Providing a definition for the deprecated _symmetry_cell_setting

[James Hester]

To be fair, the definition I have given does not provide any new mechanism
to automatically remove _symmetry_cell_setting, as there is no DDLm
attribute that can signal deprecation and no machine-readable specification
to transform a _symmetry_cell_setting value to a
_space_group.crystal_system value.  This essentially forces archives to
preserve the _symmetry_cell_setting entry.

To specify how to convert _symmetry_cell_setting to the updated dataname, a
dREL method can be added to _space_group.crystal_system to derive the value
from the _symmetry_cell_setting value, as follows:

with sg as space_group {
   final_val = sg.deprecated_cell_setting
   if (final_val == "rhombohedral") final_val = "trigonal"
}
   space_group.crystal_system = final_val

However, this concerns me somewhat, as (1) we are signalling that the value
of a dataname depends on the value of a deprecated dataname and (2) we
could always write instead a dREL method that determines the crystal system
from the space group, which would be more informative.

For completeness I note also the option of defining new dataname
'_space_group.Bravais_system' (IT Vol A p722) as the precise equivalent of
_symmetry_cell_setting.

James.

On 7 April 2017 at 01:35, Brown, David <idbrown at mcmaster.ca> wrote:

> _symmetry_cell_setting was a most unfortunate name with an equally
> unfortunate definition. Getting rid of this item was one of the driving
> forces behind preparing the space_group dictionary. James has proposed a
> very elegant way of dealing with this problem. My hope is that the problem
> will eventually fade away. James' solution provides a way in which the
> presence of the deprecated item can be virtually corrected as an entry is
> retrieved from the archive.
>
> David
>
> I. David Brown
> Professor Emeritus
> Department of Physics and Astronomy
> McMaster University
> Hamilton, Ontario, Canada
> ------------------------------
> *From:* coreDMG [coredmg-bounces at iucr.org] on behalf of James Hester [
> jamesrhester at gmail.com]
> *Sent:* April 6, 2017 01:54
> *To:* Distribution list of the IUCr COMCIFS Core Dictionary Maintenance
> Group
> *Subject:* Providing a definition for the deprecated
> _symmetry_cell_setting
>
> Dear Core DMG,
>
> A sharp-eyed reader of the new DDLm core_CIF dictionary has noted that
> _space_group.crystal_system has _symmetry_cell_setting as an alias, even
> though _symmetry_cell_setting includes 'rhombohedral' as a possible value
> whereas _space_group.crystal_system does not.  As the set of possible
> values is different, these two data items are not strictly equivalent.
> Therefore, _symmetry_cell_setting should be removed as an alias of
> _space_group.crystal_system.
>
> However, we cannot simply drop _symmetry_cell_setting. For better or
> worse, there are over 800 CIF files in the COD which have
> _symmetry_cell_setting as 'rhombohedral' instead of the recommended
> '_space_group_crystal_system' of 'trigonal' (one has
> '_space_group_crystal_system' of 'rhombohedral' as well!).  Of these, over
> 100 were produced in the last 5 years, although the deprecation has been in
> place since 2005.
>
> In order to interpret these "legacy" files, we need to preserve a
> definition for _symmetry_cell_setting somewhere.
>
> I suggest that we create an additional definition in the DDLm dictionary
> as below.  Note that
> (1) I have deliberately not provided a new dataname in <category>.<object>
> form, instead retaining the legacy dataname
> (2) I have placed the dataname in the space_group category
> (3) I have deliberately included the word deprecated in the object_id
> (this is only relevant for dREL methods).
>
> Please comment.  The period for comments will be 3 weeks, after which this
> change will be accepted unless there are outstanding issues.
>
> James.
> ======================
>
> save_symmetry_cell_setting
>
> _definition.id    '_symmetry_cell_setting'
> _name.category_id 'space_group'
> _name.object_id   'deprecated_cell_setting'
> _description.text
> ;
>      This dataname is superseded by _space_group.crystal_system and is
> retained here only to aid in interpreting
>      legacy archives. Do not use it.
>
>      Original definition: The cell setting for this space group symmetry.
> ;
>
> _type.purpose                           State
> _type.source                            Assigned
> _type.container                         Single
> _type.contents                          Code
> loop_
>   _enumeration_set.state
>          triclinic
>          monoclinic
>          orthorhombic
>          tetragonal
>          trigonal
>          hexagonal
>          cubic
>          rhombohedral
> save_
>
>
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> F +61 (02) 9717 3145 <+61%202%209717%203145>
> M +61 (04) 0249 4148
>
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>


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