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RE: Core CIF dictionary in DDLm


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.


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 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


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.

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