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_ATOM_SITE_FOURIER_WAVE_VECTOR_[]
CIF
Data items in the ATOM_SITE_FOURIER_WAVE_VECTOR category record
details about the wave vectors of the Fourier terms used in the structural model.
Example:
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.568 'First harmonic' 2 1.136 'Second harmonic'
_atom_site_Fourier_wave_vector_description
CIF
A description of the linear combination involved in a given
Fourier wave vector used to describe the atomic modulation functions.
Example:
q(4)=q(1)+q(2)
_atom_site_Fourier_wave_vector_seq_id
CIF
A numeric code identifying the wave vectors defined in
_atom_site_Fourier_wave_vector_.
_atom_site_Fourier_wave_vector
CIF
Data names: _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_y _atom_site_Fourier_wave_vector_z
Wave vectors of the Fourier terms used in the structural model
to describe the atomic modulation functions, expressed with
respect to the three-dimensional reciprocal basis that spans
the lattice of main reflections. They are linear combinations
with integer coefficients of the independent wave vectors given
in the _cell_wave_vector_ list. Therefore, a generic Fourier wave
vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given
by _cell_modulation_dimension. In the case of composites
described in a single data block, these wave vectors are
expressed with respect to the three-dimensional reciprocal
basis of each subsystem (see _cell_subsystem_matrix_W_).
_ATOM_SITE_U_FOURIER_[]
CIF
Data items in the ATOM_SITE_U_FOURIER category record details
about the Fourier components describing the modulation of the atomic thermal parameters in a modulated structure.
Example:
loop_ _atom_site_U_Fourier_id _atom_site_U_Fourier_atom_site_label _atom_site_U_Fourier_tens_elem _atom_site_U_Fourier_wave_vector_seq_id Mn_U11_2 Mn U11 2 Mn_U22_2 Mn U22 2 Mn_U33_2 Mn U33 2 Mn_U12_2 Mn U12 2 Mn_U13_2 Mn U13 2 Mn_U23_2 Mn U23 2 Cl1_U11_2 Cl1 U11 2 Cl1_U22_2 Cl1 U22 2 Cl1_U33_2 Cl1 U33 2 Cl1_U12_2 Cl1 U12 2 Cl1_U13_2 Cl1 U13 2 Cl1_U23_2 Cl1 U23 2
# - - - - data truncated for brevity - - - -
_atom_site_U_Fourier_atom_site_label
CIF
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive
modulation), the atomic occupation (occupational modulation)
and/or the atomic anisotropic (or isotropic) displacement
parameters (referred to as modulation of thermal parameters,
since the term 'displacement parameters' is ambiguous in this
context). _atom_site_U_Fourier_atom_site_label is the code that
identifies an atom in a loop in which the Fourier components of
its thermal-parameters modulation are listed. This code must
match the _atom_site_label of the associated coordinate list
and conform to the rules described in _atom_site_label.
_atom_site_U_Fourier_id
CIF
A code identifying each Fourier component used to describe the
modulation of the atomic thermal parameters.
_atom_site_U_Fourier_tens_elem
CIF
A label identifying the temperature tensor element U(ij) of a
given atom or rigid group whose modulation is being parameterized by Fourier series.
_atom_site_U_Fourier_wave_vector_seq_id
CIF
A numeric code identifying the wave vectors of the Fourier terms
used to describe the modulation functions corresponding to the
temperature factors of an atom or rigid group. This code must
match _atom_site_Fourier_wave_vector_seq_id.
_ATOM_SITE_U_FOURIER_PARAM_[]
CIF
Data items in the ATOM_SITE_U_FOURIER category record details
about the coefficients of the Fourier series used to describe the modulation of the atomic thermal parameters in a modulated structure. The Fourier components are defined in the category ATOM_SITE_U_FOURIER and are listed separately.
Example:
loop_ _atom_site_U_Fourier_param_id _atom_site_U_Fourier_param_modulus _atom_site_U_Fourier_param_phase Mn_U11_2 0.003(3) 0.0 Mn_U22_2 0.0 0.0 Mn_U33_2 0.017(2) 0.0 Mn_U12_2 0.0 0.0 Mn_U13_2 0.00(2) 0.5 Mn_U23_2 0.0 0.0 Cl1_U11_2 0.003(3) 0.5 Cl1_U22_2 0.005(3) 0.0 Cl1_U33_2 0.020(3) 0.0 Cl1_U12_2 0.008(3) 0.0 Cl1_U13_2 0.02(2) 0.75 Cl1_U23_2 0.03(3) 0.25
# - - - - data truncated for brevity - - - -
_atom_site_U_Fourier_param_cos
CIF
The modulation of the atomic thermal parameters is usually
parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, U(ij)c cos(2 k r)+U(ij)s sin(2 k r), and the modulus-argument form, |U(ij)| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_U_Fourier_param_cos is the cosine coefficient [U(ij)c], in angstroms squared, corresponding to the Fourier term defined by _atom_site_U_Fourier_atom_site_label, _atom_site_U_Fourier_tens_elem and _atom_site_U_Fourier_wave_vector_seq_id.
_atom_site_U_Fourier_param_id
CIF
A code identifying the (in general complex) coefficient of each
term present in the Fourier series describing the modulation of
the atomic thermal parameters. This code must match
_atom_site_U_Fourier_id.
_atom_site_U_Fourier_param_modulus
CIF
The modulation of the atomic thermal parameters is usually
parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, U(ij)c cos(2 k r)+U(ij)s sin(2 k r), and the modulus-argument form, |U(ij)| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_U_Fourier_param_modulus is the modulus [|U(ij)|], in angstroms squared, of the complex amplitudes corresponding to the Fourier term defined by _atom_site_U_Fourier_atom_site_label, _atom_site_U_Fourier_tens_elem and _atom_site_U_Fourier_wave_vector_seq_id.
_atom_site_U_Fourier_param_phase
CIF
The modulation of the atomic thermal parameters is usually
parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, U(ij)c cos(2 k r)+U(ij)s sin(2 k r), and the modulus-argument form, |U(ij)| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_U_Fourier_param_phase is the phase (/2), in cycles, of the complex amplitude corresponding to the Fourier term defined by _atom_site_U_Fourier_atom_site_label, _atom_site_U_Fourier_tens_elem and _atom_site_U_Fourier_wave_vector_seq_id.
_atom_site_U_Fourier_param_sin
CIF
The modulation of the atomic thermal parameters is usually
parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, U(ij)c cos(2 k r)+U(ij)s sin(2 k r), and the modulus-argument form, |U(ij)| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_U_Fourier_param_sin is the sine coefficient [U(ij)s], in angstroms squared, corresponding to the Fourier term defined by _atom_site_U_Fourier_atom_site_label, _atom_site_U_Fourier_tens_elem and _atom_site_U_Fourier_wave_vector_seq_id.
_ATOM_SITE_[MS]
CIF
Data items in the ATOM_SITE category record details about
the atom sites in a crystal structure, such as the positional coordinates, atomic displacement parameters, and magnetic moments and directions. This category exists in the core CIF dictionary but is extended in this dictionary by the addition of some items that may appear in the main looped list of atom-site information.
_atom_site_displace_modulation_flag
CIF
A code that signals whether the structural model includes the
modulation of the positional coordinates of a given atom site.
_atom_site_occ_modulation_flag
CIF
A code that signals whether the structural model includes the
modulation of the occupation of a given atom site.
_atom_site_subsystem_code
CIF
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_[ms]). It must match one of the labels specified for _cell_subsystem_code.
_atom_site_U_modulation_flag
CIF
A code that signals whether the structural model includes the
modulation of the thermal parameters of a given atom site.
_ATOM_SITE_DISPLACE_FOURIER_[]
CIF
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 category ATOM_SITE_DISPLACE_FOURIER_PARAM and are listed separately.
Examples:
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.568 'First harmonic' 2 1.136 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1 Nb1 z 1 Nb1x2 Nb1 x 2 Nb1y2 Nb1 y 2 S1x1 S1 x 1 S1y1 S1 y 1 S1z1 S1 z 1 S1x2 S1 x 2 S1y2 S1 y 2 S1z2 S1 z 2
# NbS2 subsystem has been chosen as reference, i.e. its # W matrix is the unit matrix.
loop_ _cell_subsystem_code _cell_subsystem_description _cell_subsystem_matrix_W_1_1 _cell_subsystem_matrix_W_1_4 _cell_subsystem_matrix_W_2_2 _cell_subsystem_matrix_W_3_3 _cell_subsystem_matrix_W_4_1 _cell_subsystem_matrix_W_4_4 NbS2 '1st subsystem' 1 0 1 1 0 1 LaS '2nd subsystem' 0 1 1 1 1 0
# The modulation wave vectors are referred to the reciprocal # basis of each subsystem. They are related to the reciprocal # basis used to index the whole diffraction pattern through # the W matrices.
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_z _atom_site_Fourier_wave_vector_description 1 0.568 0 'First harmonic' 2 1.136 0 'Second harmonic' 3 1.761 0.5 'First harmonic' 4 3.522 1.0 'Second harmonic'
# The modulation coefficients given below are referred to # each subsystem.
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1_NbS2 Nb1 z 1 Nb1x2_NbS2 Nb1 x 2 Nb1y2_NbS2 Nb1 y 2 S1x1_NbS2 S1 x 1 S1y1_NbS2 S1 y 1 S1z1_NbS2 S1 z 1 S1x2_NbS2 S1 x 2 S1y2_NbS2 S1 y 2 S1z2_NbS2 S1 z 2 La1x3_LaS La1 x 3 La1y3_LaS La1 y 3 La1z3_LaS La1 z 3 La1x4_LaS La1 x 4 La1y4_LaS La1 y 4 La1z4_LaS La1 z 4 S2x3_LaS S2 x 3 S2y3_LaS S2 y 3 S2z3_LaS S2 z 3 S2x4_LaS S2 x 4 S2y4_LaS S2 y 4 S2z4_LaS S2 z 4
# # The same structural data but expressed using a set of # linked data blocks #
# Items concerning the modulated structure of the first # subsystem
data_LaSNbS2_MOD_NbS2
_audit_block_code 1997-07-24|LaSNbS2|G.M.|_MOD_NbS2
loop_ _audit_link_block_code _audit_link_block_description 1997-07-24|LaSNbS2|G.M.| 'common experimental and publication data' 1997-07-24|LaSNbS2|G.M.|_REFRNCE 'reference structure (common data)' 1997-07-21|LaSNbS2|G.M.|_MOD 'modulated structure (common data)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_NbS2 'reference structure (1st subsystem)' . 'modulated structure (1st subsystem)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_LaS 'reference structure (2nd subsystem)' 1997-07-21|LaSNbS2|G.M.|_MOD_LaS 'modulated structure (2nd subsystem)'
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.568 'First harmonic' 2 1.136 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1 Nb1 z 1 Nb1x2 Nb1 x 2 Nb1y2 Nb1 y 2 S1x1 S1 x 1 S1y1 S1 y 1 S1z1 S1 z 1 S1x2 S1 x 2 S1y2 S1 y 2 S1z2 S1 z 2
#### End of modulated structure first subsystem data ######
# Items concerning the modulated structure of the second # subsystem
data_LaSNbS2_MOD_LaS
_audit_block_code 1997-07-24|LaSNbS2|G.M.|_MOD_LaS
loop_ _audit_link_block_code _audit_link_block_description 1997-07-24|LaSNbS2|G.M.| 'common experimental and publication data' 1997-07-24|LaSNbS2|G.M.|_REFRNCE 'reference structure (common data)' 1997-07-21|LaSNbS2|G.M.|_MOD 'modulated structure (common data)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_NbS2 'reference structure (1st subsystem)' 1997-07-21|LaSNbS2|G.M.|_MOD_NbS2 'modulated structure (1st subsystem)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_LaS 'reference structure (2nd subsystem)' . 'modulated structure (2nd subsystem)'
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_z _atom_site_Fourier_wave_vector_description 1 1.761 0.5 'First harmonic' 2 3.522 1.0 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id La1x1 La1 x 1 La1y1 La1 y 1 La1z1 La1 z 1 La1x2 La1 x 2 La1y2 La1 y 2 La1z2 La1 z 2 S2x1 S2 x 1 S2y1 S2 y 1 S2z1 S2 z 1 S2x2 S2 x 2 S2y2 S2 y 2 S2z2 S2 z 2
### End of modulated structure second subsystem data ######
_atom_sites_displace_Fourier_axes_description
; a1 and a2 are respectively the long molecular axis
and the axis normal to the mean molecular plane.
;
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Byphenyl_a1_1 Biphenyl a1 1
_atom_site_displace_Fourier_atom_site_label
CIF
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive modulation), the atomic occupation (occupational modulation) and/or the atomic anisotropic (or isotropic) displacement parameters (referred to as modulation of thermal parameters, since the term 'displacement parameters' is ambiguous in this context). _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.
_atom_site_displace_Fourier_axis
CIF
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. a1, a2 and a3 are defined by
_atom_sites_displace_Fourier_axes_description.
_atom_site_displace_Fourier_id
CIF
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.
_atom_site_displace_Fourier_wave_vector_seq_id
CIF
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.
_ATOM_SITE_DISPLACE_FOURIER_PARAM_[]
CIF
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 category ATOM_SITE_DISPLACE_FOURIER and are listed separately.
Examples:
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.568 'First harmonic' 2 1.136 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1 Nb1 z 1 Nb1x2 Nb1 x 2 Nb1y2 Nb1 y 2 S1x1 S1 x 1 S1y1 S1 y 1 S1z1 S1 z 1 S1x2 S1 x 2 S1y2 S1 y 2 S1z2 S1 z 2
loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Nb1z1 -0.0006(2) 0. Nb1x2 0. 0.0078(17) Nb1y2 -0.0014(7) 0. S1x1 0. -0.0134(85) S1y1 -0.0022(12) 0. S1z1 0.0014(14) 0. S1x2 0. -0.0129(27) S1y2 -0.0073(27) 0. S1z2 -0.0012(3) 0.
# NbS2 subsystem has been chosen as reference, i.e. its # W matrix is the unit matrix.
loop_ _cell_subsystem_code _cell_subsystem_description _cell_subsystem_matrix_W_1_1 _cell_subsystem_matrix_W_1_4 _cell_subsystem_matrix_W_2_2 _cell_subsystem_matrix_W_3_3 _cell_subsystem_matrix_W_4_1 _cell_subsystem_matrix_W_4_4 NbS2 '1st subsystem' 1 0 1 1 0 1 LaS '2nd subsystem' 0 1 1 1 1 0
# The modulation wave vectors are referred to the reciprocal # basis of each subsystem. They are related to the reciprocal # basis used to index the whole diffraction pattern through # the W matrices.
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_z _atom_site_Fourier_wave_vector_description 1 0.568 0 'First harmonic' 2 1.136 0 'Second harmonic' 3 1.761 0.5 'First harmonic' 4 3.522 1.0 'Second harmonic'
# The modulation coefficients given below are referred to # each subsystem.
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1_NbS2 Nb1 z 1 Nb1x2_NbS2 Nb1 x 2 Nb1y2_NbS2 Nb1 y 2 S1x1_NbS2 S1 x 1 S1y1_NbS2 S1 y 1 S1z1_NbS2 S1 z 1 S1x2_NbS2 S1 x 2 S1y2_NbS2 S1 y 2 S1z2_NbS2 S1 z 2 La1x3_LaS La1 x 3 La1y3_LaS La1 y 3 La1z3_LaS La1 z 3 La1x4_LaS La1 x 4 La1y4_LaS La1 y 4 La1z4_LaS La1 z 4 S2x3_LaS S2 x 3 S2y3_LaS S2 y 3 S2z3_LaS S2 z 3 S2x4_LaS S2 x 4 S2y4_LaS S2 y 4 S2z4_LaS S2 z 4
loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Nb1z1_NbS2 -0.0006(2) 0. Nb1x2_NbS2 0. 0.0078(17) Nb1y2_NbS2 -0.0014(7) 0. S1x1_NbS2 0. -0.0134(85) S1y1_NbS2 -0.0022(12) 0. S1z1_NbS2 0.0014(14) 0. S1x2_NbS2 0. -0.0129(27) S1y2_NbS2 -0.0073(27) 0. S1z2_NbS2 -0.0012(3) 0. La1x3_LaS 0. -0.0010(22) La1y3_LaS 0.0174(4) 0. La1z3_LaS -0.0005(3) 0. La1x4_LaS 0. 0.0144(7) La1y4_LaS 0.0001(14) 0. La1z4_LaS 0.0008(3) 0. S2x3_LaS 0. 0.0059(70) S2y3_LaS 0.0081(16) 0. S2z3_LaS 0.0009(12) 0. S2x4_LaS 0. -0.0030(30) S2y4_LaS 0.0002(56) 0. S2z4_LaS 0.0007(10) 0.
# # The same structural data but expressed using a set of linked data blocks #
# Items concerning the modulated structure of the first # subsystem
data_LaSNbS2_MOD_NbS2
_audit_block_code 1997-07-24|LaSNbS2|G.M.|_MOD_NbS2
loop_ _audit_link_block_code _audit_link_block_description 1997-07-24|LaSNbS2|G.M.| 'common experimental and publication data' 1997-07-24|LaSNbS2|G.M.|_REFRNCE 'reference structure (common data)' 1997-07-21|LaSNbS2|G.M.|_MOD 'modulated structure (common data)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_NbS2 'reference structure (1st subsystem)' . 'modulated structure (1st subsystem)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_LaS 'reference structure (2nd subsystem)' 1997-07-21|LaSNbS2|G.M.|_MOD_LaS 'modulated structure (2nd subsystem)'
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.568 'First harmonic' 2 1.136 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Nb1z1 Nb1 z 1 Nb1x2 Nb1 x 2 Nb1y2 Nb1 y 2 S1x1 S1 x 1 S1y1 S1 y 1 S1z1 S1 z 1 S1x2 S1 x 2 S1y2 S1 y 2 S1z2 S1 z 2
loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Nb1z1 -0.0006(2) 0. Nb1x2 0. 0.0078(17) Nb1y2 -0.0014(7) 0. S1x1 0. -0.0134(85) S1y1 -0.0022(12) 0. S1z1 0.0014(14) 0. S1x2 0. -0.0129(27) S1y2 -0.0073(27) 0. S1z2 -0.0012(3) 0.
#### End of modulated structure first subsystem data ######
# Items concerning the modulated structure of the second # subsystem
data_LaSNbS2_MOD_LaS
_audit_block_code 1997-07-24|LaSNbS2|G.M.|_MOD_LaS
loop_ _audit_link_block_code _audit_link_block_description 1997-07-24|LaSNbS2|G.M.| 'common experimental and publication data' 1997-07-24|LaSNbS2|G.M.|_REFRNCE 'reference structure (common data)' 1997-07-21|LaSNbS2|G.M.|_MOD 'modulated structure (common data)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_NbS2 'reference structure (1st subsystem)' 1997-07-21|LaSNbS2|G.M.|_MOD_NbS2 'modulated structure (1st subsystem)' 1997-07-24|LaSNbS2|G.M.|_REFRNCE_LaS 'reference structure (2nd subsystem)' . 'modulated structure (2nd subsystem)'
loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_z _atom_site_Fourier_wave_vector_description 1 1.761 0.5 'First harmonic' 2 3.522 1.0 'Second harmonic'
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id La1x1 La1 x 1 La1y1 La1 y 1 La1z1 La1 z 1 La1x2 La1 x 2 La1y2 La1 y 2 La1z2 La1 z 2 S2x1 S2 x 1 S2y1 S2 y 1 S2z1 S2 z 1 S2x2 S2 x 2 S2y2 S2 y 2 S2z2 S2 z 2
loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin La1x1 0. -0.0010(22) La1y1 0.0174(4) 0. La1z1 -0.0005(3) 0. La1x2 0. 0.0144(7) La1y2 0.0001(14) 0. La1z2 0.0008(3) 0. S2x1 0. 0.0059(70) S2y1 0.0081(16) 0. S2z1 0.0009(12) 0. S2x2 0. -0.0030(30) S2y2 0.0002(56) 0. S2z2 0.0007(10) 0.
### End of modulated structure second subsystem data ######
_atom_sites_displace_Fourier_axes_description
; a1 and a2 are respectively the long molecular axis
and the axis normal to the mean molecular plane.
;
loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Byphenyl_a1_1 Biphenyl a1 1
loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_modulus _atom_site_displace_Fourier_param_phase Byphenyl_a1_1 0.035(5) 0.
_atom_site_displace_Fourier_param_cos
CIF
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 k r)+As sin(2 k r), and the modulus-argument form, |A| cos(2 k r+), 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 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 _atom_sites_displace_Fourier_axes_description.
_atom_site_displace_Fourier_param_id
CIF
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.
_atom_site_displace_Fourier_param_modulus
CIF
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 k r)+As sin(2 k r), and the modulus-argument form, |A| cos(2 k r+), 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 _atom_sites_displace_Fourier_axes_description.
_atom_site_displace_Fourier_param_phase
CIF
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 k r)+As sin(2 k r), and the modulus-argument form, |A| cos(2 k r+), 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 (/2) 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.
_atom_site_displace_Fourier_param_sin
CIF
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 k r)+As sin(2 k r), and the modulus-argument form, |A| cos(2 k r+), 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 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 _atom_sites_displace_Fourier_axes_description.
_ATOM_SITE_DISPLACE_SPECIAL_FUNC_[]
CIF
Data items in the ATOM_SITE_DISPLACE_SPECIAL_FUNC category record
details about the displacive modulation of an atom site in a modulated structure when it is not described by Fourier series. Special functions are effective in some cases where the modulations are highly anharmonic, since the number of parameters is drastically reduced. However, they are in general discontinuous or with discontinuous derivatives and therefore these functions describe an ideal situation that never occurs in a real modulated crystal. Up to now, only a few types of special functions have been used and all of them come from the JANA suite of programs. Although this approach is far from being general, it has the advantage that the functions are tightly defined and therefore the atomic displacements and occupations can be calculated easily. In this dictionary, only the special functions available in JANA2000 have been included. These are:
(1) Sawtooth functions for atomic displacive modulation along x, y and z. (2) Crenel functions for the occupational modulation of atoms and rigid groups. Both of these only apply to one-dimensional modulated structures.
Example:
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # In this example the displacive modulation of the O(4) # atom was modelled using a sawtooth-shaped function. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - loop_ _atom_site_displace_special_func_atom_site_label _atom_site_displace_special_func_sawtooth_ax _atom_site_displace_special_func_sawtooth_ay _atom_site_displace_special_func_sawtooth_az _atom_site_displace_special_func_sawtooth_c _atom_site_displace_special_func_sawtooth_w O(4) -0.270(6) 0.022(9) 0.014(2) 0.42(2) 1.07(2)
_atom_site_displace_special_func_atom_site_label
CIF
The code that identifies an atom in a loop in which the special
function that describes its displacive modulation is being defined. This code must match the _atom_site_label of the associated coordinate list and conform to the rules described in _atom_site_label.
_atom_site_displace_special_func_sawtooth
CIF
Data names: _atom_site_displace_special_func_sawtooth_ax _atom_site_displace_special_func_sawtooth_ay _atom_site_displace_special_func_sawtooth_az _atom_site_displace_special_func_sawtooth_c _atom_site_displace_special_func_sawtooth_w
_atom_site_displace_special_func_sawtooth_ items are the
adjustable parameters of a sawtooth function.
A displacive sawtooth function along the internal space is defined as follows:
ux=2*ax[(x4-c)/w] uy=2*ay[(x4-c)/w] uz=2*az[(x4-c)/w]
for x4 belonging to the interval [c-(w/2), c+(w/2)], where ax, ay and az are the amplitudes (maximum displacements) along each crystallographic axis, w is its width, x4 is the internal coordinate and c is the centre of the function in internal space. ux, uy and uz must be expressed in relative units. The use of this function is restricted to one-dimensional modulated structures. For more details, see the manual for JANA2000 (Petricek & Dusek, 2000).
Reference: Petricek, V. & Dusek, M. (2000). JANA2000. The crystallographic computing system. Institute of Physics, Prague, Czech Republic.
_ATOM_SITE_OCC_FOURIER_[]
CIF
Data items in the ATOM_SITE_OCC_FOURIER category record details
about the Fourier components of the occupational modulation of the atom sites in a modulated structure. The (in general complex) coefficients of each Fourier component belong to the category ATOM_SITE_OCC_FOURIER_PARAM and are listed separately.
Example:
loop_ _atom_site_occ_Fourier_id _atom_site_occ_Fourier_atom_site_label _atom_site_occ_Fourier_wave_vector_seq_id CuBr4_1 CuBr4 1 NC4_1_1 (NC4)1 1 NC4_2_1 (NC4)2 1
_atom_site_occ_Fourier_atom_site_label
CIF
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive
modulation), the atomic occupation (occupational modulation)
and/or the atomic anisotropic (or isotropic) displacement
parameters (referred to as modulation of thermal parameters,
since the term 'displacement parameters' is ambiguous in this
context). _atom_site_occ_Fourier_atom_site_label is the code that
identifies an atom in a loop in which the Fourier components of
its occupational modulation are listed. This code must
match the _atom_site_label of the associated coordinate list and
conform to the rules described in _atom_site_label.
_atom_site_occ_Fourier_id
CIF
A code identifying each component of the occupational modulation
of a given atom or rigid group when the modulation is expressed in terms of Fourier series.
_atom_site_occ_Fourier_wave_vector_seq_id
CIF
A numeric code identifying the wave vectors of the Fourier terms
used in the structural model to describe the modulation functions
corresponding to the occupational part of the distortion. This
code must match _atom_site_Fourier_wave_vector_seq_id.
_ATOM_SITE_OCC_FOURIER_PARAM_[]
CIF
Data items in the ATOM_SITE_OCC_FOURIER_PARAM category record
details about the coefficients of the Fourier series used to describe the occupational modulation of the atom sites in a modulated structure. The Fourier components are defined in the category ATOM_SITE_OCC_FOURIER and are listed separately.
Example:
loop_ _atom_site_occ_Fourier_param_id _atom_site_occ_Fourier_param_modulus _atom_site_occ_Fourier_param_phase CuBr4_1 0.397(11) 0.392(6) NC4_1_1 0.216(42) -0.047(33) NC4_2_1 0.208(48) 0.132(27)
_atom_site_occ_Fourier_param_cos
CIF
The occupational distortion of a given atom or rigid group is
usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Pc cos(2 k r)+Ps sin(2 k r), and the modulus-argument form, |P| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_occ_Fourier_param_cos is the cosine coefficient (Pc) corresponding to the Fourier term defined by _atom_site_occ_Fourier_atom_site_label and _atom_site_occ_Fourier_wave_vector_seq_id.
_atom_site_occ_Fourier_param_id
CIF
A code identifying the (in general complex) coefficient of each
term present in the Fourier series describing the occupational
modulation of a given atom or rigid group. This code must match
_atom_site_occ_Fourier_id.
_atom_site_occ_Fourier_param_modulus
CIF
The occupational distortion of a given atom or rigid group is
usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Pc cos(2 k r)+Ps sin(2 k r), and the modulus-argument form, |P| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_occ_Fourier_param_modulus is the modulus (|P|) of the complex amplitude corresponding to the Fourier term defined by _atom_site_occ_Fourier_atom_site_label and _atom_site_occ_Fourier_wave_vector_seq_id.
_atom_site_occ_Fourier_param_phase
CIF
The occupational distortion of a given atom or rigid group is
usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Pc cos(2 k r)+Ps sin(2 k r), and the modulus-argument form, |P| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_occ_Fourier_param_phase is the phase (/2) in cycles corresponding to the Fourier term defined by _atom_site_occ_Fourier_atom_site_label and _atom_site_occ_Fourier_wave_vector_seq_id.
_atom_site_occ_Fourier_param_sin
CIF
The occupational distortion of a given atom or rigid group is
usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Pc cos(2 k r)+Ps sin(2 k r), and the modulus-argument form, |P| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_occ_Fourier_param_sin is the sine coefficient (Ps) corresponding to the Fourier term defined by _atom_site_occ_Fourier_atom_site_label and _atom_site_occ_Fourier_wave_vector_seq_id.
_ATOM_SITE_OCC_SPECIAL_FUNC_[]
CIF
Data items in the ATOM_SITE_DISPLACE_OCC_SPECIAL_FUNC category
record details about the occupational modulation of a given atom or rigid group in a modulated structure when it is not described by Fourier series. Special functions are effective in some cases where the modulations are highly anharmonic, since the number of parameters is drastically reduced. However, they are in general discontinuous or with discontinuous derivatives and therefore these functions describe an ideal situation that never occurs in a real modulated crystal. Up to now, only a few types of special functions have been used and all of them come from the JANA suite of programs. Although this approach is far from being general, it has the advantage that the functions are tightly defined and therefore the atomic displacements and occupations can be calculated easily. In this dictionary, only the special functions available in JANA2000 have been included. These are:
(1) Sawtooth functions for atomic displacive modulation along x, y and z. (2) Crenel functions for the occupational modulation of atoms and rigid groups. Both of these only apply to one-dimensional modulated structures.
Example:
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # In this example the occupational modulation of the Mn(2) # atom was modelled using a square-wave crenel function. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - loop_ _atom_site_occ_special_func_atom_site_label _atom_site_occ_special_func_crenel_c _atom_site_occ_special_func_crenel_w Mn(2) 0.25 0.623(4)
_atom_site_occ_special_func_atom_site_label
CIF
The code that identifies an atom or rigid group in a loop in
which the parameters of the special function that describes its occupational modulation are listed. This code must match the _atom_site_label of the associated coordinate list and conform to the rules described in _atom_site_label.
_atom_site_occ_special_func_crenel
CIF
Data names: _atom_site_occ_special_func_crenel_c _atom_site_occ_special_func_crenel_w
_atom_site_occ_special_func_crenel_ items are the adjustable
parameters of a crenel function.
An occupational crenel function along the internal space is defined as follows:
p(x4)=1 if x4 belongs to the interval [c-w/2,c+w/2] p(x4)=0 if x4 is outside the interval [c-w/2,c+w/2],
where x4 is the internal coordinate, c is the centre of the function in internal space and w is its width. The use of this function is restricted to one-dimensional modulated structures. For more details, see the manual for JANA2000 (Petricek & Dusek, 2000).
Reference: Petricek, V. & Dusek, M. (2000). JANA2000. The crystallographic computing system. Institute of Physics, Prague, Czech Republic.
_ATOM_SITE_PHASON_[]
CIF
Data items in the ATOM_SITE_PHASON category record details
about the atomic phason correction. Although this kind of correction is intended to be overall, some refinement programs (for example, JANA2000) allow for this (theoretically dubious) atom-dependent phason treatment.
_atom_site_phason_atom_site_label
CIF
The code that identifies an atom or rigid group in a loop in
which the phason coefficients are listed. Although this kind of correction is intended to be overall, some refinement programs (for example, JANA2000) allow an independent phason correction for each atom or rigid group. In this case, _atom_site_phason_formula and _atom_site_phason_coeff should be used (see also _refine_ls_mod_overall_phason_). This code must match the _atom_site_label of the associated coordinate list and conform to the rules described in _atom_site_label.
_atom_site_phason_coeff
CIF
The phason coefficient used to calculate (with the appropriate
expression given in _atom_site_phason_formula) the atomic phason correction. Although this kind of correction is intended to be overall, some refinement programs (for example, JANA2000) allow an independent phason correction for each atom or rigid group. In this case, _atom_site_phason_formula and _atom_site_phason_coeff should be used (see also _refine_ls_mod_overall_phason_).
_atom_site_phason_formula
CIF
The formula used for the phason correction. Although both kinds
of corrections are intended to be overall, some refinement programs (for example, JANA2000) allow an independent phason correction for each atom or rigid group. In this case, _atom_site_phason_formula and _atom_site_phason_coeff should be used (see also _refine_ls_mod_overall_phason_).
_ATOM_SITE_ROT_FOURIER_[]
CIF
Data items in the ATOM_SITE_ROT_FOURIER category record details
about the Fourier components present in the rotational part of the displacive modulation of a given rigid group. The translational part would appear in a separate list of items belonging to the ATOM_SITE_DISPLACE_FOURIER category. The (in general complex) coefficients of each Fourier component belong to the category ATOM_SITE_ROT_FOURIER_PARAM and are listed separately.
Examples:
loop_ _atom_site_rot_Fourier_id _atom_site_rot_Fourier_atom_site_label _atom_site_rot_Fourier_axis _atom_site_rot_Fourier_wave_vector_seq_id SeO4_x_1 SeO4 x 1 SeO4_y_1 SeO4 y 1
_atom_sites_rot_Fourier_axes_description ; a1 and a2 are respectively the long molecular axis and the axis normal to the mean molecular plane. ; loop_ _atom_site_rot_Fourier_id _atom_site_rot_Fourier_atom_site_label _atom_site_rot_Fourier_axis _atom_site_rot_Fourier_wave_vector_seq_id Ph1_a1_1 Phenyl1 a1 1 Ph2_a1_1 Phenyl2 a1 1 Bph_a2_1 Biphenyl a2 1
_atom_site_rot_Fourier_atom_site_label
CIF
Modulation parameters are usually looped in separate lists.
Modulated parameters are the atom positions (displacive modulation), the atomic occupation (occupational modulation) and/or the atomic anisotropic (or isotropic) displacement parameters (referred to as modulation of thermal parameters, since the term 'displacement parameters' is ambiguous in this context). _atom_site_rot_Fourier_atom_site_label is the code that identifies a rigid group in a loop in which the Fourier components of the rotational part of its displacive modulation are listed. The translational part (if any) would appear in a separate list (see _atom_site_displace_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.
_atom_site_rot_Fourier_axis
CIF
A label identifying the rotation component around a fixed point
of a given rigid group whose modulation 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
_atom_sites_rot_Fourier_axes_description.
_atom_site_rot_Fourier_id
CIF
A code identifying each component of the rotational modulation of
a given rigid group when the modulation is expressed in terms of Fourier series.
_atom_site_rot_Fourier_wave_vector_seq_id
CIF
A numeric code identifying the wave vectors of the Fourier terms
used in the structural model to describe the modulation functions
corresponding to the rotational distortion of a rigid group. This
code must match _atom_site_Fourier_wave_vector_seq_id.
_ATOM_SITE_ROT_FOURIER_PARAM_[]
CIF
Data items in the ATOM_SITE_ROT_FOURIER_PARAM category record
details about the coefficients of the Fourier series used to describe the rotational component of the displacive modulation of 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 category ATOM_SITE_ROT_FOURIER and are listed separately.
Examples:
loop_ _atom_site_rot_Fourier_param_id _atom_site_rot_Fourier_param_cos _atom_site_rot_Fourier_param_sin SeO4_x_1 -4.2(1) 0.91(3) SeO4_y_1 4.3(1) 0.
_atom_sites_rot_Fourier_axes_description ; a1 and a2 are respectively the long molecular axis and the axis normal to the mean molecular plane. ; loop_ _atom_site_rot_Fourier_param_id _atom_site_rot_Fourier_param_modulus _atom_site_rot_Fourier_param_phase Ph1_a1_1 11.0(2) 0. Ph2_a1_1 11.0(2) 0.5 Bph_a2_1 1.0(1) 0.25
_atom_site_rot_Fourier_param_cos
CIF
The displacive distortion of a given rigid group is not
completely described by _atom_site_displace_Fourier_. The rigid rotation of the group around a given axis passing through a fixed point (for example, the centre of mass of the group) is usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Rc cos(2 k r)+Rs sin(2 k r), and the modulus-argument form, |R| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_rot_Fourier_param_cos is the cosine coefficient (Rc) in degrees corresponding to the Fourier term defined by _atom_site_rot_Fourier_atom_site_label, _atom_site_rot_Fourier_axis and _atom_site_rot_Fourier_wave_vector_seq_id.
_atom_site_rot_Fourier_param_id
CIF
A code identifying the (in general complex) coefficient of each
term present in the Fourier series describing the rotational part
of the displacive modulation of a given rigid group. This code
must match _atom_site_rot_Fourier_id.
_atom_site_rot_Fourier_param_modulus
CIF
The displacive distortion of a given rigid group is not
completely described by _atom_site_displace_Fourier_. The rigid rotation of the group around a given axis passing through a fixed point (for example, the centre of mass of the group) is usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Rc cos(2 k r)+Rs sin(2 k r), and the modulus-argument form, |R| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_rot_Fourier_param_modulus is the modulus (|R|) in degrees of the complex amplitude corresponding to the Fourier term defined by _atom_site_rot_Fourier_atom_site_label, _atom_site_rot_Fourier_axis and _atom_site_rot_Fourier_wave_vector_seq_id.
_atom_site_rot_Fourier_param_phase
CIF
The displacive distortion of a given rigid group is not
completely described by _atom_site_displace_Fourier_. The rigid rotation of the group around a given axis passing through a fixed point (for example, the centre of mass of the group) is usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Rc cos(2 k r)+Rs sin(2 k r), and the modulus-argument form, |R| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_rot_Fourier_param_phase is the phase (/2) in cycles of the complex amplitude corresponding to the Fourier term defined by _atom_site_rot_Fourier_atom_site_label, _atom_site_rot_Fourier_axis and _atom_site_rot_Fourier_wave_vector_seq_id.
_atom_site_rot_Fourier_param_sin
CIF
The displacive distortion of a given rigid group is not
completely described by _atom_site_displace_Fourier_. The rigid rotation of the group around a given axis passing through a fixed point (for example, the centre of mass of the group) is usually parameterized by Fourier series. Each term of the series commonly adopts two different representations: the sine-cosine form, Rc cos(2 k r)+Rs sin(2 k r), and the modulus-argument form, |R| cos(2 k r+), where k is the wave vector of the term and r is the atomic average position. _atom_site_rot_Fourier_param_sin is the sine coefficient (Rs) in degrees corresponding to the Fourier term defined by _atom_site_rot_Fourier_atom_site_label, _atom_site_rot_Fourier_axis and _atom_site_rot_Fourier_wave_vector_seq_id.
_ATOM_SITES_DISPLACE_FOURIER_[]
CIF
Data items in the ATOM_SITES_DISPLACE_FOURIER category record
details common to the displacive modulation of atom sites in a modulated structure.
Details for individual atom sites are described by data items in the ATOM_SITE_DISPLACE_FOURIER category.
Example:
_atom_sites_displace_Fourier_axes_description
; a1 and a2 are respectively the long molecular axis
and the axis normal to the mean molecular plane.
;
_atom_sites_displace_Fourier_axes_description
CIF
The definition of the axes used for describing the displacive
modulation, parameterized by Fourier series, when they are other than the crystallographic axes.
Example:
a1 and a2 are respectively the long molecular axis and the axis normal to the mean molecular plane.
_ATOM_SITES_MODULATION_[]
CIF
Data items in the ATOM_SITES_MODULATION category record details
common to the modulation of atom sites in a modulated structure.
_atom_sites_modulation_global_phase_t
CIF
Data names: _atom_sites_modulation_global_phase_t_1 _atom_sites_modulation_global_phase_t_2 _atom_sites_modulation_global_phase_t_3 _atom_sites_modulation_global_phase_t_4 _atom_sites_modulation_global_phase_t_5 _atom_sites_modulation_global_phase_t_6 _atom_sites_modulation_global_phase_t_7 _atom_sites_modulation_global_phase_t_8
The initial phases, in cycles, of the modulation waves. For
incommensurate structures they are irrelevant. However, they are essential for the description of commensurate structures within the superspace formalism, since they determine the space group of the commensurate superstructure [see Perez-Mato, Madariaga, Zuiga & Garcia Arribas (1987) or van Smaalen (1995)]. Note that for composites described using a single data block, the initial phases for each subsystem are derived using the W matrices (see _cell_subsystem_matrix_W_) from a unique set of global phases whose values are assigned to _atom_sites_modulation_global_phase_t_. Detailed information can be found in van Smaalen (1995).
Ref: Perez-Mato, J. M., Madariaga, G., Zuiga, F. J. & Garcia Arribas, A. (1987). Acta Cryst. A43, 216-226. Smaalen, S. van (1995). Crystallogr. Rev. 4, 79-202.
_ATOM_SITES_ROT_FOURIER_[]
CIF
Data items in the ATOM_SITES_ROT_FOURIER category record
details about the rotational component of the displacive modulation of a given rigid group as a whole.
Details for individual atom sites are described by data items in the ATOM_SITES_ROT_FOURIER category.
Example:
_atom_sites_rot_Fourier_axes_description
; a1 and a2 are respectively the long molecular axis
and the axis normal to the mean molecular plane.
;
_atom_sites_rot_Fourier_axes_description
CIF
The definition of the axes used for describing the rotational
part of the displacive modulation of a given rigid group, parameterized by Fourier series, when they are other than the crystallographic axes.
Example:
a1 and a2 are respectively the long molecular axis and the axis normal to the mean molecular plane.
_AUDIT_LINK_[MS]
CIF
This category description does NOT introduce a new category; instead, it describes the recommended practice for using block codes as described in the core AUDIT_LINK category for descriptions of modulated structures.
The value of _audit_block_code may be associated with a data block in the same file or in a different file related to the current data block. The value of _audit_block_code should be unique.
It is recommended that data blocks are named as follows:
<string> The name of the data block containing those items that, for a particular material, are independent of the specific structure (modulated, reference etc.). For example, the experimental set-up or publication details would be described here.
<string>_REFRNCE The name of the data block that contains specific details of the reference (unmodulated) structure if it was refined separately using only main reflections. In the case of composites, this data block may contain those items that are common to the reference structures of all subsystems.
<string>_MOD The name of the data block in which specific details of the modulated structure are given. In the case of composites, this data block may include either those items that are common to the modulated structures of all subsystems or the whole modulated structure if it is described implicitly through the *_subsystem_code pointers.
A trailing code following the reserved words MOD or REFRNCE
indicates that the corresponding data block includes
structural information corresponding to the modulated or
reference structures of the subsystem labelled by
_cell_subsystem_code. A recommended format for <string>
is given in the definitions of _pd_block_[pd] and
_pd_block_id in the dictionary extension cif_pd.dic
(http://www.iucr.org/cif/pd/index.html).
Examples:
loop_ _audit_link_block_code _audit_link_block_description . 'publication details' K2SEO4_COM 'experimental data common to ref./mod. structures' K2SEO4_REFRNCE 'reference structure' K2SEO4_MOD 'modulated structure'
_audit_link_block_code 'PbSVS2_MOD_VS2'
_CELL_[MS]
CIF
Data items in the CELL category record details about
the crystallographic cell parameters and their measurement. This category is already defined in the core CIF dictionary but is extended in this dictionary by the addition of some items that are specific for modulated and composite structures.
_cell_modulation_dimension
CIF
Number of additional reciprocal vectors needed to index the
whole diffraction pattern using integer Miller indices.
_cell_reciprocal_basis_description
CIF
Definition of the higher-dimensional basis with respect to which
the Miller indices are defined. The three-dimensional basis used to index the additional wave vectors should be clearly indicated.
Examples:
a*,b*,c* (reciprocal basis spanning the lattice of main reflections) and q (incommensurate with respect to a*,b*,c*)
The diffraction pattern can be indexed with four integers based on the reciprocal vectors a*~1~=a*~11~, a*~2~=a*~12~, a*~3~=a*~13~, a*~4~=a*~21~. a*~1j~ (j=1,2,3) index the main reflections of the 1st subsystem. a*~21~ is incommensurate with a*~11~.
_CELL_SUBSYSTEM_[MS]
CIF
Data items in the CELL_SUBSYSTEM category record details about
the crystallographic cell parameters of each subsystem present in a composite.
Example:
_cell_subsystems_number 2 loop_ _cell_subsystem_code _cell_subsystem_description _cell_subsystem_matrix_W_1_1 _cell_subsystem_matrix_W_1_4 _cell_subsystem_matrix_W_2_2 _cell_subsystem_matrix_W_3_3 _cell_subsystem_matrix_W_4_1 _cell_subsystem_matrix_W_4_4 NbS2 '1st subsystem' 1 0 1 1 0 1 LaS '2nd subsystem' 0 1 1 1 1 0
_cell_subsystem_code
CIF
The code identifying uniquely a certain composite subsystem.
This code is used to identify the data blocks that contain the structural information associated with the subsystem.
Example:
NbS2
_cell_subsystem_description
CIF
Description of each subsystem defining a composite structurally.
The number of definitions must match the number given in
_cell_subsystems_number.
Example:
NbS2 part of the layer compound (LaS)~1.14~NbS~2~
_cell_subsystem_matrix_W
CIF
Data names: _cell_subsystem_matrix_W_1_1 _cell_subsystem_matrix_W_1_2 _cell_subsystem_matrix_W_1_3 _cell_subsystem_matrix_W_1_4 _cell_subsystem_matrix_W_1_5 _cell_subsystem_matrix_W_1_6 _cell_subsystem_matrix_W_1_7 _cell_subsystem_matrix_W_1_8 _cell_subsystem_matrix_W_1_9 _cell_subsystem_matrix_W_1_10 _cell_subsystem_matrix_W_1_11 _cell_subsystem_matrix_W_2_1 _cell_subsystem_matrix_W_2_2 _cell_subsystem_matrix_W_2_3 _cell_subsystem_matrix_W_2_4 _cell_subsystem_matrix_W_2_5 _cell_subsystem_matrix_W_2_6 _cell_subsystem_matrix_W_2_7 _cell_subsystem_matrix_W_2_8 _cell_subsystem_matrix_W_2_9 _cell_subsystem_matrix_W_2_10 _cell_subsystem_matrix_W_2_11 _cell_subsystem_matrix_W_3_1 _cell_subsystem_matrix_W_3_2 _cell_subsystem_matrix_W_3_3 _cell_subsystem_matrix_W_3_4 _cell_subsystem_matrix_W_3_5 _cell_subsystem_matrix_W_3_6 _cell_subsystem_matrix_W_3_7 _cell_subsystem_matrix_W_3_8 _cell_subsystem_matrix_W_3_9 _cell_subsystem_matrix_W_3_10 _cell_subsystem_matrix_W_3_11 _cell_subsystem_matrix_W_4_1 _cell_subsystem_matrix_W_4_2 _cell_subsystem_matrix_W_4_3 _cell_subsystem_matrix_W_4_4 _cell_subsystem_matrix_W_4_5 _cell_subsystem_matrix_W_4_6 _cell_subsystem_matrix_W_4_7 _cell_subsystem_matrix_W_4_8 _cell_subsystem_matrix_W_4_9 _cell_subsystem_matrix_W_4_10 _cell_subsystem_matrix_W_4_11 _cell_subsystem_matrix_W_5_1 _cell_subsystem_matrix_W_5_2 _cell_subsystem_matrix_W_5_3 _cell_subsystem_matrix_W_5_4 _cell_subsystem_matrix_W_5_5 _cell_subsystem_matrix_W_5_6 _cell_subsystem_matrix_W_5_7 _cell_subsystem_matrix_W_5_8 _cell_subsystem_matrix_W_5_9 _cell_subsystem_matrix_W_5_10 _cell_subsystem_matrix_W_5_11 _cell_subsystem_matrix_W_6_1 _cell_subsystem_matrix_W_6_2 _cell_subsystem_matrix_W_6_3 _cell_subsystem_matrix_W_6_4 _cell_subsystem_matrix_W_6_5 _cell_subsystem_matrix_W_6_6 _cell_subsystem_matrix_W_6_7 _cell_subsystem_matrix_W_6_8 _cell_subsystem_matrix_W_6_9 _cell_subsystem_matrix_W_6_10 _cell_subsystem_matrix_W_6_11 _cell_subsystem_matrix_W_7_1 _cell_subsystem_matrix_W_7_2 _cell_subsystem_matrix_W_7_3 _cell_subsystem_matrix_W_7_4 _cell_subsystem_matrix_W_7_5 _cell_subsystem_matrix_W_7_6 _cell_subsystem_matrix_W_7_7 _cell_subsystem_matrix_W_7_8 _cell_subsystem_matrix_W_7_9 _cell_subsystem_matrix_W_7_10 _cell_subsystem_matrix_W_7_11 _cell_subsystem_matrix_W_8_1 _cell_subsystem_matrix_W_8_2 _cell_subsystem_matrix_W_8_3 _cell_subsystem_matrix_W_8_4 _cell_subsystem_matrix_W_8_5 _cell_subsystem_matrix_W_8_6 _cell_subsystem_matrix_W_8_7 _cell_subsystem_matrix_W_8_8 _cell_subsystem_matrix_W_8_9 _cell_subsystem_matrix_W_8_10 _cell_subsystem_matrix_W_8_11 _cell_subsystem_matrix_W_9_1 _cell_subsystem_matrix_W_9_2 _cell_subsystem_matrix_W_9_3 _cell_subsystem_matrix_W_9_4 _cell_subsystem_matrix_W_9_5 _cell_subsystem_matrix_W_9_6 _cell_subsystem_matrix_W_9_7 _cell_subsystem_matrix_W_9_8 _cell_subsystem_matrix_W_9_9 _cell_subsystem_matrix_W_9_10 _cell_subsystem_matrix_W_9_11 _cell_subsystem_matrix_W_10_1 _cell_subsystem_matrix_W_10_2 _cell_subsystem_matrix_W_10_3 _cell_subsystem_matrix_W_10_4 _cell_subsystem_matrix_W_10_5 _cell_subsystem_matrix_W_10_6 _cell_subsystem_matrix_W_10_7 _cell_subsystem_matrix_W_10_8 _cell_subsystem_matrix_W_10_9 _cell_subsystem_matrix_W_10_10 _cell_subsystem_matrix_W_10_11 _cell_subsystem_matrix_W_11_1 _cell_subsystem_matrix_W_11_2 _cell_subsystem_matrix_W_11_3 _cell_subsystem_matrix_W_11_4 _cell_subsystem_matrix_W_11_5 _cell_subsystem_matrix_W_11_6 _cell_subsystem_matrix_W_11_7 _cell_subsystem_matrix_W_11_8 _cell_subsystem_matrix_W_11_9 _cell_subsystem_matrix_W_11_10 _cell_subsystem_matrix_W_11_11
In the case of composites, for each subsystem the matrix W as
defined in van Smaalen (1991); see also van Smaalen (1995). Its dimension must match (_cell_modulation_dimension+3)*(_cell_modulation_dimension+3).
Intergrowth compounds are composed of several periodic substructures in which the reciprocal lattices of two different subsystems are incommensurate in at least one direction. The indexing of the whole diffraction diagram with integer indices requires more than three reciprocal basic vectors. However, the distinction between main reflections and satellites is not as obvious as in normal incommensurate structures. Indeed, true satellites are normally difficult to locate for composites and the modulation wave vectors are reciprocal vectors of the other subsystem(s) referred to the reciprocal basis of one of them. The choice of the enlarged reciprocal basis {a*, b*, c*, q~1~,..., q~d~} is completely arbitrary, but the reciprocal basis of each subsystem is always known through the W matrices. These matrices [(3+d)x(3+d)-dimensional], one for each subsystem, can be blocked as follows:
(Z^^~3~ Z^^~d~) W^^= ( ) (V^^~3~ V^^~d~),
the dimension of each block being (3x3), (3xd), (dx3) and (dxd) for Z^^~3~, Z^^~d~, V^^~3~ and V^^~d~, respectively. For example, Z^^ expresses the reciprocal basis of each subsystem in terms of the basis {a*, b*, c*, q~1~ ,..., q~d~}. W^^ also gives the irrational components of the modulation wave vectors of each subsystem in its own three-dimensional reciprocal basis {a~~*, b~~*, c~~*} and the superspace group of a given subsystem from the unique superspace group of the composite.
The structure of these materials is always described by a set of incommensurate structures, one for each subsystem. The atomic coordinates, modulation parameters and wave vectors used for describing the modulation(s) are always referred to the (direct or reciprocal) basis of each particular subsystem. Although expressing the structural results in the chosen common basis is possible (using the matrices W), it is less confusing to use this alternative description. Atomic coordinates are only referred to a common basis when interatomic distances are calculated. Usually, the reciprocal vectors {a*, b* and c*} span the lattice of main reflections of one of the subsystems and therefore its W matrix is the unit matrix.
For composites described in a single data block using
*_subsystem_code pointers, the cell parameters, the superspace
group and the measured modulation wave vectors (see
CELL_WAVE_VECTOR below) correspond to the reciprocal basis
described in _cell_reciprocal_basis_description and coincide
with the reciprocal basis of the specific subsystem (if any)
whose W matrix is the unit matrix. The cell parameters and the
symmetry of the remaining subsystems can be derived using the
appropriate W matrices. In any case (single or multiblock CIF),
the values assigned to the items describing the atomic parameters
(including the wave vectors used to describe the modulations)
are always the same and are referred to the basis of each
particular subsystem. Such a basis will be explicitly given in a
multiblock CIF or should be calculated (with the appropriate W
matrix) in the case of a single block description of the
composite.
Ref: Smaalen, S. van (1991). Phys. Rev. B, 43, 11330-11341. Smaalen, S. van (1995). Crystallogr. Rev. 4, 79-202.
_CELL_SUBSYSTEMS_[MS]
CIF
Data items in the CELL_SUBSYSTEMS category describe the gross
structure of the subsystems present in a composite.
Example:
_cell_subsystems_number 2
_cell_subsystems_number
CIF
The number of subsystems used to define the structural model of
a composite structure.
_CELL_WAVE_VECTOR_[MS]
CIF
Data items in the CELL_WAVE_VECTOR category list the
independent modulation wave vectors q~i~. The diffraction vectors are indexed in the form ha*+kb*+lc*+sum~i~ (m~i~q~i~). sum~i~ is taken over all wave vectors. In this version of the dictionary, the index i has been restricted to be less than 9.
Example:
loop_ _cell_wave_vector_seq_id _cell_wave_vector_x 1 0.318(5)
_cell_wave_vector_seq_id
CIF
A numeric code to identify each independent wave vector. These
codes define uniquely the reciprocal basis and, therefore, force the order of the Miller indices assigned to intensities, crystal faces etc.
_cell_wave_vector
CIF
Data names: _cell_wave_vector_x _cell_wave_vector_y _cell_wave_vector_z
Independent modulation wave vector(s) with which the whole
diffraction pattern is indexed, expressed as fractions of the three reciprocal basis vectors of the reference structure. In the case of composites, the modulation wave vectors of each subsystem are expressed in terms of the reciprocal basis of its corresponding reference structure. Their number must match _cell_modulation_dimension. In the case of composites described in a single data block, the wave vectors are expressed in the three-dimensional basis chosen as reference in _cell_reciprocal_basis_description, which would correspond to the subsystem (if any) whose W matrix is the {(_cell_modulation_dimension + 3)* (_cell_modulation_dimension + 3)} unit matrix. In this case, the wave vectors used to describe the modulation of each subsystem are referred to their own reciprocal basis via the W matrices (for details see _cell_subsystem_matrix_W_ and _atom_site_Fourier_wave_vector_).
_CELL_WAVE_VECTORS_[MS]
CIF
Data items in the CELL_WAVE_VECTORS category record details
about the set of independent modulation wave vectors q~i~ and their measurement. The diffraction vectors are indexed in the form ha*+kb*+lc*+sum~i~ (m~i~q~i~). sum~i~ is taken over all wave vectors. In this version of the dictionary, the index i has been restricted to be less than 9.
Example:
_cell_wave_vectors_meas_details 'Determined from profiles along q'
_cell_wave_vectors_meas_details
CIF
Details about the method used to determine the independent
modulation wave vector(s).
_cell_wave_vectors_pressure
CIF
Data names: _cell_wave_vectors_pressure_max _cell_wave_vectors_pressure_min
The maximum and minimum values of the pressure in kilopascals
defining the interval within which the modulation wave vector(s) were measured.
_cell_wave_vectors_temp
CIF
Data names: _cell_wave_vectors_temp_max _cell_wave_vectors_temp_min
The maximum and minimum values of the temperature in kelvins
defining the interval within which the modulation wave vector(s) were measured.
_cell_wave_vectors_variation
CIF
Details concerning the behaviour (and its experimental
detection) of the wave vector(s) with temperature and/or pressure within the ranges specified by _cell_wave_vectors_pressure_max, _cell_wave_vectors_pressure_min, _cell_wave_vectors_temp_max and _cell_wave_vectors_temp_min.
_DIFFRN_REFLN_[MS]
CIF
Data items in the DIFFRN_REFLN category record details about
the intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. (The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLNS data items are not looped.) Data items in this category are extensions of the core CIF dictionary definitions to the indexing of diffraction intensities by higher-dimensional components.
_diffrn_refln_index_m
CIF
Data names: _diffrn_refln_index_m_1 _diffrn_refln_index_m_2 _diffrn_refln_index_m_3 _diffrn_refln_index_m_4 _diffrn_refln_index_m_5 _diffrn_refln_index_m_6 _diffrn_refln_index_m_7 _diffrn_refln_index_m_8
Additional Miller indices needed to write the reciprocal vector
of a certain reflection in the basis described in _cell_reciprocal_basis_description. Following the usual convention, such a vector would be expressed as H=h*a*+k*b*+l*c*+m1*q(1)+...+m8*q(8), where h,k,l are the usual _diffrn_refln_index_, and q(1)...q(8) represent the independent wave vectors given by _cell_wave_vector_ and identified by _cell_wave_vector_seq_id. Therefore, the total number of indices of a given reflection must match (_cell_modulation_dimension + 3) and the order of the additional indices must be consistent with the codes given in _cell_wave_vector_seq_id . These indices need not match _refln_index_m_ values if a transformation of the original measured cell has occurred.
_DIFFRN_REFLNS_[MS]
CIF
Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLNS data items are not looped. (The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists.) Data items in this category extend the core CIF dictionary definitions providing independent checks on the range of values recorded for each of the additional Miller indices given in the DIFFRN_REFLN category.
_diffrn_reflns_limit_index_m
CIF
Data names: _diffrn_reflns_limit_index_m_1_max _diffrn_reflns_limit_index_m_1_min _diffrn_reflns_limit_index_m_2_max _diffrn_reflns_limit_index_m_2_min _diffrn_reflns_limit_index_m_3_max _diffrn_reflns_limit_index_m_3_min _diffrn_reflns_limit_index_m_4_max _diffrn_reflns_limit_index_m_4_min _diffrn_reflns_limit_index_m_5_max _diffrn_reflns_limit_index_m_5_min _diffrn_reflns_limit_index_m_6_max _diffrn_reflns_limit_index_m_6_min _diffrn_reflns_limit_index_m_7_max _diffrn_reflns_limit_index_m_7_min _diffrn_reflns_limit_index_m_8_max _diffrn_reflns_limit_index_m_8_min
Maximum and minimum values of the additional Miller indices
appearing in _diffrn_refln_index_m_. The number of ranges must match _cell_modulation_dimension. The order of the additional indices must be consistent with the codes given in _cell_wave_vector_seq_id.
_diffrn_reflns_satellite_order_max
CIF
Maximum order of observed satellites.
_DIFFRN_STANDARD_REFLN_[MS]
CIF
Data items in the DIFFRN_STANDARD_REFLN category record
details about the reflections treated as standards during the measurement of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. Data items in this category are extensions of the core CIF dictionary definitions to the indexing of standard reflections by higher-dimensional components.
_diffrn_standard_refln_index_m
CIF
Data names: _diffrn_standard_refln_index_m_1 _diffrn_standard_refln_index_m_2 _diffrn_standard_refln_index_m_3 _diffrn_standard_refln_index_m_4 _diffrn_standard_refln_index_m_5 _diffrn_standard_refln_index_m_6 _diffrn_standard_refln_index_m_7 _diffrn_standard_refln_index_m_8
Additional Miller indices needed to write the reciprocal vectors
of the standard intensities used in the diffraction measurement process, in the basis described in _cell_reciprocal_basis_description. The total number of indices of a given standard reflection must match (_cell_modulation_dimension + 3) and the order of the additional indices must be consistent with the codes given in _cell_wave_vector_seq_id.
_EXPTL_CRYSTAL_[MS]
CIF
Data items in the EXPTL_CRYSTAL category record
details about experimental measurements on the crystal or crystals used, such as shape, size and density. The new data item added to this category specifies whether the structure is crystalline, modulated or composite.
_exptl_crystal_type_of_structure
CIF
The type of structure. This is used to check the consistency of a
CIF: the data blocks that are expected and/or certain characteristic parameters depend on whether the material is classified as crystalline (periodic in three dimensions), modulated or composite.
_EXPTL_CRYSTAL_FACE_[MS]
CIF
Data items in the EXPTL_CRYSTAL_FACE category record
details of the crystal faces. Data items in this category are extensions of the core CIF dictionary definitions to the indexing of crystal faces by higher-dimensional components.
_exptl_crystal_face_index_m
CIF
Data names: _exptl_crystal_face_index_m_1 _exptl_crystal_face_index_m_2 _exptl_crystal_face_index_m_3 _exptl_crystal_face_index_m_4 _exptl_crystal_face_index_m_5 _exptl_crystal_face_index_m_6 _exptl_crystal_face_index_m_7 _exptl_crystal_face_index_m_8
Additional Miller indices of the crystal face associated with the
value _exptl_crystal_face_perp_dist when the face is indexed using a multidimensional scheme. The total number of indices must match (_cell_modulation_dimension + 3). The order of the indices must be consistent with the codes given in _cell_wave_vector_seq_id.
_GEOM_ANGLE_[MS]
CIF
Data items in the GEOM_ANGLE category record
details about the bond angles, as calculated from the ATOM, CELL and SYMMETRY data. These extensions to the core CIF dictionary definitions record the maximum, minimum and average values of angles and extend the symmetry-operation code used in angle listings to the higher-dimensional superspace form.
_geom_angle
CIF
Data names: _geom_angle_max _geom_angle_min _geom_angle_av
Maximum, minimum and average angles in degrees bounded by
_geom_angle_atom_site_label_1, *_2, and *_3. The site at *_2 is at the apex of the angle.
_geom_angle_site_ssg_symmetry
CIF
Data names: _geom_angle_site_ssg_symmetry_1 _geom_angle_site_ssg_symmetry_2 _geom_angle_site_ssg_symmetry_3
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 that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. 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 translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used.
Examples:
4
7_6455
_GEOM_BOND_[MS]
CIF
Data items in the GEOM_BOND category record
details about bonds, as calculated from the ATOM, CELL and SYMMETRY data. These extensions to the core CIF dictionary definitions record the maximum, minimum and average lengths of bonds and extend the symmetry-operation code used in bond listings to the higher-dimensional superspace form.
_geom_bond_distance
CIF
Data names: _geom_bond_distance_max _geom_bond_distance_min _geom_bond_distance_av
Maximum, minimum and average values of the intramolecular bond
distance in angstroms.
_geom_bond_site_ssg_symmetry
CIF
Data names: _geom_bond_site_ssg_symmetry_1 _geom_bond_site_ssg_symmetry_2
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 that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the bond. 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 translations, the translation number may be omitted. If no symmetry operations or translations are applicable then a single full stop '.' is used.
Examples:
4
7_6455
_GEOM_CONTACT_[MS]
CIF
Data items in the GEOM_CONTACT category record
details about interatomic contacts, as calculated from the ATOM, CELL and SYMMETRY data. These extensions to the core CIF dictionary definitions record the maximum, minimum and average values of contact distances and extend the symmetry-operation code used in contact-distance listings to the higher-dimensional superspace form.
_geom_contact_distance
CIF
Data names: _geom_contact_distance_max _geom_contact_distance_min _geom_contact_distance_av
Maximum, minimum and average values of the interatomic contact
distance in angstroms.
_geom_contact_site_ssg_symmetry
CIF
Data names: _geom_contact_site_ssg_symmetry_1 _geom_contact_site_ssg_symmetry_2
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 that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the contact. 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 translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used.
Examples:
4
7_6455
_GEOM_TORSION_[MS]
CIF
Data items in the GEOM_TORSION category record
details about torsion angles, as calculated from the ATOM, CELL and SYMMETRY data. These extensions to the core CIF dictionary definitions record the maximum, minimum and average values of torsion angles and extend the symmetry-operation code used in torsion-angle listings to the higher-dimensional superspace form.
_geom_torsion
CIF
Data names: _geom_torsion_max _geom_torsion_min _geom_torsion_av
Maximum, minimum and average torsion angles in degrees bounded
by the four atom sites identified by the _geom_torsion_atom_site_label_ codes. These must match labels specified as _atom_site_label in the atom list. The torsion- angle definition should be that of Klyne and Prelog (1960).
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
_geom_torsion_site_ssg_symmetry
CIF
Data names: _geom_torsion_site_ssg_symmetry_1 _geom_torsion_site_ssg_symmetry_2 _geom_torsion_site_ssg_symmetry_3 _geom_torsion_site_ssg_symmetry_4
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 that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. 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 translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used.
Examples:
4
7_6455
_REFINE_[MS]
CIF
Data items in the REFINE category record
details about the structure refinement parameters. The new items in this category extend those of the core CIF dictionary and are specific to the refinement of modulated structures.
_refine_ls_mod_func_description
CIF
Types of modulation present in the structural model and their
parameterization.
Examples:
Only displacive modulation. Fourier series.
Modulation of atom S(1) described by a non-standard linear sawtooth function
_refine_ls_mod_hydrogen_treatment
CIF
Treatment of hydrogen-atom modulation parameters in the
refinement.
_refine_ls_mod_overall_phason_coeff
CIF
The phason coefficient used to calculate the overall phason
correction.
_refine_ls_mod_overall_phason_formula
CIF
The expression for the overall phason correction, if used.
_REFLN_[MS]
CIF
Data items in the REFLN category record details about the
reflections used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Data items in this category are extensions of the core CIF dictionary definitions to the indexing of reflections used in the refinement by higher-dimensional components.
_refln_index_m
CIF
Data names: _refln_index_m_1 _refln_index_m_2 _refln_index_m_3 _refln_index_m_4 _refln_index_m_5 _refln_index_m_6 _refln_index_m_7 _refln_index_m_8
Additional Miller indices of a particular reflection in the basis
described in _cell_reciprocal_basis_description. The total number of indices must match (_cell_modulation_dimension + 3). The order of the additional indices must be consistent with the codes given in _cell_wave_vector_seq_id.
_REFLNS_[MS]
CIF
Data items in the REFLNS category record details about the
reflections used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Data items in this category extend the core CIF dictionary definitions providing independent checks on the range of values recorded for each of the additional Miller indices given in the REFLN category.
_reflns_limit_index_m
CIF
Data names: _reflns_limit_index_m_1_max _reflns_limit_index_m_1_min _reflns_limit_index_m_2_max _reflns_limit_index_m_2_min _reflns_limit_index_m_3_max _reflns_limit_index_m_3_min _reflns_limit_index_m_4_max _reflns_limit_index_m_4_min _reflns_limit_index_m_5_max _reflns_limit_index_m_5_min _reflns_limit_index_m_6_max _reflns_limit_index_m_6_min _reflns_limit_index_m_7_max _reflns_limit_index_m_7_min _reflns_limit_index_m_8_max _reflns_limit_index_m_8_min
Maximum and minimum values of the additional Miller indices
appearing in _refln_index_m_. The number of ranges must match _cell_modulation_dimension. The order of the additional indices must be consistent with the codes given in _cell_wave_vector_seq_id. These need not be the same as the _diffrn_reflns_limit_index_m_.
_SPACE_GROUP_[MS]
CIF
The SPACE_GROUP category introduced in the symmetry CIF
dictionary (cif_sym.dic) is intended to replace the original core SYMMETRY category. For modulated structures, superspace- group descriptions may be included in the same category, but include the _ssg_ flag to indicate their dimensionality of > 3.
_space_group_ssg_IT_number
CIF
Superspace-group number from International Tables for
Crystallography, Vol. C (2004). Valid only for one-dimensional modulated structures.
Ref: International Tables for Crystallography (2004). Vol. C, Chapter 9.8. Dordrecht: Kluwer Academic Publishers.
_space_group_ssg_name
CIF
Superspace-group symbol conforming to an alternative definition
from that given in _space_group_ssg_name_IT and _space_group_ssg_name_WJJ for one-dimensional modulated structures or to the superspace-group name for higher dimensions. When necessary, indicate the origin and the setting. Use a colon ':' as a separator between the different parts of the superspace-group symbol. Within each part, leave a space between each component. Rules for the notation for Hermann-Mauguin and Hall symbols (if present) are given in the symmetry CIF dictionary (cif_sym.dic) and, partially, in _space_group_ssg_name_IT and _space_group_ssg_name_WJJ. For composites described in a single data block, the superspace group describes the symmetry of the whole structure. The symmetry of each subsystem can be derived using the appropriate W matrices.
Example:
Hall's notation W:-P -2xb -2ya:q q
_space_group_ssg_name_IT
CIF
Superspace-group symbol as given in International Tables for
Crystallography, Vol. C (2004). Valid only for one-dimensional modulated structures. The symbol is divided into three parts: the Hermann-Mauguin space-group symbol of the reference structure, the modulation wave vector and the phase shift (or internal translation) associated with each component of the space group. Each component of the space-group name is separated by a space. Subscripts should appear without special symbols and bars should be given as negative signs. The components of the modulation wave vector (in parentheses) and the phase shifts are also separated by a space. For composites described in a single data block, the superspace group describes the symmetry of the whole structure. The symmetry of each subsystem can be derived using the appropriate W matrices.
Ref: International Tables for Crystallography (2004). Vol. C, Chapter 9.8. Dordrecht: Kluwer Academic Publishers.
Example:
P n m a (0 0 ) 0 s 0
_space_group_ssg_name_WJJ
CIF
Superspace-group symbol as given by de Wolff, Janssen & Janner
(1981). Valid only for one-dimensional modulated structures. The symbol is divided into three parts separated by colons ':': the superspace lattice symbol, the Hermann-Mauguin space-group symbol of the reference structure and the phase shift (or internal translation) associated with each component of the space group. Each component of the space-group name is separated by a space. Subscripts should appear without special symbols and bars should be given as negative signs. The phase shifts are also separated by a space. For composites described in a single data block, the superspace group describes the symmetry of the whole structure. The symmetry of each subsystem can be derived using the appropriate W matrices.
Ref: Wolff, P. M. de, Janssen, T. & Janner, A. (1981). Acta Cryst. A37, 625-636.
Example:
P:P c m n:s s -1
_space_group_ssg_WJJ_code
CIF
Superspace-group code as given by de Wolff, Janssen & Janner
(1981). Valid only for one-dimensional modulated structures.
Ref: Wolff, P. M. de, Janssen, T. & Janner, A. (1981). Acta Cryst. A37, 625-636.
Example:
28a.10.1/2
_SPACE_GROUP_SYMOP_[MS]
CIF
The SPACE_GROUP_SYMOP category introduced in the symmetry CIF
dictionary (cif_sym.dic) is intended to replace the original core SYMMETRY_EQUIV category. It contains information about the symmetry operations of the space group. For modulated structures, superspace-group descriptions may be included in the same category, but include the _ssg_ flag to indicate their dimensionality of > 3.
Example:
loop_ _space_group_symop_ssg_id _space_group_symop_ssg_operation_algebraic 1 x1,x2,x3,x4 2 1/2+x1,1/2-x2,1/2-x3,x4 3 1/2-x1,1/2+x2,-x3,1/2-x4 4 -x1,-x2,1/2+x3,1/2-x4 5 -x1,-x2,-x3,-x4 6 1/2-x1,1/2+x2,1/2+x3,-x4 7 1/2+x1,1/2-x2,x3,1/2+x4 8 x1,x2,1/2-x3,1/2+x4
_space_group_symop_ssg_id
CIF
A numeric code identifying each entry in the
_space_group_symop_ssg_operation_algebraic list.
_space_group_symop_ssg_operation_algebraic
CIF
A parsable string giving one of the symmetry operations of the
superspace group in algebraic form. These data will generally be
repeated in a loop. Use symbols as necessary according to
_cell_modulation_dimension.
All symmetry operations should be entered, including the
identity operation, those for lattice centring and that for
a centre of symmetry, if present. The symbolic notation for
coordinates is such that the identity operation is expressed
as x1,x2,x3,...,xn.
_space_group_symop_ssg_operation_algebraic must always be present
in a CIF corresponding to a modulated structure.
Example:
x1,-x2,x3,1/2+x4
Revision history
1994-09-12 Initial definitions G. Madariaga
1994-09-19 Several corrections I.D. Brown
1994-09-19 Loops with mixed categories removed G. Madariaga
1994-09-20 Addition of W for composites S. van Smaalen
1995-03-21 A new way of labelling parameters G. Madariaga
1995-03-21 Extensive use of _type_construct G. Madariaga
1995-04-05 Does _type_construct allow structured items? G. Madariaga
1995-04-06 New entries G. Madariaga
1995-04-10 Block identifiers added G. Madariaga
1997-05-26 _units_extension, _units_description and
_units_conversion substituted by _units and
_units_detail G. Madariaga
1997-05-26 Units included in the definitions G. Madariaga
1997-05-26 _symm_ substituted by _symmetry_ G. Madariaga
1997-05-26 category SYMMETRY_EQUIV added G. Madariaga
1997-05-27 explicit definition of _cell_matrix_W_ G. Madariaga
1997-05-27 _cell_matrix_W_organization removed G. Madariaga
1997-05-27 _enumeration_range 1:8 added to _cell_modulation_dimension G. Madariaga
1997-05-27 _enumeration_range 4:11 modified in
_cell_reciprocal_basis_vect_numb G. Madariaga
1997-05-27 _diffrn_refln_indices
_diffrn_reflns_limit_indices
_diffrn_standard_refln_indices
_exptl_crystal_face_indices
_refln_indices and _reflns_limit_indices_
replaced by _diffrn_refln_extra_index_
_diffrn_reflns_limit_extra_index_
_diffrn_standard_refln_extra_index_
_exptl_crystal_face_extra_index_
_refln_extra_index_ and
_diffrn_reflns_limit_extra_index_ G. Madariaga
1997-05-28 _block_id substituted by _audit_block_code,
_audit_link_block_code and
_audit_link_block_description G. Madariaga
1997-05-28 added _refine_ls_by_class_R_Fsqd_factor and
_refine_ls_by_class_R_I_factor G. Madariaga
1997-05-28 added _refine_ls_by_class_d_res_ G. Madariaga
1997-05-29 deleted _refine_ls_Fourier_term and
_refine_ls_Fourier_term_code G. Madariaga
1997-06-03 deleted _atom_site_coeff_,
_atom_site_Fourier_label_,
_atom_site_Fourier_phase_ G. Madariaga
1997-06-03 added the new datanames _atom_site_Fourier_
according to David's suggestions G. Madariaga
1997-07-14 complete revision of _atom_site_Fourier_ items G. Madariaga
1997-07-18 added the new datanames
_atom_site_spec_func_disp_label,
_atom_site_spec_func_occ_label,
_atom_site_spec_func_temp_label G. Madariaga
1997-07-18 *_special_func_ -> *_spec_func_
*_special_par_ -> *_spec_param_
*_special_param_ -> *_spec_param_ G. Madariaga
1997-07-18 deleted *_special_npar_ G. Madariaga
1997-07-18 _atom_site_spec_label_ substituted by
_atom_site_spec_param_
added the following parent/child relationships
_refine_ls_spec_param_disp_code and
_atom_site_spec_param_disp_code,
_refine_ls_spec_param_occ_code and
_atom_site_spec_param_occ_code,
_refine_ls_spec_param_temp_code and
_atom_site_spec_param_temp_code G. Madariaga
1997-07-18 redefined _atom_site_phason_label, added _atom_site_phason_formula G. Madariaga
1997-07-21 added _refine_ls_spec_param_rot_ and
_atom_site_spec_param_rot_, together with the
corresponding parent/child links. G. Madariaga
1997-07-21 added _audit_link_external_block_ items G. Madariaga
1997-07-21 added _reflns_shell_by_class_ items G. Madariaga
1997-07-22 added _atom_site_spec_func_disp_axis and
_atom_site_spec_func_rot_axis G. Madariaga
1997-07-22 added new *_wave_vector *_wave_vector_seq_id
and *_wave_vector_ items G. Madariaga
1997-07-22 added *_temp_element_ items G. Madariaga
1997-07-23 *_sup_spac_sy_ items reworded as
*_superspace_symm_.
_refine_ls_mod_funct_description reworded as
_refine_ls_modulation_function. G. Madariaga
1997-07-23 *_wave_vector_ items changed:
defined generic _atom_site_Fourier_wave_vector_
and new link/parent relationships with
*_disp_wave_vector_seq_id,
*_occ_wave_vector_seq_id,
*_rot_wave_vector_seq_id,
*_temp_wave_vector_seq_id. G. Madariaga
1997-07-24 added _atom_site_spec_param_temp_B and
_atom_site_spec_param_temp_U G. Madariaga
1997-07-24 ********Cyclops test passed*********** G. Madariaga
1997-07-28 _refine_ls_subsystem_ items renamed to
_cell_subsystem_. _cell_numb_of_subsystems
renamed to _cell_subsystem_number G. Madariaga
1997-07-29 _cell_reciprocal_basis_vect_numb renamed to
_cell_reciprocal_basis_vect_number.
_diffrn_reflns_number_of_classes renamed to
_diffrn_reflns_class_number G. Madariaga
1997-11-12 References to the B form of temperature
factors removed I.D. Brown
1997-11-12 Some spelling mistakes corrected. I.D. Brown
1997-12-12 _atom_site_Fourier_disp_sin removed from
_list_reference of _atom_site_Fourier_disp_cos.
_atom_site_Fourier_disp_phase removed from
_list_reference of _atom_site_Fourier_disp_modulus.
_atom_site_Fourier_disp_modulus removed from
_list_reference of _atom_site_Fourier_disp_phase.
_atom_site_Fourier_disp_cos removed from
_list_reference of _atom_site_Fourier_disp_sin.
_atom_site_Fourier_occ_sin removed from
_list_reference of _atom_site_Fourier_occ_cos.
_atom_site_Fourier_occ_phase removed from
_list_reference of _atom_site_Fourier_occ_modulus.
_atom_site_Fourier_occ_modulus removed from
_list_reference of _atom_site_Fourier_occ_phase.
_atom_site_Fourier_occ_cos removed from
_list_reference of _atom_site_Fourier_occ_sin.
_atom_site_Fourier_rot_sin removed from
_list_reference of _atom_site_Fourier_rot_cos.
_atom_site_Fourier_rot_phase removed from
_list_reference of _atom_site_Fourier_rot_modulus.
_atom_site_Fourier_rot_modulus removed from
_list_reference of _atom_site_Fourier_rot_phase.
_atom_site_Fourier_rot_cos removed from
_list_reference of _atom_site_Fourier_rot_sin.
_atom_site_Fourier_temp_sin_U_ removed from
_list_reference of _atom_site_Fourier_cos_U_.
_atom_site_Fourier_temp_phase_U_ removed from
_list_reference of _atom_site_Fourier_modulus_U_.
_atom_site_Fourier_temp_modulus_U_ removed from
_list_reference of _atom_site_Fourier_phase_U_.
_atom_site_Fourier_temp_cos_U_ removed from
_list_reference of _atom_site_Fourier_sin_U_. B. McMahon
P. Edgington
1997-12-12 Several typos corrected P. Edgington
1997-12-12 Tabs removed P. Edgington
1997-12-15 _enumeration_range 0.0: added to the following items: _atom_site_Fourier_disp_modulus _atom_site_Fourier_occ_modulus _atom_site_Fourier_rot_modulus _atom_site_Fourier_temp_modulus_U_ _atom_site_phason_coeff _cell_wave_vector_pressure_ _cell_wave_vector_temp_ _refine_ls_overall_phason_coeff. _enumeration_range 0: added to the following items: _diffrn_reflns_by_class_number _reflns_shell_by_class_number_measured_all _reflns_shell_by_class_number_measured_obs _enumeration_range 1:192 added to _symmetry_equiv_position_number _enumeration_range 1.1: added to _symmetry_superspace_group_numb_IT P. Edgington
1997-12-15 'obs' and 'observed' changed to 'gt'. References
to '_reflns_observed_criterion' changed to
'_reflns_threshold_expression' B. McMahon
1997-12-15 Items including *_superspace_symm_, _superspace_
and _symmetry_, renamed to _ssg_symmetry_ or
_symmetry_ssg_ (where appropriate). 'ssg' holds
for 'superspace group' I.D. Brown
G. Madariaga
B. McMahon
1997-12-15 _symmetry_ssg_numb_WJJ renamed to
_symmetry_ssg_code_WJJ G. Madariaga
1997-12-16 _atom_site_mod_refinement_flags split into
_atom_site_disp_refinement_flag,
_atom_site_occ_refinement_flag,
_atom_site_temp_refinement_flag I.D. Brown
P. Edgington
1997-12-17 The following items:
_atom_site_spec_param_disp_code,
_atom_site_spec_param_occ_code,
_atom_site_spec_param_rot_code,
_atom_site_spec_param_temp_code,
_atom_site_spec_param_disp,
_atom_site_spec_param_occ,
_atom_site_spec_param_rot,
_atom_site_spec_param_temp_U,
_cell_matrix_W_
renamed as:
_atom_site_spec_func_disp_param_code,
_atom_site_spec_func_occ_param_code,
_atom_site_spec_func_rot_param_code,
_atom_site_spec_func_temp_param_code,
_atom_site_spec_func_disp_param,
_atom_site_spec_func_occ_param,
_atom_site_spec_func_rot_param,
_atom_site_spec_func_temp_param_U,
_cell_subsystem_matrix_W_
for a better introduction of new categories G. Madariaga
1997-12-18 new categories defined:
ATOM_SITE_FOURIER_DISP, ATOM_SITE_FOURIER_OCC,
ATOM_SITE_FOURIER_ROT, ATOM_SITE_FOURIER_TEMP,
ATOM_SITE_FOURIER-WAVE_VECTOR,
ATOM_SITE_SPEC_FUNC_DISP,
ATOM_SITE_SPEC_FUNC_OCC, ATOM_SITE_SPEC_FUNC_ROT,
ATOM_SITE_SPEC_FUNC_TEMP, CELL_SUBSYSTEM,
CELL_WAVE_VECTOR, DIFFRN_REFLNS_CLASS,
REFINE_LS_CLASS, REFINE_LS_SPEC_FUNC_DISP,
REFINE_LS_SPEC_FUNC_OCC, REFINE_LS_SPEC_FUNC_ROT,
REFINE_LS_SPEC_FUNC_TEMP, REFINE_LS_SPEC_PARAM_DISP,
REFINE_LS_SPEC_PARAM_OCC, REFINE_LS_SPEC_PARAM_ROT,
REFINE_LS_SPEC_PARAM_TEMP, REFLNS_CLASS,
REFINE_SHELL_CLASS, SYMMETRY_SSG_EQUIV B. McMahon
1997-12-18 added the appropriate items belonging to
CATEGORY_OVERVIEW and some examples. Dictionary
arranged a la Core. G. Madariaga
1997-12-18 ********vcif test passed*********** G. Madariaga
1998-01-08 *_U_ items converted to *_U (redundancy) G. Madariaga
1998-05-20 Major changes: The abbreviation 'temp' for 'temperature factor' has been substituted by 'U'. It affects the following categories and datanames: ATOM_SITE_FOURIER_TEMP _atom_site_Fourier_temp_label _atom_site_Fourier_temp_element_U _atom_site_Fourier_temp_cos_U _atom_site_Fourier_temp_modulus_U _atom_site_Fourier_temp_phase_U _atom_site_Fourier_temp_sin_U _atom_site_Fourier_temp_wave_vector_seq_id ATOM_SITE_SPEC_FUNC_TEMP _atom_site_spec_func_temp_element_U _atom_site_spec_func_temp_label _atom_site_spec_func_temp_param_code _atom_site_spec_func_temp_param_U REFINE_LS_SPEC_FUNC_TEMP _refine_ls_spec_func_temp _refine_ls_spec_func_temp_code REFINE_LS_SPEC_PARAM_TEMP _refine_ls_spec_param_temp _refine_ls_spec_param_temp_code _diffrn_reflns_by_class_number renamed to _diffrn_reflns_class_number_of_reflns _reflns_by_class_number_ renamed to _reflns_class_number_of_reflns_ The part '_by_class' has been substituted by 'class' for a better link to the category name. Affected datanames are: _diffrn_reflns_by_class_av_R_eq _diffrn_reflns_by_class_av_sgI/I _diffrn_reflns_by_class_number _diffrn_reflns_by_class_th_ _refine_ls_by_class_res_ _refine_ls_by_class_R_factor_ _refine_ls_by_class_R_Fsqd_factor _refine_ls_by_class_R_I_factor _refine_ls_by_class_wR_factor_ _reflns_by_class_number_ _reflns_shell_by_class_d_res_ _reflns_shell_by_class_meanI_over_sigI_ _reflns_shell_by_class_number_measured_ _reflns_shell_by_class_number_possible _reflns_shell_by_class_number_unique_ _reflns_shell_by_class_percent_possible_ _reflns_shell_by_class_Rmerge_ *_extra_index_ renamed to *_index_m_. list of affected datanames: _diffrn_refln_extra_index_ _diffrn_reflns_limit_extra_index_ _diffrn_standard_refln_extra_index_ _exptl_crystal_face_extra_index_ _refln_extra_index_ _reflns_limit_extra_index_ _diffrn_reflns_class renamed to _diffrn_reflns_class_description. _diffrn_reflns_class_number renamed to _diffrn_reflns_number_of_classes. _diffrn_reflns_sat_maximum_order renamed to _diffrn_reflns_satellite_order_max. _diffrn_symmetry renamed to _diffrn_symmetry_description _refine_ls_class_wR_factor_gt removed. _symmetry_ssg_equiv_position_number renamed to _symmetry_ssg_equiv_positions_number. I.D. Brown
1998-05-20 Less major and minor changes:
Several examples looped correctly. Some typos
corrected. I.D. Brown
1998-05-21 _enumeration_range of _atom_site_rot_modulus
changed from 0.0:360.0 to 0.0:
Added _enumeration_default 0 to
_cell_subsystem_matrix_W_ I.D. Brown
1998-05-21 More major changes:
_disp substituted by _displace since the latter
abbreviation already exists in coreCIF. However
some datanames (like
_atom_site_Fourier_displace_wave_vector_seq_id)
are probably too long. Let's try anyway.
_atom_site_Fourier_displace_,
_atom_site_Fourier_occ_,
_atom_site_Fourier_rot_ and
_atom_site_Fourier_U_ items renamed to:
_atom_site_displace_Fourier_,
_atom_site_occ_Fourier_,
_atom_site_rot_Fourier_ and
_atom_site_U_Fourier_. The corresponding
categories have been similarly changed I.D. Brown
1998-05-21 _atom_site_Fourier_wave_vector_seq_id included as _list_reference of _atom_site_Fourier_wave_vector_ G. Madariaga
1998-05-21 *_spec_func_ -> *_special_func_ I.D. Brown
1998-05-22 *_spec_param_ -> *_special_param_ I.D. Brown
1998-05-22 _atom_site_special_func_displace_,
_atom_site_special_func_occ_,
_atom_site_special_func_rot_ and
_atom_site_special_func_U_ items renamed to:
_atom_site_displace_special_func_,
_atom_site_occ_special_func_,
_atom_site_rot_special_func_ and
_atom_site_U_special_func_.
_refine_ls_special_func_displace_,
_refine_ls_special_func_occ_,
_refine_ls_special_func_rot_ and
_refine_ls_special_func_U_ items renamed to:
_refine_ls_displace_special_func_,
_refine_ls_occ_special_func_,
_refine_ls_rot_special_func_ and
_refine_ls_U_special_func_.
_refine_ls_special_param_displace_,
_refine_ls_special_param_occ_,
_refine_ls_special_param_rot_ and
_refine_ls_special_param_U_ items renamed to:
_refine_ls_displace_special_param_,
_refine_ls_occ_special_param_,
_refine_ls_rot_special_param_ and
_refine_ls_U_special_param_. The corresponding
categories have been similarly changed G. Madariaga
1998-05-22 *_Fourier_label -> *_Fourier_atom_site_label
*_special_func_label ->
*_special_func_atom_site_label
'element' referred to the temperature factor U
changed to 'tens_elem' I.D. Brown
1998-05-25 *_refinement_flag -> *_modulation_flag I.D. Brown
1998-05-25 _refine_ls_*_special_param_ items renamed to
_refine_ls_*_special_func_param_ G. Madariaga
1998-05-26 _refine_ls_restrained_wR_gt deleted G. Madariaga
1998-05-27 _diffrn_reflns_th_ renamed to
_diffrn_reflns_class_d_res_ I.D. Brown
1998-05-27 _symmetry_ssg_equiv_pos_as_fract_coord renamed
to _symmetry_ssg_equiv_pos_as_xyz I.D. Brown
1998-08-03 Fixed some typos; removed global_ block B. McMahon
1998-08-04 Moved _diffrn_pressure_history and _diffrn_thermal_history
to core as _exptl_crystal_pressure_history and
_exptl_crystal_thermal_history; moved
_diffrn_symmetry_description and REFINE_LS_CLASS to core
B. McMahon
1998-12-08 Version spellchecked and checked with vcif and cyclops, then
returned to Gotzon B. McMahon
1998-12-23 Categories involving special functions cross-
referenced. Some examples enlarged. I.D. Brown
1998-12-23 Some items and categories alphabetically
reordered. G. Madariaga
1998-12-23 _atom_site_phason_label renamed to _atom_site_phason_atom_site_label G. Madariaga
1998-12-23 _diffrn_reflns_number_of_classes removed. G. Madariaga
1998-12-23 Merging of the following pairs of definitions:
_reflns_shell_class_d_res_high and
_reflns_shell_class_d_res_low
_reflns_shell_class_meanI_over_sigI_all and
_reflns_shell_class_meanI-over_sigI_gt
_reflns_shell_class_number_measured_all and
_reflns_shell_class_number_measured_gt
_reflns_shell_class_number_unique_all and
_reflns_shell_class_number_unique_gt
_reflns_shell_class_percent_possible_all and
_reflns_shell_class_percent_possible_gt
_reflns_shell_class_Rmerge_F_all and
_reflns_shell_class_Rmerge_F_gt
_reflns_shell_class_Rmerge_I_all and
_reflns_shell_class_Rmerge_I_gt. H. Flack
1998-12-27 Modified the definitions of:
_atom_site_Fourier_wave_vector_,
_cell_wave_vector_,
_cell_subsystem_matrix_W_,
_symmetry_ssg_name,
_symmetry_ssg_name_IT and
_symmetry_ssg_name_WJJ G. Madariaga
1999-01-14 Added the following datanames:
_atom_site_phason_subsystem_code
_atom_site_aniso_subsystem_code
_atom_site_displace_Fourier_subsystem_code
_atom_site_occ_Fourier_subsystem_code
_atom_site_rot_Fourier_subsystem_code
_atom_site_U_Fourier_subsystem_code
_atom_site_displace_special_func_subsystem_code
_atom_site_occ_special_func_subsystem_code
_atom_site_rot_special_func_subsystem_code
_atom_site_U_special_func_subsystem_code
_geom_angle_atom_site_subsystem_code_
_geom_bond_atom_site_subsystem_code_
_geom_contact_atom_site_subsystem_code_
_geom_torsion_atom_site_subsystem_code_ V. Petricek
1999-01-24 More examples added to
ATOM_SITE_DISPLACE_FOURIER G. Madariaga
1999-02-28 _enumeration list of: _atom_site_displace_Fourier_axis, _atom_site_rot_Fourier_axis, _atom_site_displace_special_func_axis and _atom_site_rot_special_func_axis enlarged to cover arbitrary axes different from the crystallographic ones. G. Madariaga
1999-02-28 New datanames:
_atom_site_displace_Fourier_axes_description,
_atom_site_rot_Fourier_axes_description,
_atom_site_displace_special_func_axes_description
and _atom_site_rot_special_func_axes_description.
G. Madariaga
1999-02-28 Modified the definitions of:
_atom_site_displace_Fourier_cos,
_atom_site_displace_Fourier_modulus and
_atom_site_displace_Fourier_sin G. Madariaga
1999-02-28 A new example added to ATOM_SITE_ROT_FOURIER
and ATOM_SITE_DISPLACE_FOURIER G. Madariaga
1999-04-01 Some cosmetic rearrangement of line endings to
improve the formatted version B. McMahon
1999-04-19 DIFFRN_REFLNS_CLASS and REFLNS_CLASS removed (already in cif_core.dic 2.1) _atom_site_Fourier_wave_vector renamed to _atom_site_Fourier_wave_vector_description _cell_reciprocal_basis renamed to _cell_reciprocal_basis_description _cell_subsystem renamed to _cell_subsystem_description _refine_ls_hydrogen_mod_param renamed to _refine_ls_hydrogen_mod_flag _refine_ls_*_special_func renamed to _refine_ls_*_special_func_description. I.D. Brown
1999-04-19 _symmetry_equiv_position_number:
_enumeration_range 1:192 changed to
_enumeration_range 1: I.D. Brown
1999-04-19 _refine_ls_*_special_func_param renamed to
_refine_ls_*_special_func_param_description. G. Madariaga
1999-07-26 New datanames:
_atom_site_modulation_global_phase_t_ G. Madariaga
1999-07-29 A caution about the names of the items belonging
to SYMMETRY and SYMMETRY_SSG_EQUIV categories I.D. Brown
1999-07-29 Definition of _atom_site_Fourier_wave_vector_
reworded G. Madariaga
1999-07-29 Definition of _cell_subsystem_matrix_W_
completely reworded G. Madariaga
1999-07-29 ********vcif test passed*********** G. Madariaga
2000-04-20 merged Gotzon's revisions/my cosmetic changes B. McMahon
2000-07-06 _aver -> _av in several _geom definitions
_type_construct entries commented out pending
some software implementation of
_type_construct validation
new categories added in several cases to house
data items that give collective descriptions of
other items individually looped together; new
categories are ATOM_SITES_DISPLACE_FOURIER,
ATOM_SITES_DISPLACE_SPECIAL_FUNC,
ATOM_SITES_ROT_FOURIER, ATOM_SITES_ROT_SPECIAL_FUNC,
CELL_WAVE_VECTORS
several stylistic and punctuation changes B. McMahon
2000-07-19 Some further changes during COMCIFS review: removed _audit_link_external_block_code and *_description pending reworking of core AUDIT_LINK category to include external blocks. Description of the recommended usage for block codes in modulated structures moved to the discussion in data_audit_link_[ms]. [ms] added consistently to category descriptions specific to this dictionary REFLNS_SHELL_CLASS category removed because this functionality is met in the Core by REFLNS_CLASS moved _refine_ls_F_calc_accuracy, *_details, *_formula, _refine_ls_restrained_wR_all, *_weighting_scheme to core _refine_ls_hydrogen_mod_flag, _refine_ls_modulation_func_description, _refine_ls_overall_phason_coeff, _refine_ls_overall_phason_formula renamed as _refine_ls_mod_hydrogen_treatment, _refine_ls_mod_func_description, _refine_ls_mod_overall_phason_coeff, _refine_ls_mod_overall_phason_formula, respectively First attempt to rename symmetry data names in with the symcif proposals by changing _symmetry_ to _space_group_ throughout. The thinking is that the _ssg_ flag will indicate superspace group within the existing (draft) SPACE_GROUP category. I.D.Brown suggests that there is no need for a special category for equivalent positions; but I'm not sure at this stage, and retain Gotzon's proposal until further consideration is given to how to phase out the old core _symmetry_ names _symmetry_ssg_equiv_pos_as_xyz renamed _space_group_ssg_equiv_pos_algebraic for greater generality Added example to _space_group_ssg_code_WJJ B. McMahon
2000-10-16 Some additional changes: -symmetry items. Changes consistent with cif_sym.0.07: _space_group_ssg_numb_IT changed to _space_group_ssg_IT_number. SPACE_GROUP_SSG_EQUIV category changed to SPACE_GROUP_SYMOP. _space_group_ssg_equiv_pos_algebraic, _space_group_ssg_equiv_pos_seg_id changed to _space_group_symop_ssg_operation_algebraic, _space_group_symop_ssg_id. _space_group_equivalent_position_number changed to _space_group_symop_ssg_operations_number and therefore changed from SPACE_GROUP to SPACE_GROUP_SYMOP 'equivalent position' replaced by 'symmetry operation' where neccessary (see _geom_*_site_symmetry_ items). -New category ATOM_SITES_MODULATION. It contains only the _atom_sites_modulation_global_phase_t_ items. -Some minors changes. Reference to JANA98 changed to JANA2000. Some references corrected. G. Madariaga
2001-04-19 Treatment of special functions completely changed. The categories: ATOM_SITE_ROT_SPECIAL_FUNC ATOM_SITE_U_SPECIAL_FUNC ATOM_SITES_DISPLACE_SPECIAL_FUNC ATOM_SITES_ROT_SPECIAL_FUNC REFINE_LS_DISPLACE_SPECIAL_FUNC REFINE_LS_DISPLACE_SPECIAL_FUNC_PARAM REFINE_LS_OCC_SPECIAL_FUNC REFINE_LS_OCC_SPECIAL_FUNC_PARAM REFINE_LS_ROT_SPECIAL_FUNC REFINE_LS_ROT_SPECIAL_FUNC_PARAM REFINE_LS_U_SPECIAL_FUNC REFINE_LS_U_SPECIAL_FUNC_PARAM have been removed. The categories ATOM_SITE_DISPLACE_SPECIAL_FUNC and ATOM_SITE_OCC_SPECIAL_FUNC have suffered the following changes: _atom_site_displace_special_func_axis, _atom_site_displace_special_func_param, _atom_site_displace_special_func_param_code, _atom_site_displace_occ_func_param, _atom_site_displace_occ_func_param_code have been removed and substituted by: _atom_site_displace_special_func_sawtooth_, _atom_site_occ_special_func_crenel_. All the examples have been accordingly changed. The categories: ATOM_SITE_DISPLACE_FOURIER, ATOM_SITE_OCC_FOURIER, ATOM_SITE_ROT_FOURIER, ATOM_SITE_U_FOURIER have been split. There are four new categories: ATOM_SITE_DISPLACE_FOURIER_PARAM, ATOM_SITE_OCC_FOURIER_PARAM, ATOM_SITE_ROT_FOURIER_PARAM, ATOM_SITE_U_FOURIER_PARAM linked with the former ones through two new items: _atom_site_displace_Fourier_id, _atom_site_displace_Fourier_param_id which are the _list_reference for the all the items in each category. The examples have been changed and some definitions slightly reworded. Added the new category ATOM_SITE_PHASON. Some cosmetic changes. I.D. Brown J.Westbrook
2001-05-12 *_subsystem_code items deleted except for _atom_site_subsystem_code; corrected _list_reference for _atom_site_Fourier_wave_vector_description and _list_link_parent for _atom_site_U_Fourier_param_id; moved _space_group_symop_ssg_operations_number to category space_group as _space_group_ssg_symops_number (all suggestions of IDB) B. McMahon
2001-05-28 _space_group_ssg_symops_number and _cell_reciprocal_basis_vect_number now appear as comments. They are only useful for some _type_construct regex. _cell_reciprocal_basis_vect_number has been substituted by (_cell_modulation_dimension + 3) in some definitions. G. Madariaga
2002-02-28 Definitions of: _space_group_[ms], _space_group_ssg_name, _space_group_ssg_name_IT, _space_group_ssg_name_WJJ and _space_group_symop_[ms] reworded according to the rules given in the dictionary cif_sym 1.0. G. Madariaga
2002-02-04 Release version 1.0. IUCr (B. McMahon)
2002-03-04 Cosmetic edits for formatted version B. McMahon
2004-06-10 Further cosmetic edits for formatting in
International Tables Volume G B. McMahon
2005-01-06 Some realphabetisation B. McMahon
2005-01-17 NJ Ashcroft: minor corrections to hyphenation, spelling and punctuation _audit_link_[ms]: definition edited slightly _cell_wave_vectors_pressure_, _cell_wave_vectors_temp_: definition edited slightly _exptl_crystal_type_of_structure: definition edited _space_group_ssg_IT_number, data_space_group_ssg_name_IT: reference to Vol. C updated _geom_torsion_: reference changed from Endeavour to Experientia
2005-03-27 Addition of changes included in ITCG chapter 4.3 G. Madariaga
2005-06-16 Category overviews added for all categories NJ Ashcroft