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Re: Providing a definition for the deprecated _symmetry_cell_setting

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Re: Providing a definition for the deprecated _symmetry_cell_setting
  • From: James Hester <jamesrhester@gmail.com>
  • Date: Fri, 7 Apr 2017 15:01:46 +1000
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  • In-Reply-To: <2D96ACB4B332484AAC57FEC68EBC49A136528105@FHSDB2D11-2.csu.mcmaster.ca>
  • References: <CAM+dB2dhnEfJiPW=Uj-H1tgM2gew65U8XK4O2nHrAryf1KxwXw@mail.gmail.com><2D96ACB4B332484AAC57FEC68EBC49A136528105@FHSDB2D11-2.csu.mcmaster.ca>
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.


On 7 April 2017 at 01:35, Brown, David <idbrown@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.


I. David Brown
Professor Emeritus
Department of Physics and Astronomy
McMaster University
Hamilton, Ontario, Canada
From: coreDMG [coredmg-bounces@iucr.org] on behalf of James Hester [jamesrhester@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.



_definition.id    '_symmetry_cell_setting'
_name.category_id 'space_group'
_name.object_id   'deprecated_cell_setting'
     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

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