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cif_core.dic
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#\#CIF_2.0
##########################################################################
# #
# CIF CORE DICTIONARY #
# #
##########################################################################
data_CIF_CORE
_dictionary.title CIF_CORE
_dictionary.class Instance
_dictionary.version 3.3.0
_dictionary.date 2024-11-12
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic
_dictionary.ddl_conformance 4.2.0
_dictionary.namespace CifCore
_description.text
;
The CIF_CORE dictionary defines data items that are common to all domains
of crystallographic studies. These definitions are mostly used within the
Crystallographic Information Framework (CIF).
;
save_CIF_CORE_HEAD
_definition.id CIF_CORE_HEAD
_definition.scope Category
_definition.class Head
_definition.update 2024-05-15
_description.text
;
The CIF_CORE_HEAD category is the top-level category for all categories in
the CIF_CORE dictionary.
;
_name.category_id CIF_CORE
_name.object_id CIF_CORE_HEAD
save_
save_DIFFRACTION
_definition.id DIFFRACTION
_definition.scope Category
_definition.class Set
_definition.update 2024-05-15
_description.text
;
The DICTIONARY group encompassing the CORE DIFFRACTION data items defined
and used within the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE_HEAD
_name.object_id DIFFRACTION
save_
save_DIFFRN
_definition.id DIFFRN
_definition.scope Category
_definition.class Set
_definition.update 2022-05-09
_description.text
;
The CATEGORY of data items used to describe the diffraction experiment.
;
_name.category_id DIFFRACTION
_name.object_id DIFFRN
_category_key.name '_diffrn.id'
save_
save_diffrn.ambient_environment
_definition.id '_diffrn.ambient_environment'
_alias.definition_id '_diffrn_ambient_environment'
_definition.update 2012-11-26
_description.text
;
The gas or liquid environment of the crystal sample, if not air.
;
_name.category_id diffrn
_name.object_id ambient_environment
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'He'
'vacuum'
'mother liquor'
save_
save_diffrn.ambient_pressure
_definition.id '_diffrn.ambient_pressure'
_alias.definition_id '_diffrn_ambient_pressure'
_definition.update 2023-01-13
_description.text
;
Mean hydrostatic pressure at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_pressure
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save_diffrn.ambient_pressure_su
_definition.id '_diffrn.ambient_pressure_su'
loop_
_alias.definition_id
'_diffrn_ambient_pressure_su'
'_diffrn.ambient_pressure_esd'
_definition.update 2023-07-01
_description.text
;
Standard uncertainty of _diffrn.ambient_pressure.
;
_name.category_id diffrn
_name.object_id ambient_pressure_su
_name.linked_item_id '_diffrn.ambient_pressure'
_units.code kilopascals
_import.get [{'file':templ_attr.cif 'save':general_su}]
save_
save_diffrn.ambient_pressure_gt
_definition.id '_diffrn.ambient_pressure_gt'
_alias.definition_id '_diffrn_ambient_pressure_gt'
_definition.update 2012-12-13
_description.text
;
Mean hydrostatic pressure above which intensities were measured.
These items allow for a pressure range to be given.
_diffrn.ambient_pressure should be used in preference to this
item when possible.
;
_name.category_id diffrn
_name.object_id ambient_pressure_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save_diffrn.ambient_pressure_lt
_definition.id '_diffrn.ambient_pressure_lt'
_alias.definition_id '_diffrn_ambient_pressure_lt'
_definition.update 2012-12-13
_description.text
;
Mean hydrostatic pressure below which intensities were measured.
These items allow for a pressure range to be given.
_diffrn.ambient_pressure should be used in preference to this
item when possible.
;
_name.category_id diffrn
_name.object_id ambient_pressure_lt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save_diffrn.ambient_temperature
_definition.id '_diffrn.ambient_temperature'
loop_
_alias.definition_id
'_diffrn_ambient_temperature'
'_diffrn_ambient_temp'
'_diffrn.ambient_temp'
_definition.update 2012-11-26
_description.text
;
Mean temperature at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_temperature
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save_diffrn.ambient_temperature_su
_definition.id '_diffrn.ambient_temperature_su'
loop_
_alias.definition_id
'_diffrn_ambient_temperature_su'
'_diffrn_ambient_temp_su'
'_diffrn.ambient_temp_esd'
_definition.update 2021-03-03
_description.text
;
Standard uncertainty of _diffrn.ambient_temperature.
;
_name.category_id diffrn
_name.object_id ambient_temperature_su
_name.linked_item_id '_diffrn.ambient_temperature'
_units.code kelvins
_import.get [{'file':templ_attr.cif 'save':general_su}]
save_
save_diffrn.ambient_temperature_details
_definition.id '_diffrn.ambient_temperature_details'
loop_
_alias.definition_id
'_diffrn_ambient_temp_details'
'_diffrn.ambient_temp_details'
_definition.update 2014-06-12
_description.text
;
A description of special aspects of temperature control during
data collection.
;
_name.category_id diffrn
_name.object_id ambient_temperature_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_diffrn.ambient_temperature_gt
_definition.id '_diffrn.ambient_temperature_gt'
loop_
_alias.definition_id
'_diffrn_ambient_temp_gt'
'_diffrn_ambient_temperature_gt'
'_diffrn.ambient_temp_gt'
_definition.update 2012-12-13
_description.text
;
Mean temperature above which intensities were measured.
These items allow for a temperature range to be given.
_diffrn.ambient_temperature should be used in preference to
this item when possible.
;
_name.category_id diffrn
_name.object_id ambient_temperature_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save_diffrn.ambient_temperature_lt
_definition.id '_diffrn.ambient_temperature_lt'
loop_
_alias.definition_id
'_diffrn_ambient_temp_lt'
'_diffrn_ambient_temperature_lt'
'_diffrn.ambient_temp_lt'
_definition.update 2012-12-13
_description.text
;
Mean temperature below which intensities were measured.
These items allow for a temperature range to be given.
_diffrn.ambient_temperature should be used in preference to
this item when possible.
;
_name.category_id diffrn
_name.object_id ambient_temperature_lt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save_diffrn.crystal_id
_definition.id '_diffrn.crystal_id'
_definition.update 2022-05-09
_description.text
;
Identifier for the crystal from which diffraction data were
collected. This is a pointer to _exptl_crystal.id.
;
_name.category_id diffrn
_name.object_id crystal_id
_name.linked_item_id '_exptl_crystal.id'
_type.purpose Link
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_diffrn.crystal_support
_definition.id '_diffrn.crystal_support'
_definition.update 2014-06-12
_description.text
;
The physical device used to support the crystal during data
collection.
;
_name.category_id diffrn
_name.object_id crystal_support
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
save_diffrn.crystal_treatment
_definition.id '_diffrn.crystal_treatment'
_alias.definition_id '_diffrn_crystal_treatment'
_definition.update 2012-11-26
_description.text
;
Remarks about how the crystal was treated prior to intensity measurement.
Particularly relevant when intensities were measured at low temperature.
;
_name.category_id diffrn
_name.object_id crystal_treatment
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
save_
save_diffrn.id
_definition.id '_diffrn.id'
_definition.update 2022-05-09
_description.text
;
Unique identifier for a diffraction data set collected under
particular diffraction conditions.
;
_name.category_id diffrn
_name.object_id id
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_diffrn.measured_fraction_theta_full
_definition.id '_diffrn.measured_fraction_theta_full'
_alias.definition_id '_diffrn_measured_fraction_theta_full'
_definition.update 2013-01-20
_description.text
;
Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns.theta_full.
;
_name.category_id diffrn
_name.object_id measured_fraction_theta_full
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save_diffrn.measured_fraction_theta_max
_definition.id '_diffrn.measured_fraction_theta_max'
_alias.definition_id '_diffrn_measured_fraction_theta_max'
_definition.update 2013-01-20
_description.text
;
Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns.theta_max.
;
_name.category_id diffrn
_name.object_id measured_fraction_theta_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save_diffrn.special_details
_definition.id '_diffrn.special_details'
loop_
_alias.definition_id
'_diffrn_special_details'
'_diffrn.details'
_definition.update 2012-11-26
_description.text
;
Special details of the diffraction measurement process. Should include
information about source instability, crystal motion, degradation, etc.
;
_name.category_id diffrn
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
_description_example.case
;
The results may not be entirely reliable as the measurement was
made during a heat wave when the air-conditioning had failed.
;
save_
save_diffrn.symmetry_description
_definition.id '_diffrn.symmetry_description'
_alias.definition_id '_diffrn_symmetry_description'
_definition.update 2012-11-26
_description.text
;
Recorded diffraction point symmetry, systematic absences and possible
space group(s) or superspace group(s) compatible with these.
;
_name.category_id diffrn
_name.object_id symmetry_description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_CELL
_definition.id CELL
_definition.scope Category
_definition.class Set
_definition.update 2023-03-02
_description.text
;
The CATEGORY of data items used to describe the parameters of
the crystal unit cell.
;
_name.category_id DIFFRN
_name.object_id CELL
_category_key.name '_cell.diffrn_id'
save_
save_cell.angle_alpha
_definition.id '_cell.angle_alpha'
_alias.definition_id '_cell_angle_alpha'
_name.category_id cell
_name.object_id angle_alpha
_import.get [{'file':templ_attr.cif 'save':cell_angle}]
save_
save_cell.angle_alpha_su
_definition.id '_cell.angle_alpha_su'
loop_
_alias.definition_id
'_cell_angle_alpha_su'
'_cell.angle_alpha_esd'
_name.category_id cell
_name.object_id angle_alpha_su
_name.linked_item_id '_cell.angle_alpha'
_import.get
[{'file':templ_attr.cif 'save':cell_angle_su}]
save_
save_cell.angle_beta
_definition.id '_cell.angle_beta'
_alias.definition_id '_cell_angle_beta'
_name.category_id cell
_name.object_id angle_beta
_import.get [{'file':templ_attr.cif 'save':cell_angle}]
save_
save_cell.angle_beta_su
_definition.id '_cell.angle_beta_su'
loop_
_alias.definition_id
'_cell_angle.beta_su'
'_cell_angle_beta_su'
'_cell.angle_beta_esd'
_name.category_id cell
_name.object_id angle_beta_su
_name.linked_item_id '_cell.angle_beta'
_import.get
[{'file':templ_attr.cif 'save':cell_angle_su}]
save_
save_cell.angle_gamma
_definition.id '_cell.angle_gamma'
_alias.definition_id '_cell_angle_gamma'
_name.category_id cell
_name.object_id angle_gamma
_import.get [{'file':templ_attr.cif 'save':cell_angle}]
save_
save_cell.angle_gamma_su
_definition.id '_cell.angle_gamma_su'
loop_
_alias.definition_id
'_cell_angle.gamma_su'
'_cell_angle_gamma_su'
'_cell.angle_gamma_esd'
_name.category_id cell
_name.object_id angle_gamma_su
_name.linked_item_id '_cell.angle_gamma'
_import.get
[{'file':templ_attr.cif 'save':cell_angle_su}]
save_
save_cell.atomic_mass
_definition.id '_cell.atomic_mass'
_definition.update 2012-11-22
_description.text
;
Atomic mass of the contents of the unit cell. This calculated
from the atom sites present in the ATOM_TYPE list, rather than
the ATOM_SITE lists of atoms in the refined model.
;
_name.category_id cell
_name.object_id atomic_mass
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code dalton
_method.purpose Evaluation
_method.expression
;
mass = 0.
Loop t as atom_type {
mass += t.number_in_cell * t.atomic_mass
}
_cell.atomic_mass = mass
;
save_
save_cell.convert_uij_to_betaij
_definition.id '_cell.convert_Uij_to_betaij'
_definition.update 2021-09-24
_description.text
;
The reciprocal space matrix for converting the U(ij) matrix of
atomic displacement parameters to a dimensionless beta(IJ) matrix.
The ADP factor in a structure factor expression:
t = exp - 2π^2^ ( U11 h h a* a* + ...... 2 U23 k l b* c* )
t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* )
= exp - ( β11 h h + ............ 2 β23 k l )
The conversion of the U or B matrices to the β matrix
β = C U C = C B C /8π^2^
where C is conversion matrix defined here.
;
_name.category_id cell
_name.object_id convert_Uij_to_betaij
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code reciprocal_angstroms
_method.purpose Evaluation
_method.expression
;
With c as cell
_cell.convert_Uij_to_betaij = 1.4142 * Pi *
Matrix([[ c.reciprocal_length_a, 0, 0 ],
[ 0, c.reciprocal_length_b, 0 ],
[ 0, 0, c.reciprocal_length_c ]])
;
save_
save_cell.convert_uij_to_betaij_su
_definition.id '_cell.convert_Uij_to_betaij_su'
_definition.update 2023-07-01
_description.text
;
Standard uncertainty of _cell.convert_Uij_to_betaij.
;
_name.category_id cell
_name.object_id convert_Uij_to_betaij_su
_name.linked_item_id '_cell.convert_Uij_to_betaij'
_type.purpose SU
_type.source Related
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code reciprocal_angstroms
save_
save_cell.convert_uiso_to_uij
_definition.id '_cell.convert_Uiso_to_Uij'
_definition.update 2021-07-07
_description.text
;
The reciprocal space matrix for converting the isotropic Uiso
atomic displacement parameter to the anisotropic matrix Uij.
| 1 cos(γ*) cos(β*) |
U[i,j] = Uiso * | cos(γ*) 1 cos(α*) |
| cos(β*) cos(α*) 1 |
;
_name.category_id cell
_name.object_id convert_Uiso_to_Uij
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code none
_method.purpose Evaluation
_method.expression
;
With c as cell
_cell.convert_Uiso_to_Uij = [[ 1.,
Cosd(c.reciprocal_angle_gamma), Cosd(c.reciprocal_angle_beta) ],
[ Cosd(c.reciprocal_angle_gamma), 1.,
Cosd(c.reciprocal_angle_alpha) ], [
Cosd(c.reciprocal_angle_beta), Cosd(c.reciprocal_angle_alpha), 1. ]]
;
save_
save_cell.convert_uiso_to_uij_su
_definition.id '_cell.convert_Uiso_to_Uij_su'
_definition.update 2023-07-01
_description.text
;
Standard uncertainty of _cell.convert_Uiso_to_Uij.
;
_name.category_id cell
_name.object_id convert_Uiso_to_Uij_su
_name.linked_item_id '_cell.convert_Uiso_to_Uij'
_type.purpose SU
_type.source Related
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code none
save_
save_cell.diffrn_id
_definition.id '_cell.diffrn_id'
_definition.update 2023-02-01
_description.text
;
A pointer to the diffraction conditions to which this cell has been applied,
for example, to locate and extract diffraction peaks. These will normally be
the same conditions as those under which the cell was measured, but some
legacy data sets may have used a cell measured under differing conditions,
in which case those conditions should be indicated using the
_cell_measurement.condition_id data item.
;
_name.category_id cell
_name.object_id diffrn_id
_name.linked_item_id '_diffrn.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Word
save_
save_cell.formula_units_z
_definition.id '_cell.formula_units_Z'
_alias.definition_id '_cell_formula_units_Z'
_definition.update 2021-03-01
_description.text
;
The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
_chemical_formula.sum.
;
_name.category_id cell
_name.object_id formula_units_Z
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_cell.length_a
_definition.id '_cell.length_a'
_alias.definition_id '_cell_length_a'
_name.category_id cell
_name.object_id length_a
_import.get [{'file':templ_attr.cif 'save':cell_length}]
save_
save_cell.length_a_su
_definition.id '_cell.length_a_su'
loop_
_alias.definition_id
'_cell_length_a_su'
'_cell.length_a_esd'
_name.category_id cell
_name.object_id length_a_su
_name.linked_item_id '_cell.length_a'
_import.get
[{'file':templ_attr.cif 'save':cell_length_su}]
save_
save_cell.length_b
_definition.id '_cell.length_b'
_alias.definition_id '_cell_length_b'
_name.category_id cell
_name.object_id length_b
_import.get [{'file':templ_attr.cif 'save':cell_length}]
save_
save_cell.length_b_su
_definition.id '_cell.length_b_su'
loop_
_alias.definition_id
'_cell_length_b_su'
'_cell.length_b_esd'
_name.category_id cell
_name.object_id length_b_su
_name.linked_item_id '_cell.length_b'
_import.get
[{'file':templ_attr.cif 'save':cell_length_su}]
save_
save_cell.length_c
_definition.id '_cell.length_c'
_alias.definition_id '_cell_length_c'
_name.category_id cell
_name.object_id length_c
_import.get [{'file':templ_attr.cif 'save':cell_length}]
save_
save_cell.length_c_su
_definition.id '_cell.length_c_su'
loop_
_alias.definition_id
'_cell_length_c_su'
'_cell.length_c_esd'
_name.category_id cell
_name.object_id length_c_su
_name.linked_item_id '_cell.length_c'
_import.get
[{'file':templ_attr.cif 'save':cell_length_su}]
save_
save_cell.metric_tensor
_definition.id '_cell.metric_tensor'
_definition.update 2021-07-07
_description.text
;
The direct space (covariant) metric tensor used to transform
vectors and coordinates from real (direct) to reciprocal space.
;
_name.category_id cell
_name.object_id metric_tensor
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code angstrom_squared
_method.purpose Evaluation
_method.expression
;
with c as cell
_cell.metric_tensor = [[ c.vector_a*c.vector_a,
c.vector_a*c.vector_b, c.vector_a*c.vector_c ],
[ c.vector_b*c.vector_a, c.vector_b*c.vector_b, c.vector_b*c.vector_c ],
[ c.vector_c*c.vector_a, c.vector_c*c.vector_b,
c.vector_c*c.vector_c ]]
;
save_
save_cell.orthogonal_matrix
_definition.id '_cell.orthogonal_matrix'
_definition.update 2021-07-07
_description.text
;
Orthogonal matrix of the crystal unit cell. Definition uses
Rollet's axial assignments with cell vectors a,b,c aligned
with orthogonal axes X,Y,Z so that c||Z and b in plane YZ.
;
_name.category_id cell
_name.object_id orthogonal_matrix
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.dimension '[3,3]'
_type.contents Real
_units.code angstroms
_method.purpose Evaluation
_method.expression
;
With c as cell
_cell.orthogonal_matrix = [
[ c.length_a*Sind(c.angle_beta)*Sind(c.reciprocal_angle_gamma), 0,
0 ], [
-c.length_a*Sind(c.angle_beta)*Cosd(c.reciprocal_angle_gamma),
c.length_b*Sind(c.angle_alpha), 0 ], [
c.length_a*Cosd(c.angle_beta),
c.length_b*Cosd(c.angle_alpha), c.length_c ]]
;
save_
save_cell.reciprocal_angle_alpha
_definition.id '_cell.reciprocal_angle_alpha'
_alias.definition_id '_cell_reciprocal_angle_alpha'
_definition.update 2013-01-18
_description.text
;
Reciprocal of the angle between _cell.length_b and _cell.length_c.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_name.category_id cell
_name.object_id reciprocal_angle_alpha
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:180.0
_units.code degrees
_method.purpose Evaluation
_method.expression
;
With c as cell
_cell.reciprocal_angle_alpha =
Acosd((Cosd(c.angle_beta)*Cosd(c.angle_gamma)-Cosd(c.angle_alpha))/
(Sind(c.angle_beta)*Sind(c.angle_gamma)))
;
save_
save_cell.reciprocal_angle_alpha_su
_definition.id '_cell.reciprocal_angle_alpha_su'
loop_
_alias.definition_id
'_cell_reciprocal_angle_alpha_su'
'_cell.reciprocal_angle_alpha_esd'
_definition.update 2021-03-03
_description.text
;
Standard uncertainty of _cell.reciprocal_angle_alpha.
;
_name.category_id cell
_name.object_id reciprocal_angle_alpha_su
_name.linked_item_id '_cell.reciprocal_angle_alpha'
_units.code degrees
_import.get [{'file':templ_attr.cif 'save':general_su}]
save_
save_cell.reciprocal_angle_beta