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The review period having well and truly finished, it is now approved and will be sent off for technical editing. My thanks to Vladislav Blatov and Davide Proserpio for initiating this project.
Re: Topology CIF dictionary for discussion and review
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: Re: Topology CIF dictionary for discussion and review
- From: James Hester <jamesrhester@gmail.com>
- Date: Mon, 4 Jun 2018 15:08:21 +1000
- Cc: Vladislav Blatov <blatov@gmail.com>,Davide Proserpio <davide.proserpio@unimi.it>
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Dear COMCIFS,
The discussion period for the Topological CIF dictionary saw some important issues raised and resolved. The final updated version is at https://github.com/COMCIFS/TopoCif/blob/master/Topology.dic. , and differs primariliy from the review version in having dropped most datanames connected with entanglement pending resolution within the community on the best way to describe it.The review period having well and truly finished, it is now approved and will be sent off for technical editing. My thanks to Vladislav Blatov and Davide Proserpio for initiating this project.
best wishes,
JamesOn 27 February 2018 at 16:11, James Hester <jamesrhester@gmail.com> wrote:
James.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/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/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 .TopoCif/issues ), or by you forwarding an email from them to this list.TopoCif/blob/master/Topology. dic --T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
#\#CIF_2.0
############################################################ #####################
#Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ÂÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â #
#         Topology CIF dictionary                   Â                         #
#Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ÂÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â #
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data_TOPOLOGY_CIF
_dictionary.title            Â         TOPOLOGY_CIF
_dictionary.class            Â         Instance
_dictionary.version          Â         0.4
_dictionary.ddl_conformance  Â         3.13.1
_dictionary.date             Â         2018-02-27
_description.text            Â        Â
;
 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               Â         TOPOLOGY
_definition.scope            Â         Category
_definition.class            Â         Head
_description.text
                             'This category is the parent of all categories in the dictionary'
_name.object_id              Â         TOPOLOGY
_name.category_id            Â         TOPOLOGY_CIF
save_
save_topol
_definition.id               Â         topol
_name.category_id            Â         TOPOLOGY
_name.object_id              Â         topol
_definition.update           Â         2018-01-30
_definition.scope            Â         Category
_definition.class            Â         Set
_description.text            Â        Â
;Â Â Â Â Â Â Â Â Â Â Â Â
             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
;Â
  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
;
;Â
  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
;
;Â
  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               Â         '_topol.repres_occurrence_ total'
_name.category_id            Â         topol
_name.object_id              Â         repres_occurrence_total
_definition.update           Â         2018-02-13
_description.text            Â        Â
;
    The total number of occurrences in literature and databases of the
    underlying net topology at the time the data file was prepared.
;
_type.contents               Â         Count
_type.purpose                Â         Number
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol.special_details
_definition.id               Â         '_topol.special_details'
_name.category_id            Â         topol
_name.object_id              Â         special_details
_definition.update           Â         2018-01-30
_description.text            Â        Â
;Â Â Â
    The description of topological information not covered by the
    existing data names in the topology categories.
;
_type.contents               Â         Text
_type.purpose                Â         Describe
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save_topol_link
_definition.id               Â         topol_link
_name.category_id            Â         TOPOLOGY
_name.object_id              Â         topol_link
_definition.update           Â         2018-01-30
_definition.scope            Â         Category
_definition.class            Â         Loop
_description.text            Â        Â
;Â Â Â Â Â Â Â Â Â
          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               Â         '_topol_link.node_label_1'
_name.category_id            Â         topol_link
_name.object_id              Â         node_label_1
_definition.update           Â         2018-01-30
_type.contents               Â         Code
_description.text            Â        Â
;Â Â Â
    The labels of two nodes that form a link. These must match
    nodes specified in topol_repres_node
;
_type.purpose                Â         Link
_type.source                 Â         Related
_type.container              Â         Single
_name.linked_item_id         Â         '_topol_repres_node.label'
save_
save__topol_link.node_label_2
_definition.id               Â         '_topol_link.node_label_2'
_name.category_id            Â         topol_link
_name.object_id              Â         node_label_2
_definition.update           Â         2018-01-30
_type.contents               Â         Code
_description.text            Â        Â
;Â Â Â
    The labels of two nodes that form a link. These must match
    nodes specified in topol_repres_node
;
_type.purpose                Â         Link
_type.source                 Â         Related
_type.container              Â         Single
_name.linked_item_id         Â         '_topol_repres_node.label'
save_
save_topol_link.distance
_definition.id               Â         '_topol_link.distance'
_name.category_id            Â         topol_link
_name.object_id              Â         distance
_definition.update           Â         2018-01-30
_description.text            Â         'The link length in angstroms.'
_enumeration.range           Â         0.:
_type.contents               Â         Real
_type.purpose                Â         Measurand
_type.source                 Â         Derived
_type.container              Â         Single
_units.code                  Â         angstroms
save_
save_topol_link.id
_definition.id               Â         '_topol_link.id'
_name.category_id            Â         topol_link
_name.object_id              Â         id
_definition.update           Â         2018-01-30
_description.text            Â         'The identifier of the link.'
_type.contents               Â         Code
_type.purpose                Â         Key
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save_topol_link.multiplicity
_definition.id               Â         '_topol_link.multiplicity'
_name.category_id            Â         topol_link
_name.object_id              Â         multiplicity
_definition.update           Â         2018-01-30
_description.text            Â         'The number of these links in the unit cell.'
_enumeration.range           Â         1:
_type.contents               Â         Integer
_type.purpose                Â         Number
_type.source                 Â         Derived
_type.container              Â         Single
save_
save_topol_link.site_symmetry_1
_definition.id               Â         '_topol_link.site_symmetry_1'
_name.category_id            Â         topol_link
_name.object_id              Â         site_symmetry_1
_definition.update           Â         2018-01-30
_type.contents               Â         Code
_description.text            Â        Â
;Â Â Â
    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                Â         Encode
_type.source                 Â         Derived
_type.container              Â         Single
save_
save_topol_link.site_symmetry_2
_definition.id               Â         '_topol_link.site_symmetry_2'
_name.category_id            Â         topol_link
_name.object_id              Â         site_symmetry_2
_definition.update           Â         2018-01-30
_type.contents               Â         Code
_description.text            Â        Â
;
    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                Â         Encode
_type.source                 Â         Derived
_type.container              Â         Single
save_
save_topol_link.type
_definition.id               Â         '_topol_link.type'
_name.category_id            Â         topol_link
_name.object_id              Â         type
_definition.update           Â         2018-02-06
_type.container              Â         Single
_type.purpose                Â         State
_description.text            Â        Â
;
    The chemical bond type associated with the connection between the
    two sites.
;
_type.contents               Â         Code
loop_
 _enumeration_set.state
 _enumeration_set.detail
        sg       'single bond'     Â
        db       'double bond'     Â
        tr       'triple bond'     Â
        qd       'quadruple bond'  Â
        ar       'aromatic bond'   Â
        dl       'delocalized double bond'   Â
        v        'valence bond'    Â
        pi       'pi bond'         Â
        hb       'hydrogen bond'   Â
        s        'specific bond'   Â
        hg       'halogen bond'    Â
        vw       'van der Waals contact'     Â
        no       'no bond'         Â
        ab       'any kind of bond (unspecified)'
_type.source                 Â         Assigned
save_
save_topol_link.voronoi_solidangle
_definition.id               Â         '_topol_link.voronoi_ solidangle'
_name.category_id            Â         topol_link
_name.object_id              Â         voronoi_solidangle
_definition.update           Â         2018-02-06
_enumeration.range           Â         1:50
_description.text            Â        Â
;
    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               Â         Real
_type.purpose                Â         Measurand
_type.source                 Â         Derived
_type.container              Â         Single
_units.code                  Â         none
save_
save_topol_repres
_definition.id               Â         topol_repres
_name.category_id            Â         TOPOLOGY
_name.object_id              Â         topol_repres
_definition.update           Â         2018-01-30
_definition.scope            Â         Category
_definition.class            Â         Set
_description.text            Â        Â
;
    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               Â         '_topol_repres.genus'
_name.category_id            Â         topol_repres
_name.object_id              Â         genus
_definition.update           Â         2018-02-06
_description.text            Â        Â
;Â Â Â
    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               Â         Index
_type.purpose                Â         Number
_type.source                 Â         Derived
_type.container              Â         Single
save_
save__topol_repres.overall_topology
_definition.id               Â         '_topol_repres.overall_ topology'
_name.category_id            Â         topol_repres
_name.object_id              Â         overall_topology
_definition.update           Â         2018-01-30
_description.text            Â        Â
;
    The overall topology symbol in an arbitrary form.
;
_type.contents               Â         Text
loop_
 _description_example.case
        'face-centered cubic topology'
_type.purpose                Â         Describe
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol_repres.overall_topology_EPINET
_definition.id               Â         '_topol_repres.overall_ topology_EPINET'
_name.category_id            Â         topol_repres
_name.object_id              Â         overall_topology_EPINET
_definition.update           Â         2018-01-30
_description.text            Â        Â
;
    The identifier for the overall topology as listed
    in the EPINET database at http://epinet.anu.edu.au
;
_type.contents               Â         Text
loop_
 _description_example.case
        sqc6
_type.purpose                Â         Encode
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol_repres.overall_topology_RCSR
_definition.id               Â         '_topol_repres.overall_ topology_RCSR'
_name.category_id            Â         topol_repres
_name.object_id              Â         overall_topology_RCSR
_definition.update           Â         2018-01-30
_description.text            Â        Â
;
    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               Â         Text
loop_
 _description_example.case
        dia
_type.purpose                Â         Encode
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol_repres.overall_topology_SP
_definition.id               Â         '_topol_repres.overall_ topology_SP'
_name.category_id            Â         topol_repres
_name.object_id              Â         overall_topology_SP
_definition.update           Â         2018-01-30
_description.text            Â        Â
;
    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               Â         Text
loop_
 _description_example.case
        4/6/c1
_type.purpose                Â         Encode
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol_repres.overall_topology_TOPOS
_definition.id               Â         '_topol_repres.overall_ topology_TOPOS'
_name.category_id            Â         topol_repres
_name.object_id              Â         overall_topology_TOPOS
_definition.update           Â         2018-02-06
_description.text            Â        Â
;
    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               Â         Text
loop_
 _description_example.case
        '3,3,4T3'
_description_example.detail  Â        Â
;
   The third three-periodic trinodal net with two 3-coordinated and one
   4-coordinated independent nodes
;
_type.purpose                Â         Encode
_type.source                 Â         Assigned
_type.container              Â         Single
save_
save__topol_repres.period
_definition.id               Â         '_topol_repres.period'
_name.category_id            Â         topol_repres
_name.object_id              Â         period
_definition.update           Â         2018-01-30
_type.container              Â         Single
_type.purpose                Â         State
_description.text            Â        Â
;
    Periodicity of the underlying net. The allowed data values
    have the following meaning:
        0        0-periodic (finite)       Â
        1        1-periodic (chain)       Â
        2        2-periodic (layer)        Â
        3        3-periodic (framework)
;
_type.contents               Â         Count
_enumeration.range           Â         0:3