Providing a definition for the deprecated _symmetry_cell_setting
James Hester
jamesrhester at gmail.com
Mon May 15 07:08:18 BST 2017
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
F +61 (02) 9717 3145
M +61 (04) 0249 4148
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