Arrangement of the dictionary

Madariaga, G.

doi:10.1107/97809553602060000736

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.4, pp. 132-137

Section 3.4.3. Arrangement of the dictionary

G. Madariaga^a ^*

^a Departamento de Física de la Materia Condensada, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, 48080 Bilbao, Spain
Correspondence e-mail: gotzon.madariaga@ehu.es

3.4.3. Arrangement of the dictionary

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The msCIF dictionary detailed in Chapter 4.3 includes 19 new categories. Another 18 already exist in the core CIF dictionary, but include new items (16) or revised definitions (2). The category structure of the msCIF dictionary is summarized in Table 3.4.2.1 and is listed in full in Appendix 3.4.1. The appendix also lists for each category the section of this chapter in which the category is described.

Table 3.4.2.1 | top | pdf |
Category groups defined in the msCIF dictionary

The groups are listed in the order in which they are described in this chapter.

Section	Category group	Subject covered
(a) Experimental measurements
3.4.3.1.1	CELL	The unit cell, especially cell subsystems for composite structures
3.4.3.1.2	DIFFRN	Multi-dimensional diffraction pattern
3.4.3.1.3	EXPTL	Details of the experiment specific to modulated and composite structures

(b) Analysis
3.4.3.2.1	REFINE	Refinement procedures
3.4.3.2.2	REFLN	Reflection measurements indexed in higher-dimensional space

(c) Atomicity, chemistry and structure
3.4.3.3.1 to 3.4.3.3.3	ATOM	Atom sites in a modulated structure
3.4.3.3.4	GEOM	Geometry of a structure in superspace
3.4.3.3.5	SYMMETRY	Symmetry information

(d) File metadata
3.4.3.4	AUDIT	The structure of the CIF

Many of the modifications to categories that already exist in the core CIF dictionary result from the need to use more than three integer indices to label the diffracted intensities (in the cases of CELL, DIFFRN_REFLN, DIFFRN_REFLNS, DIFFRN_STANDARD_REFLN and EXPTL_CRYSTAL_FACE) or the need to use superspace symmetry (in the cases of GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_TORSION, SPACE_GROUP and SPACE_GROUP_SYMOP). Apart from the categories that describe the atomic modulation functions, there are two that are specific to composite structures (CELL_SUBSYSTEM and CELL_SUBSYSTEMS).

The rest of this section summarizes the contents of the dictionary, organized by categories within the functional groups outlined in Table 3.1.10.1 . As in the other chapters in this part of the volume, the classification is under the headings Experimental measurements (Section 3.4.3.1), Analysis (Section 3.4.3.2), Atomicity, chemistry and structure (Section 3.4.3.3) and File metadata (Section 3.4.3.4). The msCIF dictionary adds no new data items concerned with the publication or reporting of structures to those already present in the core CIF dictionary.

The data items within each category are listed in the detailed commentary below. Where relevant, data items that represent a unique identifier for a looped list (`category keys') are listed first and are marked by a bullet ( $[\bullet]$ ). The remaining data items in each category are listed alphabetically.

3.4.3.1. Experimental measurements

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The categories relevant to a structure determination experiment are in the CELL, DIFFRN and EXPTL groups. Most of the items extend the existing core CIF categories, but the categories describing cell subsystems are new.

3.4.3.1.1. Cell and modulation wave vectors

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The categories describing the unit cell (or cells for composite structures), the wave vectors of the modulations and, for composites, the cell subsystems are as follows:

CELL group

CELL¶

CELL_SUBSYSTEM

CELL_SUBSYSTEMS

CELL_WAVE_VECTOR

CELL_WAVE_VECTORS

Categories marked with ¶ are already defined in the core CIF dictionary.

The data items in these categories are as follows:

(a) CELL [Scheme scheme1]

(b) CELL_SUBSYSTEM [Scheme scheme2] $[\vdots]$

(and _cell_subsystem_matrix_W_m_n for all combinations $[1 \le m,n \le 11]$ )

$[\vdots]$ [Scheme scheme3]

(d) CELL_WAVE_VECTOR [Scheme scheme5]

(e) CELL_WAVE_VECTORS [Scheme scheme6]

As explained in Section 3.4.2, the msCIF dictionary arbitrarily allows an upper limit of 11 for the dimension of superspace for which data names are defined. _cell_modulation_dimension specifies the number of additional reciprocal vectors needed to index the whole diffraction pattern and has values d ranging from 1 to 8 to express the dimensionality (3 + d) of the superspace. _cell_reciprocal_basis_description is a text field allowing a free description of the higher-dimensional basis chosen.

For a composite structure, different cell subsystems may be specified. Each such subsystem is identified and characterized by the data items in the CELL_SUBSYSTEM category (see Section 3.4.4.1). _cell_subsystems_number gives the number of such subsystems as an independent check of the completeness of the description.

Data items in the CELL_WAVE_VECTOR category specify the wave vectors of the modulation (see Section 3.4.4.1). In accordance with the limits on dimensionality of the current version of the msCIF dictionary, no more than eight additional modulation wave vectors may be specified. The number used must agree with the value of _cell_modulation_dimension.

The data items in the CELL_WAVE_VECTORS category describe the experimental conditions during the determination of the independent modulation wave vectors.

3.4.3.1.2. Data collection

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The categories describing data collection are as follows:

DIFFRN group

DIFFRN_REFLN ¶

DIFFRN_REFLNS ¶

DIFFRN_STANDARD_REFLN ¶

Categories marked with ¶ are already defined in the core CIF dictionary.

New data items in these categories are as follows:

(a) DIFFRN_REFLN [Scheme scheme7]

(b) DIFFRN_REFLNS [Scheme scheme8]

The data items in these categories are straightforward extensions of the core CIF dictionary definitions to the indexing of diffraction intensities by higher-dimensional components. The _diffrn_refln_index_m_* items are the additional Miller indices [m_i] indexing the modulation wave vectors $[{\bf q}_i]$ when the diffraction wave vector is written as $[{\bf H}=h {\bf a}^{*}+k {\bf b}^{*}+ l{\bf c}^{*}+ \textstyle\sum_i m_{i} {\bf q}_{i}]$ .

The upper limit of 8 was chosen arbitrarily to limit the number of data items defined in the msCIF dictionary.

_diffrn_reflns_limit_index_m_* items provide independent checks on the range of values recorded for each of the additional Miller indices [m_i] . _diffrn_standard_refln_index_m_* items allow the higher-dimensional Miller indices of standard reflections to be recorded.

3.4.3.1.3. Experimental measurements on the crystal

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The categories describing measurements on the crystal or crystals used in the experiment are as follows:

EXPTL group

EXPTL_CRYSTAL ¶

EXPTL_CRYSTAL_FACE ¶

Categories marked with ¶ are already defined in the core CIF dictionary.

New data items in these categories are as follows:

(a) EXPTL_CRYSTAL [Scheme scheme10]

(b) EXPTL_CRYSTAL_FACE [Scheme scheme11]

_exptl_crystal_type_of_structure specifies the structure type as cryst (crystalline), mod (modulated) or comp (composite). These are the only three types of structure handled at present by the msCIF dictionary.

The extensions to the EXPTL_CRYSTAL_FACE category permit the indexing of crystal faces using the higher-dimensional Miller indices introduced for aperiodic structures.

3.4.3.2. Analysis

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The categories related to refinement that have been extended in this dictionary are as follows:

Refinement techniques and results (§3.4.3.2.1

)

REFINE ¶

The reflections used in the refinement (§3.4.3.2.2

)

REFLN ¶

REFLNS ¶

Categories marked with ¶ are already defined in the core CIF dictionary.

3.4.3.2.1. Refinement techniques and results

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New data items in this category are as follows:

REFINE [Scheme scheme12]

During the early stages of the development of the msCIF dictionary, several sets of data items were defined to accommodate the need to specify residual R factors for the different sets of main reflections and satellite reflections. It was then recognized that the binning of reflection classes had more general application, and these new data items were transferred to the core CIF dictionary, where, of course, they are still available for use in an msCIF.

The new items in the REFINE category in the msCIF dictionary are specific to the refinement of modulated structures. _refine_ls_mod_func_description allows a free-text description of the types of modulation present in the structural model and how they are handled. The treatment of hydrogen-atom modulation parameters is specified by _refine_ls_mod_hydrogen_treatment. Information on an overall phason correction (the use of which should in general be discouraged) may be given using the _refine_ls_mod_overall_phason_* items.

3.4.3.2.2. The reflections used in the refinement

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New data items in these categories are as follows:

(a) REFLN [Scheme scheme13]

(b) REFLNS [Scheme scheme14]

As with the _diffrn_refln_* and _diffrn_reflns_* items (Section 3.4.3.1.2), these data names extend the corresponding core data items into the higher-dimensional space used in the treatment of modulated structures and composites. They apply to the list of reflections used in the refinement, as distinct from the experimentally collected set of intensities described by the _diffrn_* data items.

3.4.3.3. Atomicity, chemistry and structure

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The categories relevant to the description of the structural model are as follows:

ATOM group

Atom sites (§3.4.3.3.1

)

ATOM_SITE ¶

ATOM_SITE_PHASON

Modulation functions as Fourier series (§3.4.3.3.2

)

ATOM_SITE_DISPLACE_FOURIER

ATOM_SITE_DISPLACE_FOURIER_PARAM

ATOM_SITE_FOURIER_WAVE_VECTOR

ATOM_SITE_OCC_FOURIER

ATOM_SITE_OCC_FOURIER_PARAM

ATOM_SITE_ROT_FOURIER

ATOM_SITE_ROT_FOURIER_PARAM

ATOM_SITE_U_FOURIER

ATOM_SITE_U_FOURIER_PARAM

ATOM_SITES_DISPLACE_FOURIER

ATOM_SITES_MODULATION

ATOM_SITES_ROT_FOURIER

Special modulation functions (§3.4.3.3.3

)

ATOM_SITE_DISPLACE_SPECIAL_FUNC

ATOM_SITE_OCC_SPECIAL_FUNC

Molecular or packing geometry (§3.4.3.3.4

)

GEOM group

GEOM_ANGLE ¶

GEOM_BOND ¶

GEOM_CONTACT ¶

GEOM_TORSION ¶

Symmetry information (§3.4.3.3.5

)

SYMMETRY group

SPACE_GROUP ¶

SPACE_GROUP_SYMOP ¶

Categories marked with ¶ are already defined in the core CIF dictionary.

Most of the new categories introduced to the msCIF dictionary appear here, since their function is to describe in great detail the modulation of the atom-site properties. They fall naturally into families describing the modulation of atomic displacement, of site occupation or of thermal parameters.

New data items are added to several categories in the core CIF dictionary that describe molecular or packing geometry. There are also new data items to describe superspace-group symmetry.

3.4.3.3.1. Atom sites

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Data items in these categories are as follows:

(a) ATOM_SITE [Scheme scheme15]

(b) ATOM_SITE_PHASON [Scheme scheme16]

The bullet ( $[\bullet]$ ) indicates a category key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

The ATOM_SITEcategory is extended in the msCIF dictionary by the addition of a small number of items that may appear in the main looped list of atom-site information (see Section 3.2.4.1.1 ). The *_flag items indicate whether each individual atom site has been modelled through modulation of atomic displacement, site occupation or thermal parameters. In each case, the default value of the item is no, so that any or all of the flags may be omitted when that particular type of modulation has not been applied to the structural model.

_atom_site_subsystem_code identifies the cell subsystem to which the atom site must be assigned in the description of composite structures. Each value of _atom_site_subsystem_code must match one of the values of _cell_subsystem_code in the overall description of the subsystems defined for a composite.

The ATOM_SITE_PHASON category allow details of an atom-dependent phason correction, as implemented in JANA2000, to be given. The use of these phason corrections is discouraged.

3.4.3.3.2. Modulation functions as Fourier series

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Data items in these categories are as follows:

(a) ATOM_SITE_DISPLACE_FOURIER [Scheme scheme17]

(b) ATOM_SITE_DISPLACE_FOURIER_PARAM [Scheme scheme18]

(d) ATOM_SITE_OCC_FOURIER [Scheme scheme20]

(e) ATOM_SITE_OCC_FOURIER_PARAM [Scheme scheme21]

(f) ATOM_SITE_ROT_FOURIER [Scheme scheme22]

(g) ATOM_SITE_ROT_FOURIER_PARAM [Scheme scheme23]

(h) ATOM_SITE_U_FOURIER [Scheme scheme24]

(i) ATOM_SITE_U_FOURIER_PARAM [Scheme scheme25]

(j) ATOM_SITES_DISPLACE_FOURIER [Scheme scheme26]

(k) ATOM_SITES_MODULATION [Scheme scheme27]

(l) ATOM_SITES_ROT_FOURIER [Scheme scheme28]

The bullet ( $[\bullet]$ ) indicates a category key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

It is common to represent a modulated structure using a reference periodic structure on which are superimposed atomic modulation functions expanded as Fourier series. (A full discussion of this is given in Section 3.4.4.3.) The msCIF dictionary provides separate categories for listing the modulated parameters that apply to atom positions, site occupancies and thermal parameters. The structuring of the data items within each of these categories follows a similar pattern.

For example, consider the modulation of the atomic displacements. The ATOM_SITE_DISPLACE_FOURIER category allows a listing of the axis along which the displacement occurs (*_axis) and the wave vectors contributing to that displacement component (*_wave_vector_seq_id) for each relevant atom site (labelled by _atom_site_displace_Fourier_atom_site_label). *_wave_vector_seq_id is a pointer to the description of the separate modulation wave vectors and must match one of the identifiers _atom_site_Fourier_wave_vector_seq_id listed separately in the ATOM_SITE_FOURIER_WAVE_VECTOR category. Likewise, the *_atom_site_label data item must match a value of _atom_site_label in the main list of atom positions. This is how the modulation is linked to the atom list. The item _atom_site_displace_Fourier_id is the formal key for the ATOM_SITE_DISPLACE_FOURIER category. It is used to locate the matching Fourier coefficients in the ATOM_SITE_DISPLACE_FOURIER_PARAM category. The coefficients may be reported in a sine–cosine ( _atom_site_displace_Fourier_param_sin, *_cos) or modulus–argument (*_mod, *_phase) representation.

Where a group of atoms is treated as a rigid group, the categories above describe only the translational part of the positional distortion. ATOM_SITE_ROT_FOURIER and ATOM_SITE_ROT_FOURIER_PARAM are used to describe the rotational components.

ATOM_SITE_OCC_FOURIER and ATOM_SITE_U_FOURIER, and their associated *_PARAM categories, are the analogous categories for the modulation of site occupation and thermal parameters.

All the categories above describe the properties of individual atom sites. Larger-scale descriptions of the displacive modulation or of the rotational component of a rigid group are covered by the categories ATOM_SITES_DISPLACE_FOURIER and ATOM_SITES_ROT_FOURIER, each of which at present contains one descriptive data item.

The ATOM_SITES_MODULATION category contains data items describing the initial phases of the modulation waves, which are essential for determining the space group of the commensurate superstructure. More details are given in the dictionary.

3.4.3.3.3. Special modulation functions

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Data items in these categories are as follows:

(a) ATOM_SITE_DISPLACE_SPECIAL_FUNC [Scheme scheme29]

(b) ATOM_SITE_OCC_SPECIAL_FUNC [Scheme scheme30]

The bullet ( $[\bullet]$ ) indicates a category key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

Several data items cover modulation functions that are not expressed as Fourier expansions. The examples in the current msCIF dictionary are restricted to the one-dimensional modulations (sawtooth displacive and occupational crenel functions) implemented in the program JANA2000 (see Section 3.4.2).

3.4.3.3.4. Molecular or packing geometry

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New data items in these categories are as follows:

(a) GEOM_ANGLE [Scheme scheme31]

(b) GEOM_BOND [Scheme scheme32]

(d) GEOM_TORSION [Scheme scheme34]

For each of the geometry categories, there are two groups of extensions. One set covers maximum, minimum and average values of bonds, contact distances, angles and torsion angles. The other extends the symmetry-operation code used in geometry listings in the core CIF dictionary (see Section 3.2.4.3.2 ) to the higher-dimensional superspace form.

3.4.3.3.5. Symmetry information

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New data items in these categories are as follows:

(a) SPACE_GROUP [Scheme scheme35]

(b) SPACE_GROUP_SYMOP [Scheme scheme36]

At present, the msCIF dictionary extends the core CIF dictionary symmetry categories to describe superspace groups for one-dimensional modulated structures in four ways: as the superspace-group number in Janssen et al. (2004) ( _space_group_ssg_IT_number), as the International Tables superspace-group symbol (*_ssg_name_IT), as one of the notations from de Wolff et al. (1981) (*_ssg_name_WJJ, *_ssg_WJJ_code), or in some other formalism (*_ssg_name). At present, superspace-group names for higher dimensions can only be indicated using _space_group_ssg_name.

Symmetry operations in the superspace group are specified in the SPACE_GROUP_SYMOP category by an obvious extension to the method used in the core dictionary. These items must always be present in a CIF corresponding to a modulated or composite structure.

3.4.3.4. File metadata

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The categories modified in the msCIF dictionary to formalize the construction of a multi-block description of modulated or composite structures are as follows :

AUDIT group

AUDIT ¶

AUDIT_LINK ¶

Categories marked with ¶ are already defined in the core CIF dictionary.

Data items revised in these categories are as follows:

(a) AUDIT [Scheme scheme37]

(b) AUDIT_LINK [Scheme scheme38]

The core dictionary definitions of these items are revised in order to formalize the relationships between multiple data blocks representing reference and modulated structures. Guidance is provided in the msCIF dictionary on how to label data blocks in a way that makes their mutual relationships clear.

References

Janssen, T., Janner, A., Looijenga-Vos, A. & de Wolff, P. M. (2004). Incommensurate and commensurate modulated structures. International Tables for Crystallography, Volume C, Mathematical, chemical and physical tables, 3rd ed., edited by E. Prince, ch. 9.8. Dordrecht: Kluwer Academic Publishers.Google Scholar

Wolff, P. M. de, Janssen, T. & Janner, A. (1981). The superspace groups for incommensurate crystal structures with a one-dimensional modulation. Acta Cryst. A37, 625–636.Google Scholar

International Tables for Crystallography (2006). Vol. G. ch. 3.4, pp. 132-137