Providing a definition for the deprecated _symmetry_cell_setting
James Hester
jamesrhester at gmail.com
Fri Jun 9 06:08:25 BST 2017
Dear Core CIF maintainers:
Following acceptance of a dataname to indicate deprecation, I have updated
cif_core.dic to include a '_symmetry.cell_setting' dataname that is marked
as 'deprecated'. The full text is as follows:
save__symmetry.cell_setting
_definition.id '_symmetry.cell_setting'
_alias.definition_id '_symmetry_cell_setting'
_definition.update 2017-06-09
_definition.replaced_by '_space_group.crystal_system'
_description.text
;
This dataname should not be used and is DEPRECATED as it is
ambiguous.
The original definition is as follows:
The cell settings for this space-group symmetry.
;
_name.category_id space_group
_name.object_id deprecated_setting
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_enumeration_set.state
triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
save_
On 15 May 2017 at 16:08, James Hester <jamesrhester at gmail.com> wrote:
> To answer my own question: the list of cell settings in the old
> '_symmetry_cell_setting' corresponds to no well-defined concept, including
> 'Bravais system', as 'Bravais system' does not have 'trigonal'.
> 'Hexagonal' may mean 'hexagonal Bravais system' or 'hexagonal crystal
> system', which are different sets (see table 8.1 in Volume A).
> Consequently, the pseudocode included in my previous email is incomplete as
> it does not (and cannot) cover 'hexagonal' cases.
>
> I will pursue addition of a DDLm attribute for deprecation to handle this
> item, and will not bother this group further on this topic.
>
> James.
>
>
> On 28 April 2017 at 08:51, James Hester <jamesrhester at gmail.com> wrote:
>
>> 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_
>>>>
>>>>
>>>> --
>>>> T +61 (02) 9717 9907 <+61%202%209717%209907>
>>>> F +61 (02) 9717 3145 <+61%202%209717%203145>
>>>> M +61 (04) 0249 4148
>>>>
>>>> _______________________________________________
>>>> coreDMG mailing list
>>>> coreDMG at iucr.org
>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg
>>>>
>>>>
>>>
>>>
>>> --
>>> T +61 (02) 9717 9907 <+61%202%209717%209907>
>>> F +61 (02) 9717 3145 <+61%202%209717%203145>
>>> M +61 (04) 0249 4148
>>>
>>
>>
>>
>> --
>> T +61 (02) 9717 9907 <+61%202%209717%209907>
>> F +61 (02) 9717 3145 <+61%202%209717%203145>
>> M +61 (04) 0249 4148
>>
>
>
>
> --
> T +61 (02) 9717 9907 <+61%202%209717%209907>
> F +61 (02) 9717 3145 <+61%202%209717%203145>
> M +61 (04) 0249 4148
>
--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
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