Index

Topology dictionary (topoCIF) version 0.9.6

Revision history

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Version 0.3.0 ()
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       Changed topol_bond to topol_link using node labels instead of atom
       labels. Added coordinates, multiplicity and Wyckoff symbol to topol_node.
       Added in type and linking information. (J Hester.)

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Version 0.4.0 ()
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       Added long-form examples provided by V Blatov. Version for review.

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Version 0.5.0 ()
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       Added InChI, SMILES structural formulas and replaced symops with explicit
       symmetry operator ids and vector translations. Clarified bond types.

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Version 0.9.0 ()
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       Version for final approval after review. Removed most tags from
       TOPOL_ENTANGL and subcategories.

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Version 0.9.1 ()
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       Fixed a few typos. (B. McMahon)

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Version 0.9.2 ()
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       Replaced TOPOL_REPRES category by TOPOL_NET; all TOPOL_REPRES categories
       are moved to TOPOL category; Examples 4 and 5 added

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Version 0.9.3 ()
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       Added CIF-1.0 equivalents for _topol_link.site_symmetry_translation_1,
       _topol_link.site_symmetry_translation_2, and
       _topol_node.coordination_sequence (B. Hanson and V. Blatov)

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Version 0.9.4 ()
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       Added TOPOL_ATOM subcategory, _topol_link.node_id_1,
       _topol_link.node_id_2, _topol_link.structural_formula_InChI,
       _topol_link.structural_formula_SMILES, and _topol_node.id items
       Removed TOPOL_EDGE subcategory
       Renamed _topol_link.site_symmetry_symop_1(2) to _topol_link.symop_1(2)
       _topol_link.site_symmetry_translation_1(2)
       to _topol_link.translation_1(2)
       _topol_node.site_symmetry_symop_1(2) to _topol_node.symop_1(2)
       _topol_node.site_symmetry_translation_1(2)
       to _topol_node.translation_1(2)
       (V. Blatov)
       editorial adjustments, formatting (B. Hanson)

       Corrected the definitions of the _topol_node.fract_x,
       _topol_node.fract_y and _topol_node.fract_z data items. (A. Vaitkus)

       added _topol_net.label
       changing "dataname" to "tag" as per VOl. G 2.2.3.3.4 and 2.2.2(2)
       changing "field" to "data value" or "value" as per Vol. G 2.2.3.1.5
       and 2.2.3.1.7
       changing various terms to "loop" as per Vol. g 2.2.2(4) and 2.2.3.1.7
       updated Example 5 for net.id being a number
       temporarily replaced examples 1-4 with TODO as a reminder to get these
       updated
       changing ATOM_SITE.label to _atom_site.label
       changed "block" or "section" to "data items" or "category"
       changed elemental_symbol to element_symbol
       added _topol_link.net_id
       updated examples 2-4 for _chemical_formula_sum  and ATOM_TYPE
       (B. Hanson)

       added new tags (V. Blatov)
       _topol_link.label
       _topol_net.overall_topology_IZA
       _topol_tiling.id
       _topol_tiling.net_id
       _topol_tiling_tile.tiling_id
       added Example 5; renamed old Example 5 to Example 6 (V. Blatov)

       switched _topol_*.id to Integer/enum 1: (B. Hanson)

       Renamed data items _topol_atom.symop, _topol_link.symop_1 and
       _topol_link.symop_2 to _topol_atom.symop_id, _topol_link.symop_id_1
       and _topol_link.symop_id_2 respectively. Adjusted multiple examples
       and data item definitions to reflect this change. (A. Vaitkus)

       Added an enumeration range of 0: to the _topol_tiling_tile.count
       and _topol_tiling_faces.count data items. (A. Vaitkus)

       Renamed data item _topol_net.overall_topology_rscr to
       _topol_net.overall_topology_RCSR. (A. Vaitkus)

       Updated several descriptions by replacing the term 'tag' with
       'data item' and correcting data item references. (A. Vaitkus)

       Added _topol_node.symop_id and _topol_node.translation* (B. Hanson)

       issue #37 Removed method for _topol_node.fract_* (B. Hanson)

       Added DOIs to multiple references. (A. Vaitkus)

       Renamed _topol_tiling.Dsize to _topol_tiling.d_size and
       _topol_link.Voronoi_solidangle to _topol_link.Voronoi_solid_angle.
       (A. Vaitkus)

       Added enumeration range of 1: to the _topol_tiling.d_size data item.
       Redefined the _topol_net.period data item as an enumeration set.
       (A. Vaitkus)

       Restricted the _topol_node.Wyckoff_symbol data item values
       to a set of case-sensitive enumeration values. (A. Vaitkus)
       Added the _dictionary.uri attribute. (A. Vaitkus)
       Added the 'none' measurement units to the definitions of multiple
       data items. (A. Vaitkus)

       Added multiple standard uncertainty (SU) data items. (A. Vaitkus)

       Added the _dictionary.namespace attribute and changed the DDL
       conformance version from 3.13.1 to 4.1.0.

       Declared the TOPOL_TILING category as looped. (A. Vaitkus)

       Removed the _topol_link.atom_label_1, _topol_link.atom_label_2,
       _topol_link.chemical_formula_IUPAC, _topol_link.chemical_formula_moiety,
       _topol_link.chemical_formula_sum, _topol_link.structural_formula_InChI,
       _topol_link.structural_formula_SMILES, _topol_node.atom_label,
       _topol_node.chemical_formula_IUPAC, _topol_node.chemical_formula_moiety,
       _topol_node.chemical_formula_sum, _topol_node.structural_formula_InChI,
       _topol_node.structural_formula_SMILES, _topol_node.symop_id,
       _topol_node.translation, _topol_node.translation_x,
       _topol_node.translation_y and _topol_node.translation_z data items.
       Adjusted related definitions accordingly. (A. Vaitkus)

       TODO: adjust _category_key.name to allow for optional id in all
       TOPOL_* categories with _topol_*.id, as in CHEMICAL_CONN_BOND

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Version 0.9.5 ()
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       Removed _topol_net.occurrence_total                  (B. Hanson)
       Removed TOPOL_OCCURRENCE                             (B. Hanson)
       Removed TOPOL_TILING_FACES and TOPOL_TILING_TILE     (B. Hanson)
       Added _topol_link.type 'gl' (generic link)           (B. Hanson)

       Added machine-readable default values to the definitions
       of multiple data items. (A. Vaitkus)

       NOTE: _topol_net.total_point_symbol
       should display { } correctly in {4.6^2}2{4^2.6^10.8^3}

       NOTE: all ^ should be that mark in the dictionary examples.

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Version 0.9.6 ()
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       Updated the _topol_atom.atom_label, _topol_atom.symop_id,
       _topol_link.symop_id_1 and _topol_link.symop_id_2 data items
       to be compatible with the data items that they are linked to.
       (A. Vaitkus)

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