Moving symmetry dictionary into DDLm

[James Hester]

This sounds like a sensible idea. I will liaise with David to coordinate
this effort and we will presumably report back once we are finished or if
we have issues. If anybody else would like to be involved, let me know.

James.
---------- Forwarded message ----------
From: Brown, David <idbrown at mcmaster.ca>
Date: 13 April 2016 at 05:55
Subject: RE: Core CIF dictionary in DDLm
To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group
<coredmg at iucr.org>


James,

Thank you for circulating the draft DDLm core dictionary.  This is
magnificent work and a great step forward. I have just one suggestion for a
change, and that is one that I would strongly urge the core dictionary
maintenance group to adopt.

When we prepared the symmetry dictionary, we discovered that the _symmetry
items in the core dictionary were designed in such a way that they could
not be expanded into a coherent set of items that would properly reflect
the mathematics of space group theory. Consequently we created the
space_group categories in a separate symmetry dictionary, but with the
recommendation that the _symmetry items in the core be retired and replaced
by items in the space_group categories. We ensured that every _symmetry
item had a corresponding item in the space_group categories. However, the
relevant _space_group items were never moved into the core, but the
development of the DDLm dictionaries provides an ideal opportunity to
remove the ill-defined _symmetry items, and replace them with the
corresponding _space_group items, perhaps enhanced with a few extra
_space_group items to allow for a fuller description of the crystal
symmetry. The DDLm specification ensures that the old names (which will
undoubtedly be used for many years to come) can be included as aliases in
the _space_group items, making for a seamless transition.

This is a change that is needed if we want the DDLm dictionaries to contain
a coherent description of crystallography. I am willing to assist in moving
the relevant _space_group items into the core, collaborating with whoever
is overseeing the conversion.

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 11, 2016 10:30
*To:* Distribution list of the IUCr COMCIFS Core Dictionary Maintenance
Group
*Subject:* Core CIF dictionary in DDLm

Dear Core CIF Dictionary Management Group,

Many of you will be aware that COMCIFS decided at the Montreal meeting to
move all IUCr-maintained DDL1 dictionaries to the new DDLm standard. The
core CIF dictionary, as the basis upon which most other dictionaries are
expressed, is the first in line to be approved. I would therefore like you
to look over the attached draft core CIF DDLm dictionary and raise any
issues in this mailing list.  You may find the short introduction to
reading DDLm dictionaries at
http://www.iucr.org/resources/cif/ddl/ddlm/docs/intro helpful, and the full
set of DDLm attributes is provided in the latest ddl.dic file at
ftp://ftp.iucr.org/pub/cifdics/DDLm_3.11.09.dic (itself a small DDLm
dictionary). I have also provided a short overview of the DDLm core CIF
dictionary below. Note that the dictionary makes use of the definition
templates and default data found in the auxiliary dictionaries
templ_enum.dic and templ_attr.dic (also attached).

I propose a minimum 6 week discussion period (starting today) with any
significant changes that have been accepted by the active members of this
group automatically initiating a further 6 week wait from the date of the
proposed change before being considered approved. Following approval by
this group, the dictionary will be forwarded to COMCIFS for a formal
approval.  It would of course be desirable for members of this group to
positively indicate approval rather than remain silent. I note that the
dictionary is large (over 1000 definitions) so I suggest that those of you
who lack the time or expertise to review the whole dictionary review as
many categories as you can deal with and indicate to us that you are
commenting only on those particular categories.

It would be particularly helpful if you were to start a separate email
thread for every significant issue. This makes it easier for those who come
later to follow our discussion.

best wishes,
James Hester (acting Core CIF DMG chair)

DDL Core CIF dictionary overview
===========================

History

This draft DDLm core CIF dictionary was originally drafted by the Perth
group, led by Syd Hall, and has been lightly edited by James Hester to
bring it into line with the new CIF2 syntax and updates to the DDLm
standard.

Major differences from DDL1

(1) Recommended datanames (the _definition.id attribute) are in
<category>.<object> notation (i.e. contain a dot). The previous DDL1
datanames are still valid and are listed using the _alias tags. Where
possible the recommended datanames should match their equivalents from the
mmCIF dictionary (which are also in <category>.<object> notation.
(2) The dictionary makes use of the DDLm import mechanism to remove
repetitive material from the dictionary proper into auxiliary files
(templ_enum and templ_attr)
(3) Datanames may now be of vector or matrix type. So e.g. U_ij can be
defined using a single dataname _atom_site_aniso.matrix_U
(4) The mathematical relationships connecting datanames are expressed using
dREL methods. It is therefore possible to calculate F_calc using
dictionary-aware software (e.g. look at the method for _refln.F_complex).
These methods have been extensively tested by myself and the Perth group.
If you are happy working with Python, the latest version of the PyCIFRW
software fully understands these methods and can be used to test them.
(4a) The templ_enum dictionary contains all of the data required to perform
the F_calc calculation, including all of the form factor coefficients and
neutron scattering lengths.
(4b) Some new datanames have been created to record intermediate values in
such calculation chains.
(5) DDLm 'nested' categories have been used to create 'splittable' loops.
For example, atom_site_aniso is a category nested inside atom_site. This
means that the anisotropic displacement parameters may either be listed
separately, or together with the atom sites.
(6) Every loop category always has a single dataname that acts as a key.

-- 
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148

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-- 
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
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