.case
_description_example.detail
'{6^6}' 'Point symbol for diamond'
'{4.6^2}_2{4^2.6^10.8^3}' '3,6-coordinated underlying net of
TiO2'
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save_topol_repres_edge
_definition.id topol_repres_edge
_name.category_id TOPOLOGY
_name.object_id topol_repres_edge
_definition.update 2018-01-30
_definition.scope Category
_definition.class Loop
_description.text
;
The TOPOL_REPRES_EDGE category describes the chemical composition of
the edges of the underlying net.
;
_category_key.name '_topol_repres_edge.id'
save_
save__topol_repres_edge.chemical_formula_iupac
_definition.id
'_topol_repres_edge.chemical_formula_iupac'
_name.category_id topol_repres_edge
_name.object_id chemical_formula_iupac
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node
expressed in conformance with IUPAC rules.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_edge.chemical_formula_moiety
_definition.id
'_topol_repres_edge.chemical_formula_moiety'
_name.category_id topol_repres_edge
_name.object_id chemical_formula_moiety
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node.
The formula is written in accordance with the rules of the
_chemical_formula_moiety tag.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_edge.chemical_formula_sum
_definition.id
'_topol_repres_edge.chemical_formula_sum'
_name.category_id topol_repres_edge
_name.object_id chemical_formula_sum
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node.
The formula is written in accordance with the rules of the
_chemical_formula_sum tag.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_edge.id
_definition.id '_topol_repres_edge.id'
_name.category_id topol_repres_edge
_name.object_id id
_definition.update 2018-01-30
_description.text
;The label of the edge. These must match labels
specified as _topol_link.id in the topol_link list.
;
_name.linked_item_id '_topol_link.id'
_type.contents Code
_type.purpose Link
_type.source Related
_type.container Single
save_
save_topol_repres_entangl
_definition.id topol_repres_entangl
_name.category_id TOPOLOGY
_name.object_id topol_repres_entangl
_definition.update 2018-01-30
_definition.scope Category
_definition.class Set
_description.text
;The TOPOL_REPRES_ENTANGL category describes entanglements in the
underlying net. An entangled net can be separated into two or
more motifs.
;
save_
save__topol_repres_entangl.interp_class
_definition.id '_topol_repres_entangl.interp_class'
_name.category_id topol_repres_entangl
_name.object_id interp_class
_definition.update 2018-01-30
_type.container Single
_type.purpose State
_description.text
;
The class of the interpenetration as defined in Baburin I. A.,
Blatov V. A., Carlucci L., Ciani G., Proserpio D. M. J. (2005)
Solid State Chem., 178, 2452-2474. The classes are determined
based on the way in which the overall net is generated from
individual identical motifs using combinations of translations
and symmetry elements.
;
_type.contents Text
loop_
_enumeration_set.state
_enumeration_set.detail
Ia 'all nets generated by a single translation'
Ib 'at least two vectors required to generate all
nets'
IIa 'all nets related by a single symmetry element'
IIb 'at least two symmetry elements required to generate all
nets'
IIIa 'all nets generated by a combination of a single
translation and single non-translating symmetry element'
IIIb 'all nets generated by a combination of at least two
translations and a single non-translating symmetry element'
IIIc 'all nets generated by a combination of a single
translation and at least two non-translating symmetry elements'
IIId 'a combination of at least two translations and at least
two non-translating symmetry elements required to generate all nets'
_type.source Assigned
save_
save__topol_repres_entangl.interp_deg
_definition.id '_topol_repres_entangl.interp_deg'
_name.category_id topol_repres_entangl
_name.object_id interp_deg
_definition.update 2018-01-30
_description.text 'The finite number of
interpenetrating nets.'
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save__topol_repres_entangl.period
_definition.id '_topol_repres_entangl.period'
_name.category_id topol_repres_entangl
_name.object_id period
_definition.update 2018-01-30
_type.container Single
_description.text
;
Periodicity of the entangled array. Integers are interpreted as
follows:
0 '0-periodic (finite)'
1 '1-periodic (chain)'
2 '2-periodic (layer)'
3 '3-periodic (framework)'
;
_enumeration.range 0:3
_type.contents Count
_type.purpose Number
_type.source Assigned
save_
save__topol_repres_entangl.type
_definition.id '_topol_repres_entangl.type'
_name.category_id topol_repres_entangl
_name.object_id type
_definition.update 2018-01-30
_type.container Single
_type.purpose State
_description.text
;The type of the entanglement as described in Proserpio, D. M.
(2010) Nat. Chem. 2, 435-436 and Carlucci L., Ciani G.,
Proserpio D. M., Mitina T. G., Blatov V. A. (2014) Chem.
Rev. 114, 7557-7580
;
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
borr Borromean
brun Brunnian
caten catenation
interp interpenetration
polycat_inc 'inclined polycatenation'
polycat_par 'parallel polycatenation'
polythread polythreading
selfcat self-catenation
undef 'no special type is assigned'
_type.source Assigned
save_
save_topol_repres_entangl_ERN
_definition.id topol_repres_entangl_ERN
_name.category_id TOPOLOGY
_name.object_id topol_repres_entangl_ERN
_definition.update 2018-02-13
_definition.scope Category
_definition.class Loop
_description.text
;
Topology of the entanglement described as an extended ring net (ERN).
The name of the extended ring net is specified in one or more of the
standard nomenclatures.
;
_category_key.name
'_topol_repres_entangl_ERN.nomenclature'
save_
save_topol_repres_entangl_ERN.name
_definition.id '_topol_repres_entangl_ERN.name'
_name.category_id topol_repres_entangl_ERN
_name.object_id name
_definition.update 2018-02-13
_description.text
;
The symbol or name of the extended ring net in the specified
nomenclature.
;
_type.contents Text
_type.purpose Describe
_type.source Assigned
_type.container Single
save_
save_topol_repres_entangl_ERN.nomenclature
_definition.id
'_topol_repres_entangl_ERN.nomenclature'
_name.category_id topol_repres_entangl_ERN
_name.object_id nomenclature
_definition.update 2018-02-13
_description.text
;
The nomenclature used to describe the extended ring net. See the
TOPOL_REPRES
category for detailed information on the source for the nomenclatures.
;
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
TOPOS 'The TOPOS nomenclature'
SP 'Sphere packing'
RCSR 'RCSR nomenclature'
Epinet 'Epinet database identifier'
Arbitrary 'Non-standard identifier'
_type.purpose Key
_type.source Assigned
_type.container Single
save_
save_topol_repres_entangl_HRN
_definition.id topol_repres_entangl_HRN
_name.category_id TOPOLOGY
_name.object_id topol_repres_entangl_HRN
_definition.update 2018-02-13
_definition.scope Category
_definition.class Loop
_description.text
;Topology of the entanglement described as a Hopf ring net (HRN).
The name of the extended ring net is specified in one or more of the
standard nomenclatures.
;
_category_key.name
'_topol_repres_entangl_HRN.nomenclature'
save_
save_topol_repres_entangl_HRN.name
_definition.id '_topol_repres_entangl_HRN.name'
_name.category_id topol_repres_entangl_HRN
_name.object_id name
_definition.update 2018-02-13
_description.text
'The symbol or name of the Hopf
ring net in the specified nomenclature.'
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save_topol_repres_entangl_HRN.nomenclature
_definition.id
'_topol_repres_entangl_HRN.nomenclature'
_name.category_id topol_repres_entangl_HRN
_name.object_id nomenclature
_definition.update 2018-02-13
_description.text
;The nomenclature used to describe the Hopf ring net. See the TOPOL_REPRES
category for detailed information on the source for the nomenclatures.
;
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
TOPOS 'The TOPOS nomenclature'
SP 'Sphere packing'
RCSR 'RCSR nomenclature'
Epinet 'Epinet database identifier'
Arbitrary 'Non-standard identifier'
_type.purpose Key
_type.source Assigned
_type.container Single
save_
save_topol_repres_node
_definition.id topol_repres_node
_name.category_id TOPOLOGY
_name.object_id topol_repres_node
_definition.update 2018-02-06
_definition.scope Category
_definition.class Set
_description.text
;The TOPOL_REPRES_NODE category describes the chemical composition,
structure
and topological properties of the nodes of the underlying net.
See Blatov V.A., O'Keeffe M., Proserpio D. M. CrystEngComm, 2010, 12,
44-48.
Nodes may be specified by reference to atom sites, or by explicitly
giving their
coordinates.
;
loop_
_category_key.name
'_topol_repres_node.label'
save_
save__topol_repres_node.atom_label
_definition.id '_topol_repres_node.atom_label'
_name.object_id atom_label
_name.category_id topol_repres_node
_definition.class Datum
_description.text
'The atom label corresponding to
this node. Not all nodes have to coincide with atom sites.'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
_name.linked_item_id '_atom_site.label'
save_
save__topol_repres_node.chemical_formula_iupac
_definition.id
'_topol_repres_node.chemical_formula_iupac'
_name.category_id topol_repres_node
_name.object_id chemical_formula_iupac
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node
expressed in conformance with IUPAC rules.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_node.chemical_formula_moiety
_definition.id
'_topol_repres_node.chemical_formula_moiety'
_name.category_id topol_repres_node
_name.object_id chemical_formula_moiety
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node.
The formula is written in accordance with the rules of the
_chemical_formula_moiety tag.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_node.chemical_formula_sum
_definition.id
'_topol_repres_node.chemical_formula_sum'
_name.category_id topol_repres_node
_name.object_id chemical_formula_sum
_definition.update 2018-01-30
_description.text
;Formula of the residue or ion, which corresponds to the node.
The formula is written in accordance with the rules of the
_chemical_formula_sum tag.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_node.CS
_definition.id '_topol_repres_node.CS'
_name.category_id topol_repres_node
_name.object_id CS
_definition.update 2018-02-06
_description.text
;The coordination sequence is a sequence of numbers counting the
atoms in the 1st, 2nd, 3rd etc. coordination shells of any given
node in the net. In other words, the kth entry in the list is the
number of vertices linked to the node by a path of exactly k
steps. It is usually listed up to k=10
;
_type.contents Integer
_type.container List
loop_
_description_example.case
_description_example.detail
[4 12 24 42 64 92 124 162 204 252] 'The diamond coordination
sequence'
_type.purpose Number
_type.source Derived
save_
save__topol_repres_node.ES
_definition.id '_topol_repres_node.ES'
_name.category_id topol_repres_node
_name.object_id ES
_definition.update 2018-02-06
_description.text
;The extended point symbol of the node lists all shortest circuits
for each angle for each non-equivalent atom. A(b).B(c)... there
are b A-rings and c B-rings for all the N(N-1) circuits per node.
It is sorted so shortest rings came first For 4-coordinated
nodess only, the angles are grouped in opposite pairs; ab,cd and
ac,bd and ad,bc (written in lexicographic order smallest numbers
first).
;
_type.contents Text
loop_
_description_example.case
_description_example.detail
6(2).6(2).6(2).6(2).6(2).6(2) 'ES for a vertex in the
diamond structure'
4.6(2).4.8(3).6(2).6(2) 'ES for one vertex of feldspar
net'
7(2).9(2).7(3).7(3).7(3).7(3) 'ES for the vertex of qzd
net'
4.4.4.4.6(3).6(3).6(5).6(5).6(5).6(5) 'ES for the vertex of 5-c
sqp net'
_type.purpose Encode
_type.source Derived
_type.container Single
save_
save__topol_repres_node.fract_x
_definition.id '_topol_repres_node.fract_x'
_name.object_id fract_x
_name.category_id topol_repres_node
_definition.class Datum
_import.get [{'save':fract_coord 'file':templ_attr.cif}]
save_
save__topol_repres_node.fract_y
_definition.id '_topol_repres_node.fract_y'
_name.object_id fract_y
_name.category_id topol_repres_node
_definition.class Datum
_import.get [{'save':fract_coord 'file':templ_attr.cif}]
save_
save__topol_repres_node.fract_z
_definition.id '_topol_repres_node.fract_z'
_name.object_id fract_z
_name.category_id topol_repres_node
_definition.class Datum
_import.get [{'save':fract_coord 'file':templ_attr.cif}]
save_
save__topol_repres_node.label
_definition.id '_topol_repres_node.label'
_name.category_id topol_repres_node
_name.object_id label
_definition.update 2018-01-30
_description.text
;The label of the node, which corresponds to a particular
node of the crystal structure representation.
;
_type.contents Text
_type.purpose Key
_type.source Assigned
_type.container Single
save_
save__topol_repres_node.point_symbol
_definition.id '_topol_repres_node.point_symbol'
_name.category_id topol_repres_node
_name.object_id point_symbol
_definition.update 2018-02-06
_description.text
;The (short) point symbol of the node. This lists the number and size of
the shortest closed chains of connected nodes (circuits) starting from
any non-equivalent node in the net. For a N-coordinated node there are
N(N-1) circuits
;
_type.contents Text
loop_
_description_example.case
_description_example.detail
6^6 'Point symbol for a diamond vertex'
4^2.6^3.8 'Point symbol for a feldspar 4-coordinated
vertex'
7^5.9 'Point symbol for the vertex of 4-c qzd net'
4^4.6^6 'Point symbol for the vertex of 5-c sqp net'
_type.purpose Encode
_type.source Derived
_type.container Single
save_
save__topol_repres_node.symmetry_multiplicity
_definition.id
'_topol_repres_node.symmetry_multiplicity'
_name.object_id symmetry_multiplicity
_name.category_id topol_repres_node
_definition.class Datum
_description.text
;The number of different sites that are generated by the
application of the space-group symmetry to the coordinates
given for this site. It is equal to the multiplicity given
for this Wyckoff site in International Tables for Cryst.
Vol. A (2002).
;
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Index
_enumeration.range 1:192
_definition.update 2018-02-23
save_
save__topol_repres_node.VS
_definition.id '_topol_repres_node.VS'
_name.category_id topol_repres_node
_name.object_id VS
_definition.update 2018-02-06
_description.text
;The vertex symbol of a node provides similar information to the
extended point symbol, but only for rings, which are circuits
that contain no shortcuts, that is, are not the sum of two
smaller circuits. There may be circuits that cannot be rings. If
there are no rings meeting at a particular angle of the node, the
symbol '*' is used instead of the A^a symbol. It is sorted so
shortest rings came first For 4-coordinated nodess only, the
angles are grouped in opposite pairs; ab,cd and ac,bd and ad,bc
(written in lexicographic order smallest numbers first). In the
ordering the symbol '*' is equivalent to zero.
;
_type.contents Text
loop_
_description_example.case
_description_example.detail
6(2).6(2).6(2).6(2).6(2).6(2) 'Vertex symbol for
diamond'
4.6(2).4.8.6.6(2) 'VS for one vertex of feldspar net'
7(2).*.7(3).7(3).7(3).7(3) 'VS for the vertex of qzd
net'
4.4.4.4.6.6.6(5).6(5).6(5).6(5) 'VS for the vertex of 5-c
sqp net'
_type.purpose Encode
_type.source Derived
_type.container Single
save_
save__topol_repres_node.Wyckoff_symbol
_definition.id '_topol_repres_node.Wyckoff_symbol'
_name.object_id Wyckoff_symbol
_name.category_id topol_repres_node
_definition.class Datum
_description.text
;The Wyckoff symbol (letter) as listed in the space-group section
of International Tables for Crystallography, Vol. A (1987).
;
_definition.update 2018-02-23
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save_topol_repres_occurrence
_definition.id topol_repres_occurrence
_name.category_id TOPOLOGY
_name.object_id topol_repres_occurrence
_definition.update 2018-01-30
_definition.scope Category
_definition.class Loop
_description.text
;The TOPOL_REPRES_OCCURRENCE category describes the occurrence of the
underlying net topology in crystal structures.
;
_category_key.name '_topol_repres_occurrence.id'
save_
save__topol_repres_occurrence.refcode
_definition.id '_topol_repres_occurrence.refcode'
_name.category_id topol_repres_occurrence
_name.object_id refcode
_definition.update 2018-01-30
_description.text
;Reference code in a crystallographic database to the
crystallographic data of the crystal structure with the
underlying net topology.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_occurrence.reference
_definition.id '_topol_repres_occurrence.reference'
_name.category_id topol_repres_occurrence
_name.object_id reference
_definition.update 2018-01-30
_description.text
;Reference to a publication, where a crystal structure with the
underlying net topology was characterized.
;
_type.contents Text
_type.purpose Describe
_type.source Assigned
_type.container Single
save_
save_topol_repres_occurrence.id
_definition.id '_topol_repres_occurrence.id'
_name.category_id topol_repres_occurrence
_name.object_id id
_definition.update 2018-02-13
_description.text 'A unique identifier for the
literature or database reference'
_type.contents Text
_type.purpose Key
_type.source Assigned
_type.container Single
save_
save_topol_repres_tiling
_definition.id topol_repres_tiling
_name.category_id TOPOLOGY
_name.object_id topol_repres_tiling
_definition.update 2018-02-06
_definition.scope Category
_definition.class Set
_description.text
;
The TOPOL_REPRES_TILING category describes the natural tiling
corresponding to the underlying net. A tiling is a
partition of crystal space using generalised polyhedra, and a
natural tiling is one for which tiles are the smallest possible
that conserve the full symmetry of the net and for which the
faces are all locally strong rings. This means that there is no
single largest face (face with the largest number of vertices)
as such a face will be the some of the other smaller faces.
The tile signature contains the sizes of the tile faces and
the number of faces of a given size in the tile.
See: Blatov V. A., Delgado-Friedrichs, O., O'Keeffe M.,
Proserpio D. M. Acta Cryst. 2007, A63, 418-425
;
save_
save__topol_repres_tiling.Dsize
_definition.id '_topol_repres_tiling.Dsize'
_name.category_id topol_repres_tiling
_name.object_id Dsize
_definition.update 2018-01-30
_description.text
;
The number of distinct (not symmetry-related) chambers in the
tiling.
;
_type.contents Index
_type.purpose Number
_type.source Derived
_type.container Single
save_
save__topol_repres_tiling.dual
_definition.id '_topol_repres_tiling.dual'
_name.category_id topol_repres_tiling
_name.object_id dual
_definition.update 2018-01-30
_description.text
;
The overall topology symbol of the dual net, which corresponds
to the net of the dual of the natural tiling.
;
_type.contents Text
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_tiling.edges
_definition.id '_topol_repres_tiling.edges'
_name.category_id topol_repres_tiling
_name.object_id edges
_definition.update 2018-01-30
_description.text
;
Number of independent tile edges in the natural tiling.
;
_type.contents Index
_type.purpose Number
_type.source Recorded
_type.container Single
save_
save__topol_repres_tiling.faces
_definition.id '_topol_repres_tiling.faces'
_name.category_id topol_repres_tiling
_name.object_id faces
_definition.update 2018-01-30
_description.text
;
Number of independent tile faces in the natural tiling.
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save__topol_repres_tiling.signature
_definition.id '_topol_repres_tiling.signature'
_name.category_id topol_repres_tiling
_name.object_id signature
_definition.update 2018-02-06
_description.text
;
The tiling signature, written in the form \a[A^a^ . B^b^ ...]+\b[C^c^
. D^d^ ...]+...,
where square brackets envelop tile symbols, \a,\b,... are
stoichiometric
coefficients, A, B, C, D, ... are sizes of tile faces, a,b,c,d, ... are
numbers of the faces of a given size in the tile.
The signature is written in a lexicographic order, smallest numbers
first:
5[6^4^]+[6^3^] = 56463 better than [6^3^]+5[6^4^] = 63564
;
_type.contents Text
loop_
_description_example.case
_description_example.detail
'[6^4]' 'Natural tiling for diamond'
'3[4^6]+[4^6.6^8]+[4^12.6^8.8^6]' 'Natural tiling for
zeolite LTA'
_type.purpose Encode
_type.source Assigned
_type.container Single
save_
save__topol_repres_tiling.tiles
_definition.id '_topol_repres_tiling.tiles'
_name.category_id topol_repres_tiling
_name.object_id tiles
_definition.update 2018-01-30
_description.text
;
Number of independent tiles in the natural tiling.
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save__topol_repres_tiling.vertices
_definition.id '_topol_repres_tiling.vertices'
_name.category_id topol_repres_tiling
_name.object_id vertices
_definition.update 2018-01-30
_description.text
;
Number of independent tile vertices in the natural tiling.
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save_topol_repres_tiling_faces
_definition.id topol_repres_tiling_faces
_name.category_id TOPOLOGY
_name.object_id topol_repres_tiling_faces
_definition.update 2018-02-13
_definition.scope Category
_definition.class Loop
_description.text
;
The TOPOL_REPRES_TILING_FACES category tabulates the faces
belonging to each tile in the tiling. Together with the
TOPOL_REPRES_TILING_TILES category it tabulates the information
contained in _topol_repres_tiling.signature. See the
TOPOL_REPRES_TILING category for further information.
;
loop_
_category_key.name
'_topol_repres_tiling_faces.tile_id'
'_topol_repres_tiling_faces.size'
loop_
_description_example.detail
_description_example.case
'Expanded description of 3[4^6^]+[4^6^.6^8^]+[4^12^.6^8^.8^6^]
tiling'
;
loop_
_topol_repres_tiling_tile.id
_topol_repres_tiling_tile.count
a 3
b 1
c 1
loop_
_topol_repres_tiling_faces.tile_id
_topol_repres_tiling_faces.size
_topol_repres_tiling_faces.count
a 4 6
b 4 6
b 6 8
c 4 12
c 6 8
c 8 6
;
save_
save_topol_repres_tiling_faces.count
_definition.id '_topol_repres_tiling_faces.count'
_name.category_id topol_repres_tiling_faces
_name.object_id count
_definition.update 2018-02-13
_description.text
;
The number of faces of this size in the tile
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save_topol_repres_tiling_faces.size
_definition.id '_topol_repres_tiling_faces.size'
_name.category_id topol_repres_tiling_faces
_name.object_id size
_definition.update 2018-02-13
_description.text
;
The size of the tile face.
;
_type.contents Count
_enumeration.range 3:
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save_topol_repres_tiling_faces.tile_id
_definition.id '_topol_repres_tiling_faces.tile_id'
_name.category_id topol_repres_tiling_faces
_name.object_id tile_id
_definition.update 2018-02-13
_description.text
;
The tile to which this face belongs. It must be one of the values
provided
in _topol_repres_tiling_tile.id
;
_type.contents Code
_name.linked_item_id '_topol_repres_tiling_tile.id'
_type.purpose Link
_type.source Related
_type.container Single
save_
save_topol_repres_tiling_tile
_definition.id topol_repres_tiling_tile
_name.category_id TOPOLOGY
_name.object_id topol_repres_tiling_tile
_definition.update 2018-02-13
_definition.scope Category
_definition.class Loop
_description.text
;
The TOPOL_REPRES_TILING_TILE category provides information on
each of the tiles in the tiling. Together with the
TOPOL_REPRES_TILING_FACES category it tabulates the information
contained in _topol_repres_tiling.signature. See the
TOPOL_REPRES_TILING category for further information.
;
_category_key.name '_topol_repres_tiling_tile.id'
save_
save_topol_repres_tiling_tile.count
_definition.id '_topol_repres_tiling_tile.count'
_name.category_id topol_repres_tiling_tile
_name.object_id count
_definition.update 2018-02-13
_description.text
;
The number of this kind of tile in the tiling.
;
_type.contents Index
_type.purpose Number
_type.source Assigned
_type.container Single
save_
save_topol_repres_tiling_tile.id
_definition.id '_topol_repres_tiling_tile.id'
_name.category_id topol_repres_tiling_tile
_name.object_id id
_definition.update 2018-02-13
_description.text
;
An arbitrary, unique identifier for this tile type.
;
_type.contents Code
_type.purpose Key
_type.source Assigned
_type.container Single
save_
loop_
_dictionary_audit.version
_dictionary_audit.date
_dictionary_audit.revision
0.3 2018-02-23
;
Changed topol_bond to topol_link using node labels instead of atom
labels.
Added coordinates, multiplicity and Wyckoff symbol to
topol_repres_node. Added
in type and linking information. (J Hester.)
;
0.4 2018-02-27
;
Added long-form examples provided by V Blatov. Version for review.
;
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