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vaitkus committed Sep 8, 2023
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12 changes: 12 additions & 0 deletions README.md
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# The Modulated Structures dictionary

A repository for developing CIF definitions for describing modulated and composite structures. Do
not rely on the contents of this repository for authoritative information about data names. You
may rely on released versions, or versions found on
[the IUCr website](https://www.iucr.org/resources/cif/dictionaries/cif_ms) for this purpose.

## Contributing

Please feel free to raise issues, including asking questions about dictionary usage
and suggestions of new data names, using the usual Github mechanisms. Participation
in ongoing discussions of issues and PRs is also welcome.
69 changes: 34 additions & 35 deletions cif_ms.dic
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#\#CIF_2.0
###############################################################################
################################################################################
# #
# CIF Dictionary for Modulated Structures #
# --------------------------------------- #
Expand Down Expand Up @@ -49,7 +49,7 @@ save_MS_GROUP
;
_name.category_id CIF_MS
_name.object_id MS_GROUP
_import.get [{"file":"cif_core.dic" "save":"CIF_CORE" "mode":"Full"}]
_import.get [{"file":"cif_core.dic" "save":"CIF_CORE" "mode":"Full" "dupl":"Ignore"}]

save_

Expand Down Expand Up @@ -399,8 +399,8 @@ save_atom_site_displace_Fourier_param.cos
cosine coefficient (Ac) corresponding to the Fourier term defined
_atom_site_displace_Fourier.atom_site_label,
_atom_site_displace_Fourier.axis and
_atom_site_displace_Fourier.wave_vector.seq_id. Atomic or rigid-
group displacements must be expressed as fractions of the unit
_atom_site_displace_Fourier.wave_vector.seq_id. Atomic or rigid-group
displacements must be expressed as fractions of the unit
cell or in angstroms if the modulations are referred to some
special axes defined by the items belonging to the ATOM_SITES_AXES
category, through _atom_site_displace_Fourier.matrix_seq_id.
Expand Down Expand Up @@ -479,8 +479,8 @@ save_atom_site_displace_Fourier_param.modulus
Fourier term defined by
_atom_site_displace_Fourier.atom_site_label,
_atom_site_displace_Fourier.axis and
_atom_site_displace_Fourier.wave_vector_seq_id. Atomic or rigid-
group displacements must be expressed as fractions of the unit
_atom_site_displace_Fourier.wave_vector_seq_id. Atomic or rigid-group
displacements must be expressed as fractions of the unit
cell or in angstroms if the modulations are referred to some
special axes defined by the items belonging to the ATOM_SITES_AXES
category, through _atom_site_displace_Fourier.matrix_seq_id.
Expand Down Expand Up @@ -579,8 +579,8 @@ save_atom_site_displace_Fourier_param.sin
sine coefficient (As) corresponding to the Fourier term defined
_atom_site_displace_Fourier.atom_site_label,
_atom_site_displace_Fourier.axis, and
_atom_site_displace_Fourier.wave_vector_seq_id. Atomic or rigid-
group displacements must be expressed as fractions of the unit
_atom_site_displace_Fourier.wave_vector_seq_id. Atomic or rigid-group
displacements must be expressed as fractions of the unit
cell or in angstroms if the modulations are referred to some
special axes defined by
the items belonging to the ATOM_SITES_AXES
Expand Down Expand Up @@ -647,7 +647,6 @@ save_ATOM_SITE_DISPLACE_LEGENDRE
ATOM_SITE_ROT_LEGENDRE category. The coefficients of each Legendre function
belong to the category ATOM_SITE_DISPLACE_LEGENDRE_PARAM and are listed
separately.
.

References: Petricek, V., Van Der Lee & Evain, M. (1995).
Acta Cryst. A51, 529-535. DOI 10.1107/S0108767395000365
Expand Down Expand Up @@ -741,7 +740,7 @@ save_atom_site_displace_Legendre.coeff
_atom_site_displace_Legendre.axis and _atom_site_displace_Legendre.order.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_Legendre.matrix_seq_id.
;
_name.category_id atom_site_displace_Legendre
Expand Down Expand Up @@ -855,7 +854,7 @@ save_atom_site_displace_Legendre_param.coeff
_atom_site_displace_Legendre.axis and _atom_site_displace_Legendre.order.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_Legendre.matrix_seq_id.
;
_name.category_id atom_site_displace_Legendre_param
Expand Down Expand Up @@ -1001,7 +1000,7 @@ save_atom_site_displace_ortho.coeff
_atom_site_displace_ortho.axis and _atom_site_displace_ortho.func_id.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_ortho.matrix_seq_id.
;
_name.category_id atom_site_displace_ortho
Expand Down Expand Up @@ -1029,7 +1028,7 @@ save_atom_site_displace_ortho.func_id
;
_name.category_id atom_site_displace_ortho
_name.object_id func_id
_name.linked_item_id '_atom_sites_ortho.func_id '
_name.linked_item_id '_atom_sites_ortho.func_id'
_type.purpose Link
_type.source Related
_type.container Single
Expand Down Expand Up @@ -1117,7 +1116,7 @@ save_atom_site_displace_ortho_param.coeff
_atom_site_displace_ortho.axis and _atom_site_displace_ortho.func_id.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_ortho.matrix_seq_id.
;
_name.category_id atom_site_displace_ortho_param
Expand Down Expand Up @@ -1859,7 +1858,7 @@ save_atom_site_displace_xharm.coeff
_atom_site_displace_xharm.axis and _atom_site_displace_xharm.order.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_xharm.matrix_seq_id.
;
_name.category_id atom_site_displace_xharm
Expand Down Expand Up @@ -1970,7 +1969,7 @@ save_atom_site_displace_xharm_param.coeff
_atom_site_displace_xharm.axis and _atom_site_displace_xharm.order.
Atomic or rigid-group displacements must be expressed as fractions
of the unit cell or in angstroms if the modulations are referred to some
special axes defined by defined by the items belonging to the
special axes defined by the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_xharm.matrix_seq_id.
;
_name.category_id atom_site_displace_xharm_param
Expand Down Expand Up @@ -3419,7 +3418,7 @@ save_atom_site_occ_ortho.func_id
;
_name.category_id atom_site_occ_ortho
_name.object_id func_id
_name.linked_item_id '_atom_sites_ortho.func_id '
_name.linked_item_id '_atom_sites_ortho.func_id'
_type.purpose Link
_type.source Related
_type.container Single
Expand Down Expand Up @@ -4159,7 +4158,7 @@ save_ATOM_SITE_ROT_FOURIER_PARAM
a given rigid group. The translational part would appear in a
separate list of items belonging to the
ATOM_SITE_DISPLACE_FOURIER_PARAM category. The Fourier components
are defined in the parent category ATOM_SITE_ROT_FOURIER Notice
are defined in the parent category ATOM_SITE_ROT_FOURIER. Notice
that items in this category may be listed together with those of the
ATOM_SITE_DISPLACE_FOURIER category.
;
Expand Down Expand Up @@ -4656,7 +4655,7 @@ save_ATOM_SITE_ROT_ORTHO
Data items in the ATOM_SITE_ROT_ORTHO category record
details about the orthogonalized functions defined to solve
correlation problems during the refinement of displacive
modulations when the the atomic domain of a given atom is
modulations when the atomic domain of a given atom is
restricted by a crenel function. The functions are constructed
selecting Fourier harmonics until the desired degree of
orthogonality and completeness is reached (see
Expand Down Expand Up @@ -4758,7 +4757,7 @@ save_atom_site_rot_ortho.func_id
;
_name.category_id atom_site_rot_ortho
_name.object_id func_id
_name.linked_item_id '_atom_sites_ortho.func_id '
_name.linked_item_id '_atom_sites_ortho.func_id'
_type.purpose Link
_type.source Related
_type.container Single
Expand Down Expand Up @@ -6395,7 +6394,7 @@ save_atom_site_U_ortho.func_id
;
_name.category_id atom_site_U_ortho
_name.object_id func_id
_name.linked_item_id '_atom_sites_ortho.func_id '
_name.linked_item_id '_atom_sites_ortho.func_id'
_type.purpose Link
_type.source Related
_type.container Single
Expand Down Expand Up @@ -6740,7 +6739,7 @@ save_ATOM_SITES_AXES
_name.category_id MS_GROUP
_name.object_id ATOM_SITES_AXES
loop_
_category_key.name '_atom_site_sites_axes.matrix_seq_id'
_category_key.name '_atom_sites_axes.matrix_seq_id'
save_

save_atom_sites_axes.matrix
Expand Down Expand Up @@ -7175,9 +7174,9 @@ save_atom_sites_modulation.global_phase_list
& Garcia Arribas, A. (1987). Acta Cryst. A43, 216-226.
On the structure and symmetry of incommensurate phases.
A practical formulation
Smaalen, S. van(1995). Crystallogr. Rev. 4, 79-202.
Smaalen, S. van (1995). Crystallogr. Rev. 4, 79-202.
Incommensurate crystal structures
Smaalen, S. van(2012).
Smaalen, S. van (2012).
Incommensurate Crystallography. Oxford University Press.
;
_name.category_id atom_sites_modulation
Expand Down Expand Up @@ -7512,7 +7511,7 @@ save_atom_sites_ortho.coeff_sin_list
vector list given by _atom_sites_ortho.wave_vector_seq_id_list
;
_name.category_id atom_sites_ortho
_name.object_id coeff_sin
_name.object_id coeff_sin_list
_type.purpose Number
_type.source Assigned
_type.container List
Expand All @@ -7524,7 +7523,7 @@ save_

save_atom_sites_ortho.func_id

_definition.id '_atom_sites_ortho.func_id '
_definition.id '_atom_sites_ortho.func_id'
_definition.update 2017-03-11
_description.text
;
Expand Down Expand Up @@ -7892,7 +7891,7 @@ save_cell_subsystem.matrix_W
Smaalen, S. van (1995).
Crystallogr. Rev. 4, 79-202.
Incommensurate crystal structures
Smaalen, S. van(2012).
Smaalen, S. van (2012).
Incommensurate Crystallography. Oxford University Press.

;
Expand Down Expand Up @@ -9301,7 +9300,7 @@ save_cell_wave_vectors.meas_details
_name.category_id cell_wave_vectors
_name.object_id meas_details
_type.purpose Describe
_type.source Asd
_type.source Assigned
_type.container Single
_type.contents Text

Expand Down Expand Up @@ -10353,7 +10352,7 @@ save_exptl_crystal_face.index_m_list
_name.object_id index_m_list
_type.purpose Number
_type.source Assigned
_type.container Single
_type.container List
_type.contents Integer
_type.dimension '[8]'
loop_
Expand Down Expand Up @@ -10609,7 +10608,7 @@ save_function.Sawtooth
2* a * ((x4-c)/w)

for x4 belonging to the interval [c-(w/2), c+(w/2)], where a is the array
containing the the amplitudes (maximum displacements) along each
containing the amplitudes (maximum displacements) along each
crystallographic axis, w is the width of the sawtooth, x4 is a particular value
of the internal coordinate and c is the centre of the function in
internal space. The use of this function is restricted to one-dimensional
Expand Down Expand Up @@ -10690,7 +10689,7 @@ save_function.Zigzag

for x4 in the interval [c+1/2-(w/2), c+1/2+(w/2)]

where a is the array containing the the amplitudes (maximum displacements)
where a is the array containing the amplitudes (maximum displacements)
along each crystallographic axis, w is the width of the zigzag, x4 is a
particular value of the internal coordinate and c is the centre of the function
in internal space. The use of this function is restricted to one-dimensional
Expand Down Expand Up @@ -10863,7 +10862,7 @@ _units.code degrees

save_

save_save_geom_angle.site_ssg_symmetry_1
save_geom_angle.site_ssg_symmetry_1

_definition.id '_geom_angle.site_ssg_symmetry_1'
_definition.update 2014-06-27
Expand Down Expand Up @@ -10899,9 +10898,9 @@ save_save_geom_angle.site_ssg_symmetry_1
loop_
_description_example.case
_description_example.detail
"." 'no symmetry or translation to site'
"4" '4th symmetry operation applied'
"7_645" '7th symmetry position; +a on x, -b on y'
. 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symmetry position; +a on x, -b on y'

save_

Expand Down

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