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Re: COMCIFS approval of proposal to flag dataname redefinition

This seems reasonable to me.
Jim Kaduk
On 2017-03-22 20:38, James Hester wrote:> Dear COMCIFS,> > As per the my email of last December (see> http://www.iucr.org/__data/iucr/lists/comcifs-l/msg00736.html) a> simple mechanism has now been developed to clearly flag the presence> of redefined datanames in a datafile.  Neither the ddlm-group nor the> core CIF DMG have raised objections. The full proposal is reproduced> below, and can be read in a more nicely formatted form at> https://github.com/COMCIFS/comcifs.github.io/blob/master/audit.formalism_proposal.md> > All comments are welcome. If no objections are received within 3> weeks, this proposal will be considered approved.> > James Hester (chair).> > ==========================================> > # Proposal for new dataname and attribute to cover differing models> > ## Introduction> > The following proposal implements part of a solution to incorporating> multiple models into CIF, discussed> [here](changing_meanings_discussion_paper.md [1]).  It should be read> in> conjunction with that document.> > ## New datanames: `_audit.formalism` and `_audit.formalism_version`> > Each value of `_audit.formalism` corresponds to a particular way of> deriving some set of CIF datanames from other datanames defined in the> same, or imported, dictionaries.  For better interoperability, we> stipulate that datanames may only be redefined by dictionaries if the> redefined datanames take values with the same units and domain as the> original datanames.  So, for example, `_refln.F_complex` for magnetic> structures is calculated differently to `_refln.F.complex` for core> CIF, but has the same units and domain (positive real numbers), so it> is acceptable for a magnetic dictionary to redefine> `_refln.F_complex`.> > `_audit.formalism_version` is provided to allow secondary parameters> to be added to the model without changing the overall formalism. As a> guide, parameters are considered secondary if they do not require the> addition of new columns to any category, and do not significantly> change the final calculated values in "typical" cases.> > All CIF datablocks should include these new datanames when they take> non-default values; the default values correspond to the> single-crystal model described in core CIF.  Any CIF reading programs> that perform calculations should check `_audit.formalism` and> `_audit.formalism_version`> datanames in order to avoid miscalculating derived values.> > The choice of the word `formalism` is purely to avoid clashing with> the widespread use of `model` in core CIF to refer to the particular> arrangement of atoms. There may be a better word.  See the appendix> for formal DDLm definitions.> > ## New DDLm attributes: `_dictionary.formalism` and> `_dictionary.formalism_version`> > These attributes associate a dictionary with a particular formalism.> > ## Treatment of current dictionaries> > ### Modulated structures> > The modulated structures dictionary is assigned formalism `modulated`> and redefines `_refln.F_complex`, `_refln.sin_theta_over_lambda` and> `_refln.symmetry_multiplicity`.> > ### Magnetism> > The magnetism dictionary builds on the modulated structures> dictionary.> It is assigned formalism `magnetic` and redefines `_refln.F_complex`> only.> > ### Powder> > The powder dictionary calculates structure factors from information> that may be held in a different datablock.  It therefore redefines> `_refln.F_complex`.  `_refln.F_meas` is also redefined as the> determination of this from the powder observations is markedly> different to the way in which it is derived from single-crystal spots,> not least because of pervasive overlap.> > Separate formalisms are necessary for each possible combination of> powder with other formalisms, for example `_audit.formalism` can> take values `powder-magnetic`, `powder-modulated` and> `powder-multipole`.> > ### Electron density> > The electron density dictionary allows parameterisation of the> electron density around each atom in terms of multipoles.> `_refln.F_complex` is redefined, and a formalism of `multipole` is> assigned.> > ### Constraints and restraints> > This dictionary relates only to the method of determination of the> final parameters and therefore does not affect the definitions of> the final datanames.> > ### Twinning> > Twinning does not change the structural model, but it may change the> way `_refln.F_meas` is calculated from the observations. A formalism> of `twinning` is assigned, and as for powder separate formalisms need> to be assigned for each distinct structural model.> > ### Image CIF> > ImgCIF relates only to raw data and is not affected by these changes.> > ### mmCIF> > mmCIF is based on the core CIF model and is therefore unaffected by> these changes.> > ## Treatment of other techniques> > ### Laue> > A Laue experiment measures distinct spots, but each spot is produced> by a distinct wavelength, and spots sometimes overlap.> `_refln.wavelength` therefore becomes an additional key column in> `refln`. This change by itself is easily covered by defining a> different `_audit.schema`.  However, a Laue dictionary must also> redefine `_refln.F_meas` as the extraction of notional observed> intensities will depend on the model for wavelength distribution, and> so we must assign a separate `_audit.formalism`. As for powder and> twinning, there will be a separate `formalism` for each distinct> structural model.> > ## Discussion> > ### Mixing and matching not possible> > It is tempting to define something like `_audit.technique` to cover> the technique-based differences, so that `_audit.technique` and> `_audit.formalism` could correspond to different dictionaries that> could be mixed and matched. So, instead of a `powder-magnetism`> formalism, there would simply be a `powder` technique combined with a> `magnetism` formalism, with both dictionaries being separately> imported> and notionally orthogonal to one another.> > However, any `formalism` that adds keys to the `refln` category will> also require the `technique` to be aware of those keys in order to> explain how `_refln.F_meas` is determined.  For example, a powder> experiment on a modulated structure will calculate the `_refln.F_meas`> value differently to a powder experiment on a non-modulated structure> as the calculations of peak position require different numbers of> indices.  Therefore, it is not possible to generally separate the> technique from the structural model, although it may be possible in> particular cases.> > ### Just use `_audit_conform`?> > Core CIF has long provided the `_audit_conform_dict_*` tags to state> which> dictionary or dictionaries a datablock conforms to.  This appears> almost> as simple as the proposed `_audit.formalism` tag, so the need for a> separate tag may not be apparent.> > While the `_audit_conform` mechanism must remain the> canonical source of information, the proposed dataname provides a> simplified route to the same information. In order for a CIF reading> program to confirm that none of the dictionaries listed in a CIF block> change any of the definitions relied upon by that program, it must in> general download the stated versions of the dictionary or dictionaries> from the canonical IUCr site, parse and merge them, and then find any> definitions that have (apparently) been replaced.  Compared to this> procedure, the `_audit.formalism` tag is a much simpler way for the> datablock writer to specify to the datablock reader a particular set> of dataname interpretations that may never change.> > Note that the `_audit_conform_*` mechanism is almost never used. As of> May 28, 2016, there were 195 modulated structures in the> Crystallographic Open Database (as determined by the presence of> `Fourier_wave_vector` in a file). Of these, zero had an> `_audit_conform` entry, which in theory would be required to explain> the adjusted interpretation of the `refln` category and new datanames.> We conclude that introduction of `_audit.formalism` should be> accompanied by an education and outreach program as well.> > ### Interaction with `_audit.schema`> > `_audit.schema` essentially allows fixed parameters to vary. It> is therefore orthogonal to `_audit.formalism`: a given formalism> may have many possible schemas, and many schemas may apply to> multiple formalisms if they share the same parameters.> > In other words, a suitably-written program can handle a variety of> schemas for a single formalism without needing to change the way in> which any dataname is calculated, whereas a program must change the> way> in which the redefined datanames are calculated if the formalism> changes.> > # Appendix I: New core definitions> > ## _audit.formalism> > ```> save_audit.formalism> > _definition.id [2]       '_audit.formalism'> _name.category_id    audit> _name.object_id      formalism> _description.text> ;> >      The CIF dictionaries listed in _audit.dictionary may redefine>      datanames. _audit.formalism is provided as an efficient>      alternative to parsing and checking those dictionaries. It>      identifies commonly-used sets of meanings for datanames. In>      general, each value taken by _audit.formalism is linked to a>      particular technique and/or structural approach.  The>      dictionaries for the datablock (see _audit.dictionary) must be>      compatible with the value of _audit.formalism.> > ;> _type.contents          Text> _type.purpose           State> _type.container         Single> _type.source            Assigned> loop_> _enumeration_set.state> _enumeration_set.detail>     Base                'Single crystal model from core CIF'>     Modulated           'Single crystal modulated structure'>     Magnetic            'Single crystal magnetic structure,> potentially modulated'>     Powder              'Powder diffraction experiment'>     Twinned             'Twinned crystal using core CIF model'>     Multipole           'Single crystal model with multipole> coefficients'>     Laue                'Laue experiment on single crystal'>     Powder-Modulated    'Powder experiment on a modulated structure'>     Powder-Magnetic     'Powder experiment on a modulated magnetic> structure'>     Powder-Multipole    'Powder experiment modelled with multipoles'>     Laue-Magnetic       'Laue experiment on magnetic structure'>     Laue-Modulated      'Laue experiment on modulated non-magnetic> structure'>     Laue-Multipole      'Laue experiment modelled with multipoles'>     Twinned-Magnetic    'Twinned magnetic single crystal structure'>     Twinned-Modulated   'Twinned modulated single crystal structure'>     Laue-Twinned        'Laue experiment on twinned single crystal'>     Laue-Twinned-Modulated 'Laue experiment on twinned modulated> structure'>     Custom              'Examine dictionaries provided in> _audit_conform'>     Local               'Locally modified dictionaries. These> datafiles should not be distributed'> _enumeration.default    Base> save_> ```> > ## _audit.formalism_version> > ```> save_audit.formalism_version> > _definition.id [2]       '_audit.formalism_version'> _name.category_id    audit> _name.object_id      formalism_version> _description.text> ;> >      The version of the given formalism (see `_audit.formalism`). The> version>      number of a formalism is incremented when new model parameters> are>      added that do not significantly affect the model values in> typical cases.> > ;> _type.contents          Text> _type.purpose           State> _type.container         Single> _type.source            Assigned> _enumeration.default    1.0> save_> ```> > ## _dictionary.formalism> > ```> save_dictionary.formalism> >     _definition.id [2]               '_dictionary.formalism'>     _definition.class            Attribute>     _definition.update           2016-12-17>     _description.text> ;> >      The value of this attribute is associated with the set of>      dataname meanings contained in this dictionary.> > ;>     _name.category_id            dictionary>     _name.object_id              formalism>     _type.purpose                Audit>     _type.source                 Assigned>     _type.container              Single>     _type.contents               Text> > save_> ```> > # Appendix II: a full hybrid dictionary> > A complete dictionary using the above mechanisms is presented below.> > ```> #\#CIF_2.0> ####################################################> #                                                  #> #    Dictionary for modulated powder diffraction   #> #                                                  #> ####################################################> > data_MODPOW> > _dictionary.title             MODPOW> _dictionary.formalism         Powder-Modulated> _dictionary.class             Instance> _dictionary.version           1.0> _dictionary.date              2016-12-19> _dictionary.ddl_conformance   3.12> _dictionary.namespace         MODPOW> _description.text> ;> >     The modulated powder diffraction dictionary redefines datanames>     for use when presenting the results of a powder diffraction>     experiment using a modulated structure model.  The remainder of> the>     relevant definitions are found in the modulated structures>     dictionary and the powder diffraction dictionary.> > ;> > save_MODPOW_GROUP> >     _definition.id [2]       MODPOW_GROUP>     _definition.scope    Category>     _definition.class    Head>     _definition.update   2016-12-19>     _description.text> ;>     This category is the parent category for all definitions>     in the MODPOW dictionary> ;> >     _name.category_id     MODPOW>     _name.object_id       MODPOW_GROUP> >     # The following import reads in and reparents all powder and>     # modulated structure definitions to the MODPOW_GROUP category. As> cif_ms is>     # read second, the refln category will have the extra modulation> indices>     # defined.> >     _import.get           [{"file":"cif_pow.dic" "save":"PD_GROUP"> "mode":"Full"}>                            {"file":"cif_ms.dic"  "save":"MS_GROUP"> "mode":"Full"}]> > save_> > save__refln.F_complex> > _definition.id [2]                          '_refln.F_complex'> loop_>   _alias.definition_id>          '_refln.F_complex'>          '_refln_F_complex'> _definition.update                      2016-12-19> _description.text> ;>      The structure factor vector for the reflection calculated from>      the modulated structure given in the datablock identified by>      _refln.phase_id> ;> _name.category_id                       refln> _name.object_id                         F_complex> _type.purpose                           Measurand> _type.source                            Derived> _type.container                         Single> _type.contents                          Complex> _enumeration.default                    0.> > #> #  A complete dREL expression for F_complex can be provided here,> using all of the> #  parameters provided in the powder and modulated structure> dictionaries.> #> save_> > save__refln.F_meas> > _definition.id [2]                          '_refln.F_meas'> loop_>   _alias.definition_id>          '_refln.F_meas'>          '_refln_F_meas'> _definition.update                      2016-12-19> _description.text> ;>      The structure factor amplitude for the modulated reflection based> on>      partitioning of each observed powder diffraction intensity> between>      contributing reflections in proportion to the model reflection> contributions.> ;> _name.category_id                       refln> _name.object_id                         F_meas> _type.purpose                           Measurand> _type.source                            Derived> _type.container                         Single> _type.contents                          Real> _enumeration.default                    0.> #> # A complete dREL expression for calculating F_meas from an observed> powder diffractogram can be given here.> #> save_> > --> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148> > Links:> ------> [1] http://changing_meanings_discussion_paper.md> [2] http://definition.id> _______________________________________________> comcifs mailing list> comcifs@iucr.org> http://mailman.iucr.org/cgi-bin/mailman/listinfo/comcifs_______________________________________________comcifs mailing listcomcifs@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/comcifs

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