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Added templates for modulated structure dictionary. #508

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Added templates for modulated structure dictionary. #508

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ad8fda2
Added templates for modulated structure dictionary.
Dec 12, 2024
c2d630f
Fix formatting
jamesrhester Dec 13, 2024
58291c1
Fix formatting
jamesrhester Dec 13, 2024
0dec5de
Fix formatting
jamesrhester Dec 13, 2024
483125a
Fix formatting
jamesrhester Dec 13, 2024
445c8e0
Fix formatting
jamesrhester Dec 13, 2024
937c86a
Use modern data names
jamesrhester Dec 13, 2024
83fa030
Use modern data names
jamesrhester Dec 13, 2024
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101 changes: 95 additions & 6 deletions templ_attr.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ data_TEMPL_ATTR
_dictionary.title TEMPL_ATTR
_dictionary.class Template
_dictionary.version 1.4.11
_dictionary.date 2024-07-17
_dictionary.date 2024-12-12
_dictionary.uri https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif
_dictionary.ddl_conformance 4.2.0
_description.text
Expand Down Expand Up @@ -167,7 +167,6 @@ save_matrix_w
_units.code none
save_


save_ms_index

_definition.update 2014-06-27
Expand All @@ -183,6 +182,70 @@ save_ms_index
_type.contents Integer
save_

save_q_coeff_element

_definition.update 2024-08-06
_description.text
;
Element of the matrix _atom_site_Fourier_wave_vector.q_coeff.
Notation of the elements is identical to the one used in magCIF.
However, in magCIF the number of elements is limited to 3.
;
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.default 0
save_
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save_q_coeff_seq_id

_definition.update 2024-07-26
_description.text
;
Element of the matrix _atom_site_Fourier_wave_vector.q_coeff_seq_id.
Must match those given in _cell_wave_vector.seq_id.
;
_name.linked_item_id '_cell_wave_vector.seq_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
save_
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save_site_ssg_symmetry

_definition.update 2024-12-12
_description.text
;
The symmetry code of each atom site as the symmetry operation
number 'n' and the higher-dimensional translation 'm1...mp'.
These numbers are combined to form the code 'n m1...mp' or
n_m1...mp. The character string n_m1...mp is composed as follows:
'n' refers to the symmetry operation that is applied to the
superspace coordinates. It must match a number given in
_space_group_symop_ssg_id. 'm1...mp' refer to the translations
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that are subsequently applied to the symmetry-transformed
coordinates to generate the atom used in calculating the angle.
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The "used in calculating the angle" part here is probably a bit too specific. I assume that this save frame will also be imported by items that do not deal with angles, e.g. _geom_bond.site_ssg_symmetry_1.

These translations (t1,...tp) are related to (m1...mp) by the
relations m1=5+t1, ..., mp=5+tp. By adding 5 to the translations,
the use of negative numbers is avoided. The number 'p' must agree
with (_cell_modulation_dimension + 3). If there are no cell
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translations, the translation number may be omitted. If no
symmetry operations or translations are applicable, then a single
full stop '.' is used.
;
_type.purpose Composite
_type.source Derived
_type.container Single
_type.contents Symop
loop_
_description_example.case
_description_example.detail
'.' 'no symmetry or translation to site'
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Suggested change
'.' 'no symmetry or translation to site'
. 'no symmetry or translation to site'

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The special value should not be quoted to distinguish it from a full stop. The same approach is taken in the 'site_symmetry' save frame.

'4' '4th symmetry operation applied'
'7_645' '7th symmetry position; +a on x, -b on y'
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@vaitkus vaitkus Dec 12, 2024 •
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The '7_645' example may be incompatible with the provided definition since the translation part consists of only 3 elements (p = 3).

The definition states that:

The number 'p' must agree with (_cell_modulation_dimension + 3).

The _cell_modulation_dimension is currently defined to have values in the range of 1..8, thus leaving the minimal p value at 4.

Also, having an example with at least 4 translations would be useful to showcases the difference from the conventional 3D symmetry code data item.

save_
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save_index_limit_max

Expand All @@ -197,8 +260,7 @@ save_index_limit_max
_type.container Single
_type.contents Integer
_units.code none
save_

save_
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save_index_limit_min

Expand Down Expand Up @@ -784,7 +846,6 @@ save_orient_matrix
_units.code none
save_


save_transf_matrix

_definition.update 2012-05-07
Expand All @@ -801,6 +862,30 @@ save_transf_matrix
_units.code none
save_

save_transf_matrix_id

_description.text
;
A numeric code identifying the transformation matrix that defines
the arbitrary axes a1, a2 and a3 in terms of the crystallographic axes.
This code must match _atom_sites_axes.matrix_seq_id.
;
_name.linked_item_id '_atom_sites_axes.matrix_seq_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
save_
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save_general_mod_param

_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0

save_

save_face_angle

Expand Down Expand Up @@ -1023,7 +1108,7 @@ save_display_colour

Updated description of _site_symmetry.
;
1.4.11 2024-07-17
1.4.11 2024-12-12
;
# Please update the date above and describe the change below until
# ready for the next release
Expand All @@ -1046,4 +1131,8 @@ save_display_colour

Changed the enumeration range of in the 'cell_length' save frame from
'1.0:' to '0.0:' (av).

Added transf_matrix_id, general_mod_param, site_ssg_symmetry,
q_coeff_element and q_coeff_seq_id for use in modulated structures
dictionary.
;
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