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cif_ms.dic
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#\#CIF_2.0
################################################################################
# #
# CIF Dictionary for Modulated Structures #
# --------------------------------------- #
# #
# CIF data definitions specifically for Modulated Structures. These are in #
# addition to those defined in the CIF Core Dictionary version 2.3 (2003). #
# #
# The data included in this dictionary are intended to fulfil the Checklist #
# for the Description of Incommensurate Modulated Crystal Structures, #
# published by the Commission on Aperiodic Crystals. Acta Cryst. (1997), #
# A53, 95-100. #
# #
# #
# #
# The DDL1 version of this dictionary was converted to DDLm on 27 June 2014. #
# #
################################################################################
data_CIF_MS
_dictionary.title CIF_MS
_dictionary.formalism Modulated
_dictionary.class Instance
_dictionary.version 3.2.1
_dictionary.date 2024-05-17
_dictionary.uri http://www.iucr.org/cif/dic/cif_ms.dic
_dictionary.ddl_conformance 3.13.1
_dictionary.namespace ModStruct
_description.text
;
The DICTIONARY group encompassing the definitions of data items
for the study of modulated structures with the Crystallographic
Information Framework (CIF).
;
save_CIF_MS_HEAD
_definition.id CIF_MS_HEAD
_definition.scope Category
_definition.class Head
_definition.update 2024-05-17
_description.text
;
The CIF_MS_HEAD category is the top-level category for all categories
in the CIF_MS dictionary. Head categories from other dictionaries are
reparented to this category.
;
_name.category_id CIF_MS
_name.object_id CIF_MS_HEAD
_import.get
[
{'dupl':Ignore 'file':cif_core.dic 'mode':Full 'save':CIF_CORE_HEAD}
]
save_
save_atom_site.displace_modulation_flag
_definition.id '_atom_site.displace_modulation_flag'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_modulation_flag'
_description.text
;
A code that signals whether the structural model includes the
modulation of the positional coordinates of a given atom site.
;
_name.category_id atom_site
_name.object_id displace_modulation_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'displacive modulation'
y 'abbreviation for "yes"'
no 'no displacive modulation'
n 'abbreviation for "no"'
_enumeration.default no
save_
save_atom_site.occ_modulation_flag
_definition.id '_atom_site.occ_modulation_flag'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_occ_modulation_flag'
_description.text
;
A code that signals whether the structural model includes the
modulation of the occupation of a given atom site.
;
_name.category_id atom_site
_name.object_id occ_modulation_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'occupational modulation'
y 'abbreviation for "yes"'
no 'no occupational modulation'
n 'abbreviation for "no"'
_enumeration.default no
save_
save_atom_site.subsystem_code
_definition.id '_atom_site.subsystem_code'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_subsystem_code'
_description.text
;
A code that links a given atom or rigid-group site to one of the
subsystems present in a composite. This code provides an
alternative description for composites which is less explicit
than that based on linked data blocks (see the description in
this dictionary of audit_link.*). It must match one of
the labels specified for _cell_subsystem.code.
;
_name.category_id atom_site
_name.object_id subsystem_code
_name.linked_item_id '_cell_subsystem.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site.U_modulation_flag
_definition.id '_atom_site.U_modulation_flag'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_U_modulation_flag'
_description.text
;
A code that signals whether the structural model includes the
modulation of the ADP of a given atom site.
;
_name.category_id atom_site
_name.object_id U_modulation_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'modulation of ADP'
y 'abbreviation for "yes"'
no 'no modulation of ADP'
n 'abbreviation for "no"'
_enumeration.default no
save_
save_ATOM_SITE_DISPLACE_FOURIER
_definition.id ATOM_SITE_DISPLACE_FOURIER
_definition.scope Category
_definition.class Loop
_definition.update 2024-05-17
_description.text
;
Data items in the ATOM_SITE_DISPLACE_FOURIER category record
details about the Fourier components of the displacive modulation
of an atom site in a modulated structure. In the case of rigid
groups, items in this category would only include the
translational part of the modulation. The rotational part would
appear in a separate list of items belonging to the
ATOM_SITE_ROT_FOURIER category. The (in general complex)
coefficients of each Fourier component belong to the child category
ATOM_SITE_DISPLACE_FOURIER_PARAM and may be listed separately.
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITE_DISPLACE_FOURIER
loop_
_category_key.name '_atom_site_displace_Fourier.id'
save_
save_atom_site_displace_Fourier.atom_site_label
_definition.id '_atom_site_displace_Fourier.atom_site_label'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_atom_site_label'
_description.text
;
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive
modulation), the atomic occupation (occupational modulation)
and/or the anisotropic (or isotropic) ADP.
_atom_site_displace_Fourier.atom_site_label is the
code that identifies an atom or rigid group in a loop in which
the Fourier components of its displacive modulation are listed.
In the case of a rigid group, this list would only include the
translational part of its displacive modulation. The rotational
part (if any) would appear in a separate list (see
_atom_site_rot_Fourier.atom_site_label). This code must match
the _atom_site.label of the associated coordinate list and
conform to the rules described in _atom_site.label.
;
_name.category_id atom_site_displace_Fourier
_name.object_id atom_site_label
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Fourier.axis
_definition.id '_atom_site_displace_Fourier.axis'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_axis'
_description.text
;
A label identifying the displacement component of a given atom
or rigid group that is being parameterized by Fourier series. a,
b and c are the basic lattice vectors of the reference structure.
For composites they refer to the reference structure of each
subsystem. a~1~, a~2~ and a~3~ are defined by the
items belonging to the ATOM_SITES_AXES category, through
_atom_site_displace_Fourier.matrix_seq_id.
Use of _atom_sites_displace_Fourier.axes_description is deprecated
and retained only for backward compatibility.
;
_name.category_id atom_site_displace_Fourier
_name.object_id axis
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
x 'displacement along the a axis'
y 'displacement along the b axis'
z 'displacement along the c axis'
a1 'displacement along an arbitrary a1 axis'
a2 'displacement along an arbitrary a2 axis'
a3 'displacement along an arbitrary a3 axis'
save_
save_atom_site_displace_Fourier.id
_definition.id '_atom_site_displace_Fourier.id'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_id'
_description.text
;
A code identifying each component of the displacive modulation of
a given atom or rigid group when the modulation is expressed in
terms of Fourier series. In the case of a rigid group, it
applies only to the translational part of the distortion.
;
_name.category_id atom_site_displace_Fourier
_name.object_id id
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Fourier.matrix_seq_id
_definition.id '_atom_site_displace_Fourier.matrix_seq_id'
_definition.update 2017-09-28
_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.category_id atom_site_displace_Fourier
_name.object_id matrix_seq_id
_name.linked_item_id '_atom_sites_axes.matrix_seq_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Fourier.wave_vector_seq_id
_definition.id '_atom_site_displace_Fourier.wave_vector_seq_id'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_wave_vector_seq_id'
_description.text
;
A numeric code identifying the wave vectors of the Fourier terms
used in the structural model to describe the displacive
modulation of an atom or rigid group. In the case of a rigid
group, it applies only to the translational part of the
distortion. This code must match
_atom_site_Fourier_wave_vector.seq_id.
;
_name.category_id atom_site_displace_Fourier
_name.object_id wave_vector_seq_id
_name.linked_item_id '_atom_site_Fourier_wave_vector.seq_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_ATOM_SITE_DISPLACE_FOURIER_PARAM
_definition.id ATOM_SITE_DISPLACE_FOURIER_PARAM
_definition.scope Category
_definition.class Loop
_definition.update 2014-06-27
_description.text
;
Data items in the ATOM_SITE_DISPLACE_FOURIER_PARAM category
record details about the coefficients of the Fourier series
used to describe the displacive modulation of an atom or rigid
group. In the case of rigid groups, items in this category would
only include the translational part of the modulation. The
rotational part would appear in a separate list of items
belonging to the ATOM_SITE_ROT_FOURIER_PARAM category. The
Fourier components are defined in the parent category
ATOM_SITE_DISPLACE_FOURIER. Notice that items in this category
may be listed together with those of the ATOM_SITE_DISPLACE_FOURIER
category.
;
_name.category_id ATOM_SITE_DISPLACE_FOURIER
_name.object_id ATOM_SITE_DISPLACE_FOURIER_PARAM
loop_
_category_key.name '_atom_site_displace_Fourier_param.id'
save_
save_atom_site_displace_Fourier_param.cos
_definition.id '_atom_site_displace_Fourier_param.cos'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_param_cos'
_description.text
;
The displacive distortion of a given atom or rigid group (see
also _atom_site_rot_Fourier_param.cos) is usually parameterized
by Fourier series. Each term of the series commonly adopts two
different representations: the sine-cosine form,
Ac cos(2\\p k r)+As sin(2\\p k r),
and the modulus-argument form,
|A| cos(2\\p k r+\\f),
where k is the wave vector of the term and r is the atomic
average position. _atom_site_displace_Fourier_param.cos is the
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
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.
Use of _atom_sites_displace_Fourier.axes_description is deprecated
and retained only for backward compatibility.
;
_name.category_id atom_site_displace_Fourier_param
_name.object_id cos
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
loop_
_method.purpose
_method.expression
Evaluation
;
With p as atom_site_displace_Fourier_param
atom_site_displace_Fourier_param.cos = p.modulus*Cos(TwoPi*p.phase)
;
save_
save_atom_site_displace_Fourier_param.id
_definition.id '_atom_site_displace_Fourier_param.id'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_param_id'
_description.text
;
A code identifying the (in general complex) coefficient of each
term present in the Fourier series describing the displacive
modulation of a given atom or rigid group. In the case of a rigid
group, it applies only to the translational part of the
distortion. This code must match _atom_site_displace_Fourier.id.
;
_name.category_id atom_site_displace_Fourier_param
_name.object_id id
_name.linked_item_id '_atom_site_displace_Fourier.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Fourier_param.modulus
_definition.id '_atom_site_displace_Fourier_param.modulus'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_param_modulus'
_description.text
;
The displacive distortion of a given atom or rigid group (see
also _atom_site_rot_Fourier_param.modulus) is usually
parameterized by Fourier series. Each term of the series commonly
adopts two different representations: the sine-cosine form,
Ac cos(2\\p k r)+As sin(2\\p k r),
and the modulus-argument form,
|A| cos(2\\p k r+\\f),
where k is the wave vector of the term and r is the atomic
average position. _atom_site_displace_Fourier_param.modulus is
the modulus (|A|) of the complex amplitude corresponding to the
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
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.
Use of _atom_sites_displace_Fourier.axes_description is deprecated
and retained only for backward compatibility.
;
_name.category_id atom_site_displace_Fourier_param
_name.object_id modulus
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
_enumeration.range 0.0:
loop_
_method.purpose
_method.expression
Evaluation
;
With p as atom_site_displace_Fourier_param
atom_site_displace_Fourier_param.modulus = Sqrt(p.cos**2 + p.sin**2)
;
save_
save_atom_site_displace_Fourier_param.phase
_definition.id '_atom_site_displace_Fourier_param.phase'
_definition.update 2014-06-27
loop_
_alias.definition_id
'_atom_site_displace_Fourier_param_phase'
_description.text
;
The displacive distortion of a given atom or rigid group (see
also _atom_site_rot_Fourier_param.phase) is usually parameterized
by Fourier series. Each term of the series commonly adopts two
different representations: the sine-cosine form,
Ac cos(2\\p k r)+As sin(2\\p k r),
and the modulus-argument form,
|A| cos(2\\p k r+\\f),
where k is the wave vector of the term and r is the atomic
average position. _atom_site_displace_Fourier_param.phase is the
phase (\f/2\\p) in cycles of the complex amplitude corresponding\
to the 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.
;
_name.category_id atom_site_displace_Fourier_param
_name.object_id phase
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
_enumeration.range -1.0:1.0
_units.code cycles
loop_
_method.purpose
_method.expression
Evaluation
;
With p as atom_site_displace_Fourier_param
atom_site_displace_Fourier_param.phase = Phase(Complex(p.cos,-p.sin)/2/Pi
;
save_
save_atom_site_displace_Fourier_param.sin
_definition.id '_atom_site_displace_Fourier_param.sin'
_definition.update 2017-09-28
loop_
_alias.definition_id
'_atom_site_displace_Fourier_param_sin'
_description.text
;
The displacive distortion of a given atom or rigid group (see
also _atom_site_rot_Fourier_param.sin) is usually parameterized
by Fourier series. Each term of the series commonly adopts two
different representations: the sine-cosine form,
Ac cos(2\\p k r)+As sin(2\\p k r),
and the modulus-argument form,
|A| cos(2\\p k r+\\f),
where k is the wave vector of the term and r is the atomic
average position. _atom_site_displace_Fourier_param.sin is the
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
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.
Use of _atom_sites_displace_Fourier.axes_description is deprecated
and retained only for backward compatibility.
;
_name.category_id atom_site_displace_Fourier_param
_name.object_id sin
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
loop_
_method.purpose
_method.expression
Evaluation
;
With p as atom_site_displace_Fourier_param
atom_site_displace_Fourier_param.sin = -p.modulus*Sin(TwoPi*p.phase)
;
save_
save_ATOM_SITE_DISPLACE_LEGENDRE
_definition.id ATOM_SITE_DISPLACE_LEGENDRE
_definition.scope Category
_definition.class Loop
_definition.update 2024-05-17
_description.text
;
The set of harmonic functions used in the Fourier series describing the
Modulation functions is orthogonal and complete in the interval [0,1).
However within the x4 interval defined by a Crenel function orthogonality
is no longer preserved and therefore the Fourier coefficients are correlated
and the refinement becomes fragile. There are several ways to avoid this
technical problem (see Petricek et al., 2016). One of them is to use
orthogonal or orthogonalized sets of functions defined within the Crenel
interval. This procedure is more robust than the orthogonalization of harmonics
described in *_ORTHO. categories. Moreover these sets of functions are
complete. Two different sets of orthogonal or orthogonalized functions have
been implemented in JANA2006: Legendre polynomials and the so-called X-
harmonics. Legendre polynomials are orthogonal in the Crenel interval and can
be easily calculated by the recurrence relation:
P~0~(x) = 1
P~1~(x) (x) = x
(n+1)P~n+1~(x) = (2n+1)x P~n~(x) - nP~n-1~(x)
Notice that Legendre polynomials are restricted to one-dimensional cases and
include as a particular case the sawtooth modulation.
Data items in the ATOM_SITE_DISPLACE_LEGENDRE category record
details about the Legendre polynomials used to describe the displacive
modulations when the atomic domain of a given atom is restricted
by a Crenel function. In the case of rigid groups, items in this category would
only include the translational part of the modulation. The rotational
part would appear in a separate list of items belonging to the
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
On the Use of Crenel Functions for Occupationally Modulated
Structures
Petricek, V., Eigner, V., Dusek, M. & Cejchan, A. (2016). Z.
Kristallogr. 231(5), 301-312. DOI 10.1515/zkri-2015-1913
Discontinuous modulation functions and their application for
analysis of modulated structures with the computing system JANA2006
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITE_DISPLACE_LEGENDRE
loop_
_category_key.name '_atom_site_displace_Legendre.id'
save_
save_atom_site_displace_Legendre.atom_site_label
_definition.id '_atom_site_displace_Legendre.atom_site_label'
_definition.update 2017-09-28
_description.text
;
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive
modulation), the atomic occupation (occupational modulation)
and/or the anisotropic (or isotropic) ADP.
_atom_site_displace_Legendre.atom_site_label is the
code that identifies an atom or rigid group in a loop in which
the Legendre components of its displacive modulation are listed.
In the case of a rigid group, this list would only include the
translational part of its displacive modulation. The rotational
part (if any) would appear in a separate list (see
_atom_site_rot_Legendre.atom_site_label). This code must match
the _atom_site.label of the associated coordinate list and
conform to the rules described in _atom_site.label.
;
_name.category_id atom_site_displace_Legendre
_name.object_id atom_site_label
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Legendre.axis
_definition.id '_atom_site_displace_Legendre.axis'
_definition.update 2017-09-28
_description.text
;
A label identifying the displacement component of a given atom
or rigid group that is being parameterized by Legendre polynomials.
a, b and c are the basic lattice vectors of the reference
structure. For composites they refer to the reference structure of
each subsystem. a~1~, a~2~ and a~3~ are defined by the
items belonging to the ATOM_SITES_AXES category, through
_atom_site_displace_Legendre.matrix_seq_id.
;
_name.category_id atom_site_displace_Legendre
_name.object_id axis
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
x 'displacement along the a axis'
y 'displacement along the b axis'
z 'displacement along the c axis'
a1 'displacement along an arbitrary a1 axis'
a2 'displacement along an arbitrary a2 axis'
a3 'displacement along an arbitrary a3 axis'
save_
save_atom_site_displace_Legendre.coeff
_definition.id '_atom_site_displace_Legendre.coeff'
_definition.update 2017-09-28
_description.text
;
The coefficient corresponding to the Legendre function
defined by _atom_site_displace_Legendre.atom_site_label,
_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 the items belonging to the
ATOM_SITES_AXES category, through _atom_site_rot_Legendre.matrix_seq_id.
;
_name.category_id atom_site_displace_Legendre
_name.object_id coeff
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
save_
save_atom_site_displace_Legendre.id
_definition.id '_atom_site_displace_Legendre.id'
_definition.update 2017-09-28
_description.text
;
A code identifying each component of the displacive modulation of
a given atom or rigid group when the modulation is expressed in
terms of Legendre polynomials. In the case of a rigid group, it
applies only to the translational part of the distortion.
;
_name.category_id atom_site_displace_Legendre
_name.object_id id
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Legendre.matrix_seq_id
_definition.id '_atom_site_displace_Legendre.matrix_seq_id'
_definition.update 2017-09-28
_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.category_id atom_site_displace_Legendre
_name.object_id matrix_seq_id
_name.linked_item_id '_atom_sites_axes.matrix_seq_id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_Legendre.order
_definition.id '_atom_site_displace_Legendre.order'
_definition.update 2019-09-25
_description.text
;
The order of the Legendre polynomial.
;
_name.category_id atom_site_displace_Legendre
_name.object_id order
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range 0:
save_
save_ATOM_SITE_DISPLACE_LEGENDRE_PARAM
_definition.id ATOM_SITE_DISPLACE_LEGENDRE_PARAM
_definition.scope Category
_definition.class Loop
_definition.update 2024-05-17
_description.text
;
Data items in the ATOM_SITE_DISPLACE_LEGENDRE_PARAM category
record details about the coefficients of the Legendre polynomials
functions defined in ATOM_SITE_DISPLACE_LEGENDRE and used to
describe the displacive modulation of an atom or rigid group.
In the case of rigid groups, items in this category would
only include the translational part of the modulation. The
rotational part would appear in a separate list of items
belonging to the ATOM_SITE_ROT_LEGENDRE_PARAM category.
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITE_DISPLACE_LEGENDRE_PARAM
loop_
_category_key.name '_atom_site_displace_Legendre_param.id'
save_
### JRH Notes: is there any reason to have this as a separate category
### if there is a one-to-one relationship between the id of this category
### and the id of the parent category?
save_atom_site_displace_Legendre_param.coeff
_definition.id '_atom_site_displace_Legendre_param.coeff'
_definition.update 2017-09-28
_description.text
;
The coefficient corresponding to the Legendre function
defined by _atom_site_displace_Legendre.atom_site_label,
_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 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
_name.object_id coeff
_type.purpose Measurand
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
save_
save_atom_site_displace_Legendre_param.id
_definition.id '_atom_site_displace_Legendre_param.id'
_definition.update 2017-09-28
_description.text
;
A code identifying the coefficient of each Legendre polynomial describing the displacive
modulation of a given atom or rigid group. In the case of a rigid
group, it applies only to the translational part of the
distortion. This code must match _atom_site_displace_Legendre.id.
;
_name.category_id atom_site_displace_Legendre_param
_name.object_id id
_name.linked_item_id '_atom_site_displace_Legendre.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_ATOM_SITE_DISPLACE_ORTHO
_definition.id ATOM_SITE_DISPLACE_ORTHO
_definition.scope Category
_definition.class Loop
_definition.update 2024-05-17
_description.text
;
Data items in the ATOM_SITE_DISPLACE_ORTHO category record
details about the orthogonalized functions defined to solve
correlation problems during the refinement of displacive
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
_atom_site_occ_special_func.crenel_ortho_eps).
In the case of rigid groups, items in this category would only
include the translational part of the modulation. The rotational
part would appear in a separate list of items belonging to the
ATOM_SITE_ROT_ORTHO category. The coefficients of each
orthogonalized function belong to the category
ATOM_SITE_DISPLACE_ORTHO_PARAM and are listed separately.
Notice that the global results could also be expressed (losing
information) using the data items defined in the categories
ATOM_SITE_DISPLACE_FOURIER and ATOM_SITE_DISPLACE_FOURIER_PARAM.
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITE_DISPLACE_ORTHO
loop_
_category_key.name '_atom_site_displace_ortho.id'
save_
save_atom_site_displace_ortho.atom_site_label
_definition.id '_atom_site_displace_ortho.atom_site_label'
_definition.update 2017-09-28
_description.text
;
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive
modulation), the atomic occupation (occupational modulation)
and/or the anisotropic (or isotropic) ADP.
_atom_site_displace_ortho.atom_site_label is the
code that identifies an atom or rigid group in a loop in which
the ortho components of its displacive modulation are listed.
In the case of a rigid group, this list would only include the
translational part of its displacive modulation. The rotational
part (if any) would appear in a separate list (see
_atom_site_rot_ortho.atom_site_label). This code must match
the _atom_site.label of the associated coordinate list and
conform to the rules described in _atom_site.label.
;
_name.category_id atom_site_displace_ortho
_name.object_id atom_site_label
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_atom_site_displace_ortho.axis
_definition.id '_atom_site_displace_ortho.axis'
_definition.update 2017-09-28
_description.text
;
A label identifying the displacement component of a given atom
or rigid group that is being parameterized by orthogonalized
functions. a, b and c are the basic lattice vectors of the reference
structure. For composites they refer to the reference structure of
each subsystem. a~1~, a~2~ and a~3~ are defined by the
items belonging to the ATOM_SITES_AXES category, through
_atom_site_displace_ortho.matrix_seq_id.
;
_name.category_id atom_site_displace_ortho
_name.object_id axis
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
x 'displacement along the a axis'
y 'displacement along the b axis'
z 'displacement along the c axis'
a1 'displacement along an arbitrary a1 axis'
a2 'displacement along an arbitrary a2 axis'
a3 'displacement along an arbitrary a3 axis'
save_
save_atom_site_displace_ortho.coeff
_definition.id '_atom_site_displace_ortho.coeff'
_definition.update 2014-06-27
_description.text
;