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Updated proposal for _audit.formalism to ease restrictions on
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redefinition.
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James.Hester committed Mar 7, 2017
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Expand Up @@ -12,12 +12,13 @@ conjunction with that document.
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, for
some values of the datanames from which the redefined datanames are
calculated, the derived dataname takes the values that the original
dataname would have taken. So, for example, if `_atom_site.moment` is
zero, `_refln.F_complex` has the same values as in core CIF, so it is
acceptable for a magnetic dictionary to redefine `_refln.F_complex`.
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
Expand All @@ -27,9 +28,9 @@ 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. Most CIF reading programs
should check these datanames in order to avoid miscalculating derived
values.
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
Expand Down Expand Up @@ -59,7 +60,7 @@ only.
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 clearly
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.

Expand All @@ -71,9 +72,7 @@ take values `powder-magnetic`, `powder-modulated` and
### Electron density

The electron density dictionary allows parameterisation of the
electron density around each atom in terms of multipoles. With
appropriate choice of coefficients this reduces to the spherical atom
model used in core CIF, so is an acceptable redefinition.
electron density around each atom in terms of multipoles.
`_refln.F_complex` is redefined, and a formalism of `multipole` is
assigned.

Expand All @@ -85,8 +84,8 @@ the final datanames.

### Twinning

Twinning does not change the structural model, but it does change the
way of determining `_refln.F_meas` from the observations. A formalism
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.

Expand Down Expand Up @@ -143,7 +142,7 @@ 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.

However, while the `_audit_conform` mechanism must remain the
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
Expand All @@ -155,13 +154,14 @@ 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.

Notably, the `_audit_conform_*` mechanism is almost never used. As of
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. We conclude that introduction of
`_audit.formalism` should be accompanied by an education and outreach
program as well.
`_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`

Expand All @@ -174,7 +174,7 @@ 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
expands.
changes.

# Appendix I: New core definitions

Expand Down

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