Providing a definition for the deprecated _symmetry_cell_setting

[James Hester]

Can anyone advise why "Bravais system" (IT Vol A p722) would not be
suitable as a replacement for _symmetry_cell_cetting? That is,
"_symmetry_cell_setting" would be aliased to new dataname
"_space_group.Bravais_system".

On 7 April 2017 at 15:01, James Hester <jamesrhester at gmail.com> wrote:

> 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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>> M +61 (04) 0249 4148
>>
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>>
>>
>
>
> --
> T +61 (02) 9717 9907 <+61%202%209717%209907>
> F +61 (02) 9717 3145 <+61%202%209717%203145>
> M +61 (04) 0249 4148
>



-- 
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