#\#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. ;