Re: [magCIF] magCIF working group
- To: Discussion list for the magnetic CIF dictionary project <magcif@iucr.org>
- Subject: Re: [magCIF] magCIF working group
- From: "Campbell, Branton" <branton@physics.byu.edu>
- Date: Wed, 18 Jun 2014 00:35:40 +0000
- Accept-Language: en-US
- In-Reply-To: <53A0695A.1070307@mcmaster.ca>
- References: <430A6277358CE34E95A8748DCB3548670270C3D0@POLARIS.physics.byu.edu><CAM+dB2dyONwGRDYhakki+=DNeifd0SOh4gu-HLBFmaX7Yc1D8g@mail.gmail.com><430A6277358CE34E95A8748DCB35486702793B5F@POLARIS.physics.byu.edu><002b01cf8946$a14d2fa0$e3e78ee0$@fzu.cz> <53A0695A.1070307@mcmaster.ca>
Regarding Vaclav’s inquiry: It’s normal to combine tags from different dictionaries in the same CIF output file, even if those dictionaries are written in different
DDL versions. This is already commonly done when using tags from the symCIF dictionary (DDL2) together with tags from the coreCIF (DDL1) dictionary. Regarding David’s comment on merging multiple dictionaries: Does the “_atom_site_fract_x”
tag name in the DDLm version of the core dictionary get changed to “_atom_site.fract_x”? And how about the case where the DDL1 core dictionary gets merged into a composite DDLm dictionary – do the “_” separators get changed to “.” in that case? Branton From: magcif-bounces@iucr.org [mailto:magcif-bounces@iucr.org]
On Behalf Of David Brown I agree with the comments so far in this discussion. I would just like to point out that DDLm was designed to be able to read any CIFs written in DDL1 or DDL2. There is already a version of the core
dictionary written in DDLm. Many programs are written with the data names hard copied into the code, and for these the dictionary is irrelevant. They will have no problem reading CIFs written using DDLm dictionaries provided the CIFs do not contain matrices
and vectors written as single data items. The only time that the dictionary becomes relevant is when a program uses the dictionary itself in order to recognize the datanames, e.g., programs like checkcif. I imagine that by the time our dictionary is complete,
Chester will have DDLm compatible versions of its programs running. DDLm can create seamless virtual dictionaries by reading and merging all the required dictionaries, e.g., magCIF, coreCIF, symCIF etc. The coreCIF DDLm dictionary already exists. It may
be necessary to generate a DDLm version of symCIF, but that will eventually be needed in any case. Dear magCIF members, After returning from a short holiday I have found several new important contributions from James and Branton. I would like write my opinion: 1.
After comparing advantages and disadvantages of creating a separate dictionary and adding to existing dictionaries I would prefer a new separate magnetic
dictionary. 2.
Concerning the type of dictionary I like the newest DDLm format with possibility of _alias.definition_id.
3.
I do not see problems to read into Jana CIF files having as category/item separators ‘.’ or ‘_’.
I think this is in accordance with the last answer from James. 4.
A little bit is how to create as an output CIF file. One possibility is to offer a user three possibilities – pure DDL1, pure DDL2 or mixed output derived
from the original (standard) definition of each dictionary. With best wishes, Vaclav From:
magcif-bounces@iucr.org [mailto:magcif-bounces@iucr.org]
On Behalf Of Campbell, Branton I appreciate the positive comments from James. Suppose that we use category.item for tags in the new magCIF dictionary. Then also suppose that half the relevant magnetic software packages in the world are
willing to read/write category.item, but that the other half decide to read/write category_item instead for the same tags (not an unlikely scenario). If I want my own software to be compatible with all relevant software packages, what am I to do? It seems
that I must simultaneously read/write both category.item and category_item for the same tag, which would be very unpleasant. Best, Branton From:
magcif-bounces@iucr.org [mailto:magcif-bounces@iucr.org]
On Behalf Of James Hester Dear magCIF members, Let me clarify and expand on a few of Branton's points. Note that officially, neither '.' nor '_' carry any syntactical or semantic meaning in a dataname. Conventionally in DDL2 and DDLm dictionaries a '.' separates the category from the object name, but this is
purely convention and therefore software should not rely on it. Furthermore, because in DDL1 datanames no such convention applies, '.' is just another character and datanames containing '.' are in no way more or less acceptable. Therefore, I would strongly
urge that all new magCIF datanames contain a '.' according to the DDL2/m convention, as such datanames conform with DDL1, DDL2 and DDLm conventions. There is absolutely no practical issue with datafiles containing datanames some of which have '.' and some
of which don't. I imagine that software authors in the magCIF domains will simply treat the dataname as a string of characters (as they should) that they use to read/write a value in a file, and the presence or absence of '.'
or '_' should be completely irrelevant in this form of usage. Given this, I do not see the point of defining two new datanames for each concept. For what it's worth, I think Branton's suggestion of developing the basic information in a simple ASCII file is by far the best way to proceed. all the best, (COMCIFS chair) On Fri, Jun 13, 2014 at 1:01 PM, Campbell, Branton <branton@physics.byu.edu> wrote: Dear magCIF working group members (and others),
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