From 3b2464579f769f53a974b202ecc731a2d89af565 Mon Sep 17 00:00:00 2001 From: "James.Hester" Date: Thu, 27 Feb 2014 14:59:12 +1100 Subject: [PATCH] Added draft DDLm dictionaries --- cif_core_ddlm.dic | 112 + core_diffr.dic | 5780 +++++++++++++++++++++++++++++++++++++++++++++ core_exptl.dic | 4578 +++++++++++++++++++++++++++++++++++ core_funct.dic | 383 +++ core_model.dic | 2398 +++++++++++++++++++ core_publn.dic | 4022 +++++++++++++++++++++++++++++++ core_struc.dic | 4583 +++++++++++++++++++++++++++++++++++ templ_attr.cif | 452 ++++ templ_enum.cif | 1531 ++++++++++++ 9 files changed, 23839 insertions(+) create mode 100755 cif_core_ddlm.dic create mode 100755 core_diffr.dic create mode 100755 core_exptl.dic create mode 100644 core_funct.dic create mode 100755 core_model.dic create mode 100755 core_publn.dic create mode 100755 core_struc.dic create mode 100755 templ_attr.cif create mode 100755 templ_enum.cif diff --git a/cif_core_ddlm.dic b/cif_core_ddlm.dic new file mode 100755 index 0000000..2c1a9a9 --- /dev/null +++ b/cif_core_ddlm.dic @@ -0,0 +1,112 @@ +############################################################################## +# # +# CIF CORE DICTIONARY # +# # +############################################################################## + +data_CIF_CORE + + _dictionary.title CIF_CORE + _dictionary.class Instance + _dictionary.version 1.4.02 + _dictionary.date 2012-12-18 + _dictionary.uri www.iucr.org/cif/dic/cif_core.dic + _dictionary.ddl_conformance 3.10.3 + _dictionary.namespace CifCore + _description.text +; + Dictionary shell for the definitions of COMCIFS-approved CORE data + used within the Crystallographic Information Framework. +; + +save_CIF_CORE + _definition.id CIF_CORE + _definition.scope Category + _definition.class Head + _definition.update 2012-12-18 + _description.text +; + The DICTIONARY group encompassing all CORE data items defined and + used with in the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_DIC + _name.object_id CIF_CORE + + _import.get + [{"save":'EXPERIMENTAL', "file":'core_exptl.dic', "mode":'full' }, + {"save":'DIFFRACTION', "file":'core_diffr.dic', "mode":'full' }, + {"save":'STRUCTURE', "file":'core_struc.dic', "mode":'full' }, + {"save":'MODEL', "file":'core_model.dic', "mode":'full' }, + {"save":'PUBLICATION', "file":'core_publn.dic', "mode":'full' }, + {"save":'FUNCTION', "file":'core_funct.dic', "mode":'full' }] + + + save_ #---------- close of CIF_CORE category + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.0.0 2005-12-12 +; + Initial version created from the CORE_3 version 3.5.02. +; + 1.0.01 2006-02-06 +; + Place all _import_dictionary.id components into a tuple. +; + 1.1.01 2006-02-08 +; + Remove save frame from dictionary definition attributes. + Add definition id to the import dictionary tuple. +; + 1.1.02 2006-02-12 +; + Add attribute _dictionary.parent_id +; + 1.1.03 2006-02-12 +; + Change loop_ of _import_dictionary.id to a tuple. +; + 1.2.01 2006-02-21 +; + Basic change in dictionary structure where the dictionary data block now + contains a saveframe defining the category of the DICTIONRY to which + contained data categories are linked. It differs from other CATEGORY + definitions in that its name is NOT part of the child data tags. + This change allows imported dictionaries to be inserted without their + data block header or non-savedframed attributes. +; + 1.2.02 2006-02-30 +; + Apply the DDL 3.6.05 attribute changes. +; + 1.2.03 2006-11-13 +; + Apply the DDL 3.6.10 attribute changes. +; + 1.2.04 2008-02-12 +; + Updated the IMPORT values as per ddl.dic 3.07.09 +; + 1.2.05 2008-05-18 +; + Changed looped list of imports to _import_list.id syntax. +; + 1.3.01 2011-06-07 +; + Place all import lists into [[......]] +; + 1.4.01 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 1.4.02 2012-12-18 +; + Add import for FUNCTION category containing all function definitions. +; diff --git a/core_diffr.dic b/core_diffr.dic new file mode 100755 index 0000000..51893fe --- /dev/null +++ b/core_diffr.dic @@ -0,0 +1,5780 @@ +############################################################################## +# # +# CIF CORE DIFFRACTION DICTIONARY # +# # +############################################################################## + +data_CORE_DIFFR + + _dictionary.title CORE_DIFFR + _dictionary.class Instance + _dictionary.version 1.5.10 + _dictionary.date 2013-02-21 + _dictionary.uri www.iucr.org/cif/dic/core_diffr.dic + _dictionary.ddl_conformance 3.10.04 + _dictionary.namespace CoreDiffr + _description.text +; + This dictionary contains the definitions of data items that + are considered CORE to the description of DIFFRACTION data. +; + + +save_DIFFRACTION + _definition.id DIFFRACTION + _definition.scope Category + _definition.class Head + _definition.update 2012-11-26 + _description.text +; + The DICTIONARY group encompassing the CORE DIFFRACTION data items defined + and used with in the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_CORE + _name.object_id DIFFRACTION + +#============================================================================ + +save_DIFFRN + + _definition.id DIFFRN + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of data items used to describe the diffraction experiment. +; + _name.category_id DIFFRACTION + _name.object_id DIFFRN + + +save_diffrn.ambient_environment + _definition.id '_diffrn.ambient_environment' + loop_ + _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 Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'He' 'vacuum' 'mother liquor' + save_ + + +save_diffrn.ambient_pressure + _definition.id '_diffrn.ambient_pressure' + loop_ + _alias.definition_id '_diffrn_ambient_pressure' + _definition.update 2012-11-26 + _description.text +; + Mean hydrostatic pressure at which intensities were measured. +; + _description.common 'AmbientPressure' + _name.category_id diffrn + _name.object_id ambient_pressure + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kilopascals + save_ + + +save_diffrn.ambient_pressure_gt + _definition.id '_diffrn.ambient_pressure_gt' + loop_ + _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 Quantity + _type.source Observed + _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' + loop_ + _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 Quantity + _type.source Observed + _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. +; + _description.common 'AmbientTemperature' + _name.category_id diffrn + _name.object_id ambient_temperature + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_diffrn.ambient_temperature_gt + _definition.id '_diffrn.ambient_temperature_gt' + loop_ + _alias.definition_id '_diffrn_ambient_temperature_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 Quantity + _type.source Observed + _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_temperature_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 Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + +save_diffrn.crystal_treatment + _definition.id '_diffrn.crystal_treatment' + loop_ + _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. +; + _description.common 'CrystalTreatment' + _name.category_id diffrn + _name.object_id crystal_treatment + _type.purpose Describe + _type.source Assigned + _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.measured_fraction_theta_full + _definition.id '_diffrn.measured_fraction_theta_full' + loop_ + _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. +; + _description.common 'DiffrnCompletionThetaFull' + _name.category_id diffrn + _name.object_id measured_fraction_theta_full + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_diffrn.measured_fraction_theta_max + _definition.id '_diffrn.measured_fraction_theta_max' + loop_ + _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. +; + _description.common 'DiffrnCompletionThetaMax' + _name.category_id diffrn + _name.object_id measured_fraction_theta_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + 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. +; + _description.common 'DiffrnMeasDetails' + _name.category_id diffrn + _name.object_id special_details + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _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' + loop_ + _alias.definition_id '_diffrn_symmetry_description' + _definition.update 2012-11-26 + _description.text +; + Observed diffraction point symmetry, systematic absences and possible + space group(s) or superspace group(s) compatible with these. +; + _description.common 'DiffrnSymmetryDetails' + _name.category_id diffrn + _name.object_id symmetry_description + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + +#---------------------------------------------------------------------- + +save_DIFFRN_ATTENUATOR + + _definition.id diffrn_attenuator + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the attenuators used in the + diffraction source. +; + _name.category_id DIFFRN + _name.object_id ATTENUATOR + _category.key_id '_diffrn_attenuator.key' + + +save_diffrn_attenuator.key + _definition.id '_diffrn_attenuator.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_ATTENUATOR items + in a looped list. +; + _description.common 'Key to beam attenuator values' + _name.category_id attenuator + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_attenuator.code) +; + Evaluation +; _diffrn_attenuator.key = _diffrn_attenuator.code +; + save_ + + +save_diffrn_attenuator.code + _definition.id '_diffrn_attenuator.code' + loop_ + _alias.definition_id '_diffrn_attenuator_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying a particular attenuator setting; referenced by the + _diffrn_refln.attenuator_code which is stored with the intensities. +; + _description.common 'DiffrnAttenuatorCode' + _name.category_id attenuator + _name.object_id code + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_diffrn_attenuator.material + _definition.id '_diffrn_attenuator.material' + loop_ + _alias.definition_id '_diffrn_attenuator_material' + _definition.update 2012-11-26 + _description.text +; + Description of the material from which the attenuator is made. +; + _description.common 'DiffrnAttenuator' + _name.category_id attenuator + _name.object_id material + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_diffrn_attenuator.scale + _definition.id '_diffrn_attenuator.scale' + loop_ + _alias.definition_id '_diffrn_attenuator_scale' + _definition.update 2012-11-26 + _description.text +; + The scale factor applied to a measured intensity if it is reduced by + an attenuator identified by _diffrn_attenuator.code. +; + _description.common 'DiffrnAttenuatorScale' + _name.category_id attenuator + _name.object_id scale + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 1.0: + save_ + + save_ #------ close DIFFRN_ATTENUATOR category + + +#---------------------------------------------------------------------- + +save_DIFFRN_DETECTOR + + _definition.id diffrn_detector + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the detectors used in the + in the measurement of diffraction intensities. +; + _name.category_id DIFFRN + _name.object_id DETECTOR + + +save_diffrn_detector.description + _definition.id '_diffrn_detector.description' + loop_ + _alias.definition_id '_diffrn_radiation_detector' + '_diffrn_detector' + '_diffrn_detector.detector' + _definition.update 2012-11-26 + _description.text +; + Description of the type of diffraction radiation detector. +; + _description.common 'DetectorClass' + _name.category_id detector + _name.object_id description + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'photographic film' + 'scintillation counter' + 'CCD plate' + 'BF~3~ counter' + save_ + + +save_diffrn_detector.area_resol_mean + _definition.id '_diffrn_detector.area_resol_mean' + loop_ + _alias.definition_id '_diffrn_detector_area_resol_mean' + _definition.update 2012-11-26 + _description.text +; + The resolution limit of an area diffraction radiation detector. +; + _description.common 'DetectorResolLimit' + _name.category_id detector + _name.object_id area_resol_mean + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code pixels_per_millimetre + save_ + + +save_diffrn_detector.details + _definition.id '_diffrn_detector.details' + loop_ + _alias.definition_id '_diffrn_detector_details' + _definition.update 2012-11-26 + _description.text +; + Description of special aspects of the radiation detector. +; + _description.common 'DetectorDetails' + _name.category_id detector + _name.object_id details + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_diffrn_detector.dtime + _definition.id '_diffrn_detector.dtime' + loop_ + _alias.definition_id '_diffrn_detector_dtime' + '_diffrn_radiation.detector_dtime' + '_diffrn_radiation_detector_dtime' + _definition.update 2012-11-26 + _description.text +; + The maximum time between two detector signals that cannot be resolved. +; + _description.common 'DetectorDeadTime' + _name.category_id detector + _name.object_id dtime + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code microseconds + save_ + + +save_diffrn_detector.make + _definition.id '_diffrn_detector.make' + loop_ + _alias.definition_id '_diffrn_detector_type' + '_diffrn_detector.type' + _definition.update 2012-11-26 + _description.text +; + The make, model or name of the diffraction radiation detector. +; + _description.common 'DetectorMake' + _name.category_id detector + _name.object_id make + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + save_ #------ close DIFFRN_DETECTOR category + +#---------------------------------------------------------------------------- + + +save_DIFFRN_MEASUREMENT + + _definition.id DIFFRN_MEASUREMENT + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the details of the + diffraction measurement. +; + _name.category_id DIFFRN + _name.object_id MEASUREMENT + + +save_diffrn_measurement.details + _definition.id '_diffrn_measurement.details' + loop_ + _alias.definition_id '_diffrn_measurement_details' + '_diffrn.measurement_details' + _definition.update 2012-11-26 + _description.text +; + Description of special aspects of the diffraction measurement. +; + _description.common 'DiffrnMeasDetails' + _name.category_id measurement + _name.object_id details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '440 frames of 0.25\%' + save_ + + +save_diffrn_measurement.device_class + _definition.id '_diffrn_measurement.device_class' + loop_ + _alias.definition_id '_diffrn_measurement_device' + '_diffrn.measurement_device_class' + '_diffrn.measurement.device' + _definition.update 2012-11-26 + _description.text +; + Type of goniometer device used to mount and orient the specimen. +; + _description.common 'DiffrnMeasDeviceClass' + _name.category_id measurement + _name.object_id device_class + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'three-circle diffractometer' + 'four-circle diffractometer' + '\k-geometry diffractometer' + 'oscillation camera' + 'precession camera' + save_ + + +save_diffrn_measurement.device_details + _definition.id '_diffrn_measurement.device_details' + loop_ + _alias.definition_id '_diffrn_measurement_device_details' + '_diffrn.measurement_device_details' + _definition.update 2012-11-26 + _description.text +; + Details of the goniometer device used in the diffraction experiment. +; + _description.common 'DiffrnMeasDeviceDetails' + _name.category_id measurement + _name.object_id device_details + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case +; commercial goniometer modified locally to + allow for 90\% \t arc +; + save_ + + +save_diffrn_measurement.device_make + _definition.id '_diffrn_measurement.device_make' + loop_ + _alias.definition_id '_diffrn_measurement_device_type' + '_diffrn.measurement_device_make' + '_diffrn_measurement_device.type' + _definition.update 2012-11-26 + _description.text +; + The make, model or name of the goniometer device used. +; + _description.common 'DiffrnMeasDeviceMake' + _name.category_id measurement + _name.object_id device_make + _type.purpose Observed + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_diffrn_measurement.method + _definition.id '_diffrn_measurement.method' + loop_ + _alias.definition_id '_diffrn_measurement_method' + '_diffrn.measurement_method' + _definition.update 2012-11-26 + _description.text +; + Description of scan method used to measure diffraction intensities. +; + _description.common 'DiffrnMeasMethod' + _name.category_id measurement + _name.object_id method + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'profile data from \q/2\q scans' + save_ + + +save_diffrn_measurement.specimen_support + _definition.id '_diffrn_measurement.specimen_support' + loop_ + _alias.definition_id '_diffrn_measurement_specimen_support' + '_diffrn.measurement_specimen_support' + _definition.update 2013-01-23 + _description.text +; + Mounting method for the crystal specimum during data collection. +; + _description.common 'DiffrnSpecimumMount' + _name.category_id measurement + _name.object_id specimen_support + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'glass capillary' + 'quartz capillary' + 'fiber' + 'metal loop' + save_ + + save_ #------ close DIFFRN_MEASUREMENT category + +#---------------------------------------------------------------------------- + + +save_DIFFRN_ORIENT + + _definition.id DIFFRN_ORIENT + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the orientation of the crystal + axes to the diffractometer goniometer. +; + _name.category_id DIFFRN + _name.object_id ORIENT + +#---------------------------------------------------------------------------- + + +save_DIFFRN_ORIENT_MATRIX + + _definition.id DIFFRN_ORIENT_MATRIX + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the matrix specifying the + orientation of the crystal axes to the diffractometer goniometer. +; + _name.category_id DIFFRN_ORIENT + _name.object_id MATRIX + + +save_diffrn_orient_matrix.type + _definition.id '_diffrn_orient_matrix.type' + loop_ + _alias.definition_id '_diffrn_orient_matrix_type' + _definition.update 2012-11-26 + _description.text +; + Description of orientation matrix and how it should be applied to define + the orientation of the crystal with respect to the diffractometer axes. +; + _description.common 'DiffrnOrientMatrixType' + _name.category_id matrix + _name.object_id type + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_diffrn_orient_matrix.UBIJ + _definition.id '_diffrn_orient_matrix.UBIJ' + _definition.update 2012-11-26 + _description.text +; + The 3x3 matrix specifying the orientation of the crystal with + respect to the diffractometer axes. +; + _description.common 'DiffrnOrientMatrix' + _name.category_id matrix + _name.object_id UBIJ + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With o as diffrn_orient_matrix + + _diffrn_orient_matrix.UBIJ = [[ o.ub_11, o.ub_12, o.ub_13 ], + [ o.ub_21, o.ub_22, o.ub_23 ], + [ o.ub_31, o.ub_32, o.ub_33 ]] +; + save_ + + +save_diffrn_orient_matrix.UB_11 + _definition.id '_diffrn_orient_matrix.UB_11' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_11' + '_diffrn_orient_matrix.UB[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_11 + save_ + + +save_diffrn_orient_matrix.UB_12 + _definition.id '_diffrn_orient_matrix.UB_12' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_12' + '_diffrn_orient_matrix.UB[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_12 + save_ + + +save_diffrn_orient_matrix.UB_13 + _definition.id '_diffrn_orient_matrix.UB_13' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_13' + '_diffrn_orient_matrix.UB[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_13 + save_ + + +save_diffrn_orient_matrix.UB_21 + _definition.id '_diffrn_orient_matrix.UB_21' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_21' + '_diffrn_orient_matrix.UB[2][1]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_21 + save_ + + +save_diffrn_orient_matrix.UB_22 + _definition.id '_diffrn_orient_matrix.UB_22' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_22' + '_diffrn_orient_matrix.UB[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_22 + save_ + + +save_diffrn_orient_matrix.UB_23 + _definition.id '_diffrn_orient_matrix.UB_23' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_23' + '_diffrn_orient_matrix.UB[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_23 + save_ + + +save_diffrn_orient_matrix.UB_31 + _definition.id '_diffrn_orient_matrix.UB_31' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_31' + '_diffrn_orient_matrix.UB[3][1]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_31 + save_ + + +save_diffrn_orient_matrix.UB_32 + _definition.id '_diffrn_orient_matrix.UB_32' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_32' + '_diffrn_orient_matrix.UB[3][2]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_32 + save_ + + +save_diffrn_orient_matrix.UB_33 + _definition.id '_diffrn_orient_matrix.UB_33' + loop_ + _alias.definition_id '_diffrn_orient_matrix_UB_33' + '_diffrn_orient_matrix.UB[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'orient_matrix'}] + _name.category_id matrix + _name.object_id UB_33 + save_ + + save_ #------ close DIFFRN_ORIENT_MATRIX category + +#---------------------------------------------------------------------------- + + +save_DIFFRN_ORIENT_REFLN + + _definition.id DIFFRN_ORIENT_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the reflections used to + calculate the matrix which gives the orientation of the crystal + axes to the diffractometer goniometer. +; + _name.category_id DIFFRN_ORIENT + _name.object_id REFLN + _category.key_id '_diffrn_orient_refln.key' + + +save_diffrn_orient_refln.key + _definition.id '_diffrn_orient_refln.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_ORIENT_REFLN items + in a looped list. +; + _description.common 'Key to orientation reflections' + _name.category_id refln + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_orient_refln.hkl) +; + Evaluation +; _diffrn_orient_refln.key = _diffrn_orient_refln.hkl +; + save_ + + +save_diffrn_orient_refln.angle_chi + _definition.id '_diffrn_orient_refln.angle_chi' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_chi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_chi + save_ + + +save_diffrn_orient_refln.angle_kappa + _definition.id '_diffrn_orient_refln.angle_kappa' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_kappa' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_kappa + save_ + + +save_diffrn_orient_refln.angle_omega + _definition.id '_diffrn_orient_refln.angle_omega' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_omega' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_omega + save_ + + +save_diffrn_orient_refln.angle_phi + _definition.id '_diffrn_orient_refln.angle_phi' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_phi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_phi + save_ + + +save_diffrn_orient_refln.angle_psi + _definition.id '_diffrn_orient_refln.angle_psi' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_psi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_psi + save_ + + +save_diffrn_orient_refln.angle_theta + _definition.id '_diffrn_orient_refln.angle_theta' + loop_ + _alias.definition_id '_diffrn_orient_refln_angle_theta' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_theta + save_ + + +save_diffrn_orient_refln.hkl + _definition.id '_diffrn_orient_refln.hkl' + _definition.update 2012-11-26 + _description.text +; + Miller indices of a reflection used to define the orientation matrix. +; + _description.common 'DiffrnOrientReflnHkl' + _name.category_id refln + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as diffrn_orient_refln + + _diffrn_orient_refln.hkl = [a.index_h, a.index_k, a.index_l] +; + save_ + + +save_diffrn_orient_refln.index_h + _definition.id '_diffrn_orient_refln.index_h' + loop_ + _alias.definition_id '_diffrn_orient_refln_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_h + save_ + + +save_diffrn_orient_refln.index_k + _definition.id '_diffrn_orient_refln.index_k' + loop_ + _alias.definition_id '_diffrn_orient_refln_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_k + save_ + + +save_diffrn_orient_refln.index_l + _definition.id '_diffrn_orient_refln.index_l' + loop_ + _alias.definition_id '_diffrn_orient_refln_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_l + save_ + + save_ #------ close DIFFRN_ORIENT_REFLN category + + save_ #------ close DIFFRN_ORIENT category + + +#---------------------------------------------------------------------------- + + +save_DIFFRN_RADIATION + + _definition.id DIFFRN_RADIATION + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the wavelength of the + radiation used in measuring diffraction intensities. Items may be + looped to identify and assign weights to distinct wavelength + components from a polychromatic beam. +; + _name.category_id DIFFRN + _name.object_id RADIATION + + +save_diffrn_radiation.collimation + _definition.id '_diffrn_radiation.collimation' + loop_ + _alias.definition_id '_diffrn_radiation_collimation' + _definition.update 2012-11-26 + _description.text +; + Description of the collimation or focusing applied to the radiation. +; + _description.common 'RadCollimator' + _name.category_id radiation + _name.object_id collimation + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case '0.3 mm double-pinhole' + '0.5 mm' + 'focusing mirrors' + save_ + + +save_diffrn_radiation.filter_edge + _definition.id '_diffrn_radiation.filter_edge' + loop_ + _alias.definition_id '_diffrn_radiation_filter_edge' + _definition.update 2012-11-26 + _description.text +; + Absorption edge of the radiation filter used. +; + _description.common 'RadFilter' + _name.category_id radiation + _name.object_id filter_edge + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_diffrn_radiation.inhomogeneity + _definition.id '_diffrn_radiation.inhomogeneity' + loop_ + _alias.definition_id '_diffrn_radiation_inhomogeneity' + _definition.update 2012-11-26 + _description.text +; + Half-width of the incident beam perpendicular to the diffraction plane. +; + _description.common 'RadHalfWidth' + _name.category_id radiation + _name.object_id inhomogeneity + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code millimetres + save_ + + +save_diffrn_radiation.monochromator + _definition.id '_diffrn_radiation.monochromator' + loop_ + _alias.definition_id '_diffrn_radiation_monochromator' + _definition.update 2012-11-26 + _description.text +; + Description of the method used to obtain monochromatic radiation. + If a monochromator crystal is used the material and the indices of + the Bragg reflection are specified. +; + _description.common 'RadMonochromator' + _name.category_id radiation + _name.object_id monochromator + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Zr filter' 'Ge 220' 'none' + 'equatorial mounted graphite' + save_ + + +save_diffrn_radiation.polarisn_norm + _definition.id '_diffrn_radiation.polarisn_norm' + loop_ + _alias.definition_id '_diffrn_radiation_polarisn_norm' + _definition.update 2012-11-26 + _description.text +; + The angle, as viewed from the specimen, between the perpendicular + component of the polarisation and the diffraction plane. +; + _description.common 'RadPolarizNorm' + _name.category_id radiation + _name.object_id polarisn_norm + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range -180.0:180.0 + _units.code degrees + save_ + + +save_diffrn_radiation.polarisn_ratio + _definition.id '_diffrn_radiation.polarisn_ratio' + loop_ + _alias.definition_id '_diffrn_radiation_polarisn_ratio' + _definition.update 2012-11-26 + _description.text +; + Polarisation ratio of the diffraction beam incident on the crystal. + It is the ratio of the perpendicularly polarised to the parallel + polarised component of the radiation. The perpendicular component + forms an angle of _diffrn_radiation.polarisn_norm to the normal to + the diffraction plane of the sample (i.e. the plane containing the + incident and reflected beams). +; + _description.common 'RadPolarizRatio' + _name.category_id radiation + _name.object_id polarisn_ratio + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_diffrn_radiation.probe + _definition.id '_diffrn_radiation.probe' + loop_ + _alias.definition_id '_diffrn_radiation_probe' + _definition.update 2012-11-26 + _description.text +; + Enumerated code for the nature of radiation used (i.e. name of + subatomic particle or region of the electromagnetic spectrum). +; + _description.common 'RadDescription' + _name.category_id radiation + _name.object_id probe + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state x-ray neutron electron gamma + _enumeration.default x-ray + save_ + + +save_diffrn_radiation.type + _definition.id '_diffrn_radiation.type' + loop_ + _alias.definition_id '_diffrn_radiation_type' + _definition.update 2012-11-26 + _description.text +; + Enumerated code for the radiation source or energy spectrum. +; + _description.common 'RadType' + _name.category_id radiation + _name.object_id type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + Cu 'Copper tube' + Mo 'Molybdinum tube' + Ag 'Silver tube' + white 'unfiltered radiation' + synch 'synchrotron radiation' + save_ + + +save_diffrn_radiation.xray_symbol + _definition.id '_diffrn_radiation.xray_symbol' + loop_ + _alias.definition_id '_diffrn_radiation_xray_symbol' + _definition.update 2012-11-26 + _description.text +; + IUPAC symbol for the X-ray wavelength for probe radiation. +; + _description.common 'RadXraySymbol' + _name.category_id radiation + _name.object_id xray_symbol + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + K-L~3~ 'K\a~1~ in older Siegbahn notation' + K-L~2~ 'K\a~2~ in older Siegbahn notation' + K-M~3~ 'K\b~1~ in older Siegbahn notation' + K-L~2,3~ 'use where K-L~3~ and K-L~2~ are not resolved' + _enumeration.default K-L~3~ + save_ + +#---------------------------------------------------------------------------- + +save_DIFFRN_RADIATION_WAVELENGTH + + _definition.id DIFFRN_RADIATION_WAVELENGTH + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the wavelength of the + radiation used in measuring diffraction intensities. Items may be + looped to identify and assign weights to distinct wavelength + components from a polychromatic beam. +; + _name.category_id DIFFRN_RADIATION + _name.object_id WAVELENGTH + _category.key_id '_diffrn_radiation_wavelength.key' + + +save_diffrn_radiation_wavelength.key + _definition.id '_diffrn_radiation_wavelength.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_RADIATION_WAVELENGTH items + in a looped list. +; + _description.common 'Key to radiation wavelengths' + _name.category_id wavelength + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_radiation_wavelength.id) +; + Evaluation +; _diffrn_radiation_wavelength.key = _diffrn_radiation_wavelength.id +; + save_ + + +save_diffrn_radiation_wavelength.value + _definition.id '_diffrn_radiation_wavelength.value' + loop_ + _alias.definition_id '_diffrn_radiation_wavelength' + '_diffrn_radiation_wavelength.wavelength' + _definition.update 2012-11-26 + _description.text +; + Wavelength of radiation used in diffraction measurements. +; + _description.common 'RadWaveLength' + _name.category_id wavelength + _name.object_id value + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_diffrn_radiation_wavelength.id + _definition.id '_diffrn_radiation_wavelength.id' + loop_ + _alias.definition_id '_diffrn_radiation_wavelength_id' + '_diffrn_radiation.wavelength_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying a radiation used in the diffraction measurements. + This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id +; + _description.common 'RadWaveLengthId' + _name.category_id wavelength + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ _description_example.case "x2" + save_ + + +save_diffrn_radiation_wavelength.details + _definition.id '_diffrn_radiation_wavelength.details' + loop_ + _alias.definition_id '_diffrn_radiation_wavelength_details' + '_diffrn_radiation.wavelength_details' + _definition.update 2012-11-26 + _description.text +; + Information about the determination of the radiation + wavelength that is not conveyed completely by an + enumerated value of _diffrn_radiation_wavelength.determination. +; + _name.category_id wavelength + _name.object_id details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_diffrn_radiation_wavelength.determination + _definition.id '_diffrn_radiation_wavelength.determination' + loop_ + _alias.definition_id '_diffrn_radiation_wavelength_determination' + '_diffrn_radiation.wavelength_determination' + _definition.update 2012-11-26 + _description.text +; + Information about the determination of the radiation + wavelength that is not conveyed completely by an + enumerated value of _diffrn_radiation_wavelength.determination. +; + _name.category_id wavelength + _name.object_id determination + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + + fundamental 'Fundamental property of matter e.g. MoK\alpha' + + estimated 'Estimated e.g. from monochromator angle or time of flight' + + refined 'Refined using a standard crystal with known cell parameters' + save_ + + +save_diffrn_radiation_wavelength.wt + _definition.id '_diffrn_radiation_wavelength.wt' + loop_ + _alias.definition_id '_diffrn_radiation_wavelength_wt' + _definition.update 2012-11-26 + _description.text +; + Relative intensity of a radiation used in the diffraction measurements. +; + _description.common 'RadWaveLengthWeight' + _name.category_id wavelength + _name.object_id wt + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + _enumeration.default 1.0 + save_ + + save_ #------ close DIFFRN_RADIATION_WAVELENGTH category + + save_ #------ close DIFFRN_RADIATION category + + +#----------------------------------------------------------------------------- + + +save_DIFFRN_REFLN + + _definition.id DIFFRN_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the reflection measurements, + prior to data reduction and merging. +; + _name.category_id DIFFRN + _name.object_id REFLN + _category.key_id '_diffrn_refln.key' + + +save_diffrn_refln.key + _definition.id '_diffrn_refln.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_REFLN items + in a looped list. +; + _description.common 'Key to measured reflection data' + _name.category_id refln + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_refln.hkl) +; + Evaluation +; _diffrn_refln.key = _diffrn_refln.hkl +; + save_ + + +save_diffrn_refln.angle_chi + _definition.id '_diffrn_refln.angle_chi' + loop_ + _alias.definition_id '_diffrn_refln_angle_chi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id diffrn_refln + _name.object_id angle_chi + save_ + + +save_diffrn_refln.angle_kappa + _definition.id '_diffrn_refln.angle_kappa' + loop_ + _alias.definition_id '_diffrn_refln_angle_kappa' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_kappa + save_ + + +save_diffrn_refln.angle_omega + _definition.id '_diffrn_refln.angle_omega' + loop_ + _alias.definition_id '_diffrn_refln_angle_omega' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_omega + save_ + + +save_diffrn_refln.angle_phi + _definition.id '_diffrn_refln.angle_phi' + loop_ + _alias.definition_id '_diffrn_refln_angle_phi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_phi + save_ + + +save_diffrn_refln.angle_psi + _definition.id '_diffrn_refln.angle_psi' + loop_ + _alias.definition_id '_diffrn_refln_angle_psi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_psi + save_ + + +save_diffrn_refln.angle_theta + _definition.id '_diffrn_refln.angle_theta' + loop_ + _alias.definition_id '_diffrn_refln_angle_theta' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id refln + _name.object_id angle_theta + save_ + + +save_diffrn_refln.attenuator_code + _definition.id '_diffrn_refln.attenuator_code' + loop_ + _alias.definition_id '_diffrn_refln_attenuator_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying any attenuator setting for this reflection. +; + _description.common 'DiffrnReflnAttenCode' + _name.category_id refln + _name.object_id attenuator_code + _name.linked_item_id '_diffrn_attenuator.code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_diffrn_refln.class_code + _definition.id '_diffrn_refln.class_code' + loop_ + _alias.definition_id '_diffrn_refln_class_code' + _definition.update 2012-11-26 + _description.text +; + Code for reflection class, if assigned. e.g. modulated structures +; + _description.common 'DiffrnReflnClass' + _name.category_id refln + _name.object_id class_code + _name.linked_item_id '_diffrn_reflns_class.code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_diffrn_refln.counts_bg_1 + _definition.id '_diffrn_refln.counts_bg_1' + loop_ + _alias.definition_id '_diffrn_refln_counts_bg_1' + _import.get [{"file":'templ_attr.cif',"save":'diffr_counts'}] + _name.category_id refln + _name.object_id counts_bg_1 + _description.common 'DiffrnReflnCountsBg1' + save_ + + +save_diffrn_refln.counts_bg_2 + _definition.id '_diffrn_refln.counts_bg_2' + loop_ + _alias.definition_id '_diffrn_refln_counts_bg_2' + _import.get [{"file":'templ_attr.cif',"save":'diffr_counts'}] + _name.category_id refln + _name.object_id counts_bg_2 + _description.common 'DiffrnReflnCountsBg2' + save_ + + +save_diffrn_refln.counts_net + _definition.id '_diffrn_refln.counts_net' + loop_ + _alias.definition_id '_diffrn_refln_counts_net' + _import.get [{"file":'templ_attr.cif',"save":'diffr_counts'}] + _name.category_id refln + _name.object_id counts_net + _description.common 'DiffrnReflnCountsNet' + save_ + + +save_diffrn_refln.counts_peak + _definition.id '_diffrn_refln.counts_peak' + loop_ + _alias.definition_id '_diffrn_refln_counts_peak' + _import.get [{"file":'templ_attr.cif',"save":'diffr_counts'}] + _name.category_id refln + _name.object_id counts_peak + _description.common 'DiffrnReflnCountsPeak' + save_ + + +save_diffrn_refln.counts_total + _definition.id '_diffrn_refln.counts_total' + loop_ + _alias.definition_id '_diffrn_refln_counts_total' + _import.get [{"file":'templ_attr.cif',"save":'diffr_counts'}] + _name.category_id refln + _name.object_id counts_total + _description.common 'DiffrnReflnCountsTotal' + save_ + + +save_diffrn_refln.crystal_id + _definition.id '_diffrn_refln.crystal_id' + loop_ + _alias.definition_id '_diffrn_refln_crystal_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying each crystal if multiple crystals are used. +; + _description.common 'DiffrnReflnCrystalId' + _name.category_id refln + _name.object_id crystal_id + _name.linked_item_id '_exptl_crystal.id' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_diffrn_refln.detect_slit_horiz + _definition.id '_diffrn_refln.detect_slit_horiz' + loop_ + _alias.definition_id '_diffrn_refln_detect_slit_horiz' + _definition.update 2012-11-26 + _description.text +; + Total slit aperture angle in the diffraction plane. +; + _description.common 'DiffrnReflnDetectSlitHoriz' + _name.category_id refln + _name.object_id detect_slit_horiz + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_refln.detect_slit_vert + _definition.id '_diffrn_refln.detect_slit_vert' + loop_ + _alias.definition_id '_diffrn_refln_detect_slit_vert' + _definition.update 2012-11-26 + _description.text +; + Total slit aperture angle perpendicular to the diffraction plane. +; + _description.common 'DiffrnReflnDetectSlitVert' + _name.category_id refln + _name.object_id detect_slit_vert + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_refln.elapsed_time + _definition.id '_diffrn_refln.elapsed_time' + loop_ + _alias.definition_id '_diffrn_refln_elapsed_time' + _definition.update 2012-11-26 + _description.text +; + Elapsed time from the start to the end of the intensity measurement. +; + _description.common 'DiffrnReflnElapseTime' + _name.category_id refln + _name.object_id elapsed_time + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code minutes + save_ + + +save_diffrn_refln.hkl + _definition.id '_diffrn_refln.hkl' + _definition.update 2012-11-26 + _description.text +; + Miller indices of a measured reflection. These need not match the + _refln.hkl values if a transformation of the original measured + cell has taken place. +; + _description.common 'DiffrnReflnHkl' + _name.category_id refln + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as diffrn_refln + + _diffrn_refln.hkl = [a.index_h, a.index_h, a.index_l] +; + save_ + + +save_diffrn_refln.index_h + _definition.id '_diffrn_refln.index_h' + loop_ + _alias.definition_id '_diffrn_refln_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_h + save_ + + +save_diffrn_refln.index_k + _definition.id '_diffrn_refln.index_k' + loop_ + _alias.definition_id '_diffrn_refln_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_k + save_ + + +save_diffrn_refln.index_l + _definition.id '_diffrn_refln.index_l' + loop_ + _alias.definition_id '_diffrn_refln_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_l + save_ + + +save_diffrn_refln.intensity_net + _definition.id '_diffrn_refln.intensity_net' + loop_ + _alias.definition_id '_diffrn_refln_intensity_net' + _definition.update 2012-11-26 + _description.text +; + Net intensity calculated from the diffraction counts after the + attenuator and standard scales have been applied. +; + _description.common 'DiffrnReflnInet' + _name.category_id refln + _name.object_id intensity_net + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + save_ + + +save_diffrn_refln.intensity_net_su + _definition.id '_diffrn_refln.intensity_net_su' + loop_ + _alias.definition_id '_diffrn_refln_intensity_u' + '_diffrn_refln_intensity_sigma' + _definition.update 2012-12-13 + _description.text +; + Standard uncertainty of the net intensity calculated from the + diffraction counts after the attenuator and standard scales + have been applied. +; + _name.category_id refln + _name.object_id intensity_net_su + _type.purpose SU + _type.source Measured + _type.container Single + _type.contents Real + save_ + + +save_diffrn_refln.scale_group_code + _definition.id '_diffrn_refln.scale_group_code' + loop_ + _alias.definition_id '_diffrn_refln_scale_group_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying the scale applying to this reflection. +; + _description.common 'DiffrnReflnScaleGroup' + _name.category_id refln + _name.object_id scale_group_code + _name.linked_item_id '_diffrn_scale_group.code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_diffrn_refln.scan_mode + _definition.id '_diffrn_refln.scan_mode' + loop_ + _alias.definition_id '_diffrn_refln_scan_mode' + _definition.update 2012-11-26 + _description.text +; + Code identifying the mode of scanning with a diffractometer. + See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. +; + _description.common 'DiffrnReflnScanMode' + _name.category_id refln + _name.object_id scan_mode + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail om 'omega scan' + ot 'omega/2theta scan' + q 'Q-scans (arbitrary reciprocal directions)' + _enumeration.default ot + save_ + + +save_diffrn_refln.scan_mode_backgd + _definition.id '_diffrn_refln.scan_mode_backgd' + loop_ + _alias.definition_id '_diffrn_refln_scan_mode_backgd' + _definition.update 2012-11-26 + _description.text +; + Code identifying mode of scanning to measure the background intensity. +; + _description.common 'DiffrnReflnScanModeBgd' + _name.category_id refln + _name.object_id scan_mode_backgd + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail st 'stationary counter background' + mo 'moving counter background' + _enumeration.default st + save_ + + +save_diffrn_refln.scan_rate + _definition.id '_diffrn_refln.scan_rate' + loop_ + _alias.definition_id '_diffrn_refln_scan_rate' + _definition.update 2012-11-26 + _description.text +; + Angular rate of scanning a reflection to measure the intensity. +; + _description.common 'DiffrnReflnScanRate' + _name.category_id refln + _name.object_id scan_rate + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code degrees_per_minute + save_ + + +save_diffrn_refln.scan_time_backgd + _definition.id '_diffrn_refln.scan_time_backgd' + loop_ + _alias.definition_id '_diffrn_refln_scan_time_backgd' + _definition.update 2012-11-26 + _description.text +; + Time spent measuring background counts. +; + _description.common 'DiffrnReflnScanTimeBgd' + _name.category_id refln + _name.object_id scan_time_backgd + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code seconds + save_ + + +save_diffrn_refln.scan_width + _definition.id '_diffrn_refln.scan_width' + loop_ + _alias.definition_id '_diffrn_refln_scan_width' + _definition.update 2012-11-26 + _description.text +; + Angular scan width when measuring the peak intensity. +; + _description.common 'DiffrnReflnScanWidth' + _name.category_id refln + _name.object_id scan_width + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_refln.sin_theta_over_lambda + _definition.id '_diffrn_refln.sin_theta_over_lambda' + loop_ + _alias.definition_id '_diffrn_refln_sint/lambda' + '_diffrn_refln_sint_over_lambda' + _definition.update 2012-11-26 + _description.text +; + (sin theta)/lambda value for this reflection. +; + _description.common 'DiffrnReflnSinTheta/Lambda' + _name.category_id refln + _name.object_id sin_theta_over_lambda + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms + save_ + + +save_diffrn_refln.standard_code + _definition.id '_diffrn_refln.standard_code' + loop_ + _alias.definition_id '_diffrn_refln_standard_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying reflections measured repeated as standard intensity. + Must match a _diffrn_standard_refln.code values OR set to '.' if + it was not used as a intensity standard. +; + _description.common 'DiffrnReflnStandCode' + _name.category_id refln + _name.object_id standard_code + _name.linked_item_id '_diffrn_standard_refln.code' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_diffrn_refln.wavelength + _definition.id '_diffrn_refln.wavelength' + loop_ + _alias.definition_id '_diffrn_refln_wavelength' + _definition.update 2012-11-26 + _description.text +; + Mean wavelength of radiation used to measure this intensity. +; + _description.common 'DiffrnReflnWaveLength' + _name.category_id refln + _name.object_id wavelength + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_diffrn_refln.wavelength_id + _definition.id '_diffrn_refln.wavelength_id' + loop_ + _alias.definition_id '_diffrn_refln_wavelength_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying the wavelength in the diffrn_radiation_wavelength list. +; + _description.common 'DiffrnReflnRadId' + _name.category_id refln + _name.object_id wavelength_id + _name.linked_item_id '_diffrn_radiation_wavelength.id' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + save_ #------ close DIFFRN_REFLN category + + +#============================================================================ + + +save_DIFFRN_REFLNS + + _definition.id DIFFRN_REFLNS + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the overall reflection + measurement information. +; + _name.category_id DIFFRN + _name.object_id REFLNS + + +save_diffrn_reflns.av_R_equivalents + _definition.id '_diffrn_reflns.av_R_equivalents' + loop_ + _alias.definition_id '_diffrn_reflns_av_R_equivalents' + _definition.update 2012-11-26 + _description.text +; + The residual [sum av|del(I)| / sum |av(I)|] for symmetry-equivalent + reflections used to calculate the average intensity av(I). The + av|del(I)| term is the average absolute difference between av(I) and + the individual symmetry-equivalent intensities. +; + _description.common 'DiffrnResid(EquivI)' + _name.category_id reflns + _name.object_id av_R_equivalents + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_diffrn_reflns.av_sunetI_over_netI + _definition.id '_diffrn_reflns.av_sunetI_over_netI' + loop_ + _alias.definition_id '_diffrn_reflns_av_sigmaI_over_netI' + '_diffrn_reflns_av_sigmaI/netI' + '_diffrn_reflns_av_unetI/netI' + _definition.update 2012-11-26 + _description.text +; + Measured [sum |su(netI)| / sum |netI|] for all measured reflections. +; + _description.common 'DiffrnRatio(sigI/netI)' + _name.category_id reflns + _name.object_id av_sunetI_over_netI + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_diffrn_reflns.Laue_measured_fraction_full + _definition.id '_diffrn_reflns.Laue_measured_fraction_full' + loop_ + _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_full' + _definition.update 2013-01-20 + _description.text +; + Fraction of Laue_group unique reflections (symmetry-independent in + the Laue group) measured out to the resolution given in + _diffrn_reflns.resolution_full or _diffrn_reflns.theta_full. + The Laue group always contains a centre of symmetry so that + the reflection h,k,l is always equivalent to the reflection + -h,-k,-l even in space groups without a centre of symmetry. + This number should not be less than 0.95, since it represents + the fraction of reflections measured in the part of the + diffraction pattern that is essentially complete. +; + _name.category_id reflns + _name.object_id Laue_measured_fraction_full + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.95:1.0 + save_ + + +save_diffrn_reflns.Laue_measured_fraction_max + _definition.id '_diffrn_reflns.Laue_measured_fraction_max' + loop_ + _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_max' + _definition.update 2013-01-20 + _description.text +; + Fraction of Laue-group unique reflections (symmetry-independent in + the Laue group) measured out to the resolution given in + _diffrn_reflns.resolution_max or _diffrn_reflns.theta_max. + The Laue group always contains a centre of symmetry so that the + reflection h,k,l is always equivalent to the reflection -h,-k,-l + even in space groups without a centre of symmetry. +; + _name.category_id reflns + _name.object_id Laue_measured_fraction_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_diffrn_reflns.point_measured_fraction_full + _definition.id '_diffrn_reflns.point_measured_fraction_full' + loop_ + _alias.definition_id '_diffrn_reflns_point_group_measured_fraction_full' + _definition.update 2013-01-20 + _description.text +; + Fraction of crystal point-group unique reflections (i.e. + symmetry-independent in the crystal point group) measured + out to the resolution given in _diffrn_reflns.resolution_full + or _diffrn_reflns.theta_full. For space groups that do not + contain a centre of symmetry the reflections h,k,l and + -h,-k,-l are independent. This number should not be less + than 0.95, since it represents the fraction of reflections + measured in the part of the diffraction pattern that is + essentially complete. +; + _name.category_id reflns + _name.object_id point_measured_fraction_full + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.95:1.0 + save_ + + +save_diffrn_reflns.point_measured_fraction_max + _definition.id '_diffrn_reflns.point_measured_fraction_max' + loop_ + _alias.definition_id '_diffrn_reflns_point_group_measured_fraction_max' + _definition.update 2013-01-20 + _description.text +; + Fraction of crystal point-group unique reflections (i.e. + symmetry-independent in the crystal point group) measured + out to the resolution given in _diffrn_reflns.resolution_max + or _diffrn_reflns.theta_max. For space groups that do not + contain a centre of symmetry the reflections h,k,l and + -h,-k,-l are independent. +; + _name.category_id reflns + _name.object_id point_measured_fraction_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.95:1.0 + save_ + + +save_diffrn_reflns.limit_max + _definition.id '_diffrn_reflns.limit_max' + _definition.update 2013-01-15 + _description.text +; + Maximum Miller indices of measured diffraction reflections. +; + _name.category_id reflns + _name.object_id limit_max + _type.purpose Quantity + _type.source Assigned + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as diffrn_reflns + + _diffrn_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] +; + save_ + + +save_diffrn_reflns.limit_min + _definition.id '_diffrn_reflns.limit_min' + _definition.update 2013-01-15 + _description.text +; + Minimum Miller indices of meas.ued diffraction reflections. +; + _name.category_id reflns + _name.object_id limit_min + _type.purpose Quantity + _type.source Assigned + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as diffrn_reflns + + _diffrn_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] +; + save_ + + +save_diffrn_reflns.limit_h_max + _definition.id '_diffrn_reflns.limit_h_max' + loop_ + _alias.definition_id '_diffrn_reflns_limit_h_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_h_max + save_ + + +save_diffrn_reflns.limit_h_min + _definition.id '_diffrn_reflns.limit_h_min' + loop_ + _alias.definition_id '_diffrn_reflns_limit_h_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_h_min + save_ + + +save_diffrn_reflns.limit_k_max + _definition.id '_diffrn_reflns.limit_k_max' + loop_ + _alias.definition_id '_diffrn_reflns_limit_k_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_k_max + save_ + + +save_diffrn_reflns.limit_k_min + _definition.id '_diffrn_reflns.limit_k_min' + loop_ + _alias.definition_id '_diffrn_reflns_limit_k_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_k_min + save_ + + +save_diffrn_reflns.limit_l_max + _definition.id '_diffrn_reflns.limit_l_max' + loop_ + _alias.definition_id '_diffrn_reflns_limit_l_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_l_max + save_ + + +save_diffrn_reflns.limit_l_min + _definition.id '_diffrn_reflns.limit_l_min' + loop_ + _alias.definition_id '_diffrn_reflns_limit_l_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_l_min + save_ + + +save_diffrn_reflns.number + _definition.id '_diffrn_reflns.number' + loop_ + _alias.definition_id '_diffrn_reflns_number' + _definition.update 2012-11-26 + _description.text +; + Total number of measured intensities, excluding reflections that are + classed as systematically absent arising from translational symmetry + in the crystal unit cell. +; + _description.common 'DiffrnReflnsCount' + _name.category_id reflns + _name.object_id number + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_diffrn_reflns.reduction_process + _definition.id '_diffrn_reflns.reduction_process' + loop_ + _alias.definition_id '_diffrn_reflns_reduction_process' + _definition.update 2012-11-26 + _description.text +; + How intensities were reduced to structure-factor magnitudes. +; + _description.common 'DiffrnReflnsReductionDetails' + _name.category_id reflns + _name.object_id reduction_process + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'data averaged using Fisher test' + save_ + + +save_diffrn_reflns.theta_full + _definition.id '_diffrn_reflns.theta_full' + loop_ + _alias.definition_id '_diffrn_reflns_theta_full' + _definition.update 2012-11-26 + _description.text +; + Theta angle at which the count of measured reflections is almost + complete. The fraction of unique reflections measured out to + this angle is given by _diffrn.measured_fraction_theta_full. +; + _description.common 'DiffrnThetaFull' + _name.category_id reflns + _name.object_id theta_full + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_reflns.theta_max + _definition.id '_diffrn_reflns.theta_max' + loop_ + _alias.definition_id '_diffrn_reflns_theta_max' + _definition.update 2012-11-26 + _description.text +; + Maximum theta angle of the measured reflections. +; + _description.common 'DiffrnThetaMax' + _name.category_id reflns + _name.object_id theta_max + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_reflns.theta_min + _definition.id '_diffrn_reflns.theta_min' + loop_ + _alias.definition_id '_diffrn_reflns_theta_min' + _definition.update 2012-11-26 + _description.text +; + Minimum theta angle of the measured reflections. +; + _description.common 'DiffrnThetaMin' + _name.category_id reflns + _name.object_id theta_min + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_diffrn_reflns.resolution_full + _definition.id '_diffrn_reflns.resolution_full' + loop_ + _alias.definition_id '_diffrn_reflns_resolution_full' + _definition.update 2012-11-26 + _description.text +; + The resolution at which the measured reflection count is close + to complete. The fraction of unique reflections measured out + to this angle is given by _diffrn.measured_fraction_theta_full. +; + _name.category_id reflns + _name.object_id resolution_full + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code 'reciprocal_angstroms' + save_ + + +save_diffrn_reflns.resolution_max + _definition.id '_diffrn_reflns.resolution_max' + loop_ + _alias.definition_id '_diffrn_reflns_resolution_max' + _definition.update 2012-11-26 + _description.text +; + Maximum resolution of the measured diffraction pattern. + The fraction of unique reflections measured out to this angle + is given by _diffrn.measured_fraction_theta_max. +; + _name.category_id reflns + _name.object_id resolution_full + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code 'reciprocal_angstroms' + save_ + + +#---------------------------------------------------------------------------- + +save_DIFFRN_REFLNS_TRANSF_MATRIX + + _definition.id DIFFRN_REFLNS_TRANSF_MATRIX + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the elements of the matrix + used to transform the reflection indices _diffrn_refln.hkl + into _refln.hkl. + |11 12 13| + (h k l) diffraction |21 22 23| = (h' k' l') + |31 32 33| +; + _name.category_id DIFFRN_REFLNS + _name.object_id TRANSF_MATRIX + + +save_diffrn_reflns_transf_matrix.TIJ + _definition.id '_diffrn_reflns_transf_matrix.TIJ' + _definition.update 2012-11-26 + _description.text +; + Elements of the matrix used to transform the diffraction reflection + indices _diffrn_refln.hkl into the _refln.hkl indices. + |11 12 13| + (h k l) diffraction |21 22 23| = (h' k' l') + |31 32 33| +; + _description.common 'DiffrnReflnsTransformMatrix' + _name.category_id transf_matrix + _name.object_id TIJ + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as diffrn_reflns_transf_matrix + + _diffrn_reflns_transf_matrix.TIJ = [[t.11, t.12, t.13], + [t.21, t.22, t.23], + [t.31, t.32, t.33]] +; + save_ + + +save_diffrn_reflns_transf_matrix.11 + _definition.id '_diffrn_reflns_transf_matrix.11' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_11' + '_diffrn_reflns.transf_matrix[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 11 + save_ + + +save_diffrn_reflns_transf_matrix.12 + _definition.id '_diffrn_reflns_transf_matrix.12' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_12' + '_diffrn_reflns.transf_matrix[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 12 + save_ + + +save_diffrn_reflns_transf_matrix.13 + _definition.id '_diffrn_reflns_transf_matrix.13' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_13' + '_diffrn_reflns.transf_matrix[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 13 + save_ + + +save_diffrn_reflns_transf_matrix.21 + _definition.id '_diffrn_reflns_transf_matrix.21' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_21' + '_diffrn_reflns.transf_matrix[2][1]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 21 + save_ + + +save_diffrn_reflns_transf_matrix.22 + _definition.id '_diffrn_reflns_transf_matrix.22' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_22' + '_diffrn_reflns.transf_matrix[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 22 + save_ + + +save_diffrn_reflns_transf_matrix.23 + _definition.id '_diffrn_reflns_transf_matrix.23' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_23' + '_diffrn_reflns.transf_matrix[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 23 + save_ + + +save_diffrn_reflns_transf_matrix.31 + _definition.id '_diffrn_reflns_transf_matrix.31' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_31' + '_diffrn_reflns.transf_matrix[3][1]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 31 + save_ + + +save_diffrn_reflns_transf_matrix.32 + _definition.id '_diffrn_reflns_transf_matrix.32' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_32' + '_diffrn_reflns.transf_matrix[3][2]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 32 + save_ + + +save_diffrn_reflns_transf_matrix.33 + _definition.id '_diffrn_reflns_transf_matrix.33' + loop_ + _alias.definition_id '_diffrn_reflns_transf_matrix_33' + '_diffrn_reflns.transf_matrix[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'transf_matrix'}] + _name.category_id transf_matrix + _name.object_id 33 + save_ + + save_ #------ close DIFFRN_REFLNS_TRANS_MATRIX category + + +#============================================================================ + + +save_DIFFRN_REFLNS_CLASS + + _definition.id DIFFRN_REFLNS_CLASS + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify different classes of + reflections in the raw measured diffraction data. + +; + _name.category_id DIFFRN_REFLNS + _name.object_id CLASS + _category.key_id '_diffrn_reflns_class.key' + + +save_diffrn_reflns_class.key + _definition.id '_diffrn_reflns_class.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_REFLNS_CLASS items + in a looped list. +; + _description.common 'Key to class of measured refns' + _name.category_id class + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_reflns_class.code) +; + Evaluation +; _diffrn_reflns_class.key = _diffrn_reflns_class.code +; + save_ + + +save_diffrn_reflns_class.av_R_eq + _definition.id '_diffrn_reflns_class.av_R_eq' + loop_ + _alias.definition_id '_diffrn_reflns_class_av_R_eq' + _definition.update 2012-11-26 + _description.text +; + Residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent + reflections used to calculate the average intensity av(I). + The av|del(I)| term is the average absolute difference + between av(I) and the individual intensities. +; + _description.common 'DiffrnShellResid(I)' + _name.category_id class + _name.object_id av_R_eq + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_diffrn_reflns_class.av_suI_over_I + _definition.id '_diffrn_reflns_class.av_suI_over_I' + loop_ + _alias.definition_id '_diffrn_reflns_class_av_uI_over_I' + '_diffrn_reflns_class_av_uI/I' + '_diffrn_reflns_class_av_sgI/I' + _definition.update 2012-11-26 + _description.text +; + Measured [sum|su(net I)|/sum|net I|] in a reflection class. +; + _description.common 'DiffrnShellRatio(suI/netI)' + _name.category_id class + _name.object_id av_suI_over_I + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_diffrn_reflns_class.code + _definition.id '_diffrn_reflns_class.code' + loop_ + _alias.definition_id '_diffrn_reflns_class_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying a reflection class. +; + _description.common 'DiffrnShellCode' + _name.category_id class + _name.object_id code + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case "m2" + save_ + + +save_diffrn_reflns_class.description + _definition.id '_diffrn_reflns_class.description' + loop_ + _alias.definition_id '_diffrn_reflns_class_description' + _definition.update 2012-11-26 + _description.text +; + Description of a reflection class. +; + _description.common 'DiffrnShellDetails' + _name.category_id class + _name.object_id description + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'm=1 first order satellites' + save_ + + +save_diffrn_reflns_class.d_res_high + _definition.id '_diffrn_reflns_class.d_res_high' + loop_ + _alias.definition_id '_diffrn_reflns_class_d_res_high' + _definition.update 2012-11-26 + _description.text +; + Highest resolution in reflection class i.e. smallest d value in class. +; + _description.common 'DiffrnShellResolHi' + _name.category_id class + _name.object_id d_res_high + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_diffrn_reflns_class.d_res_low + _definition.id '_diffrn_reflns_class.d_res_low' + loop_ + _alias.definition_id '_diffrn_reflns_class_d_res_low' + _definition.update 2012-11-26 + _description.text +; + Lowest resolution in reflection class i.e. largest d value in class. +; + _description.common 'DiffrnShellResolLo' + _name.category_id class + _name.object_id d_res_low + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_diffrn_reflns_class.number + _definition.id '_diffrn_reflns_class.number' + loop_ + _alias.definition_id '_diffrn_reflns_class_number' + _definition.update 2012-11-26 + _description.text +; + Number of measured intensities for a reflection class, excluding + the systematic absences arising from centring translations. +; + _description.common 'DiffrnShellNumber' + _name.category_id class + _name.object_id number + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + save_ #------ close DIFFRN_REFLNS_CLASS category + + save_ #------ close DIFFRN_REFLNS category + +#---------------------------------------------------------------------------- + + +save_DIFFRN_SCALE_GROUP + + _definition.id DIFFRN_SCALE_GROUP + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the groups of reflections in + the raw measured diffraction data with different relative scales. +; + _description.common 'ScaleGroupList' + _name.category_id DIFFRN + _name.object_id SCALE_GROUP + _category.key_id '_diffrn_scale_group.key' + + +save_diffrn_scale_group.key + _definition.id '_diffrn_scale_group.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_SCALE_GROUP items + in a looped list. +; + _description.common 'Key to intensity scaling groups' + _name.category_id scale_group + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_scale_group.code) +; + Evaluation +; _diffrn_scale_group.key = _diffrn_scale_group.code +; + save_ + + +save_diffrn_scale_group.code + _definition.id '_diffrn_scale_group.code' + loop_ + _alias.definition_id '_diffrn_scale_group_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying a specific scale group of reflections (e.g. for + multi-film or multi-crystal data). The code must match a + _diffrn_refln.scale_group_code in the diffrn_refln list. + +; + _description.common 'ScaleGroupCode' + _name.category_id scale_group + _name.object_id code + _name.linked_item_id '_diffrn_refln.scale_group_code' + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case 1 2 3 s1 A B c1 c2 c3 + save_ + + +save_diffrn_scale_group.I_net + _definition.id '_diffrn_scale_group.I_net' + loop_ + _alias.definition_id '_diffrn_scale_group_I_net' + _definition.update 2012-11-26 + _description.text +; + Scale for a specific measurement group of eflections. Is multiplied + with the net intensity to place all intensities on a common scale. +; + _description.common 'ScaleGroupInet' + _name.category_id scale_group + _name.object_id I_net + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + save_ #------ close DIFFRN_SCALE_GROUP category + +#---------------------------------------------------------------------------- + +save_DIFFRN_SOURCE + + _definition.id DIFFRN_SOURCE + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify information about the + radiation source. +; + _name.category_id DIFFRN + _name.object_id SOURCE + + +save_diffrn_source.device + _definition.id '_diffrn_source.device' + loop_ + _alias.definition_id '_diffrn_source' + '_diffrn_radiation_source' + _definition.update 2012-11-26 + _description.text +; + Enumerated code for the device providing the source of radiation. +; + _description.common 'RadSourceDevice' + _name.category_id source + _name.object_id device + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _description_example.case 'sealed X-ray tube' + 'nuclear reactor' + 'spallation source' + 'electron microscope' + 'rotating-anode X-ray tube' + 'synchrotron' + save_ + + +save_diffrn_source.current + _definition.id '_diffrn_source.current' + loop_ + _alias.definition_id '_diffrn_source_current' + _definition.update 2012-11-26 + _description.text +; + Generator current at which the radiation source device was operated. +; + _description.common 'RadSourceCurrent' + _name.category_id source + _name.object_id current + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code milliamperes + save_ + + +save_diffrn_source.details + _definition.id '_diffrn_source.details' + loop_ + _alias.definition_id '_diffrn_source_details' + _definition.update 2012-11-26 + _description.text +; + General description of the radiation source device. +; + _description.common 'RadSourceDetails' + _name.category_id source + _name.object_id details + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_diffrn_source.power + _definition.id '_diffrn_source.power' + loop_ + _alias.definition_id '_diffrn_source_power' + _definition.update 2012-11-26 + _description.text +; Generator power at which the radiation source device was operated. +; + _description.common 'RadSourcePower' + _name.category_id source + _name.object_id power + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kilowatts + save_ + + +save_diffrn_source.size + _definition.id '_diffrn_source.size' + loop_ + _alias.definition_id '_diffrn_source_size' + _definition.update 2012-11-26 + _description.text +; + Description of the collimated source beam as viewed from the sample. +; + _description.common 'RadSourceSize' + _name.category_id source + _name.object_id size + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case '8mm x 0.4 mm fine-focus' + 'broad focus' + save_ + + +save_diffrn_source.take-off_angle + _definition.id '_diffrn_source.take-off_angle' + loop_ + _alias.definition_id '_diffrn_source_take-off_angle' + _definition.update 2012-11-26 + _description.text +; + The complement of the angle in degrees between the normal + to the surface of the X-ray tube target and the primary + X-ray beam for beams generated by traditional X-ray tubes. +; + _name.category_id source + _name.object_id take_off_angle + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0:90 + _units.code degrees + save_ + + +save_diffrn_source.target + _definition.id '_diffrn_source.target' + loop_ + _alias.definition_id '_diffrn_source_target' + _definition.update 2012-11-26 + _description.text +; + Chemical element symbol for the radiation source target (usually + the anode). This can be used also for spallation sources. +; + _description.common 'RadTargetElement' + _name.category_id source + _name.object_id target + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'element_symbol'}] + _enumeration.default Cu + save_ + + +save_diffrn_source.make + _definition.id '_diffrn_source.make' + loop_ + _alias.definition_id '_diffrn_source_make' + '_diffrn_source.type' + '_diffrn_source_type' + _definition.update 2012-11-26 + _description.text +; + Description of the make, model or name of the source device. +; + _description.common 'RadDeviceMake' + _name.category_id source + _name.object_id make + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'NSLS beamline X8C' 'Rigaku RU2012-05-07 ' + save_ + + +save_diffrn_source.voltage + _definition.id '_diffrn_source.voltage' + loop_ + _alias.definition_id '_diffrn_source_voltage' + _definition.update 2012-11-26 + _description.text +; + Generator voltage at which the radiation source device was operated. +; + _description.common 'RadSourceVoltage' + _name.category_id source + _name.object_id voltage + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kilovolts + save_ + + save_ #------ close DIFFRN_SOURCE category + + +#---------------------------------------------------------------------------- + + +save_DIFFRN_STANDARD + _definition.id DIFFRN_STANDARD + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify information about the + standard reflections used in the diffraction measurement process. +; + _name.category_id DIFFRN + _name.object_id STANDARD + + +save_diffrn_standard.decay_percent + _definition.id '_diffrn_standard.decay_percent' + loop_ + _alias.definition_id '_diffrn_standards_decay_%' + '_diffrn_standards.decay_%' + '_diffrn_standards_decay_percent' + _definition.update 2013-01-23 + _description.text +; + The percentage decrease in the mean of the intensities for the + standard reflections at the start to the finish of the measurement + process. This value affords a measure of the overall decay in + crystal quality during measurement. Negative values only occur in + exceptional instances where the final intensities are greater than + the initial ones. If no measurable decay has occurred, the + standard uncertainty should be quoted to indicate the maximum + possible value the decay might have. A range of 3 standard + uncertainties is considered possible. Thus 0.0(1) would indicate + a decay of less than 0.3% or an enhancement of less than 0.3%. +; + _description.common 'DiffrnStandDecay%' + _name.category_id standard + _name.object_id decay_percent + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range :100 + loop_ _description_example.case + _description_example.detail + 0.5(1) 'represents a decay between 0.2% and 0.8%' + -1(1) 'change in standards between 2% decay and 4% rise' + 0.0(2) 'change in standards between 0.6% decay and 0.6% rise. + save_ + + +save_diffrn_standard.interval_count + _definition.id '_diffrn_standard.interval_count' + loop_ + _alias.definition_id '_diffrn_standards_interval_count%' + '_diffrn_standards_interval_count' + _definition.update 2012-11-26 + _description.text +; + Reflection count between the standard reflection measurements. +; + _description.common 'DiffrnStandIntCount' + _name.category_id standard + _name.object_id interval_count + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_diffrn_standard.interval_time + _definition.id '_diffrn_standard.interval_time' + loop_ + _alias.definition_id '_diffrn_standards_interval_time' + _definition.update 2012-11-26 + _description.text +; + Time between the standard reflection measurements. +; + _description.common 'DiffrnStandIntTime' + _name.category_id standard + _name.object_id interval_time + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code minutes + save_ + + +save_diffrn_standard.number + _definition.id '_diffrn_standard.number' + loop_ + _alias.definition_id '_diffrn_standards_number' + _definition.update 2012-11-26 + _description.text +; + Number of unique standard reflections used in measurements. +; + _description.common 'DiffrnStandCount' + _name.category_id standard + _name.object_id number + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_diffrn_standard.scale_su_average + _definition.id '_diffrn_standard.scale_su_average' + loop_ + _alias.definition_id '_diffrn_standards_scale_sigma' + '_diffrn_standards.scale_sigma' + '_diffrn_standards_scale_u' + _definition.update 2013-01-20 + _description.text +; + The average standard uncertainty of the individual standard scales + applied to the intensity data. +; + _description.common 'DiffrnStandScaleSu' + _name.category_id standard + _name.object_id scale_su_average + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +#---------------------------------------------------------------------------- + +save_DIFFRN_STANDARD_REFLN + + _definition.id DIFFRN_STANDARD_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the "standard" reflections + measured repeatedly to monitor variations in intensity due to source + flux, environment conditions or crystal quality. +; + _description.common 'StandReflnList' + _name.category_id DIFFRN_STANDARD + _name.object_id REFLN + _category.key_id '_diffrn_standard_refln.key' + + +save_diffrn_standard_refln.key + _definition.id '_diffrn_standard_refln.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of DIFFRN_STANDARD_REFLN items + in a looped list. +; + _description.common 'Key to standard reflections list' + _name.category_id refln + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(diffrn_standard_refln.code) +; + Evaluation +; _diffrn_standard_refln.key = _diffrn_standard_refln.code +; + save_ + + +save_diffrn_standard_refln.code + _definition.id '_diffrn_standard_refln.code' + loop_ + _alias.definition_id '_diffrn_standard_refln_code' + '_diffrn_standard_refln.diffrn_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying a standard reflection used to monitor source + intensity variations or crystal degradation or movement during + data collection. +; + _description.common 'StandReflnCode' + _name.category_id refln + _name.object_id code + _name.linked_item_id '_diffrn_refln.standard_code' + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case "s1" + save_ + + +save_diffrn_standard_refln.hkl + _definition.id '_diffrn_standard_refln.hkl' + _definition.update 2012-11-26 + _description.text +; + Miller indices of a standard reflection. +; + _description.common 'StandReflnHkl' + _name.category_id refln + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With d as diffrn_standard_refln + + _diffrn_standard_refln.hkl = [d.index_h, d.index_h, d.index_l] +; + save_ + + +save_diffrn_standard_refln.index_h + _definition.id '_diffrn_standard_refln.index_h' + loop_ + _alias.definition_id '_diffrn_standard_refln_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_h + save_ + + +save_diffrn_standard_refln.index_k + _definition.id '_diffrn_standard_refln.index_k' + loop_ + _alias.definition_id '_diffrn_standard_refln_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_k + save_ + + +save_diffrn_standard_refln.index_l + _definition.id '_diffrn_standard_refln.index_l' + loop_ + _alias.definition_id '_diffrn_standard_refln_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_l + save_ + + save_ #------ close DIFFRN_STANDARD_REFLN category + + save_ #------ close DIFFRN_STANDARD category + + save_ #------ close DIFFRN category + +#============================================================================ + +save_REFLN + + _definition.id REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items used to describe the reflection data + used in the refinement of a crystallographic structure model. +; + _description.common 'ReflnList' + _name.category_id DIFFRACTION + _name.object_id REFLN + _category.key_id '_refln.key' + + +save_refln.key + _definition.id '_refln.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of REFLN items + in a looped list. +; + _description.common 'Key to refinement reflection list' + _name.category_id refln + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(_refln.hkl) +; + Evaluation +; _refln.key = _refln.hkl +; + save_ + + +save_refln.A_calc + _definition.id '_refln.A_calc' + loop_ + _alias.definition_id '_refln_A_calc' + _definition.update 2012-11-26 + _description.text +; + The calculated real structure-factor component A =|Fcalc|cos(phase) +; + _description.common 'ReflnCalcA' + _name.category_id refln + _name.object_id A_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + _refln.A_calc = Real ( _refln.F_complex ) +; + save_ + + +save_refln.A_meas + _definition.id '_refln.A_meas' + loop_ + _alias.definition_id '_refln_A_meas' + _definition.update 2012-11-26 + _description.text +; + The measured real structure-factor component A =|Fmeas|cos(phase) +; + _description.common 'ReflnMeasA' + _name.category_id refln + _name.object_id A_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_refln.B_calc + _definition.id '_refln.B_calc' + loop_ + _alias.definition_id '_refln_B_calc' + _definition.update 2012-11-26 + _description.text +; + The calculated imaginary structure-factor component B =|Fcalc|sin(phase) +; + _description.common 'ReflnCalcB' + _name.category_id refln + _name.object_id B_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + _refln.B_calc = Imag ( _refln.F_complex ) +; + save_ + + +save_refln.B_meas + _definition.id '_refln.B_meas' + loop_ + _alias.definition_id '_refln_B_meas' + _definition.update 2012-11-26 + _description.text +; + The measured imaginary structure-factor component B =|Fmeas|sin(phase) +; + _description.common 'ReflnMeasB' + _name.category_id refln + _name.object_id B_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_refln.class_code + _definition.id '_refln.class_code' + loop_ + _alias.definition_id '_refln_class_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying the class to which this reflection has been + assigned. This code must match a value of _reflns_class.code. + Reflections may be grouped into classes for a variety of + purposes. For example, for modulated structures each reflection + class may be defined by the number m=sum|m~i~|, where the m~i~ + are the integer coefficients that, in addition to h,k,l, index + the corresponding diffraction vector in the basis defined + for the reciprocal lattice. +; + _description.common 'ReflnClassCode' + _name.category_id refln + _name.object_id class_code + _name.linked_item_id '_reflns_class.code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_refln.crystal_id + _definition.id '_refln.crystal_id' + loop_ + _alias.definition_id '_refln_crystal_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying each crystal if multiple crystals are used. Is + used to link with crystals identified by _exptl_crystal.id. +; + _description.common 'ReflnCrystalId' + _name.category_id refln + _name.object_id crystal_id + _name.linked_item_id '_exptl_crystal.id' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_refln.d_spacing + _definition.id '_refln.d_spacing' + loop_ + _alias.definition_id '_refln_d_spacing' + _definition.update 2012-11-26 + _description.text +; + The distance in angstroms between lattice planes in the crystal + with the indices _refln.hkl for this reflection. +; + _description.common 'ReflnDspacing' + _name.category_id refln + _name.object_id d_spacing + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + _refln.d_spacing = 2. / _refln.sin_theta_over_lambda +; + save_ + + +save_refln.F_calc + _definition.id '_refln.F_calc' + loop_ + _alias.definition_id '_refln_F_calc' + _definition.update 2013-02-21 + _description.text +; + The structure factor amplitude for the reflection calculated from + the atom site data. +; + _description.common 'ReflnCalcF' + _name.category_id refln + _name.object_id F_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + Evaluation +; + _refln.F_calc = Magn ( _refln.F_complex ) +; + save_ + + +save_refln.F_complex + _definition.id '_refln.F_complex' + loop_ + _alias.definition_id '_refln_F_complex' + _definition.update 2013-02-18 + _description.text +; + The structure factor vector for the reflection calculated from + the atom site data. +; + _description.common 'ReflnComplexF' + _name.category_id refln + _name.object_id F_complex + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Complex + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + Evaluation +; + With r as refln + + fc = Complex (0., 0.) + h = r.hkl + + Loop a as atom_site { + + f = ( r.form_factor_table [a.type_symbol] * + a.site_symmetry_multiplicity * a.occupancy ) + + Loop s as symmetry_equiv { + + t = Exp(-h * s.R * a.matrix_beta * s.RT * h) + + fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T))) + } } + _refln.F_complex = fc / _symmetry.multiplicity +; + save_ + + +save_refln.F_meas + _definition.id '_refln.F_meas' + loop_ + _alias.definition_id '_refln_F_meas' + _definition.update 2013-02-21 + _description.text +; + The structure factor amplitude for the reflection derived from the + measured intensities. +; + _description.common 'ReflnMeasF' + _name.category_id refln + _name.object_id F_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + Evaluation +; + _refln.F_meas = Sqrt ( _refln.F_squared_meas ) +; + save_ + + +save_refln.F_meas_su + _definition.id '_refln.F_meas_su' + loop_ + _alias.definition_id '_refln_F_sigma' + '_refln.F_meas_sigma' + '_refln_F_meas_su' + _definition.update 2013-02-21 + _description.text +; + The standard uncertainty of the measured structure factor amplitude. +; + _description.common 'ReflnMeasFsu' + _name.category_id refln + _name.object_id F_meas_su + _name.linked_item_id '_refln.F_meas' + _type.purpose SU + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + Evaluation +; + _refln.F_meas_su = _refln.F_squared_meas_su / 2 +; + save_ + + +save_refln.F_squared_calc + _definition.id '_refln.F_squared_calc' + loop_ + _alias.definition_id '_refln_F_squared_calc' + _definition.update 2012-11-26 + _description.text +; + The structure factor amplitude squared for the reflection calculated from + the atom site data. +; + _description.common 'ReflnCalcFsqd' + _name.category_id refln + _name.object_id F_squared_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometres_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts_squared" + Else _units.code = "electrons_squared" + +; + Evaluation +; + _refln.F_squared_calc = _refln.F_calc **2 +; + save_ + + +save_refln.F_squared_meas + _definition.id '_refln.F_squared_meas' + loop_ + _alias.definition_id '_refln_F_squared_meas' + _definition.update 2013-02-21 + _description.text +; + The structure factor amplitude for the reflection derived from the + measured intensities. +; + _description.common 'ReflnMeasFsqd' + _name.category_id refln + _name.object_id F_squared_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometres_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts_squared" + Else _units.code = "electrons_squared" + +; + Evaluation +; + _refln.F_squared_meas = _refln.F_meas **2 +; + save_ + + +save_refln.F_squared_meas_su + _definition.id '_refln.F_squared_meas_su' + loop_ + _alias.definition_id '_refln_F_squared_sigma' + '_refln.F_squared_sigma' + '_refln_F_squared_meas_su' + _definition.update 2012-11-26 + _description.text +; + The standard uncertainty of the measured structure factor squared. +; + _name.category_id refln + _name.object_id F_squared_meas_su + _name.linked_item_id '_refln.F_squared_meas' + _type.purpose SU + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometres_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts_squared" + Else _units.code = "electrons_squared" + +; + Evaluation +; + _refln.F_squared_meas_su = 2. * _refln.F_meas_su +; + save_ + + +save_refln.form_factor_table + _definition.id '_refln.form_factor_table' + _definition.update 2012-11-26 + _description.text +; + Atomic scattering factor table for the scattering angle + of this diffraction vector and atom types in structure. +; + _description.common 'ReflnFormFactorTable' + _name.category_id refln + _name.object_id form_factor_table + _type.purpose Quantity + _type.source Derived + _type.container Table + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + With r as refln + + table = Table () + s = r.sin_theta_over_lambda + + Loop t as atom_type { + + If (_diffrn_radiation.probe == 'neutron') { + + f = t.length_neutron + + } Else If (s < 2.0 ) { + + c = t.Cromer_Mann_coeffs + + f = (c[0] + c[1] * Exp (-c[2] * s*s) + + c[3] * Exp (-c[4] * s*s) + + c[5] * Exp (-c[6] * s*s) + + c[7] * Exp (-c[8] * s*s)) + } Else { + + c = t.hi_ang_Fox_coeffs + + f = Exp ( c[0] + c[1]*s + c[2]*s*s + c[3]*s*s*s ) + } + table [ t.symbol ] = f + } + _refln.form_factor_table = table +; + save_ + + +save_refln.include_status + _definition.id '_refln.include_status' + loop_ + _alias.definition_id '_refln_include_status' + '_refln_observed_status' + _definition.update 2012-11-26 + loop_ + _alias.definition_id '_refln.observed_status' + _description.text +; + Code indicating how the reflection was included in the refinement + and R-factor calculations. +; + _description.common 'ReflnRefineInclusion' + _name.category_id refln + _name.object_id include_status + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + o ' ob : within _reflns.threshold_expression; within d-res limits' + < ' lt : without _reflns.threshold_expression; within d-res limits' + - ' sa : systematically absent reflection due to symmetry' + x ' du : deemed unreliable measurement -- not used' + h ' hd : above _refine_ls.d_res_high' + l ' ld : below _refine_ls.d_res_low' + _enumeration.default o + save_ + + +save_refln.hkl + _definition.id '_refln.hkl' + _definition.update 2012-11-26 + _description.text +; + The Miller indices as a reciprocal space vector. +; + _description.common 'ReflnHkl' + _name.category_id refln + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With r as refln + + _refln.hkl = [r.index_h, r.index_k, r.index_l] +; + save_ + + +save_refln.index_h + _definition.id '_refln.index_h' + loop_ + _alias.definition_id '_refln_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_h + save_ + + +save_refln.index_k + _definition.id '_refln.index_k' + loop_ + _alias.definition_id '_refln_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_k + save_ + + +save_refln.index_l + _definition.id '_refln.index_l' + loop_ + _alias.definition_id '_refln_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_l + save_ + + +save_refln.intensity_calc + _definition.id '_refln.intensity_calc' + loop_ + _alias.definition_id '_refln_intensity_calc' + _definition.update 2012-11-26 + _description.text +; + The intensity of the reflection calculated from the atom site data. +; + _description.common 'ReflnCalcI' + _name.category_id refln + _name.object_id intensity_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + _refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor +; + save_ + + +save_refln.intensity_meas + _definition.id '_refln.intensity_meas' + loop_ + _alias.definition_id '_refln_intensity_meas' + _definition.update 2012-11-26 + _description.text +; + The intensity of the reflection derived from the diffraction measurements. +; + _description.common 'ReflnMeasI' + _name.category_id refln + _name.object_id intensity_meas + _type.purpose Measurand + _type.source Observed + _type.container Single + _type.contents Real + save_ + + +save_refln.intensity_meas_su + _definition.id '_refln.intensity_meas_su' + loop_ + _alias.definition_id '_refln_intensity_meas_su' + '_refln_intensity_sigma' + _definition.update 2013-01-23 + _description.text +; + standard uncertainty of the measured intensity. +; + _name.category_id refln + _name.object_id intensity_meas_su + _name.linked_item_id '_refln.intensity_meas' + _type.purpose SU + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_refln.Lp_factor + _definition.id '_refln.Lp_factor' + loop_ + _alias.definition_id '_refln_Lp_factor' + _definition.update 2012-11-26 + _description.text +; + The Lorentz-polarization factor appropriate for the instrument + used to measure the diffraction intensity. This is applied to + convert the net intensity into the measured F squared. +; + _description.common 'ReflnLpFactor' + _name.category_id refln + _name.object_id Lp_factor + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + save_ + + +save_refln.mean_path_length_tbar + _definition.id '_refln.mean_path_length_tbar' + loop_ + _alias.definition_id '_refln_mean_path_length_tbar' + _definition.update 2012-11-26 + _description.text +; + Mean path length through the crystal for this diffraction vector. +; + _description.common 'ReflnMeanPathLength' + _name.category_id refln + _name.object_id mean_path_length_tbar + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code millimetres + save_ + + +save_refln.phase_calc + _definition.id '_refln.phase_calc' + loop_ + _alias.definition_id '_refln_phase_calc' + _definition.update 2012-11-26 + _description.text +; + The phase of the calculated structure-factor. +; + _description.common 'ReflnCalcPhase' + _name.category_id refln + _name.object_id phase_calc + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + _refln.phase_calc = Atan2d ( _refln.B_calc, _refln.A_calc ) +; + save_ + + +save_refln.phase_meas + _definition.id '_refln.phase_meas' + loop_ + _alias.definition_id '_refln_phase_meas' + _definition.update 2012-11-26 + _description.text +; + The phase of the measured structure-factor. This may be derived from + the atom site data if available or from the phase solution process + prior to determination of the structure. +; + _description.common 'ReflnMeasPhase' + _name.category_id refln + _name.object_id phase_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + save_ + + +save_refln.refinement_status + _definition.id '_refln.refinement_status' + loop_ + _alias.definition_id '_refln_refinement_status' + _definition.update 2012-11-26 + _description.text +; + Status code of reflection in the structure refinement process. +; + _description.common 'ReflnRefineStatus' + _name.category_id refln + _name.object_id refinement_status + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail incl 'included in ls process' + excl 'excluded from ls process' + extn 'excluded due to extinction' + _enumeration.default incl + save_ + + +save_refln.scale_group_code + _definition.id '_refln.scale_group_code' + loop_ + _alias.definition_id '_refln_scale_group_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying the scale (if there is more than one scale) used + convert the measured structure factor to a common absolute value. +; + _description.common 'ReflnScaleCode' + _name.category_id refln + _name.object_id scale_group_code + _name.linked_item_id '_reflns_scale.group_code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_refln.sin_theta_over_lambda + _definition.id '_refln.sin_theta_over_lambda' + loop_ + _alias.definition_id '_refln_sint/lambda' + '_refln_sin_theta_over_lambda' + '_refln.sint_over_lambda' + _definition.update 2012-11-26 + _description.text +; + The (sin theta)/lambda value for this reflection. +; + _description.common 'ReflnSinTheta/Lambda' + _name.category_id refln + _name.object_id sin_theta_over_lambda + _type.purpose Quanity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + With r as refln + h = r.hkl + G = _cell_reciprocal.metric_tensor + + r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2. +; + save_ + + +save_refln.symmetry_epsilon + _definition.id '_refln.symmetry_epsilon' + loop_ + _alias.definition_id '_refln_symmetry_epsilon' + _definition.update 2012-11-26 + _description.text +; + The symmetry reinforcement factor corresponding to the number of + times the reflection indices are generated identically from the + space-group symmetry operations. +; + _description.common 'ReflnSymmetryEpsilon' + _name.category_id refln + _name.object_id symmetry_epsilon + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + _enumeration.range 1:48 + save_ + + +save_refln.symmetry_multiplicity + _definition.id '_refln.symmetry_multiplicity' + loop_ + _alias.definition_id '_refln_symmetry_multiplicity' + _definition.update 2012-11-26 + _description.text +; + The number of reflections symmetry-equivalent under the Laue + symmetry to the present reflection. In the Laue symmetry, Friedel + opposites (h k l and -h -k -l) are equivalent. Tables of + symmetry-equivalent reflections are available in International + Tables for Crystallography, Volume A (1987), section 10.2. +; + _description.common 'ReflnSymmetryMultiplicity' + _name.category_id refln + _name.object_id symmetry_multiplicity + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + _enumeration.range 1:48 + save_ + + +save_refln.wavelength + _definition.id '_refln.wavelength' + loop_ + _alias.definition_id '_refln_wavelength' + _definition.update 2012-11-26 + _description.text +; + The mean wavelength in angstroms of radiation used to measure + this reflection. This is an important parameter for data + collected using energy-dispersive detectors or the Laue method. +; + _description.common 'ReflnWavelength' + _name.category_id refln + _name.object_id wavelength + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_refln.wavelength_id + _definition.id '_refln.wavelength_id' + loop_ + _alias.definition_id '_refln_wavelength_id' + _definition.update 2012-11-26 + _description.text +; + Code identifying the wavelength in DIFFRN_RADIATION_WAVELENGTH list. +; + _description.common 'ReflnWavelengthId' + _name.category_id refln + _name.object_id wavelength_id + _name.linked_item_id '_diffrn_radiation_wavelength.id' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + save_ #------ close REFLN category + +#============================================================================ + +save_REFLNS + + _definition.id REFLNS + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items used to specify parameters for the complete + set of reflections used in the structure refinement process. Note that + these parameters are often similar measures to those defined in the + DIFFRN categories, but differ in that the parameters refer to the + reduced/transformed reflections which have been used to refine the + atom site data in the ATOM_SITE category. The DIFFRN definitions refer + to the diffraction measurements and the raw reflection data. +; + _name.category_id DIFFRACTION + _name.object_id REFLNS + + +save_reflns.d_resolution_high + _definition.id '_reflns.d_resolution_high' + loop_ + _alias.definition_id '_reflns_d_resolution_high' + _definition.update 2012-11-26 + _description.text +; + Highest resolution for the final REFLN data set. + This corresponds to the smallest interpanar d value. +; + _description.common 'ReflnsResolHigh' + _name.category_id reflns + _name.object_id d_resolution_high + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_reflns.d_resolution_low + _definition.id '_reflns.d_resolution_low' + loop_ + _alias.definition_id '_reflns_d_resolution_low' + _definition.update 2012-11-26 + _description.text +; + Lowest resolution for the final REFLN data set. + This corresponds to the largest interpanar d value. +; + _description.common 'ReflnsResolLow' + _name.category_id reflns + _name.object_id d_resolution_low + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_reflns.Friedel_coverage + _definition.id '_reflns.Friedel_coverage' + loop_ + _alias.definition_id '_reflns_Friedel_coverage' + _definition.update 2012-11-26 + _description.text +; + The proportion of Friedel related reflections present in the number of + the 'independent reflections' specified by the item _reflns.number_total. + + This proportion is calculated as the ratio: + + [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) + + where, working from the @diffrn_refln_ list, + + N(Crystal class) is the number of reflections obtained on + averaging under the symmetry of the crystal class + N(Laue symmetry) is the number of reflections obtained on + averaging under the Laue symmetry. + + (a) For centrosymmetric structures its value is + necessarily equal to 0.0 as the crystal class + is identical to the Laue symmetry. + (b) For whole-sphere data for a crystal in the space + group P1, _reflns.Friedel_coverage is equal to 1.0, + as no reflection h k l is equivalent to -h -k -l + in the crystal class and all Friedel pairs + {h k l; -h -k -l} have been measured. + (c) For whole-sphere data in space group Pmm2, the value + will be < 1.0 because although reflections h k l and + -h -k -l are not equivalent when h k l indices are + non-zero, they are when l=0. + (d) For a crystal in the group Pmm2 measurements of the + two inequivalent octants h >= 0, k >=0, l lead to the + same value as in (c), whereas measurements of the + two equivalent octants h >= 0, k, l >= 0 will lead to + a zero value for @reflns_Friedel_coverage. +; + _description.common 'ReflnsFriedelCoverage' + _name.category_id reflns + _name.object_id Friedel_coverage + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_reflns.Friedel_fraction_full + _definition.id '_reflns.Friedel_fraction_full' + loop_ + _alias.definition_id '_reflns_Friedel_fraction_full' + _definition.update 2013-01-20 + _description.text +; + The ratio of Friedel pairs measured to _diffrn_reflns.theta_full + to the number theoretically possible (ignoring reflections in + centric projections and systematic absences throughout). + In contrast to _reflns.Friedel_coverage this can take values in + the full range 0 to 1 for any non-centrosymmetric space group, + and so one can see at a glance how completely the Friedel pairs + have been measured. For centrosymmetric space groups the value + would be given as not-applicable '.' +; + _name.category_id reflns + _name.object_id Friedel_fraction_full + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_reflns.Friedel_fraction_max + _definition.id '_reflns.Friedel_fraction_max' + loop_ + _alias.definition_id '_reflns_Friedel_fraction_max' + _definition.update 2013-01-20 + _description.text +; + The ratio of Friedel pairs measured to _diffrn_reflns.theta_max + to the number theoretically possible (ignoring reflections in + centric projections and systematic absences throughout). + In contrast to _reflns.Friedel_coverage this can take values in + the full range 0 to 1 for any non-centrosymmetric space group, + and so one can see at a glance how completely the Friedel pairs + have been measured. For centrosymmetric space groups the value + would be given as not-applicable '.' +; + _name.category_id reflns + _name.object_id Friedel_fraction_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_reflns.limit_max + _definition.id '_reflns.limit_max' + _definition.update 2013-01-15 + _description.text +; + Maximum Miller indices of refined diffraction reflections. +; + _name.category_id reflns + _name.object_id limit_max + _type.purpose Quantity + _type.source Assigned + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as reflns + + _reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] +; + save_ + + +save_reflns.limit_min + _definition.id '_reflns.limit_min' + _definition.update 2013-01-15 + _description.text +; + Minimum Miller indices of refined diffraction reflections. +; + _name.category_id reflns + _name.object_id limit_min + _type.purpose Quantity + _type.source Assigned + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as reflns + + _reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] +; + save_ + + +save_reflns.limit_h_max + _definition.id '_reflns.limit_h_max' + loop_ + _alias.definition_id '_reflns_limit_h_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_h_max + save_ + + +save_reflns.limit_h_min + _definition.id '_reflns.limit_h_min' + loop_ + _alias.definition_id '_reflns_limit_h_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_h_min + save_ + + +save_reflns.limit_k_max + _definition.id '_reflns.limit_k_max' + loop_ + _alias.definition_id '_reflns_limit_k_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_k_max + save_ + + +save_reflns.limit_k_min + _definition.id '_reflns.limit_k_min' + loop_ + _alias.definition_id '_reflns_limit_k_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_k_min + save_ + + +save_reflns.limit_l_max + _definition.id '_reflns.limit_l_max' + loop_ + _alias.definition_id '_reflns_limit_l_max' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_l_max + save_ + + +save_reflns.limit_l_min + _definition.id '_reflns.limit_l_min' + loop_ + _alias.definition_id '_reflns_limit_l_min' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id reflns + _name.object_id limit_l_min + save_ + + +save_reflns.number_gt + _definition.id '_reflns.number_gt' + loop_ + _alias.definition_id '_reflns_number_gt' + '_reflns_number_observed' + '_reflns_number_obs' + '_reflns.number_obs' + _definition.update 2012-11-26 + _description.text +; + Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which + are significantly intense (see _reflns.threshold_expression). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending to the nature of the structure and the procedures used. +; + _description.common 'ReflnsGtCount' + _name.category_id reflns + _name.object_id number_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns.number_total + _definition.id '_reflns.number_total' + loop_ + _alias.definition_id '_reflns_number_total' + '_reflns_number_all' + '_reflns.number_all' + _definition.update 2012-11-26 + _description.text +; + Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending to the nature of the structure and the procedures used. +; + _description.common 'ReflnsTotalCount' + _name.category_id reflns + _name.object_id number_total + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns.special_details + _definition.id '_reflns.special_details' + loop_ + _alias.definition_id '_reflns_special_details' + '_reflns.details' + _definition.update 2012-11-26 + _description.text +; + Description of the properties of the REFLN reflection list that is not + given in other data items. Should include details about the averaging + of symmetry-equivalent reflections including Friedel pairs. +; + _description.common 'ReflnsSpecialDetails' + _name.category_id reflns + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_reflns.threshold_expression + _definition.id '_reflns.threshold_expression' + loop_ + _alias.definition_id '_reflns_threshold_expression' + '_reflns_observed_criterion' + '_reflns.observed_criterion' + _definition.update 2012-11-26 + _description.text +; + Description of the criterion used to classify a reflection as having a + "significant intensity". This criterion is usually expressed in terms + of a u(I) or u(F) threshold. "u" is the standard uncertainty. +; + _description.common 'ReflnsThesholdExpression' + _name.category_id reflns + _name.object_id threshold_expression + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'I>2u(I)' + save_ + + +#---------------------------------------------------------------------------- + + +save_REFLNS_CLASS + + _definition.id reflns_class + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the properties of reflections + in specific classes of reflections. +; + _name.category_id REFLNS + _name.object_id CLASS + _category.key_id '_reflns_class.key' + + +save_reflns_class.key + _definition.id '_reflns_class.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of REFLNS_CLASS items + in a looped list. +; + _description.common 'Key to reflection classes' + _name.category_id class + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(reflns_class.code) +; + Evaluation +; _reflns_class.key = _reflns_class.code +; + save_ + + +save_reflns_class.code + _definition.id '_reflns_class.code' + loop_ + _alias.definition_id '_reflns_class_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying a reflection class. +; + _description.common 'ReflnsClassCode' + _name.category_id class + _name.object_id code + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case 'c1' + save_ + + +save_reflns_class.description + _definition.id '_reflns_class.description' + loop_ + _alias.definition_id '_reflns_class_description' + _definition.update 2012-11-26 + _description.text +; + Description of a reflection class. +; + _description.common 'ReflnsClassDetails' + _name.category_id class + _name.object_id description + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'H0L0 common projection reflections' + save_ + + +save_reflns_class.d_res_high + _definition.id '_reflns_class.d_res_high' + loop_ + _alias.definition_id '_reflns_class_d_res_high' + _definition.update 2012-11-26 + _description.text +; + Highest resolution for the reflections in this class. + This corresponds to the smallest interpanar d value. +; + _description.common 'ReflnsClassResolHigh' + _name.category_id class + _name.object_id d_res_high + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_reflns_class.d_res_low + _definition.id '_reflns_class.d_res_low' + loop_ + _alias.definition_id '_reflns_class_d_res_low' + _definition.update 2012-11-26 + _description.text +; + Lowest resolution for the reflections in this class. + This corresponds to the largest interpanar d value. +; + _description.common 'ReflnsClassResolLow' + _name.category_id class + _name.object_id d_res_low + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_reflns_class.number_gt + _definition.id '_reflns_class.number_gt' + loop_ + _alias.definition_id '_reflns_class_number_observed' + '_reflns_class_number_gt' + _definition.update 2012-11-26 + _description.text +; + Count of reflections in this REFLN class (not the DIFFRN_REFLN set) + which are significantly intense (see _reflns.threshold_expression). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending to the nature of the structure and the procedures used. +; + _description.common 'ReflnsClassGtCount' + _name.category_id class + _name.object_id number_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_class.number_total + _definition.id '_reflns_class.number_total' + loop_ + _alias.definition_id '_reflns_class_number_total' + _definition.update 2012-11-26 + _description.text +; + Count of reflections in this REFLN class (not the DIFFRN_REFLN set). It + may include Friedel equivalent reflections (those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending to the nature of the structure and the procedures used. +; + _description.common 'ReflnsClassTotalCount' + _name.category_id class + _name.object_id number_total + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_class.R_factor_all + _definition.id '_reflns_class.R_factor_all' + loop_ + _alias.definition_id '_reflns_class_R_factor_all' + _definition.update 2012-11-26 + _description.text +; + Residual factor for reflections in this class used in refinement. + + sum | F(meas) - F(calc) | + R(F all) = ------------------------ + sum | F(meas) | + + F(meas) = the measured structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + + and the sum is taken over the specified reflections +; + _description.common 'ReflnsClassR(F)All' + _name.category_id class + _name.object_id R_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_class.R_factor_gt + _definition.id '_reflns_class.R_factor_gt' + loop_ + _alias.definition_id '_reflns_class_R_factor_gt' + '_reflns_class_R_factor_observed' + _definition.update 2012-11-26 + _description.text +; + Residual factor for the reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. + + sum | F(meas_gt) - F(calc) | + R(F gt) = -------------------------------- + sum | F(meas_gt) | + + F(meas) = the measured structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + + and the sum is taken over the specified reflections +; + _description.common 'ReflnsClassR(F)Gt' + _name.category_id class + _name.object_id R_factor_gt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_class.R_Fsqd_factor + _definition.id '_reflns_class.R_Fsqd_factor' + loop_ + _alias.definition_id '_reflns_class_R_Fsqd_factor' + _definition.update 2012-11-26 + _description.text +; + Residual factor R(F^2^) for reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. + + sum | F(meas_gt)^2^ - F(calc)^2^ | + R(Fsqd gt) = ------------------------------------ + sum F(meas_gt)^2^ + + F(meas_gt)^2^ = square of the 'observed' structure-factor + F(calc )^2^ = square of the calculated structure-factor + + and the sum is taken over the specified reflections +; + _description.common 'ReflnsClassR(Fsqd)Gt' + _name.category_id class + _name.object_id R_Fsqd_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_class.R_I_factor + _definition.id '_reflns_class.R_I_factor' + loop_ + _alias.definition_id '_reflns_class_R_I_factor' + _definition.update 2012-11-26 + _description.text +; + Residual factor R(I) for reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. + + sum | I(meas_gt) - I(calc) | + R(I gt) = ---------------------------- + sum | I(meas_gt) | + + I(meas_gt) = the net 'observed' intensity + I(calc ) = the net calculated intensity + + and the sum is taken over the specified reflections +; + _description.common 'ReflnsClassR(I)Gt' + _name.category_id class + _name.object_id R_I_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_class.wR_factor_all + _definition.id '_reflns_class.wR_factor_all' + loop_ + _alias.definition_id '_reflns_class_wR_factor_all' + _definition.update 2012-11-26 + _description.text +; + For each reflection class, the weighted residual factors for all + reflections included in the refinement. The reflections also + satisfy the resolution limits established by + _reflns_class.d_res_high and _reflns_class.d_res_low. + + ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ + wR = ( ------------------------------- ) + ( sum w Y(meas)^2^ ) + + Y(meas) = the measured amplitudes specified by + _refine_ls.structure_factor_coef + Y(calc) = the calculated amplitudes specified by + _refine_ls.structure_factor_coef + w = the least-squares weights + + and the sum is taken over the reflections of this class. +; + _description.common 'ReflnsClassWR(F)All' + _name.category_id class + _name.object_id wR_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + save_ #------ close REFLNS_CLASS category + +#---------------------------------------------------------------------------- + +save_REFLNS_SCALE + + _definition.id REFLNS_SCALE + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the scales needed to place + measured structure factor coefficients on the same absolute scale. +; + _name.category_id REFLNS + _name.object_id SCALE + _category.key_id '_reflns_scale.key' + + +save_reflns_scale.key + _definition.id '_reflns_scale.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of REFLNS_SCALE items + in a looped list. +; + _description.common 'Key to reflection scale groups' + _name.category_id scale + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(reflns_scale.group_code) +; + Evaluation +; _reflns_scale.key = _reflns_scale.group_code +; + save_ + + +save_reflns_scale.group_code + _definition.id '_reflns_scale.group_code' + loop_ + _alias.definition_id '_reflns_scale_group_code' + _definition.update 2012-11-26 + _description.text +; + Code identifying a reflection scale group. These names need not + correspond to _diffrn_scale_group.code names. +; + _description.common 'ReflnsScaleCode' + _name.category_id scale + _name.object_id group_code + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_reflns_scale.meas_F + _definition.id '_reflns_scale.meas_F' + loop_ + _alias.definition_id '_reflns_scale_meas_F' + _definition.update 2012-11-26 + _description.text +; + Structure factor scale for this scale group. +; + _description.common 'ReflnsScaleMeasF' + _name.category_id scale + _name.object_id meas_F + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_scale.meas_F_squared + _definition.id '_reflns_scale.meas_F_squared' + loop_ + _alias.definition_id '_reflns_scale_meas_F_squared' + _definition.update 2012-11-26 + _description.text +; + Structure factor squared scale for this scale group. +; + _description.common 'ReflnsScaleMeasFsqd' + _name.category_id scale + _name.object_id meas_F_squared + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_reflns_scale.meas_intensity + _definition.id '_reflns_scale.meas_intensity' + loop_ + _alias.definition_id '_reflns_scale_meas_intensity' + _definition.update 2012-11-26 + _description.text +; + Net intensity scale for this scale group. +; + _description.common 'ReflnsScaleMeasI' + _name.category_id scale + _name.object_id meas_intensity + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + save_ #------ close REFLNS_SCALE category + +#---------------------------------------------------------------------------- + +save_REFLNS_SHELL + + _definition.id REFLNS_SHELL + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-26 + _description.text +; + The CATEGORY of data items which specify the information about + reflections divided into shells bounded by d resolution limits. +; + _name.category_id REFLNS + _name.object_id SHELL + _category.key_id '_reflns_shell.key' + + +save_reflns_shell.key + _definition.id '_reflns_shell.key' + _definition.update 2012-11-26 + _description.text +; + Value is a unique key to a set of REFLNS_SHELL items + in a looped list. +; + _description.common 'Key to reflection shells' + _name.category_id shell + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(reflns_shell.d_res_limits) +; + Evaluation +; _reflns_shell.key = _reflns_shell.d_res_limits +; + save_ + + +save_reflns_shell.d_res_limits + _definition.id '_reflns_shell.d_res_limits' + _definition.update 2012-11-26 + _description.text +; + Resolution for the reflections in this shell stored as + the list of lowest and highest values. This is the + category key. +; + _description.common 'ReflnsShellResolLimits' + _name.category_id shell + _name.object_id d_res_limits + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Real + _type.dimension [2] + loop_ + _method.purpose + _method.expression + Evaluation +; + With s as reflns_shell + + _reflns_shell.d_res_limits = [ s.d_res_low, s.d_res_high ] +; + save_ + + +save_reflns_shell.d_res_high + _definition.id '_reflns_shell.d_res_high' + loop_ + _alias.definition_id '_reflns_shell_d_res_high' + _definition.update 2012-11-26 + _description.text +; + Highest resolution for the reflections in this shell. + This corresponds to the smallest interpanar d value. +; + _description.common 'ReflnsShellResolHigh' + _name.category_id shell + _name.object_id d_res_high + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + + +save_reflns_shell.d_res_low + _definition.id '_reflns_shell.d_res_low' + loop_ + _alias.definition_id '_reflns_shell_d_res_low' + _definition.update 2012-11-26 + _description.text +; + Lowest resolution for the reflections in this shell. + This corresponds to the largest interpanar d value. +; + _description.common 'ReflnsShellResolLow' + _name.category_id shell + _name.object_id d_res_low + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_reflns_shell.meanI_over_suI_all + _definition.id '_reflns_shell.meanI_over_suI_all' + loop_ + _alias.definition_id '_reflns_shell_meanI_over_uI_all' + '_reflns_shell_meanI_over_sigI_all' + '_reflns_shell.meanI_over_sigI_all' + _definition.update 2012-11-26 + _description.text +; + Ratio of the mean intensity in a shell to the mean standard uncertainty + of the intensities in the shell. +; + _description.common 'ReflnsShellMean(I/suI)All' + _name.category_id shell + _name.object_id meanI_over_suI_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + save_ + + +save_reflns_shell.meanI_over_suI_gt + _definition.id '_reflns_shell.meanI_over_suI_gt' + loop_ + _alias.definition_id '_reflns_shell_meanI_over_sigI_obs' + '_reflns_shell.meanI_over_sigI_obs' + '_reflns_shell_meanI_over_sigI_gt' + '_reflns_shell_meanI_over_uI_gt' + _definition.update 2012-11-26 + _description.text +; + Ratio of the mean intensity of significantly intense reflections (see + _reflns.threshold_expression) in this shell to the mean standard + uncertainty of the intensities in the shell. +; + _description.common 'ReflnsShellMean(I/suI)Gt' + _name.category_id shell + _name.object_id meanI_over_suI_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + save_ + + +save_reflns_shell.number_measured_all + _definition.id '_reflns_shell.number_measured_all' + loop_ + _alias.definition_id '_reflns_shell_number_measured_all' + _definition.update 2012-11-26 + _description.text +; + Total count of reflections measured for this resolution shell. +; + _description.common 'ReflnsShellCountAll' + _name.category_id shell + _name.object_id number_measured_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_shell.number_measured_gt + _definition.id '_reflns_shell.number_measured_gt' + loop_ + _alias.definition_id '_reflns_shell_number_measured_obs' + '_reflns_shell.number_measured_obs' + '_reflns_shell_number_measured_gt' + _definition.update 2012-11-26 + _description.text +; + Number of reflections measured for this resolution shell which are + significantly intense (see _reflns.threshold_expression). +; + _description.common 'ReflnsShellCountGt' + _name.category_id shell + _name.object_id number_measured_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_shell.number_possible + _definition.id '_reflns_shell.number_possible' + loop_ + _alias.definition_id '_reflns_shell_number_possible' + '_reflns_shell.number_possible_all' + _definition.update 2012-11-26 + _description.text +; + Count of symmetry-unique reflections possible in this reflection shell. +; + _description.common 'ReflnsShellUniqueCountEst' + _name.category_id shell + _name.object_id number_possible + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + save_ + + +save_reflns_shell.number_unique_all + _definition.id '_reflns_shell.number_unique_all' + loop_ + _alias.definition_id '_reflns_shell_number_unique_all' + _definition.update 2012-11-26 + _description.text +; + Count of symmetry-unique reflections present in this reflection shell. +; + _description.common 'ReflnsShellUniqueCountAll' + _name.category_id shell + _name.object_id number_unique_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_shell.number_unique_gt + _definition.id '_reflns_shell.number_unique_gt' + loop_ + _alias.definition_id '_reflns_shell_number_unique_gt' + '_reflns_shell_number_unique_obs' + '_reflns_shell.number_unique_obs' + _definition.update 2012-11-26 + _description.text +; + Number of symmetry-unique reflections present in this reflection shell + which are significantly intense (see _reflns.threshold_expression). +; + _description.common 'ReflnsShellUniqueCountGt' + _name.category_id shell + _name.object_id number_unique_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_reflns_shell.percent_possible_all + _definition.id '_reflns_shell.percent_possible_all' + loop_ + _alias.definition_id '_reflns_shell_percent_possible_all' + _definition.update 2012-11-26 + _description.text +; + Percentage of reflections present in this shell over that possible. +; + _description.common 'ReflnsShellCoverageAll' + _name.category_id shell + _name.object_id percent_possible_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:100.0 + save_ + + +save_reflns_shell.percent_possible_gt + _definition.id '_reflns_shell.percent_possible_gt' + loop_ + _alias.definition_id '_reflns_shell_percent_possible_gt' + '_reflns_shell_percent_possible_obs' + '_reflns_shell.percent_possible_obs' + _definition.update 2012-11-26 + _description.text +; + Percentage of reflections present in this shell which are significantly + intense (see _reflns.threshold_expression), over that possible. +; + _description.common 'ReflnsShellCoverageGt' + _name.category_id shell + _name.object_id percent_possible_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:100.0 + save_ + + +save_reflns_shell.Rmerge_F_all + _definition.id '_reflns_shell.Rmerge_F_all' + loop_ + _alias.definition_id '_reflns_shell_Rmerge_F_all' + _definition.update 2012-11-26 + _description.text +; + Rmerge(F) for all reflections in a given shell. + + sum~i~ ( sum~j~ | F~j~ - | ) + Rmerge(F) = -------------------------------- + sum~i~ ( sum~j~ ) + + F~j~ = the amplitude of the jth observation of reflection i + = the mean of the amplitudes of all observations of + reflection i + + sum~i~ is taken over all reflections + sum~j~ is taken over all observations of each reflection. +; + _description.common 'ReflnsShellMergeR(F)All' + _name.category_id shell + _name.object_id Rmerge_F_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0 + save_ + + +save_reflns_shell.Rmerge_F_gt + _definition.id '_reflns_shell.Rmerge_F_gt' + loop_ + _alias.definition_id '_reflns_shell_Rmerge_F_obs' + '_reflns_shell.Rmerge_F_obs' + '_reflns_shell_Rmerge_F_gt' + _definition.update 2012-11-26 + _description.text +; + Rmerge(F) for reflections in a shell which are significantly intense + (see _reflns.threshold_expression). The residual merge expression is + shown in the _reflns_shell.Rmerge_F_all definition. +; + _description.common 'ReflnsShellMergeR(F)Gt' + _name.category_id shell + _name.object_id Rmerge_F_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0 + save_ + + +save_reflns_shell.Rmerge_I_all + _definition.id '_reflns_shell.Rmerge_I_all' + loop_ + _alias.definition_id '_reflns_shell_Rmerge_I_all' + _definition.update 2012-11-26 + _description.text +; + Rmerge(I) for all reflections in a given shell. + + sum~i~ ( sum~j~ | I~j~ - | ) + Rmerge(I) = -------------------------------- + sum~i~ ( sum~j~ ) + + I~j~ = the intensity of the jth observation of reflection i + = the mean of the intensities of all observations of + reflection i + + sum~i~ is taken over all reflections + sum~j~ is taken over all observations of each reflection. +; + _description.common 'ReflnsShellMergeR(I)All' + _name.category_id shell + _name.object_id Rmerge_I_all + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0 + save_ + + +save_reflns_shell.Rmerge_I_gt + _definition.id '_reflns_shell.Rmerge_I_gt' + loop_ + _alias.definition_id '_reflns_shell_Rmerge_I_obs' + '_reflns_shell.Rmerge_I_obs' + '_reflns_shell_Rmerge_I_gt' + _definition.update 2012-11-26 + _description.text +; + Rmerge(I) for reflections in a shell which are significantly intense + (see _reflns.threshold_expression). The residual merge expression is + shown in the _reflns_shell.Rmerge_I_all definition. +; + _description.common 'ReflnsShellMergeR(I)Gt' + _name.category_id shell + _name.object_id Rmerge_I_gt + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0 + save_ + + save_ #------ close REFLNS_SHELL category + + save_ #------ close REFLNS category + + save_ #------ close DIFFRACTION category + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.1.01 2006-03-07 +; + Initial CORE_DIFFRACTION dictionary constructed from CORE_3 v3.5.02 +; + 1.1.02 2006-03-08 +; + Insert enumeration_set into _diffrn_radiation.type +; + 1.1.03 2006-05-16 +; + In DIFFRN_STANDARD_REFLN changed the key to .code instead of .hkl +; + 1.2.01 2006-06-20 +; + Apply DDL 3.6.04 attribute changes. +; + 1.2.02 2006-06-30 +; + Apply DDL 3.6.05 attribute changes. +; + 1.2.03 2006-09-07 +; + Apply DDL 3.6.08 attribute changes. +; + 1.2.04 2006-11-13 +; + Apply DDL 3.6.10 attribute changes. + Change method.id to method.purpose; EVAL to Evaluation +; + 1.2.05 2006-12-14 +; + Apply DDL 3.7.01 attribute changes. +; + 1.3.01 2007-02-07 +; + Apply DDL 3.7.04 attribute changes. +; + 1.3.02 2007-02-09 +; + Correct TYPE in _diffrn_standards.number and + _diffrn_standards.interval_count +; + 1.3.03 2007-10-13 +; + Placed tags in _category_key.primitive lists within quotes. +; + 1.3.04 2008-01-18 +; + Replaced import_list controls with leading uppercase character. + Changed import_list [....] to [[....]] +; + 1.3.05 2008-06-18 +; + Change import_list.id to be ((.....)) + For all *.key items change _type.contents from Code to Inherited + For other *.id items some _type.purpose from Key to Identify + For all *.hkl change _type.purpose from Observed to Identify +; + 1.3.06 2008-06-19 +; + Ensure that all items with _type.contents Code are enumerated + otherwise they are Text. +; + 1.3.07 2008-06-24 +; + Change all _type.dimension values +; + 1.4.01 2011-06-07 +; + Replace category class "List" with "Loop" + Replace all "Tuple" with "List" + Replace all "Array" with "List" + Place all import lists into [[......]] +; + 1.4.02 2011-08-01 +; + Replace category class "List" with "Loop"pply nested save frames. + Apply import.get changes + Apply all the DDL 3.8 changes +; + 1.4.03 2011-08-03 +; + Change name of import file com_att.dic to templ_attr.cif + Change name of import file com_val.dic to templ_templcif +; + 1.4.04 2011-12-01 +; + Change container type from List to Matrix for relevant item definitions +; + 1.4.05 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 1.5.01 2012-05-07 +; + Apply DDL 3.10.01 changes. +; + 1.5.02 2012-10-16 +; + Apply DDL 3.10.02 changes for type.contents. + Remove type.contents "Inherited"; insert Definition method expression. +; + 1.5.03 2012-11-20 +; + Invoke container functions Matrix, List in methods scripts where needed. +; + 1.5.04 2012-11-26 +; + Add DDL1 tags as alias.definition_id values +; + 1.5.05 2012-11-30 +; + Removed {} from Definition methods of refln_F_calc and refln.F_complex +; + 1.5.06 2012-12-13 +; + Added diffrn.ambient_pressure_gt and _lt. + Added diffrn.ambient_temperature_gt and _lt. + Added diffrn_refln.intensity_net_su to alias DDL1 tags. +; + 1.5.07 2013-01-15 +; + Added diffrn_reflns.limit_max and _min +; + 1.5.08 2013-01-28 +; + Changed atom_site.symmetry_multiplicity to *.site_symmetry_multiplicity +; + 1.5.09 2013-02-18 +; + Eval method for refln.F_complex generalised to use atom_site.matrix_beta +; + 1.5.10 2013-02-21 +; + Removed {} from conditional single-line statements in methods +; diff --git a/core_exptl.dic b/core_exptl.dic new file mode 100755 index 0000000..467057d --- /dev/null +++ b/core_exptl.dic @@ -0,0 +1,4578 @@ +############################################################################## +# # +# CIF CORE EXPERIMENTAL DATA DICTIONARY # +# # +############################################################################## + +data_CORE_EXPTL + + _dictionary.title CORE_EXPTL + _dictionary.class Instance + _dictionary.version 2.3.08 + _dictionary.date 2013-01-18 + _dictionary.uri www.iucr.org/cif/dic/core_exptl.dic + _dictionary.ddl_conformance 3.10.03 + _dictionary.namespace CoreExptl + _description.text +; + This dictionary contains the definitions of data items that + are CORE to the description of the crystal identification and + classification experiments. That is crystal, cell and chemical + data. +; + + +save_EXPERIMENTAL + _definition.id EXPERIMENTAL + _definition.scope Category + _definition.class Head + _definition.update 2012-11-22 + _description.text +; + The DICTIONARY group encompassing the CORE experimental data defined + and used with in the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_CORE + _name.object_id EXPERIMENTAL + + + +#============================================================================ + +save_EXPERIMENTS + _definition.id EXPERIMENTS + _definition.scope Category + _definition.class Ref-loop + _definition.update 2012-11-22 + _description.text +; + This category is designed specifically to facilitate studies + involving multiple sets of experiments and their associated data + values. The data items are defined within the EXPTL category. + This category class is only used in an instance document when + there is more than one experiment encompassed by the category + of EXPTL items. When this is the case each set of EXPTL data, + one set per experiment, is enclosed in its own save frame. + In the instance document these are referred to as a loop of + the item _experiments.key. See a typical example below. + When only one set of experimental data exists the EXPTL items + need not be enclosed in a save frame and the reference loop is + unnecessary. +; + _name.category_id EXPERIMENTAL + _name.object_id EXPERIMENTS + _category.key_id '_experiments.key' + loop_ + _description_example.case +; + In an instance document this category is typically invoked as + + loop_ _experiments.key + ${"frame":"exptl_blue"}$ + ${"frame":"exptl_red"}$ +; + + +save_experiments.key + _definition.id '_experiments.key' + _definition.update 2012-11-22 + _description.text +; + Unique key to a set of save frames in a looped list. +; + _description.common 'Key to save frame' + _name.category_id experiments + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Ref-table + _type.contents Table + loop_ + _description_example.case '${"frame":phase1}$' + save_ + + +#============================================================================ + +save_EXPTL + + _definition.id EXPTL + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the experimental work + prior to diffraction measurements. These include crystallization + crystal measurements and absorption-correction techniques used.. +; + _name.category_id EXPERIMENTS + _name.object_id EXPTL + + + +save_exptl.id + _definition.id '_exptl.id' + _definition.update 2012-11-22 + _description.text +; + Code identifying an experiment if there are multiple sets of + experimental data. See _experiments.key. +; + _description.common 'Experiment Id' + _name.category_id exptl + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_exptl.crystals_number + _definition.id '_exptl.crystals_number' + loop_ + _alias.definition_id '_exptl_crystals_number' + _definition.update 2012-11-22 + _description.text +; + Total number of crystals used in the measurement of intensities. +; + _description.common 'CrystalsCount' + _name.category_id exptl + _name.object_id crystals_number + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 1: + save_ + + +save_exptl.special_details + _definition.id '_exptl.special_details' + loop_ + _alias.definition_id '_exptl_special_details' + '_exptl.details' + _definition.update 2012-11-22 + _description.text +; + Details of the experiment prior to intensity measurement. + See also _exptl_crystal.preparation +; + _description.common 'SpecialExptlDetails' + _name.category_id exptl + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_exptl.transmission_factor_max + _definition.id '_exptl.transmission_factor_max' + loop_ + _alias.definition_id '_exptl_transmission_factor_max' + _definition.update 2013-01-18 + _description.text +; + The calculated maximum value of the transmission factor for + the specimen. Its value does not include the effects of + absorption in the specimen mount. The presence of this + item does not imply that the structure factors have been + corrected for absorption. The applied correction should be + given by _exptl_absorpt.correction_T_max. +; + _name.category_id exptl + _name.object_id transmission_factor_max + _type.purpose Measurand + _type.source Observed + _type.container Single + _type.contents Realt + _enumeration.range 0.0:1.0 + save_ + + +save_exptl.transmission_factor_min + _definition.id '_exptl.transmission_factor_min' + loop_ + _alias.definition_id '_exptl_transmission_factor_min' + _definition.update 2013-01-18 + _description.text +; + The calculated minimum value of the transmission factor for + the specimen. Its value does not include the effects of + absorption in the specimen mount. The presence of this + item does not imply that the structure factors have been + corrected for absorption. The applied correction should be + given by _exptl_absorpt.correction_T_min. +; + _name.category_id exptl + _name.object_id transmission_factor_min + _type.purpose Measurand + _type.source Observed + _type.container Single + _type.contents Realt + _enumeration.range 0.0:1.0 + save_ + + +#============================================================================ + +save_EXPTL_CRYSTALS + _definition.id EXPTL_CRYSTALS + _definition.scope Category + _definition.class Ref-loop + _definition.update 2012-11-22 + _description.text +; + This category is designed specifically to facilitate studies + involving multiple sets of experiments and their associated data + values. The data items are defined in the EXPTL_CRYSTAL category. + This category class is only used in an instance document when + there is more than one experiment encompassed by the category of + EXPTL items. When this is the case each set of EXPTL_CRYSTALa + data, one set per experiment, is enclosed in its own save frame. + In the instance document these are referred to as a loop of + the item _experiments.key. See a typical example below. + When only one set of experimental data exists the EXPTL items + need not be enclosed in a save frame and the reference loop is + unnecessary. +; + _name.category_id EXPTL + _name.object_id CRYSTALS + _category.key_id '_exptl_crystals.key' + loop_ + _description_example.case +; + In an instance document this category is typically invoked as + + loop_ _exptl_crystals.key + ${"frame":"crystal_1"}$ + ${"frame":"crystal_2"}$ +; + + +save_exptl_crystals.key + _definition.id '_exptl_crystals.key' + _definition.update 2012-11-22 + _description.text +; + Unique key to a set of EXPTL_CRYSTAL items in a looped list. +; + _description.common 'ExptlCrystalKey' + _name.category_id crystals + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Ref-table + _type.contents Table + loop_ + _description_example.case ' ${"frame":1}$ ' + save_ + + +#---------------------------------------------------------------------------- + +save_EXPTL_CRYSTAL + + _definition.id EXPTL_CRYSTAL + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify information about a + crystal used in the diffraction measurements. +; + _name.category_id EXPTL_CRYSTALS + _name.object_id CRYSTAL + + +save_exptl_crystal.id + _definition.id '_exptl_crystal.id' + loop_ + _alias.definition_id '_exptl_crystal_id' + _definition.update 2012-11-22 + _description.text +; + Code identifying a crystal if multiple crystals are used. + See _exptl_crystals.key. +; + _description.common 'CrystalId' + _name.category_id crystal + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_exptl_crystal.colour + _definition.id '_exptl_crystal.colour' + loop_ + _alias.definition_id '_exptl_crystal_colour' + _definition.update 2012-11-22 + _description.text +; + Colour description of a crystal as a list of the allowed + exptl_crystal_appearance states for general, intensity and hue. +; + _description.common 'CrystalColourList' + _name.category_id crystal + _name.object_id colour + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Code + _type.dimension [3] + loop_ + _description_example.case "[transluscent, pale, green]" + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as exptl_crystal_appearance + + _exptl_crystal.colour = [ c.general, c.intensity, c.hue ] +; + save_ + + +save_exptl_crystal.density_diffrn + _definition.id '_exptl_crystal.density_diffrn' + loop_ + _alias.definition_id '_exptl_crystal_density_diffrn' + _definition.update 2012-11-22 + _description.text +; + Crystal density calculated from crystal unit cell and atomic content. +; + _description.common 'CrystalDensityDiffrn' + _name.category_id crystal + _name.object_id density_diffrn + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code megagrams_per_metres_cubed + loop_ + _method.purpose + _method.expression + Evaluation +; + _exptl_crystal.density_diffrn = 1.6605 * _cell.atomic_mass / _cell.volume +; + save_ + + +save_exptl_crystal.density_meas + _definition.id '_exptl_crystal.density_meas' + loop_ + _alias.definition_id '_exptl_crystal_density_meas' + _definition.update 2012-11-22 + _description.text +; + Crystal density measured using standard chemical and physical methods. +; + _description.common 'CrystalDensityMeas' + _name.category_id crystal + _name.object_id density_meas + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code megagrams_per_metres_cubed + save_ + + +save_exptl_crystal.density_meas_gt + _definition.id '_exptl_crystal.density_meas_gt' + loop_ + _alias.definition_id '_exptl_crystal_density_meas_gt' + _definition.update 2012-12-11 + _description.text +; + The value above which the density measured using standard + chemical and physical methods lies. This item is used only + when _exptl_crystal.density_meas cannot be employed. It is + intended for use in reporting information in databases and + archives which would be misleading if reported otherwise. +; + _name.category_id crystal + _name.object_id density_meas_gt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code megagrams_per_metres_cubed + save_ + + +save_exptl_crystal.density_meas_lt + _definition.id '_exptl_crystal.density_meas_lt' + loop_ + _alias.definition_id '_exptl_crystal_density_meas_lt' + _definition.update 2012-12-11 + _description.text +; + The value below which the density measured using standard + chemical and physical methods lies. This item is used only + when _exptl_crystal.density_meas cannot be employed. It is + intended for use in reporting information in databases and + archives which would be misleading if reported otherwise. +; + _name.category_id crystal + _name.object_id density_meas_lt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code megagrams_per_metres_cubed + save_ + + +save_exptl_crystal.density_meas_temp + _definition.id '_exptl_crystal.density_meas_temp' + loop_ + _alias.definition_id '_exptl_crystal_density_meas_temp' + _definition.update 2012-11-22 + _description.text +; + Temperature at which _exptl_crystal.density_meas was determined. +; + _description.common 'CrystalDensityTemperature' + _name.category_id crystal + _name.object_id density_meas_temp + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_exptl_crystal.density_meas_temp_gt + _definition.id '_exptl_crystal.density_meas_temp_gt' + loop_ + _alias.definition_id '_exptl_crystal_density_meas_temp_gt' + _definition.update 2012-12-11 + _description.text +; + Temperature above which the measured density was determined. + This item is used only when exptl_crystal.density_meas_temp + cannot be employed. It is intended for use in reporting values + from databases which would be misleading if reported otherwise. +; + _name.category_id crystal + _name.object_id density_meas_temp_gt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_exptl_crystal.density_meas_temp_lt + _definition.id '_exptl_crystal.density_meas_temp_lt' + loop_ + _alias.definition_id '_exptl_crystal_density_meas_temp_lt' + _definition.update 2012-12-11 + _description.text +; + Temperature below which the measured density was determined. + This item is used only when exptl_crystal.density_meas_temp + cannot be employed. It is intended for use in reporting values + from databases which would be misleading if reported otherwise. +; + _name.category_id crystal + _name.object_id density_meas_temp_lt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_exptl_crystal.density_method + _definition.id '_exptl_crystal.density_method' + loop_ + _alias.definition_id '_exptl_crystal_density_method' + _definition.update 2012-11-22 + _description.text +; + Description of method used to measure _exptl_crystal.density_meas. +; + _description.common 'CrystalDensityMethod' + _name.category_id crystal + _name.object_id density_method + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'flotation in aqueous KI' + save_ + + +save_exptl_crystal.description + _definition.id '_exptl_crystal.description' + loop_ + _alias.definition_id '_exptl_crystal_description' + _definition.update 2012-11-22 + _description.text +; + Description of the quality and habit of the crystal. The crystal + dimensions should appear in the exptl_crystal_size category. +; + _description.common 'CrystalDescription' + _name.category_id crystal + _name.object_id description + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + +save_exptl_crystal.F_000 + _definition.id '_exptl_crystal.F_000' + loop_ + _alias.definition_id '_exptl_crystal_F_000' + _definition.update 2012-11-22 + _description.text +; + Number of electrons in the crystal unit cell contributing to F(000). + It may contain dispersion contributions, and is calculated as + + F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ + + f~r~ = real part of the scattering factors at theta = 0 + f~i~ = imaginary part of the scattering factors at theta = 0 + + the sum is taken over each atom in the unit cell + + For X-rays, non-dispersive F(000) is a positive number and counts + the effective number of electrons in the unit cell; for neutrons, + non-dispersive F(000) (which may be negative) counts the total + nuclear scattering power in the unit cell. See + http://reference.iucr.org/dictionary/F(000) +; + _description.common 'F(000)expected' + _name.category_id crystal + _name.object_id F_000 + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_exptl_crystal.preparation + _definition.id '_exptl_crystal.preparation' + loop_ + _alias.definition_id '_exptl_crystal_preparation' + _definition.update 2012-11-22 + _description.text +; + Details of crystal growth and preparation of the crystals + (e.g. mounting) prior to the intensity measurements. +; + _description.common 'CrystalPreparation' + _name.category_id crystal + _name.object_id preparation + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'mounted in an argon-filled quartz capillary' + save_ + + +save_exptl_crystal.pressure_history + _definition.id '_exptl_crystal.pressure_history' + loop_ + _alias.definition_id '_exptl_crystal_pressure_history' + _definition.update 2012-11-22 + _description.text +; + Details concerning the pressure history of the crystals. +; + _description.common 'CrystalOriginPressure' + _name.category_id crystal + _name.object_id pressure_history + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_exptl_crystal.recrystallization_method + _definition.id '_exptl_crystal.recrystallization_method' + loop_ + _alias.definition_id '_exptl_crystal_recrystallization_method' + _definition.update 2012-12-11 + _description.text +; + Method used to recrystallize the sample. Sufficient details should + be given for the procedure to be repeated. Temperatures, solvents, + flux or carrier gases with concentrations or pressures and ambient + atmosphere details should be given. +; + _name.category_id crystal + _name.object_id recrystallization_method + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_exptl_crystal.size_length + _definition.id '_exptl_crystal.size_length' + loop_ + _alias.definition_id '_exptl_crystal_size_length' + _definition.update 2012-11-22 + _description.text +; + The length of needle/cylindrical crystals. +; + _name.category_id crystal + _name.object_id size_length + _description.common 'CrystalNeedleLength' + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code millimetres + save_ + + +save_exptl_crystal.size_max + _definition.id '_exptl_crystal.size_max' + loop_ + _alias.definition_id '_exptl_crystal_size_max' + _definition.update 2012-11-22 + _description.text +; + The maximum dimension of a crystal. +; + _name.category_id crystal + _name.object_id size_max + _description.common 'CrystalSizeMax' + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code millimetres + save_ + + +save_exptl_crystal.size_mid + _definition.id '_exptl_crystal.size_mid' + loop_ + _alias.definition_id '_exptl_crystal_size_mid' + _definition.update 2012-11-22 + _description.text +; + The median dimension of a crystal. +; + _name.category_id crystal + _name.object_id size_mid + _description.common 'CrystalSizeMedial' + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code millimetres + save_ + + +save_exptl_crystal.size_min + _definition.id '_exptl_crystal.size_min' + loop_ + _alias.definition_id '_exptl_crystal_size_min' + _definition.update 2012-11-22 + _description.text +; + The minimum dimension of a crystal. +; + _name.category_id crystal + _name.object_id size_min + _description.common 'CrystalSizeMin' + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code millimetres + save_ + + +save_exptl_crystal.size_rad + _definition.id '_exptl_crystal.size_rad' + loop_ + _alias.definition_id '_exptl_crystal_size_rad' + _definition.update 2012-11-22 + _description.text +; + The radius of a spherical or cylindrical crystal. +; + _name.category_id crystal + _name.object_id size_rad + _description.common 'CrystalRadius' + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code millimetres + save_ + + +save_exptl_crystal.thermal_history + _definition.id '_exptl_crystal.thermal_history' + loop_ + _alias.definition_id '_exptl_crystal_thermal_history' + _definition.update 2012-11-22 + _description.text +; + Details concerning the thermal history of the crystals. +; + _description.common 'CrystalOriginThermal' + _name.category_id crystal + _name.object_id thermal_history + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +#---------------------------------------------------------------------------- + +save_EXPTL_CRYSTAL_FACE + + _definition.id EXPTL_CRYSTAL_FACE + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items which specify the dimensions of the + crystals used in the diffraction measurements. +; + _name.category_id EXPTL_CRYSTAL + _name.object_id FACE + _category.key_id '_exptl_crystal_face.key' + + +save_exptl_crystal_face.key + _definition.id '_exptl_crystal_face.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of EXPTL_CRYSTAL items + in a looped list. +; + _description.common 'Crystal Faces Key' + _name.category_id face + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(exptl_crystal_face.id) +; + Evaluation +; _exptl_crystal_face.key = _exptl_crystal_face.id +; + save_ + +save_exptl_crystal_face.crystal_id + _definition.id '_exptl_crystal_face.crystal_id' + _definition.update 2012-11-22 + _description.text +; + Code identifying a crystal if multiple crystals are used. +; + _description.common 'CrystalFaceCrystalId' + _name.category_id face + _name.object_id crystal_id + _name.linked_item_id '_exptl_crystal.id' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_exptl_crystal_face.diffr_chi + _definition.id '_exptl_crystal_face.diffr_chi' + loop_ + _alias.definition_id '_exptl_crystal_face_diffr_chi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id face + _name.object_id diffr_chi + save_ + + +save_exptl_crystal_face.diffr_kappa + _definition.id '_exptl_crystal_face.diffr_kappa' + loop_ + _alias.definition_id '_exptl_crystal_face_diffr_kappa' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id face + _name.object_id diffr_kappa + save_ + + +save_exptl_crystal_face.diffr_phi + _definition.id '_exptl_crystal_face.diffr_phi' + loop_ + _alias.definition_id '_exptl_crystal_face_diffr_phi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id face + _name.object_id diffr_phi + save_ + + +save_exptl_crystal_face.diffr_psi + _definition.id '_exptl_crystal_face.diffr_psi' + loop_ + _alias.definition_id '_exptl_crystal_face_diffr_psi' + _import.get [{"file":'templ_attr.cif',"save":'diffr_angle'}] + _name.category_id face + _name.object_id diffr_psi + save_ + + +save_exptl_crystal_face.hkl + _definition.id '_exptl_crystal_face.hkl' + _definition.update 2012-11-22 + _description.text +; + Miller indices of the crystal face. +; + _description.common 'Crystal face hkl' + _name.category_id face + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With f as exptl_crystal_face + + _exptl_crystal_face.hkl = [f.index_h, f.index_h, f.index_l] +; + save_ + + +save_exptl_crystal_face.index_h + _definition.id '_exptl_crystal_face.index_h' + loop_ + _alias.definition_id '_exptl_crystal_face_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id face + _name.object_id index_h + save_ + + +save_exptl_crystal_face.index_k + _definition.id '_exptl_crystal_face.index_k' + loop_ + _alias.definition_id '_exptl_crystal_face_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id face + _name.object_id index_k + save_ + + +save_exptl_crystal_face.index_l + _definition.id '_exptl_crystal_face.index_l' + loop_ + _alias.definition_id '_exptl_crystal_face_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id face + _name.object_id index_l + save_ + + +save_exptl_crystal_face.id + _definition.id '_exptl_crystal_face.id' + _definition.update 2012-11-22 + _description.text +; + Identifier which combines the crystal id and the face indices + as a list. This is the key item of the category. +; + _description.common 'CrystalFaceId&Index' + _name.category_id face + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'Code,Matrix(Index,Index,index)' + _type.dimension [1] + loop_ + _method.purpose + _method.expression + Evaluation +; + With f as exptl_crystal_face + + _exptl_crystal_face.id = [ f.crystal_id, f.hkl ] +; + save_ + + +save_exptl_crystal_face.perp_dist + _definition.id '_exptl_crystal_face.perp_dist' + loop_ + _alias.definition_id '_exptl_crystal_face_perp_dist' + _definition.update 2012-11-22 + _description.text +; + Perpendicular distance of face to the centre of rotation of the crystal. +; + _description.common 'Crystal face perp distance' + _name.category_id face + _name.object_id perp_dist + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code millimetres + save_ + + save_ #----------- close of EXPTL_CRYSTAL_FACE category + +#------------------------------------------------------------------------------- + +save_EXPTL_CRYSTAL_APPEARANCE + + _definition.id EXPTL_CRYSTAL_APPEARANCE + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of ENUMERATION items used to specify information about the + crystal colour and appearance. +; + _name.category_id EXPTL_CRYSTAL + _name.object_id APPEARANCE + + +save_exptl_crystal_appearance.general + _definition.id '_exptl_crystal_appearance.general' + loop_ + _alias.definition_id '_exptl_crystal_colour_lustre' + _definition.update 2012-11-22 + _description.text +; + Appearance of the crystal as prescribed state codes. +; + _description.common 'CrystalColourAppearance' + _name.category_id appearance + _name.object_id general + _type.purpose State + _type.source Observed + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state 'metallic' + 'lustrous' + 'transparent' + 'transluscent' + 'opaque' + ' ' + _enumeration.default ' ' + save_ + + +save_exptl_crystal_appearance.intensity + _definition.id '_exptl_crystal_appearance.intensity' + loop_ + _alias.definition_id '_exptl_crystal_colour_modifier' + _definition.update 2012-11-22 + _description.text +; + Colour intensity of the crystal as prescribed state codes. +; + _description.common 'CrystalColourIntensity' + _name.category_id appearance + _name.object_id intensity + _type.purpose State + _type.source Observed + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state dark light intense pale + whitish blackish grayish brownish + reddish pinkish orangish yellowish + greenish bluish ' ' + _enumeration.default ' ' + save_ + + +save_exptl_crystal_appearance.hue + _definition.id '_exptl_crystal_appearance.hue' + loop_ + _alias.definition_id '_exptl_crystal_colour_primary' + _definition.update 2012-11-22 + _description.text +; + Colour hue of the crystals as prescribed state codes. +; + _description.common 'CrystalHue' + _name.category_id appearance + _name.object_id hue + _type.purpose State + _type.source Observed + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'colour_RGB'}] + _enumeration.default 'white' + save_ + + save_ #------ close EXPTL_CRYSTAL_APPEARANCE category + + save_ #------ close EXPTL_CRYSTAL category + +#--------------------------------------------------------------------------- + +save_EXPTL_ABSORPT + + _definition.id EXPTL_ABSORPT + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the experimental details + of the absorption measurements and corrections to the diffraction + data. +; + _name.category_id EXPTL_CRYSTALS + _name.object_id ABSORPT + + +save_exptl_absorpt.coefficient_mu + _definition.id '_exptl_absorpt.coefficient_mu' + loop_ + _alias.definition_id '_exptl_absorpt_coefficient_mu' + '_exptl.absorpt_coefficient_mu' + _definition.update 2012-11-22 + _description.text +; + Absorption coefficient mu calculated from the atomic content of + the cell, the density and the radiation wavelength. +; + _description.common 'AbsorbCoeffMu' + _name.category_id absorpt + _name.object_id coefficient_mu + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_millimetres + save_ + + +save_exptl_absorpt.correction_T_max + _definition.id '_exptl_absorpt.correction_T_max' + loop_ + _alias.definition_id '_exptl_absorpt_correction_T_max' + '_exptl.absorpt_correction_T_max' + _definition.update 2012-11-22 + _description.text +; + Maximum transmission factor for the crystal and radiation applied + to the measured intensities, it includes the correction for + absorption by the specimen mount and diffractometer as well + as by the specimen itself. These factors are referred to as the + absorption correction A or 1/A*. +; + _description.common 'AbsorbTmax' + _name.category_id absorpt + _name.object_id correction_T_max + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_exptl_absorpt.correction_T_min + _definition.id '_exptl_absorpt.correction_T_min' + loop_ + _alias.definition_id '_exptl_absorpt_correction_T_min' + '_exptl.absorpt_correction_T_min' + _definition.update 2012-11-22 + _description.text +; + Minimum transmission factor for the crystal and radiation applied + to the measured intensities, it includes the correction for + absorption by the specimen mount and diffractometer as well + as by the specimen itself. These factors are referred to as the +; + _description.common 'AbsorbTmin' + _name.category_id absorpt + _name.object_id correction_T_min + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_exptl_absorpt.correction_type + _definition.id '_exptl_absorpt.correction_type' + loop_ + _alias.definition_id '_exptl_absorpt_correction_type' + '_exptl.absorpt_correction_type' + _definition.update 2012-11-22 + _description.text +; + Code identifying the absorption correction type and method. + The 'empirical' approach should NOT be used if more detailed + information on the crystal shape is available. +; + _description.common 'AbsorbCorrectType' + _name.category_id absorpt + _name.object_id correction_type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail analytical 'analytical from crystal shape' + cylinder 'cylindrical' + empirical 'empirical from intensities' + gaussian 'Gaussian from crystal shape' + integration 'integration from crystal shape' + multi-scan 'symmetry-related measurements' + none 'no absorption correction applied' + numerical 'numerical from crystal shape' + psi-scan 'psi-scan corrections' + refdelf 'refined from delta-F' + sphere 'spherical' + _enumeration.default none + save_ + + +save_exptl_absorpt.process_details + _definition.id '_exptl_absorpt.process_details' + loop_ + _alias.definition_id '_exptl_absorpt_process_details' + '_exptl.absorpt_process_details' + _definition.update 2012-11-22 + _description.text +; + Description of the absorption correction process applied to the + measured intensities. A literature reference should be supplied + for psi-scan or multi-scan techniques. +; + _description.common 'AbsorbCorrectDetails' + _name.category_id absorpt + _name.object_id process_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Tompa analytical' + 'MolEN (Fair, 1990)' + '(North, Phillips & Mathews, 1968)' + save_ + + save_ #------ close EXPTL_ABSORPT category + + save_ #------ close EXPTL_CRYSTALS category + + +#============================================================================ + +save_CELL + + _definition.id CELL + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the parameters of + the crystal unit cell and their measurement. +; + _name.category_id EXPTL + _name.object_id CELL + + +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. +; + _description.common 'Cell Atomic Mass' + _name.category_id cell + _name.object_id atomic_mass + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code daltons + loop_ + _method.purpose + _method.expression + Evaluation +; + mass = 0. + + Loop t as atom_type { + + mass += t.number_in_cell * t.atomic_mass + } + _cell.atomic_mass = mass +; + save_ + + +save_cell.formula_units_Z + _definition.id '_cell.formula_units_Z' + loop_ + _alias.definition_id '_cell_formula_units_Z' + _definition.update 2012-11-22 + _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. +; + _description.common 'CellFormulaZ' + _name.category_id cell + _name.object_id formula_units_Z + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Count + _enumeration.range 1: + save_ + + +save_cell.metric_tensor + _definition.id '_cell.metric_tensor' + _definition.update 2012-11-22 + _description.text +; + The direct space (covariant) metric tensor used to transform + vectors and coordinates from real (direct) to reciprocal space. +; + _description.common 'CellMetricTensor' + _name.category_id cell + _name.object_id metric_tensor + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + with v as cell_vector + + _cell.metric_tensor = [[ v.a*v.a, v.a*v.b, v.a*v.c ], + [ v.b*v.a, v.b*v.b, v.b*v.c ], + [ v.c*v.a, v.c*v.b, v.c*v.c ]] +; + save_ + + +save_cell.orthogonal_matrix + _definition.id '_cell.orthogonal_matrix' + _definition.update 2012-11-22 + _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. +; + _description.common 'CellOthogMatrix' + _name.category_id cell + _name.object_id orthogonal_matrix + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With p as cell_length + With q as cell_angle + With r as cell_reciprocal_angle + + _cell.orthogonal_matrix = [ + [ p.a*Sind(q.beta)*Sind(r.gamma), 0, 0 ], + [ -p.a*Sind(q.beta)*Cosd(r.gamma), p.b*Sind(q.alpha), 0 ], + [ p.a*Cosd(q.beta), p.b*Cosd(q.alpha), p.c ]] +; + save_ + + +save_cell.special_details + _definition.id '_cell.special_details' + loop_ + _alias.definition_id '_cell_special_details' + _definition.update 2012-11-22 + _description.text +; + Description of special aspects of the cell choice, noting + possible alternative settings. +; + _description.common 'CellDetails' + _name.category_id cell + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_cell.volume + _definition.id '_cell.volume' + loop_ + _alias.definition_id '_cell_volume' + _definition.update 2012-11-22 + _description.text +; + Volume of the crystal unit cell. +; + _description.common 'CellVolume' + _name.category_id cell + _name.object_id volume + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms_cubed + loop_ + _method.purpose + _method.expression + Evaluation +; + With v as cell_vector + + _cell.volume = v.a * ( v.b ^ v.c ) +; + Validation +; + delVol = 0.0005 + With c as cell + if (c.hasItem('volume') ) { + print c.volume.getValue(), c.volume.evaluate() + if(Abs(c.volume.getValue()-c.volume.evaluate()) > delVol ) { + Throw (_cell.volume, 'cellVolumeWarning'); + } + } +; + save_ + +#---------------------------------------------------------------------------- + + +save_CELL_ANGLE + + _definition.id CELL_ANGLE + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the angles between + the axes in the crystal unit cell. +; + _name.category_id CELL + _name.object_id ANGLE + + +save_cell_angle.alpha + _definition.id '_cell_angle.alpha' + loop_ + _alias.definition_id '_cell_angle_alpha' + '_cell.angle_alpha' + _definition.update 2012-11-22 + _description.text +; + The angle between the cell axes _cell_length.b and _cell_length.c. +; + _description.common 'CellAngleAlpha' + _name.category_id angle + _name.object_id alpha + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0:180.0 + _enumeration.default 90.0 + _units.code degrees + save_ + + +save_cell_angle.beta + _definition.id '_cell_angle.beta' + loop_ + _alias.definition_id '_cell_angle_beta' + '_cell.angle_beta' + _definition.update 2012-11-22 + _description.text +; + The angle between the cell axes _cell_length.a and _cell_length.c. +; + _description.common 'CellAngleBeta' + _name.category_id angle + _name.object_id beta + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0:180.0 + _enumeration.default 90.0 + _units.code degrees + save_ + + +save_cell_angle.gamma + _definition.id '_cell_angle.gamma' + loop_ + _alias.definition_id '_cell_angle_gamma' + '_cell.angle_gamma' + _definition.update 2012-11-22 + _description.text +; + The angle between the cell axes _cell_length.a and _cell_length.b. +; + _description.common 'CellAngleGamma' + _name.category_id angle + _name.object_id gamma + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0:180.0 + _enumeration.default 90.0 + _units.code degrees + save_ + + save_ #-------- close of CELL_ANGLE category + + +#---------------------------------------------------------------------------- + +save_CELL_LENGTH + + _definition.id CELL_LENGTH + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the lengths of + the axes in the crystal unit cell. +; + _name.category_id CELL + _name.object_id LENGTH + + +save_cell_length.a + _definition.id '_cell_length.a' + loop_ + _alias.definition_id '_cell_length_a' + '_cell.length_a' + _definition.update 2012-11-22 + _description.text +; + The length of the crystal unit cell along the x-axis. +; + _description.common 'CellLengthA' + _name.category_id length + _name.object_id a + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _units.code angstroms + save_ + + +save_cell_length.b + _definition.id '_cell_length.b' + loop_ + _alias.definition_id '_cell_length_b' + '_cell.length_b' + _definition.update 2012-11-22 + _description.text +; + The length of the crystal unit cell along the y-axis. +; + _description.common 'CellLengthB' + _name.category_id length + _name.object_id b + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _units.code angstroms + save_ + + +save_cell_length.c + _definition.id '_cell_length.c' + loop_ + _alias.definition_id '_cell_length_c' + '_cell.length_c' + _definition.update 2012-11-22 + _description.text +; + The length of the crystal unit cell along the z-axis. +; + _description.common 'CellLengthC' + _name.category_id length + _name.object_id c + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _units.code angstroms + save_ + + save_ #-------- close of CELL_LENGTH category + + +#---------------------------------------------------------------------------- + +save_CELL_VECTOR + + _definition.id CELL_VECTOR + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the axial vectors of + the crystal unit cell. +; + _name.category_id CELL + _name.object_id VECTOR + + +save_cell_vector.a + _definition.id '_cell_vector.a' + _definition.update 2012-11-22 + _description.text +; + The cell vector along the x axis. +; + _description.common 'CellVectorA' + _name.category_id vector + _name.object_id a + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_vector.a = _cell.orthogonal_matrix * Matrix([1,0,0]) +; + save_ + + +save_cell_vector.b + _definition.id '_cell_vector.b' + _definition.update 2012-11-22 + _description.text +; + The cell vector along the y axis. +; + _description.common 'CellVectorB' + _name.category_id vector + _name.object_id b + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_vector.b = _cell.orthogonal_matrix * Matrix([0,1,0]) +; + save_ + + +save_cell_vector.c + _definition.id '_cell_vector.c' + _definition.update 2012-11-22 + _description.text +; + The cell vector along the z axis. +; + _description.common 'CellVectorC' + _name.category_id vector + _name.object_id c + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_vector.c = _cell.orthogonal_matrix * Matrix([0,0,1]) +; + save_ + + save_ #------- close of CELL_VECTOR category + +#---------------------------------------------------------------------------- + +save_CELL_MEASUREMENT + + _definition.id CELL_MEASUREMENT + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the angles between + the axes in the crystal unit cell. +; + _name.category_id CELL + _name.object_id MEASUREMENT + + +save_cell_measurement.pressure + _definition.id '_cell_measurement.pressure' + loop_ + _alias.definition_id '_cell_measurement_pressure' + _definition.update 2012-11-22 + _description.text +; + The pressure at which the unit-cell parameters were measured + (not the pressure used to synthesize the sample). +; + _description.common 'CellMeasPressure' + _name.category_id measurement + _name.object_id pressure + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kilopascals + save_ + + +save_cell_measurement.radiation + _definition.id '_cell_measurement.radiation' + loop_ + _alias.definition_id '_cell_measurement_radiation' + _definition.update 2012-11-22 + _description.text +; + Description of the radiation used to measure the unit-cell data. +; + _description.common 'CellMeasRadiation' + _name.category_id measurement + _name.object_id radiation + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'neutron' 'X-ray tube' 'synchrotron' + save_ + + +save_cell_measurement.reflns_used + _definition.id '_cell_measurement.reflns_used' + loop_ + _alias.definition_id '_cell_measurement_reflns_used' + _definition.update 2012-11-22 + _description.text +; + Total number of reflections used to determine the unit cell. + The reflections may be specified as cell_measurement_refln items. +; + _description.common 'CellMeasReflnCount' + _name.category_id measurement + _name.object_id reflns_used + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Count + save_ + + +save_cell_measurement.temperature + _definition.id '_cell_measurement.temperature' + loop_ + _alias.definition_id '_cell_measurement_temperature' + _definition.update 2012-11-22 + _description.text +; + The temperature at which the unit-cell parameters were measured + (not the temperature of synthesis). +; + _description.common 'CellMeasTemperature' + _name.category_id measurement + _name.object_id temperature + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_cell_measurement.theta_max + _definition.id '_cell_measurement.theta_max' + loop_ + _alias.definition_id '_cell_measurement_theta_max' + _definition.update 2012-11-22 + _description.text +; + Maximum theta scattering angle of reflections used to measure + the crystal unit cell. +; + _description.common 'CellMeasThetaMax' + _name.category_id measurement + _name.object_id theta_max + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_cell_measurement.theta_min + _definition.id '_cell_measurement.theta_min' + loop_ + _alias.definition_id '_cell_measurement_theta_min' + _definition.update 2012-11-22 + _description.text +; + Minimum theta scattering angle of reflections used to measure + the crystal unit cell. +; + _description.common 'CellMeasThetaMin' + _name.category_id measurement + _name.object_id theta_min + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_cell_measurement.wavelength + _definition.id '_cell_measurement.wavelength' + loop_ + _alias.definition_id '_cell_measurement_wavelength' + _definition.update 2012-11-22 + _description.text +; + Wavelength of the radiation used to measure the unit cell. + If this is not specified, the wavelength is assumed to be the + same as that given in _diffrn_radiation_wavelength.value +; + _description.common 'CellMeasWaveLength' + _name.category_id measurement + _name.object_id wavelength + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +#---------------------------------------------------------------------------- + +save_CELL_MEASUREMENT_REFLN + + _definition.id CELL_MEASUREMENT_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the reflection data + used in the measurement of the crystal unit cell. +; + _name.category_id CELL_MEASUREMENT + _name.object_id REFLN + _category.key_id '_cell_measurement_refln.key' + + +save_cell_measurement_refln.key + _definition.id '_cell_measurement_refln.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of CELL_MEASUREMENT_REFLN items + in a looped list. +; + _description.common 'Key to cell measurement reflections' + _name.category_id refln + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(cell_measurement_refln.hkl) +; + Evaluation +; _cell_measurement_refln.key = _cell_measurement_refln.hkl +; + save_ + + +save_cell_measurement_refln.hkl + _definition.id '_cell_measurement_refln.hkl' + _definition.update 2012-11-22 + _description.text +; + Miller indices of a reflection used to measure the unit cell. +; + _description.common 'CellMeasReflnHkl' + _name.category_id refln + _name.object_id hkl + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_measurement_refln + + _cell_measurement_refln.hkl = [c.index_h, c.index_k, c.index_l] +; + save_ + + +save_cell_measurement_refln.theta + _definition.id '_cell_measurement_refln.theta' + loop_ + _alias.definition_id '_cell_measurement_refln_theta' + _definition.update 2012-11-22 + _description.text +; + Theta angle of reflection used to measure the crystal unit cell. +; + _description.common 'CellMeasReflnTheta' + _name.category_id refln + _name.object_id theta + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees + save_ + + +save_cell_measurement_refln.index_h + _definition.id '_cell_measurement_refln.index_h' + loop_ + _alias.definition_id '_cell_measurement_refln_index_h' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_h + save_ + + +save_cell_measurement_refln.index_k + _definition.id '_cell_measurement_refln.index_k' + loop_ + _alias.definition_id '_cell_measurement_refln_index_k' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_k + save_ + + +save_cell_measurement_refln.index_l + _definition.id '_cell_measurement_refln.index_l' + loop_ + _alias.definition_id '_cell_measurement_refln_index_l' + _import.get [{"file":'templ_attr.cif',"save":'Miller_index'}] + _name.category_id refln + _name.object_id index_l + save_ + + save_ #------- close of CELL_MEASUREMENT_REFLN category + + save_ #------- close of CELL_MEASUREMENT category + + +#---------------------------------------------------------------------------- + + +save_CELL_RECIPROCAL + + _definition.id CELL_RECIPROCAL + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the unit cell data + in reciprocal space. +; + _name.category_id CELL + _name.object_id RECIPROCAL + + +save_cell_reciprocal.convert_U_to_beta + _definition.id '_cell_reciprocal.convert_U_to_beta' + _definition.update 2012-11-30 + _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 -2pi**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 - ( beta11 h h + ............ 2 beta23 k l ) + + The conversion of the U or B matrices to the beta matrix + + beta = C U C = C B C /8pi**2 + + where C is conversion matrix defined here. +; + _description.common 'CellRecipConvertUtoBeta' + _name.category_id reciprocal + _name.object_id convert_U_to_beta + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With r as cell_reciprocal_length + + _cell_reciprocal.convert_U_to_beta = \ + 1.4142 * Pi * Matrix([[ r.a, 0, 0 ], + [ 0, r.b, 0 ], + [ 0, 0, r.c ]]) +; + save_ + + +save_cell_reciprocal.metric_tensor + _definition.id '_cell_reciprocal.metric_tensor' + _definition.update 2012-11-22 + _description.text +; + The reciprocal (contravariant) metric tensor used to transform + vectors and coordinates from reciprocal space to real (direct) + space. +; + _description.common 'CellRecipMetricTensor' + _name.category_id reciprocal + _name.object_id metric_tensor + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + with r as cell_reciprocal_vector + + _cell_reciprocal.metric_tensor = [[ r.a*r.a, r.a*r.b, r.a*r.c ], + [ r.b*r.a, r.b*r.b, r.b*r.c ], + [ r.c*r.a, r.c*r.b, r.c*r.c ]] +; + save_ + + +save_cell_reciprocal.orthogonal_matrix + _definition.id '_cell_reciprocal.orthogonal_matrix' + _definition.update 2012-11-22 + _description.text +; + Orthogonal matrix of the reciprocal space. The matrix may be + used to transform the non-orthogonal vector h = (h,k,l) into + the orthogonal indices p = (p,q,r) + + M h = p +; + _description.common 'HklOthogMatrix' + _name.category_id reciprocal + _name.object_id orthogonal_matrix + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_reciprocal.orthogonal_matrix = Inverse( + + Transpose( _cell.orthogonal_matrix )) +; + save_ + + +#---------------------------------------------------------------------------- + + +save_CELL_RECIPROCAL_ANGLE + + _definition.id CELL_RECIPROCAL_ANGLE + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the unit cell angles + in reciprocal space. +; + _name.category_id CELL_RECIPROCAL + _name.object_id ANGLE + + +save_cell_reciprocal_angle.alpha + _definition.id '_cell_reciprocal_angle.alpha' + loop_ + _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. +; + _description.common 'CellRecipAngleAlpha' + _name.category_id angle + _name.object_id alpha + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_angle + + _cell_reciprocal_angle.alpha = Acosd( + (Cosd(c.beta)*Cosd(c.gamma)-Cosd(c.alpha))/(Sind(c.beta)*Sind(c.gamma))) +; + save_ + + +save_cell_reciprocal_angle.beta + _definition.id '_cell_reciprocal_angle.beta' + loop_ + _alias.definition_id '_cell_reciprocal_angle_beta' + _definition.update 2013-01-18 + _description.text +; + Reciprocal of the angle between _cell_length.a and _cell_length.c. + Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. + New York: John Wiley & Sons Inc. +; + _description.common 'CellRecipAngleBeta' + _name.category_id angle + _name.object_id beta + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_angle + + _cell_reciprocal_angle.beta = Acosd( + (Cosd(c.alpha)*Cosd(c.gamma)-Cosd(c.beta))/(Sind(c.alpha)*Sind(c.gamma))) +; + save_ + + +save_cell_reciprocal_angle.gamma + _definition.id '_cell_reciprocal_angle.gamma' + loop_ + _alias.definition_id '_cell_reciprocal_angle_gamma' + _definition.update 2013-01-18 + _description.text +; + Reciprocal of the angle between _cell_length.a and _cell_length.b. + Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. + New York: John Wiley & Sons Inc. +; + _description.common 'CellRecipAngleGamma' + _name.category_id angle + _name.object_id gamma + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_angle + + _cell_reciprocal_angle.gamma = Acosd( + (Cosd(c.alpha)*Cosd(c.beta)-Cosd(c.gamma))/(Sind(c.alpha)*Sind(c.beta))) +; + save_ + + save_ #--------- close of CELL_RECIPROCAL_ANGLE category + + +#---------------------------------------------------------------------------- + +save_CELL_RECIPROCAL_LENGTH + + _definition.id CELL_RECIPROCAL_LENGTH + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the unit cell lengths + in reciprocal space. +; + _name.category_id CELL_RECIPROCAL + _name.object_id LENGTH + + +save_cell_reciprocal_length.a + _definition.id '_cell_reciprocal_length.a' + loop_ + _alias.definition_id '_cell_reciprocal_length_a' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_length.a. +; + _description.common 'CellRecipLengthA' + _name.category_id length + _name.object_id a + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code reciprocal_angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_reciprocal_length.a = Norm ( _cell_reciprocal_vector.a ) +; + save_ + + +save_cell_reciprocal_length.b + _definition.id '_cell_reciprocal_length.b' + loop_ + _alias.definition_id '_cell_reciprocal_length_b' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_length.b. +; + _description.common 'CellRecipLengthB' + _name.category_id length + _name.object_id b + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code reciprocal_angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_reciprocal_length.b = Norm ( _cell_reciprocal_vector.b ) +; + save_ + + +save_cell_reciprocal_length.c + _definition.id '_cell_reciprocal_length.c' + loop_ + _alias.definition_id '_cell_reciprocal_length_c' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_length.c. +; + _description.common 'CellRecipLengthC' + _name.category_id length + _name.object_id c + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code reciprocal_angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + _cell_reciprocal_length.c = Norm ( _cell_reciprocal_vector.c ) +; + save_ + + save_ #--------- close of CELL_RECIPROCAL_LENGTH category + + +#---------------------------------------------------------------------------- + +save_CELL_RECIPROCAL_VECTOR + + _definition.id CELL_RECIPROCAL_VECTOR + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe the unit cell vectors + in reciprocal space. +; + _name.category_id CELL_RECIPROCAL + _name.object_id VECTOR + + +save_cell_reciprocal_vector.a + _definition.id '_cell_reciprocal_vector.a' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_vector.a. +; + _description.common 'CellRecipVectorA' + _name.category_id vector + _name.object_id a + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_vector + + _cell_reciprocal_vector.a = c.b ^ c.c / _cell.volume +; + save_ + + +save_cell_reciprocal_vector.b + _definition.id '_cell_reciprocal_vector.b' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_vector.b. +; + _description.common 'CellRecipVectorB' + _name.category_id vector + _name.object_id b + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_vector + + _cell_reciprocal_vector.b = c.c ^ c.a / _cell.volume +; + save_ + + +save_cell_reciprocal_vector.c + _definition.id '_cell_reciprocal_vector.c' + _definition.update 2012-11-22 + _description.text +; + Reciprocal of the _cell_vector.c. +; + _description.common 'CellRecipVectorC' + _name.category_id vector + _name.object_id c + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as cell_vector + + _cell_reciprocal_vector.c = c.a ^ c.b / _cell.volume +; + save_ + + save_ #--------- close of CELL_RECIPROCAL_VECTOR category + + save_ #--------- close of CELL_RECIPROCAL category + + save_ #--------- close of CELL category + + +#============================================================================ + +save_CHEMICAL + + _definition.id CHEMICAL + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items which describe the composition and + chemical properties of the compound under study. The formula data + items must be consistent with the density, unit-cell and Z values. +; + _name.category_id EXPTL + _name.object_id CHEMICAL + + +save_chemical.absolute_configuration + _definition.id '_chemical.absolute_configuration' + loop_ + _alias.definition_id '_chemical_absolute_configuration' + _definition.update 2012-11-22 + _description.text +; + Necessary conditions for this assignment are given by + Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, + 908-915. (http://www.iucr.org/paper?sh0129) + Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. + 33, 1143-1148. (http://www.iucr.org/paper?ks0021) +; + _description.common 'ChemAbsConfigCode' + _name.category_id chemical + _name.object_id absolute_configuration + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + rm +; 'reference molecule' Absolute configuration established by + the structure determination of a compound containing a + chiral reference molecule of known absolute configuration. +; + ad +; 'anomalous dispersion' Absolute configuration established by + a-d effects in diffraction measurements on the crystal. +; + rmad +; 'rm + ad' Absolute configuration established by the structure + determination of a compound containing a chiral reference + molecule of known absolute configuration and confirmed by + a-d effects in diffraction measurements on the crystal. +; + syn +; 'synthetic' Absolute configuration has not been established + by anomalous-dispersion effects in diffraction measurements on + the crystal. The enantiomer has been assigned by reference to + an unchanging chiral centre in the synthetic procedure. +; + unk +; 'unknown' No firm chemical or a-d evidence for an assignment + is available. An arbitrary choice of enantiomer has been made. +; + . 'inapplicable' + save_ + + +save_chemical.compound_source + _definition.id '_chemical.compound_source' + loop_ + _alias.definition_id '_chemical_compound_source' + _definition.update 2012-11-22 + _description.text +; + Description of the source of the compound under study, or of the + parent molecule if a simple derivative is studied. This includes + the place of discovery for minerals or the actual source of a + natural product. +; + _description.common 'ChemCompoundSource' + _name.category_id chemical + _name.object_id compound_source + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + save_ + + +save_chemical.enantioexcess_bulk + _definition.id '_chemical.enantioexcess_bulk' + loop_ + _alias.definition_id '_chemical_enantioexcess_bulk' + _definition.update 2013-01-18 + _description.text +; + The enantioexcess of the bulk material from which the crystals + were grown. A value of 0.0 indicates the racemate. A value of + 1.0 indicates that the compound is enantiomerically pure. + Enantioexcess is defined in the IUPAC Recommendations + (Moss et al., 1996). The composition of the crystal + and bulk must be the same. + Ref: Moss G. P. et al. (1996). Basic Terminology of + Stereochemistry. Pure Appl. Chem., 68, 2193-2222. + http://www.chem.qmul.ac.uk/iupac/stereo/index.html +; + _name.category_id chemical + _name.object_id enantioexcess_bulk + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_chemical.enantioexcess_bulk_technique + _definition.id '_chemical.enantioexcess_bulk_technique' + loop_ + _alias.definition_id '_chemical_enantioexcess_bulk_technique' + _definition.update 2013-01-18 + _description.text +; + Technique used to determine the enantioexcess of the bulk compound. +; + _name.category_id chemical + _name.object_id enantioexcess_bulk_technique + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + OA +; Enantioexcess determined by measurement of the specific rotation + of the optical activity of the bulk compound in solution. +; + CD +; Enantioexcess determined by measurement of the visible/near UV + circular dichroism spectrum of the bulk compound in solution. +; + EC +; Enantioexcess determined by enantioselective chromatography of + the bulk compound in solution. +; + other +; Enantioexcess determined by a technique not in this list. +; + save_ + + +save_chemical.enantioexcess_crystal + _definition.id '_chemical.enantioexcess_crystal' + loop_ + _alias.definition_id '_chemical_enantioexcess_crystal' + _definition.update 2013-01-18 + _description.text +; + The enantioexcess of the crystal used for the diffraction + study. A value of 0.0 indicates the racemate. A value of + 1.0 indicates that the crystal is enantiomerically pure. + Enantioexcess is defined in the IUPAC Recommendations + (Moss et al., 1996). + Ref: Moss G. P. et al. (1996). Basic Terminology of + Stereochemistry. Pure Appl. Chem., 68, 2193-2222. + http://www.chem.qmul.ac.uk/iupac/stereo/index.html +; + _name.category_id chemical + _name.object_id enantioexcess_crystal + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_chemical.enantioexcess_crystal_technique + _definition.id '_chemical.enantioexcess_crystal_technique' + loop_ + _alias.definition_id '_chemical_enantioexcess_crystal_technique' + _definition.update 2013-01-18 + _description.text +; + Technique used to determine the enantioexcess of the crystal. +; + _name.category_id chemical + _name.object_id enantioexcess_crystal_technique + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + CD +; Enantioexcess determined by measurement of the visible/near UV + circular dichroism spectrum of the crystal taken into solution. +; + EC +; Enantioexcess determined by enantioselective chromatography of + the crystal taken into solution. +; + other +; Enantioexcess determined by a technique not in this list. +; + save_ + + +save_chemical.identifier_inchi + _definition.id '_chemical.identifier_inchi' + loop_ + _alias.definition_id '_chemical_identifier_inchi' + _definition.update 2013-01-18 + _description.text +; + The IUPAC International Chemical Identifier (InChI) is a + textual identifier for chemical substances, designed to provide + a standard and human-readable way to encode molecular information + and to facilitate the search for such information in databases + and on the web. + Ref: McNaught, A. (2006). Chem. Int. (IUPAC), 28 (6), 12-14. + http://www.iupac.org/inchi/ +; + _name.category_id chemical + _name.object_id identifier_inchi + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case + _description_example.detail + InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H' naphthalene + save_ + + +save_chemical.identifier_inchi_key + _definition.id '_chemical.identifier_inchi_key' + loop_ + _alias.definition_id '_chemical_identifier_inchi_key' + _definition.update 2013-01-18 + _description.text +; + The InChIKey is a compact hashed version of the full InChI + (IUPAC International Chemical Identifier), designed to allow + for easy web searches of chemical compounds. See + http://www.iupac.org/inchi/ +; + _name.category_id chemical + _name.object_id identifier_inchi_key + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case + _description_example.detail + 'InChIKey=OROGSEYTTFOCAN-DNJOTXNNBG' codeine + save_ + + +save_chemical.identifier_inchi_version + _definition.id '_chemical.identifier_inchi_version' + loop_ + _alias.definition_id '_chemical_identifier_inchi_version' + _definition.update 2013-01-18 + _description.text +; + Version number of the InChI standard to which the associated + chemical identifier string applies. +; + _name.category_id chemical + _name.object_id identifier_inchi_version + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _description_example.case 1.03 + save_ + + +save_chemical.melting_point + _definition.id '_chemical.melting_point' + loop_ + _alias.definition_id '_chemical_melting_point' + _definition.update 2012-11-22 + _description.text +; + The temperature at which a crystalline solid changes to a liquid. +; + _description.common 'ChemMeltingPoint' + _name.category_id chemical + _name.object_id melting_point + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.melting_point_gt + _definition.id '_chemical.melting_point_gt' + loop_ + _alias.definition_id '_chemical_melting_point_gt' + _definition.update 2012-12-11 + _description.text +; + A temperature above which the melting point lies. + _chemical.melting_point should be used in preference where possible. +; + _name.category_id chemical + _name.object_id melting_point_gt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.melting_point_lt + _definition.id '_chemical.melting_point_lt' + loop_ + _alias.definition_id '_chemical_melting_point_lt' + _definition.update 2012-12-11 + _description.text +; + A temperature below which the melting point lies. + _chemical.melting_point should be used in preference where possible. +; + _name.category_id chemical + _name.object_id melting_point_lt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.name_common + _definition.id '_chemical.name_common' + loop_ + _alias.definition_id '_chemical_name_common' + _definition.update 2012-11-22 + _description.text +; + Trivial name by which the compound is commonly known. +; + _description.common 'ChemCommonName' + _name.category_id chemical + _name.object_id name_common + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_chemical.name_mineral + _definition.id '_chemical.name_mineral' + loop_ + _alias.definition_id '_chemical_name_mineral' + _definition.update 2012-11-22 + _description.text +; + Mineral name accepted by the International Mineralogical Association. + Use only for natural minerals. +; + _description.common 'ChemMineralName' + _name.category_id chemical + _name.object_id name_mineral + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_chemical.name_structure_type + _definition.id '_chemical.name_structure_type' + loop_ + _alias.definition_id '_chemical_name_structure_type' + _definition.update 2012-11-22 + _description.text +; + Commonly used structure-type name. Usually only applied to + minerals or inorganic compounds. +; + _description.common 'ChemStructuralName' + _name.category_id chemical + _name.object_id name_structure_type + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_chemical.name_systematic + _definition.id '_chemical.name_systematic' + loop_ + _alias.definition_id '_chemical_name_systematic' + _definition.update 2012-11-22 + _description.text +; + IUPAC or Chemical Abstracts full name of compound. +; + _description.common 'ChemSystemName' + _name.category_id chemical + _name.object_id name_systematic + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_chemical.optical_rotation + _definition.id '_chemical.optical_rotation' + loop_ + _alias.definition_id '_chemical_optical_rotation' + _definition.update 2012-11-22 + _description.text +; + The optical rotation in solution of the compound is + specified in the following format: + + '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' + + where: TEMP is the temperature of the measurement in degrees Celsius, + WAVE is an indication of the wavelength of the light + used for the measurement, + CONC is the concentration of the solution given as the + mass of the substance in g in 100 ml of solution, + SORT is the signed value (preceded by a + or a - sign) + of 100.\a/(l.c), where \a is the signed optical + rotation in degrees measured in a cell of length l in + dm and c is the value of CONC in g, and + SOLV is the chemical formula of the solvent. +; + _description.common 'ChemOpticalRotDetails' + _name.category_id chemical + _name.object_id optical_rotation + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)' + save_ + + +save_chemical.properties_biological + _definition.id '_chemical.properties_biological' + loop_ + _alias.definition_id '_chemical_properties_biological' + _definition.update 2012-12-11 + _description.text +; + A description of the biological properties of the material. +; + _name.category_id chemical + _name.object_id properties_biological + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case +; diverse biological activities including use as a laxative + and strong antibacterial activity against S. aureus and weak + activity against cyclooxygenase-1 (COX-1) +; +; antibiotic activity against Bacillus subtilis (ATCC 6051) but no + significant activity against Candida albicans (ATCC 14053), + Aspergillus flavus (NRRL 6541) & Fusarium verticillioides (NRRL 25457) +; +; weakly potent lipoxygenase nonredox inhibitor +; +; no influenza A virus sialidase inhibitory & plaque reduction activities +; +; low toxicity against Drosophila melanogaster +; + save_ + + +save_chemical.properties_physical + _definition.id '_chemical.properties_physical' + loop_ + _alias.definition_id '_chemical_properties_physical' + _definition.update 2012-12-11 + _description.text +; + A description of the physical properties of the material. +; + _name.category_id chemical + _name.object_id properties_physical + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case + air-sensitive moisture-sensitive hygroscopic + deliquescent oxygen-sensitive photo-sensitive + pyrophoric semiconductor + 'ferromagnetic at low temperature' 'paramagnetic and thermochromic' + save_ + + +save_chemical.temperature_decomposition + _definition.id '_chemical.temperature_decomposition' + loop_ + _alias.definition_id '_chemical_temperature_decomposition' + _definition.update 2012-12-11 + _description.text +; + The temperature at which a crystalline solid decomposes. +; + _name.category_id chemical + _name.object_id temperature_decomposition + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.temperature_decomposition_gt + _definition.id '_chemical.temperature_decomposition_gt' + loop_ + _alias.definition_id '_chemical_temperature_decomposition_gt' + _definition.update 2012-12-11 + _description.text +; + The temperature above which a crystalline solid decomposes. + _chemical.temperature_decomposition should be used in preference. +; + _name.category_id chemical + _name.object_id temperature_decomposition_gt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.temperature_decomposition_lt + _definition.id '_chemical.temperature_decomposition_lt' + loop_ + _alias.definition_id '_chemical_temperature_decomposition_lt' + _definition.update 2012-12-11 + _description.text +; + The temperature below which a crystalline solid decomposes. + _chemical.temperature_decomposition should be used in preference. +; + _name.category_id chemical + _name.object_id temperature_decomposition_lt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.temperature_sublimation + _definition.id '_chemical.temperature_sublimation' + loop_ + _alias.definition_id '_chemical_temperature_sublimation' + _definition.update 2012-12-11 + _description.text +; + The temperature at which a crystalline solid sublimates. +; + _name.category_id chemical + _name.object_id temperature_sublimation + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.temperature_sublimation_gt + _definition.id '_chemical.temperature_sublimation_gt' + loop_ + _alias.definition_id '_chemical_temperature_sublimation_gt' + _definition.update 2012-12-11 + _description.text +; + The temperature above which a crystalline solid sublimates. + _chemical.temperature_sublimation should be used in preference. +; + _name.category_id chemical + _name.object_id temperature_sublimation_gt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + + +save_chemical.temperature_sublimation_lt + _definition.id '_chemical.temperature_sublimation_lt' + loop_ + _alias.definition_id '_chemical_temperature_sublimation_lt' + _definition.update 2012-12-11 + _description.text +; + The temperature below which a crystalline solid sublimates. + _chemical.temperature_sublimation should be used in preference. +; + _name.category_id chemical + _name.object_id temperature_sublimation_lt + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins + save_ + +#============================================================================ + +save_CHEMICAL_CONN_ATOM + + _definition.id CHEMICAL_CONN_ATOM + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items which describe the 2D chemical structure of + the molecular species. They allow a 2D chemical diagram to be + reconstructed for use in a publication or in a database search + for structural and substructural relationships. In particular, + the chemical_conn_atom data items provide information about the + chemical properties of the atoms in the structure. In cases + where crystallographic and molecular symmetry elements coincide + they must also contain symmetry-generated atoms, so as to describe + a complete chemical entity. + +; + _description.common 'Chemical Connectivity List' + _name.object_id CONN_ATOM + _name.category_id CHEMICAL + _category.key_id '_chemical_conn_atom.key' + + +save_chemical_conn_atom.key + _definition.id '_chemical_conn_atom.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of CHEMICAL_CONN_ATOM items + in a looped list. +; + _description.common 'Chemical Connectivity List' + _name.category_id conn_atom + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(chemical_conn_atom.number)) +; + Evaluation +; _chemical_conn_atom.key = _chemical_conn_atom.number +; + save_ + +save_chemical_conn_atom.charge + _definition.id '_chemical_conn_atom.charge' + loop_ + _alias.definition_id '_chemical_conn_atom_charge' + _definition.update 2012-11-22 + _description.text +; + The net integer charge assigned to this atom. This is the + formal charge assignment normally found in chemical diagrams. +; + _description.common 'ChemConnAtomCharge' + _name.category_id conn_atom + _name.object_id charge + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range -6:6 + _enumeration.default 0 + save_ + + +save_chemical_conn_atom.display_x + _definition.id '_chemical_conn_atom.display_x' + loop_ + _alias.definition_id '_chemical_conn_atom_display_x' + _definition.update 2012-11-22 + _description.text +; + Cartesian coordinate (x) of the atom site in a chemical diagram. The + coordinate origin is at the lower left corner, the x axis is horizontal. +; + _description.common 'ChemConnDisplayX' + _name.category_id conn_atom + _name.object_id display_x + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_chemical_conn_atom.display_y + _definition.id '_chemical_conn_atom.display_y' + loop_ + _alias.definition_id '_chemical_conn_atom_display_y' + _definition.update 2012-11-22 + _description.text +; + Cartesian coordinate (y) of the atom site in a chemical diagram. The + coordinate origin is at the lower left corner, the y axis is vertical. +; + _description.common 'ChemConnDisplayY' + _name.category_id conn_atom + _name.object_id display_y + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_chemical_conn_atom.NCA + _definition.id '_chemical_conn_atom.NCA' + loop_ + _alias.definition_id '_chemical_conn_atom_NCA' + _definition.update 2012-11-22 + _description.text +; + Total number of connected atoms excluding terminal hydrogen atoms. +; + _description.common 'ChemConnAtomNCA' + _name.category_id conn_atom + _name.object_id NCA + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_chemical_conn_atom.NH + _definition.id '_chemical_conn_atom.NH' + loop_ + _alias.definition_id '_chemical_conn_atom_NH' + _definition.update 2012-11-22 + _description.text +; + Total number of hydrogen atoms attached to this atom, + regardless of whether they are included in the refinement or + the atom_site list. This number will be the same as + _atom_site.attached_hydrogens only if none of the hydrogen + atoms appear in the atom_site list. +; + _description.common 'ChemConnAtomNH' + _name.category_id conn_atom + _name.object_id NH + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_chemical_conn_atom.number + _definition.id '_chemical_conn_atom.number' + loop_ + _alias.definition_id '_chemical_conn_atom_number' + _definition.update 2012-11-22 + _description.text +; + The chemical sequence number to be associated with this atom. +; + _description.common 'ChemConnAtomNumber' + _name.category_id conn_atom + _name.object_id number + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Index + _enumeration.range 1: + save_ + + +save_chemical_conn_atom.type_symbol + _definition.id '_chemical_conn_atom.type_symbol' + loop_ + _alias.definition_id '_chemical_conn_atom_type_symbol' + _definition.update 2012-11-22 + _description.text +; + A code identifying the atom type. +; + _description.common 'ChemConnAtomType' + _name.category_id conn_atom + _name.object_id type_symbol + _name.linked_item_id '_atom_type.symbol' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + save_ #------ close the CHEMICAL_CONN_ATOM category + +#---------------------------------------------------------------------------- + +save_CHEMICAL_CONN_BOND + + _definition.id CHEMICAL_CONN_BOND + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items which specify the connections between + the atoms sites in the chemical_conn_atom list and the nature + of the chemical bond between these atoms. These are details about + the two-dimensional (2D) chemical structure of the molecular species. + They allow a 2D chemical diagram to be reconstructed for use in a + publication or in a database search for structural and substructural + relationships. + +; + _description.common 'ChemConnBondList' + _name.category_id CHEMICAL + _name.object_id CONN_BOND + _category.key_id '_chemical_conn_bond.key' + + +save_chemical_conn_bond.key + _definition.id '_chemical_conn_bond.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of CHEMICAL_CONN_BOND items + in a looped list. +; + _description.common 'Chemical Connectivity Bond List' + _name.category_id conn_bond + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(chemical_conn_bond.id) +; + Evaluation +; _chemical_conn_bond.key = _chemical_conn_bond.id +; + save_ + +save_chemical_conn_bond.atom_1 + _definition.id '_chemical_conn_bond.atom_1' + loop_ + _alias.definition_id '_chemical_conn_bond_atom_1' + _definition.update 2012-11-22 + _description.text +; + The first atom in a bond connecting two atom sites. +; + _name.category_id conn_bond + _name.object_id atom_1 + _name.linked_item_id '_chemical_conn_atom.number' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Index + save_ + + +save_chemical_conn_bond.atom_2 + _definition.id '_chemical_conn_bond.atom_2' + loop_ + _alias.definition_id '_chemical_conn_bond_atom_2' + _definition.update 2012-11-22 + _description.text +; + The second atom in a bond connecting two atom sites. +; + _name.category_id conn_bond + _name.linked_item_id '_chemical_conn_atom.number' + _name.object_id atom_2 + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Index + save_ + + +save_chemical_conn_bond.id + _definition.id '_chemical_conn_bond.id' + _definition.update 2012-11-22 + _description.text +; + Bond identifier composed of a list of two sequence numbers + specified as _chemical_conn_atom.number values. +; + _description.common 'ChemConnBondId' + _name.category_id conn_bond + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Integer + _type.dimension [2] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as chemical_conn_bond + + _chemical_conn_bond.id = [ c.atom_1, c.atom_2 ] +; + save_ + + +save_chemical_conn_bond.type + _definition.id '_chemical_conn_bond.type' + loop_ + _alias.definition_id '_chemical_conn_bond_type' + _definition.update 2012-11-22 + _description.text +; + Code for the chemical bond type. +; + _description.common 'ChemConnBondType' + _name.category_id conn_bond + _name.object_id type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail sing 'single bond' + doub 'double bond' + trip 'triple bond' + quad 'quadruple bond' + arom 'aromatic bond' + poly 'polymeric bond' + delo 'delocalized double bond' + pi 'pi bond' + _enumeration.default sing + save_ + + save_ #------ close the CHEMICAL_CONN_BOND category + + +#---------------------------------------------------------------------------- + +save_CHEMICAL_FORMULA + + _definition.id CHEMICAL_FORMULA + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items which specify the composition and chemical + properties of the compound. The formula data items must agree + with those that specify the density, unit-cell and Z values. + + The following rules apply to the construction of the data items + _chemical_formula.analytical, *.structural and *.sum. For the + data item *.moiety the formula construction is broken up into + residues or moieties, i.e. groups of atoms that form a molecular + unit or molecular ion. The rules given below apply within each + moiety but different requirements apply to the way that moieties + are connected (see _chemical_formula.moiety). + + 1. Only recognized element symbols may be used. + + 2. Each element symbol is followed by a 'count' number. A count of + '1' may be omitted. + + 3. A space or parenthesis must separate each cluster of (element + symbol + count). + + 4. Where a group of elements is enclosed in parentheses, the + multiplier for the group must follow the closing parentheses. + That is, all element and group multipliers are assumed to be + printed as subscripted numbers. [An exception to this rule + exists for *.moiety formulae where pre- and post-multipliers + are permitted for molecular units]. + + 5. Unless the elements are ordered in a manner that corresponds to + their chemical structure, as in _chemical_formula.structural, + the order of the elements within any group or moiety + depends on whether or not carbon is present. If carbon is + present, the order should be: C, then H, then the other + elements in alphabetical order of their symbol. If carbon is + not present, the elements are listed purely in alphabetic order + of their symbol. This is the 'Hill' system used by Chemical + Abstracts. This ordering is used in _chemical_formula.moiety + and _chemical_formula.sum. + + _chemical_formula.iupac '[Mo (C O)4 (C18 H33 P)2]' + _chemical_formula.moiety 'C40 H66 Mo O4 P2' + _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo' + _chemical_formula.sum 'C40 H66 Mo O4 P2' + _chemical_formula.weight 768.81 +; + _name.object_id FORMULA + _name.category_id CHEMICAL + + +save_chemical_formula.analytical + _definition.id '_chemical_formula.analytical' + loop_ + _alias.definition_id '_chemical_formula_analytical' + _definition.update 2012-11-22 + _description.text +; + Formula determined by standard chemical analysis including trace + elements. Parentheses are used only for standard uncertainties (su's). +; + _description.common 'ChemFormulaAnalytical' + _name.category_id formula + _name.object_id analytical + _type.purpose Describe + _type.source Observed + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Fe2.45(2) Ni1.60(3) S4' + save_ + + +save_chemical_formula.iupac + _definition.id '_chemical_formula.iupac' + loop_ + _alias.definition_id '_chemical_formula_iupac' + _definition.update 2012-11-22 + _description.text +; + Formula expressed in conformance with IUPAC rules for inorganic + and metal-organic compounds where these conflict with the rules + for any other chemical_formula entries. Typically used for + formatting a formula in accordance with journal rules. This + should appear in the data block in addition to the most + appropriate of the other chemical_formula data names. + Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. + Oxford: Blackwell Scientific Publications. +; + _description.common 'ChemFormulaIupac' + _name.category_id formula + _name.object_id iupac + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' + save_ + + +save_chemical_formula.moiety + _definition.id '_chemical_formula.moiety' + loop_ + _alias.definition_id '_chemical_formula_moiety' + _definition.update 2012-11-22 + _description.text +; + Formula with each discrete bonded residue or ion shown as a + separate moiety. See above CHEMICAL_FORMULA for rules + for writing chemical formulae. In addition to the general + formulae requirements, the following rules apply: + 1. Moieties are separated by commas ','. + 2. The order of elements within a moiety follows general rule + 5 in CHEMICAL_FORMULA. + 3. Parentheses are not used within moieties but may surround + a moiety. Parentheses may not be nested. + 4. Charges should be placed at the end of the moiety. The + Singlege '+' or '-' may be preceded by a numerical multiplier + and should be separated from the last (element symbol + + count) by a space. Pre- or post-multipliers may be used for + individual moieties. +; + _description.common 'ChemFormulaMoiety' + _name.category_id formula + _name.object_id moiety + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'C7 H4 Cl Hg N O3 S' + 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' + 'C12 H16 N2 O6, 5(H2 O1)' + "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)" + save_ + + +save_chemical_formula.structural + _definition.id '_chemical_formula.structural' + loop_ + _alias.definition_id '_chemical_formula_structural' + _definition.update 2012-11-22 + _description.text +; + This formula should correspond to the structure as reported, i.e. + trace elements not included in atom type and atom site lists should + not be included. See category description for the rules for writing + chemical formulae for inorganics, organometallics, metal complexes + etc., in which bonded groups are preserved as discrete entities + within parentheses, with post-multipliers as required. The order of + the elements should give as much information as possible about the + chemical structure. Parentheses may be used and nested as required. + This formula should correspond to the structure as actually reported, + i.e. trace elements not included in atom-type and atom-site lists + should not be included (see also _chemical_formula.analytical). +; + _description.common 'ChemFormulaStructural' + _name.category_id formula + _name.object_id structural + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' + 'Ca ((Cl O3)2 O)2 (H2 O)6' + save_ + + +save_chemical_formula.sum + _definition.id '_chemical_formula.sum' + loop_ + _alias.definition_id '_chemical_formula_sum' + _definition.update 2012-11-22 + _description.text +; + Chemical formulae in which all discrete bonded residues and ions are + summed over the constituent elements, following the ordering given + in rule 5 of the CATEGORY description. Parentheses normally not used. +; + _description.common 'ChemFormulaSum' + _name.category_id formula + _name.object_id sum + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'C18 H19 N7 O8 S' + save_ + + +save_chemical_formula.weight + _definition.id '_chemical_formula.weight' + loop_ + _alias.definition_id '_chemical_formula_weight' + _definition.update 2012-11-22 + _description.text +; + Mass corresponding to the formulae _chemical_formula.structural, + *_iupac, *_moiety or *_sum and, together with the Z value and cell + parameters yield the density given as _exptl_crystal.density_diffrn. +; + _description.common 'ChemFormulaWeight' + _name.category_id formula + _name.object_id weight + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 1.0: + _units.code daltons + save_ + + +save_chemical_formula.weight_meas + _definition.id '_chemical_formula.weight_meas' + loop_ + _alias.definition_id '_chemical_formula_weight_meas' + _definition.update 2012-11-22 + _description.text +; + Formula mass measured by a non-diffraction experiment. +; + _description.common 'ChemFormulaWeightMeas' + _name.category_id formula + _name.object_id weight_meas + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Real + _enumeration.range 1.0: + _units.code daltons + save_ + + save_ #------ close the CHEMICAL_FORMULA category + + save_ #------ close the CHEMICAL category + + +#============================================================================ + +save_SPACE_GROUPS + _definition.id SPACE_GROUPS + _definition.scope Category + _definition.class Ref-loop + _definition.update 2012-11-22 + _description.text +; + Contains all the data items that refer to the space group as a + whole, such as its name, crystal system etc. It may be looped, + for example, in a list of space groups and their properties. + + Only a subset of the SPACE_GROUP category items appear in the + core dictionary. The remainder are found in the cif_sym + dictionary. + + Space group types are identified by their International Tables + for Crystallography Vol. A number. Specific settings of the + space groups can be identified either by their Hall symbol + or by specifying their symmetry operations. + + The commonly-used Hermann-Mauguin symbol determines the + space group type uniquely but several different Hermann-Mauguin + symbols may refer to the same space group type. It contains + information on the choice of the basis, but not on the + choice of origin. Different formats for the Hermann-Mauguin + symbol are found in the cif_sym dictionary. + +; + _name.category_id EXPTL + _name.object_id SPACE_GROUPS + _category.key_id '_space_groups.key' + loop_ + _description_example.case +; + In an instance document this category is typically invoked as + + loop_ _exptl_crystals.key + ${"frame":"space_group_1"}$ + ${"frame":"space_group_2"}$ +; + + +save_space_groups.key + _definition.id '_space_groups.key' + _definition.update 2012-11-22 + _description.text +; + Unique key to a set of SPACE_GROUP items in a looped list. +; + _name.category_id space_groups + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Ref-table + _type.contents Table + loop_ + _description_example.case ' ${"frame":"sg_set_1}$ ' + save_ + +#---------------------------------------------------------------------------- + +save_SPACE_GROUP + + _definition.id SPACE_GROUP + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify space group + information about the crystal used in the diffraction measurements. +; + _name.category_id SPACE_GROUPS + _name.object_id SPACE_GROUP + + +save_space_group.id + _definition.id '_space_group.id' + loop_ + _alias.definition_id '_space_group_id' + _definition.update 2012-11-22 + _description.text +; + Code identifying a space group if multiple symmetries. + See _exptl_crystals.key. +; + _name.category_id space_group + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.contents Code + save_ + + +save_space_group.IT_number + _definition.id '_space_group.IT_number' + loop_ + _alias.definition_id '_space_group_IT_number' + _definition.update 2012-11-22 + _description.text +; + The number as assigned in International Tables for Crystallography + Vol A, specifying the proper affine class (i.e. the orientation + preserving affine class) of space groups (crystallographic space + group type) to which the space group belongs. This number defines + the space group type but not the coordinate system expressed. +; + _name.category_id space_group + _name.object_id IT_number + _type.purpose Quantity + _type.source Selected + _type.contents Integer + save_ + + +save_space_group.name_Hall + _definition.id '_space_group.name_Hall' + loop_ + _alias.definition_id '_space_group_name_Hall' + _definition.update 2012-11-22 + _description.text +; + Space group symbol defined by Hall. Each component of the + space group name is separated by a space or an underscore. + The use of space is strongly recommended because it specifies + the coordinate system. The underscore in the name is only + retained because it was used in earlier archived files. It + should not be used in new CIFs. + Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525 + [See also International Tables for Crystallography, + Vol.B (1993) 1.4 Appendix B] +; + _name.category_id space_group + _name.object_id name_Hall + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' + save_ + + +save_space_group.name_H_M_alt + _definition.id '_space_group.name_H_M_alt' + loop_ + _alias.definition_id '_space_group_name_H-M_alt' + _definition.update 2012-11-22 + _description.text +; + _space_group_name_H-M_alt allows for any Hermann-Mauguin symbol + to be given. The way in which this item is used is determined + by the user and in general is not intended to be interpreted by + computer. It may, for example, be used to give one of the + extended Hermann-Mauguin symbols given in Table 4.3.1 of + International Tables for Crystallography Vol. A (1995) or + a Hermann-Mauguin symbol for a conventional or unconventional + setting. + Each component of the space group name is separated by a + space or underscore. The use of space is strongly + recommended. The underscore is only retained because it + was used in earlier archived files. It should not be + used in new CIFs. Subscripts should appear without special + symbols. Bars should be given as negative signs before the + numbers to which they apply. + The commonly used Hermann-Mauguin symbol determines the space + group type uniquely but a given space group type may be + described by more than one Hermann-Mauguin symbol. The space + group type is best described using _space_group_IT_number. + The Hermann-Mauguin symbol may contain information on the + choice of basis though not on the choice of origin. To + define the setting uniquely use _space_group.name_Hall or + list the symmetry operations. +; + _name.category_id space_group + _name.object_id name_H_M_alt + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case + _description_example.detail + 'P 1 21/m 1' 'space group No. 10' + 'P 2/n 2/n 2/n (origin at -1)' 'space group No. 48 origin 2' + 'R -3 2/m' 'space group No. 166 rhomb' +; loop_ _space_group_id _space_group_name_H-M_alt + 1 'C m c m' + 2 'C 2/c 2/m 21/m' + 3 'A m a m' +; + 'three examples for space group No. 63' + + save_ + + +#------------------------------------------------------------------------- + +save_SPACE_GROUP_SYMOP + + _definition.id SPACE_GROUP_SYMOP + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe symmetry equivalent sites + in the crystal unit cell. +; + _name.category_id SPACE_GROUP + _name.object_id SYMOP + _category.key_id '_space_group_symop.key' + + +save_space_group_symop.key + _definition.id '_space_group_symop.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of space_group_symop items + in a looped list. +; + _name.category_id symop + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(_space_group_symop.id) +; + Evaluation +; _symmetry_equiv.key = _space_group_symop.id +; + save_ + + +save_space_group_symop.id + _definition.id '_space_group_symop.id' + loop_ + _alias.definition_id '_space_group_symop_id' + '_space_group_symop_sg_id' + _definition.update 2012-11-22 + _description.text +; + A sequential number that identifies each symmetry operation. + The identity operation (i.e. _space_group_symop.operation_xyz + set to 'x,y,z') should be set to 1. +; + _name.category_id symop + _name.object_id id + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + save_ + +save_space_group_symop.operation_xyz + _definition.id '_space_group_symop.operation_xyz' + loop_ + _alias.definition_id '_space_group_symop_operation_xyz' + _definition.update 2012-11-22 + _description.text +; + A parsable string giving one of the symmetry operations of the + space group in algebraic form. If W is a matrix representation + of the rotational part of the symmetry operation defined by the + positions and signs of x, y and z, and w is a column of + translations defined by fractions, an equivalent position + X' is generated from a given position X by the equation + + X' = WX + w + + (Note: X is used to represent bold_italics_x in International + Tables for Crystallography Vol. A, Part 5) + + When a list of symmetry operations is given, it must contain + a complete set of coordinate representatives which generates + all the operations of the space group by the addition of + all primitive translations of the space group. Such + representatives are to be found as the coordinates of + the general-equivalent position in International Tables for + Crystallography Vol. A (2002), to which it is necessary to + add any centring translations shown above the + general-equivalent position. + + That is to say, it is necessary to list explicitly all the + symmetry operations required to generate all the atoms in + the unit cell defined by the setting used. +; + _name.category_id symop + _name.object_id operation_xyz + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case + _description_example.detail + 'x,1/2-y,1/2+z' + "glide reflection through the plane (x,1/4,z) with glide vector (1/2)c" + save_ + + save_ #------- close the SPACE_GROUP_SYMOP category + + save_ #------- close the SPACE_GROUP category + + save_ #------- close the SPACE_GROUPS category + + +#======================================================================= + +save_SYMMETRY + + _definition.id SYMMETRY + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe symmetry information + used in crystallographic structure studies. +; + _name.category_id EXPTL + _name.object_id SYMMETRY + + +save_symmetry.cell_setting + _definition.id '_symmetry.cell_setting' + loop_ + _alias.definition_id '_symmetry_cell_setting' + '_space_group_crystal_system' + _definition.update 2012-11-22 + _description.text +; + Code for cell settings for this space-group symmetry. +; + _description.common 'SymmetryCellSetting' + _name.category_id symmetry + _name.object_id cell_setting + _type.purpose State + _type.source Observed + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state triclinic + monoclinic + orthorhombic + tetragonal + rhombohedral + trigonal + hexagonal + cubic + _enumeration.default triclinic + loop_ + _method.purpose + _method.expression + Validation +; + With ca as cell_angle + if(_symmetry.cell_setting == "monoclinic") { + if(Abs(ca.alpha.getValue() - 90.0) > 0.01) { + Throw (_symmetry.cell_setting, 'cellSettingWarning1') + } + if(Abs(ca.alpha.getValue() - ca.gamma.getValue()) > 0.01) { + Throw (_symmetry.cell_setting, 'cellSettingWarning2') + } + } +; + save_ + + +save_symmetry.Int_Tables_number + _definition.id '_symmetry.Int_Tables_number' + loop_ + _alias.definition_id '_symmetry_Int_Tables_number' + _definition.update 2012-11-22 + _description.text +; + Space-group number from International Tables for Cryst., Vol. A. +; + _description.common 'SymmetryIntTabNumber' + _name.category_id symmetry + _name.object_id Int_Tables_number + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + _enumeration.range 1:230 + save_ + + +save_symmetry.multiplicity + _definition.id '_symmetry.multiplicity' + _definition.update 2012-11-22 + _description.text +; + Number of unique symmetry elements in the space group. +; + _description.common 'SymmetryMultiplicity' + _name.category_id symmetry + _name.object_id multiplicity + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Count + _enumeration.range 1:192 + loop_ + _method.purpose + _method.expression + Evaluation +; + n = 0 + + Loop s as symmetry_equiv n += 1 + + _symmetry.multiplicity = n +; + save_ + + +save_symmetry.space_group_name_Hall + _definition.id '_symmetry.space_group_name_Hall' + loop_ + _alias.definition_id '_symmetry_space_group_name_Hall' + _definition.update 2012-11-22 + _description.text +; + Space-group symbol as described by Hall. This symbol gives the + space-group setting explicitly. Leave spaces between the separate + components of the symbol. + Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525. +; + _description.common 'SpaceGroupSymbolHall' + _name.category_id symmetry + _name.object_id space_group_name_Hall + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' + save_ + + +save_symmetry.space_group_name_H-M + _definition.id '_symmetry.space_group_name_H-M' + loop_ + _alias.definition_id '_symmetry_space_group_name_H-M' + _definition.update 2012-11-29 + _description.text +; + Hermann-Mauguin space-group symbol. Note that the H-M symbol does + not necessarily contain complete information about the symmetry + and the space-group origin. If used always supply the FULL symbol + from International Tables for Crystallography, Vol. A (1987) and + indicate the origin and the setting if it is not implicit. If + there is any doubt that the equivalent positions can be uniquely + deduced from this symbol specify the _symmetry_equiv.pos_as_xyz + or *_Hall data items as well. Leave spaces between symbols + referring to different axes. +; + _description.common 'SpaceGroupSymbolH-M' + _name.category_id symmetry + _name.object_id space_group_name_H-M + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'P 1 21/m 1' + 'P 2/n 2/n 2/n (origin at -1)' + 'R -3 2/m' + save_ + +#----------------------------------------------------------------------------- + +save_SYMMETRY_EQUIV + + _definition.id SYMMETRY_EQUIV + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe symmetry equivalent sites + in the crystal unit cell. +; + _name.category_id SYMMETRY + _name.object_id EQUIV + _category.key_id '_symmetry_equiv.key' + + +save_symmetry_equiv.key + _definition.id '_symmetry_equiv.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of SYMMETRY_EQUIV items + in a looped list. +; + _description.common 'Symmetry Equivalent Position List' + _name.category_id equiv + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(symmetry_equiv.pos_site_id) +; + Evaluation +; _symmetry_equiv.key = _symmetry_equiv.pos_site_id +; + save_ + +save_symmetry_equiv.pos_as_xyz + _definition.id '_symmetry_equiv.pos_as_xyz' + loop_ + _alias.definition_id '_symmetry_equiv_pos_as_xyz' + _definition.update 2012-11-22 + _description.text +; + Symmetry equivalent position in the 'xyz' representation. Except + for the space group P1, this data will be repeated in a loop. + The format of the data item is as per International Tables for + Crystallography, Vol. A. (1987). All equivalent positions should + be entered, including those for lattice centring and a centre of + symmetry, if present. +; + _description.common 'SymmetryEquivPosXyz' + _name.category_id equiv + _name.object_id pos_as_xyz + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case -y+x,-y,1/3+z + save_ + + +save_symmetry_equiv.pos_site_id + _definition.id '_symmetry_equiv.pos_site_id' + loop_ + _alias.definition_id '_symmetry_equiv_pos_site_id' + _definition.update 2012-12-30 + _description.text +; + Index identifying each entry in the _symmetry_equiv.pos_as_xyz + list. It is normally the sequence number of the entry in that + list, and should be identified with the code 'n' in the geometry + symmetry codes of the form 'n_klm'. +; + _description.common 'SymmetryEquivPosNumber' + _name.category_id equiv + _name.object_id pos_site_id + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + loop_ + _method.purpose + _method.expression + Evaluation +; + _symmetry_equiv.pos_site_id = Current_Row(_symmetry_equiv) + 1 +; + save_ + + +save_symmetry_equiv.R + _definition.id '_symmetry_equiv.R' + _definition.update 2012-11-22 + _description.text +; + A matrix containing the symmetry rotation operations of a space group + + | r11 r12 r13 | + R = | r21 r22 r23 | + | r31 r32 r33 | +; + _description.common 'SymmetryRotMatrix' + _name.category_id equiv + _name.object_id R + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + sm = _symmetry_equiv.Seitz_matrix + + _symmetry_equiv.R = [[sm[0,0],sm[0,1],sm[0,2]], + [sm[1,0],sm[1,1],sm[1,2]], + [sm[2,0],sm[2,1],sm[2,2]]] +; + save_ + + +save_symmetry_equiv.RT + _definition.id '_symmetry_equiv.RT' + _definition.update 2012-11-22 + _description.text +; + The TRANSPOSE of the symmetry rotation matrix representing the point + group opertions of the space group + + | r11 r21 r31 | + RT = | r12 r22 r32 | + | r13 r23 r33 | +; + _description.common 'SymmetryRotMatrix' + _name.category_id equiv + _name.object_id RT + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + _symmetry_equiv.RT = Transpose (_symmetry_equiv.R) +; + save_ + + +save_symmetry_equiv.Seitz_matrix + _definition.id '_symmetry_equiv.Seitz_matrix' + _definition.update 2012-11-22 + _description.text +; + A matrix containing the symmetry operations of a space group + in 4x4 Seitz format. + + | r11 r12 r13 t1 | + | R T | | r21 r22 r23 t2 | + | 0 1 | | r31 r32 r33 t3 | + | 0 0 0 1 | +; + _description.common 'SymmetrySeitzMatrix' + _name.category_id equiv + _name.object_id Seitz_matrix + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [4,4] + loop_ + _method.purpose + _method.expression + Evaluation +; + _symmetry_equiv.Seitz_matrix = SeitzFromJones (_symmetry_equiv.pos_as_xyz) +; + save_ + + +save_symmetry_equiv.T + _definition.id '_symmetry_equiv.T' + _definition.update 2012-11-22 + _description.text +; + A vector containing the symmetry translation operations of a space group. +; + _description.common 'SymmetryTranslVector' + _name.category_id equiv + _name.object_id T + _type.purpose Quantity + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + sm = _symmetry_equiv.Seitz_matrix + + _symmetry_equiv.T = [sm[0,3],sm[1,3],sm[2,3]] +; + save_ + + save_ #------- close the SYMMETRY_EQUIV category + + save_ #------- close the SYMMETRY category + + save_ #------- close the EXPTL category + + save_ #------- close the EXPERIMENTS category + + save_ #------- close the EXPERIMENTAL category + + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.0.0 2005-12-12 +; + Initial CORE_CRYSTAL dictionary constructed from CORE_3 v3.5.02 +; + 1.0.01 2005-12-20 +; + In methods change all '<-' to '='. +; + 1.1.01 2006-02-11 +; + Remove dictionary definition from save frame. +; + 1.1.02 2006-02-12 +; + Add _dictionary.parent_id. + Insert tuples for template import arguments + Change category 'core_templates' to 'template' +; + 1.2.01 2006-02-21 +; + Basic change in dictionary structure where the dictionary data block now + contains a saveframe defining the category of the DICTIONRY to which + contained data categories are linked. It differs from other CATEGORY + definitions in that its name is NOT part of the child data tags. + This change allows imported dictionaries to be inserted without their + data block header or non-savedframed attributes. +; + 1.2.02 2006-03-07 +; + Add categories CHEMICAL and SYMMETRY to complete CRYSTAL dictionary. +; + 1.3.01 2006-06-20 +; + Apply DDL 3.6.04 attribute changes. +; + 1.3.02 2006-06-30 +; + Apply DDL 3.6.05 attribute changes. +; + 1.3.03 2006-09-07 +; + Apply DDL 3.6.08 attribute changes. +; + 1.3.04 2006-11-13 +; + Apply DDL 3.6.10 attribute changes. +; + 1.4.01 2006-11-15 +; + Apply DDL 3.7.01 attribute changes. +; + 1.4.02 2006-11-16 +; + Made EXPTL_CRYSTAL with scope "Set" +; + 1.4.03 2006-12-14 +; + Apply DDL 3.7.03 attribute changes. +; + 1.4.04 2007-02-07 +; + Apply DDL 3.7.04 attribute changes. +; + 1.4.05 2007-02-09 +; + Corrected TYPE in _chemical_conn_atom.number and + _symmetry_equiv.pos_site_id +; + 1.4.06 2007-10-13 +; + Placed tags in _category_key.primitive lists within quotes. +; + 1.4.07 2007-11-22 +; + Changed the local variables in the method of _cell.orthogonal_matrix + simply for additional clarity. +; + 1.4.08 2008-01-18 +; + Replaced import_list controls with leading uppercase character. + Changed import_list [....] to [[....]] +; + 1.4.09 2008-01-22 +; + In _exptl_crystal_appearance.hue change imported state list to + colour_RBG +; + 1.4.10 2008-02-07 +; + In _exptl_crystal_appearance.hue change colour_RBG to colour_RGB +; + 1.4.11 2008-03-28 +; + Change _type.purpose for _exptl_absorpt.correction_T_min and T_max + from Limit to Measured. +; + 1.4.12 2008-06-18 +; + Change _import_list.id to be ((.....)) + For all *.key items change _type.contents from Code to Inherited + For other *.id items some _type.purpose from Key to Identify +; + 1.4.13 2008-06-19 +; + Make EXPTL_CRYSTAL a List category and add _exptl_crystal.key definition. + Ensure that all items with _type.contents Code are enumerated. +; + 1.4.14 2008-06-24 +; + Change all _type.dimension values + Add to _cell_length.*, _cell_*.*, etc. the _definition.update + and _description.text attributes. +; + 1.5.01 2011-06-07 +; + Replace category class "List" with "Loop" + Replace all "Tuple" with "List" + Replace all "Array" with "List" + Place all import lists into [[......]] +; + 2.1.01 2011-06-18 +; + Introduction of NESTED save frames and the resolution of Loop + categories which are parents of Loop categories. + Introduction of the "Reference" class of category. +; + 2.1.02 2011-06-29 +; + Reduced Reference categories to *.key and redefined item. +; + 2.1.03 2011-07-02 +; + Place name.category_id in each category definition. +; + 2.2.01 2011-07-28 +; + Make the DDL 3.08 changes +; + 2.2.02 2011-08-03 +; + Change name of import file com_att.dic to templ_attr.cif + Change name of import file com_val.dic to templ_templcif +; + 2.2.03 2011-08-15 +; + move the EXPTL_ABSORB category within the EXPTL_CRYSTALS category +; + 2.2.04 2011-12-01 +; + Change container type from List to Matrix for relevant item definitions +; + 2.2.05 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 2.3.01 2012-05-07 +; + Apply DDLm version 3.10.01 changes. +; + 2.3.02 2012-10-16 +; + Apply DDLm version 3.10.02 type.container and type.contents changes. + Remove type.contents "Inherited"; insert Definition method expression. +; + 2.3.03 2012-11-20 +; + Invoke container functions Matrix, List in methods scripts where needed. +; + 2.3.04 2012-11-22 +; + Add DDL1 tags as alias.definition_id values + Add SPACE_GROUP definitions +; + 2.3.05 2012-11-30 +; + Add "\" to method expression for cell_reciprocal.convert_U_to_beta + Doug's TEMPORARY FIX!!!!! +; + 2.3.06 2012-12-11 +; + Add chemical_properties_biological, chemical_properties_physical + chemical_melting_point_lt and _gt + chemical_temperature_decomposition, _lt and _gt + chemical_temperature_sublimation, _lt and _gt. + crystal.density_meas_gt, _lt + crystal.density_meas_temp_gt, _lt + exptl_crystal.recrystallization_method + space_group_symop.sg_id +; + 2.3.07 2012-12-30 +; + Add method for symmetry_equiv.pos_site_id using "Current_Row" funct. +; + 2.3.08 2013-01-18 +; + Add exptl.transmission_factor_max and *.min + Add chemical.enantioexcess_bulk, chemical.enantioexcess_bulk_technique + Add chemical.enantioexcess_crystal_technique + Add chemical.identifier_inchi and related items. +; diff --git a/core_funct.dic b/core_funct.dic new file mode 100644 index 0000000..4a9da78 --- /dev/null +++ b/core_funct.dic @@ -0,0 +1,383 @@ +############################################################################## +# # +# FUNCTIONS USED IN THE CORE DICTIONARIES # +# # +############################################################################## + +data_CRY_FUNC + + _dictionary.title CRY_FUNC + _dictionary.class Function + _dictionary.version 1.3.07 + _dictionary.date 2013-01-25 + _dictionary.uri www.iucr.org/cif/dic/com_func.dic + _dictionary.ddl_conformance 3.10.03 + _description.text +; + This dictionary contains the dREL FUNCTIONS used in the + methods expressions of CIF dictionaries. +; + + +save_FUNCTION + _definition.id FUNCTION + _definition.scope Category + _definition.class Functions + _definition.update 2012-12-18 + _description.text +; + The crystallographic functions the invoked in the definition + methods of CORE STRUCTURE data items defined and used with in + the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_CORE + _name.object_id FUNCTION + +#============================================================================ + + +save_function.AtomType + _definition.id '_function.AtomType' + _definition.update 2012-10-16 + _description.text +; + The function + r = AtomType( s ) + + returns an atom type symbol (element name) from the atom site label. +; + _name.category_id function + _name.object_id AtomType + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Code + loop_ + _method.purpose + _method.expression + Evaluation +; + Function AtomType( s :[Single, Code]) { # atom label + + m = Len(s) + n = 1 + If (m > 1 and s[1] not in '0123456789') n = 2 + If (m > 2 and s[2] in '+-' ) n = 3 + If (m > 3 and s[3] in '+-' ) n = 4 + + AtomType = s[0:n] + } +; + save_ + + +save_function.Closest + _definition.id '_function.Closest' + _definition.update 2012-10-16 + _description.text +; + The function + u, d = Closest( v, u ) + + returns the real coordinate vector U which is the closest cell- + translated occurence of the vector V to the vector W. D is the + cell translation vector required to move V to U. +; + _name.category_id function + _name.object_id Closest + _type.purpose Quantity + _type.source Derived + _type.container List + _type.contents Matrix(Real,Real,Real) + _type.dimension [2] + loop_ + _method.purpose + _method.expression + Evaluation +; + Function Closest( v :[Matrix, Real], # coord vector to be cell translated + w :[Matrix, Real]) { # target vector + + d = v - w + t = Int( Mod( 99.5 + d, 1.0 ) - d ) + + Closest = List ( v+t, t ) + } +; + save_ + + +save_function.SeitzFromJones + _definition.id '_function.SeitzFromJones' + _definition.update 2011-12-01 + _description.text +; + The function + s = SeitzFromJones( j ) + + returns a 4x4 Seitz matrix from the Jones faithful representation of + the equivalent position which is a character string e.g. 1/2+x,-x,z. +; + _name.category_id function + _name.object_id SeitzFromJones + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [4,4] + loop_ + _method.purpose + _method.expression + Evaluation +; + Function SeitzFromJones( j :[Single, Text]) { # Jones symmetry notation + + joneschrs = "123456xyz/,+- " + s = [[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]] + axis = 0 + sign = 1 + inum = 0 + + do i=0,Len(j)-1 { + c = j[i] + If (c not in joneschrs) print 'illegal char in symmetry xyz' + + If (c == ' ') Next + If (c == ',') { + axis += 1 + inum = 0 + sign = 1 + } + Else If (c == '+') sign = +1 + Else If (c == '-') sign = -1 + Else If (c == 'x') s[axis,0] = sign + Else If (c == 'y') s[axis,1] = sign + Else If (c == 'z') s[axis,2] = sign + Else { + If (inum == 0) m = AtoI(c) + If (inum == 1 and c != '/') print 'illegal num in symmetry xyz' + If (inum == 2) { + n = AtoI(c) + If(n == 5) print 'illegal translation in symmetry xyz' + s[axis,3] = Mod(10.+ Float(sign*m)/Float(n), 1.) + sign = 1 + } + inum += 1 + } } + SeitzFromJones = s + } +; + save_ + + +save_function.SymEquiv + _definition.id '_function.SymEquiv' + _definition.update 2012-12-14 + _description.text +; + The function + xyz' = SymEquiv( symop, xyz ) + + returns a fractional coordinate vector xyz' which is input vector + xyz transformed by the input symop 'n_pqr' applied to the symmetry + equivalent matrix extracted from the category symmetry_equiv. +; + _name.category_id function + _name.object_id SymEquiv + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + Function SymEquiv( c :[Single, Symop], # symop string n_pqr + x :[Matrix, Real] ) # fract coordinate vector + { + s = symmetry_equiv [ SymKey( c ) ] + SymEquiv = s.R * x + s.T + SymLat( c ) + } +; + save_ + + +save_function.SymKey + _definition.id '_function.SymKey' + _definition.update 2012-12-17 + _description.text +; + The function + m = SymKey( s ) + + returns an integer index to the Seitz matrices from the character + string of the form 'n_pqr'. +; + _name.category_id function + _name.object_id SymKey + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Index + loop_ + _method.purpose + _method.expression + Evaluation +; + Function SymKey( s :[Single, Symop]) { # symop string + + If (s == '.') n = 1 + Else n = AtoI(s[0]) + +########## SymKey = n - 1 # index from 0 + SymKey = n # index from 1 + } +; + save_ + + +save_function.SymLat + _definition.id '_function.SymLat' + _definition.update 2011-12-01 + _description.text +; + The function + v = SymLat( s ) + + returns a vector of the cell translations applied to the coordinates + from the character string of the form 'n_pqr'. i.e. p-5, q-5, r-5. +; + _name.category_id function + _name.object_id SymLat + _type.purpose Quantity + _type.source Derived + _type.container Matrix + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + Function SymLat( s :[Single, Symop]) { # symop string + + If (s[1] == ' ') v = [ 5, 5, 5 ] + Else v = [ AtoI(s[2]), AtoI(s[3]), AtoI(s[4]) ] + + SymLat = v - 5 + } +; + save_ + + +save_function.Symop + _definition.id '_function.Symop' + _definition.update 2006-06-30 + _description.text +; + The function + s = Symop( n, t ) + + returns a character string of the form 'n_pqr' where n is the + symmetry equivalent site number and [p,q,r] is the cell translation + vector PLUS [5,5,5]. +; + _name.category_id function + _name.object_id Symop + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Symop + loop_ + _method.purpose + _method.expression + Evaluation +; + Function Symop( n :[Single, Integer], # symmetry equivalent site number + t :[List , Integer]) { # cell translation vector + + d = t + 5 + Symop = `n` + '_' + `d[0]` + `d[1]` + `d[2]` + } +; + save_ + + save_ #----------- close of FUNCTION category + + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.1.01 2006-03-07 +; + Initial version of the FUNCTIONS dictionary created from the + definitions used in CORE_3 dictionary version 3.5.02 +; + 1.1.02 2006-06-20 +; + Apply DDL 3.6.04 attributes. +; + 1.1.03 2006-06-30 +; + Apply DDL 3.6.05 attributes. + Remove the leading underscore from definition.id value names. + Substitute = for <- in expressions. +; + 1.1.04 2006-09-20 +; + Apply DDL 3.6.08 attributes. +; + 1.1.05 2006-11-13 +; + Apply DDL 3.6.10 attributes. +; + 1.1.06 2006-12-14 +; + Apply DDL 3.7.01 attributes. +; + 1.1.07 2008-06-24 +; + Change all _type.dimension values from [..[..]] to [..][..] +; + 1.1.08 2008-08-13 +; + Change Array([.....]) to Array(.....) +; + 1.3.01 2011-06-07 +; + Replace all "Tuple" with "List" + Replace all "Array" with "List" +; + 1.3.02 2011-12-01 +; + Change container type from List to Matrix for relevant functions. +; + 1.3.03 2012-05-07 +; + Apply DDL 3.10.01 changes. +; + 1.3.04 2012-10-16 +; + Apply DDL 3.10.02 changes. +; + 1.3.05 2012-12-14 +; + Change the SymEquiv method - put category name symmetry_equiv + directly into the method; reduce args to two here and in model dic. +; + 1.3.06 2012-12-18 +; + Add an overarching saveframe and category FUNCTION for functions. +; + 1.3.07 2013-01-25 +; + Insert a leading underscore in the definition.id values. +; diff --git a/core_model.dic b/core_model.dic new file mode 100755 index 0000000..49ccf17 --- /dev/null +++ b/core_model.dic @@ -0,0 +1,2398 @@ +############################################################################# +# # +# CIF CORE MODEL DICTIONARY # +# # +############################################################################## + +data_CORE_MODEL + + _dictionary.title CORE_MODEL + _dictionary.class Instance + _dictionary.version 1.4.06 + _dictionary.date 2013-01-22 + _dictionary.uri www.iucr.org/cif/dic/core_model.dic + _dictionary.ddl_conformance 3.10.03 + _dictionary.namespace CoreModel + _description.text +; + The DICTIONARY group encompassing the CORE MODEL data items defined + and used with in the Crystallographic Information Framework (CIF). +; + + +save_MODEL + _definition.id MODEL + _definition.scope Category + _definition.class Head + _definition.update 2012-11-22 + _description.text +; + Items in the MODEL Category specify data for the crystal structure + postulated and modelled from the atomic coordinates derived and + refined from the diffraction information. The structural model is + described principally in terms of the geometry of the 'connected' + atom sites and the crystal symmetry in which they reside. +; + _name.category_id CIF_CORE + _name.object_id MODEL + +#============================================================================ + +save_GEOM + _definition.id GEOM + _definition.scope Category + _definition.class Set + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the geometry + of the structural model as derived from the atomic sites. + The geometry is expressed in terms of the interatomic + angles (GEOM_ANGLE data), covalent bond distances + (GEOM_BOND data), contact distances (GEOM_CONTACT data), + hydrogen bonds (GEOM_HBOND data) and torsion geometry + (GEOM_TORSION data). + Geometry data are usually redundant, in that they can be + calculated from other more fundamental quantities in the data + block. However, they serve the dual purposes of providing a + check on the correctness of both sets of data and of enabling + the most important geometric data to be identified for + publication by setting the appropriate publication flag. +; + _description.common 'Structural geometry' + _name.category_id MODEL + _name.object_id GEOM + + +save_geom.bond_distance_incr + _definition.id '_geom.bond_distance_incr' + _definition.update 2012-11-22 + _description.text +; + Increment added to the bond radii for the atomic species to + specify the maximum permitted "bonded" distance between two + atom sites. +; + _description.common 'GeomBondDistIncr' + _name.category_id geom + _name.object_id bond_distance_incr + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.default 0.2 + _units.code angstroms + save_ + + +save_geom.bond_distance_min + _definition.id '_geom.bond_distance_min' + _definition.update 2012-11-22 + _description.text +; + Minimum permitted "bonded" distance between two atom sites. +; + _description.common 'GeomBondDistMin' + _name.category_id geom + _name.object_id bond_distance_min + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.default 0.2 + _units.code angstroms + save_ + + +save_geom.contact_distance_incr + _definition.id '_geom.contact_distance_incr' + _definition.update 2012-11-22 + _description.text +; + Increment added to the bond radii for the atomic species to + specify the maximum permitted "contact" distance between two + "non-bonded" atom sites. +; + _description.common 'GeomContactDistIncr' + _name.category_id geom + _name.object_id contact_distance_incr + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.default 0.2 + _units.code angstroms + save_ + + +save_geom.contact_distance_min + _definition.id '_geom.contact_distance_min' + _definition.update 2012-11-22 + _description.text +; + Minimum permitted "contact" distance between two "non-bonded" atom sites. +; + _description.common 'GeomContactDistMin' + _name.category_id geom + _name.object_id contact_distance_min + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.default 0.2 + _units.code angstroms + save_ + + +save_geom.special_details + _definition.id '_geom.special_details' + loop_ + _alias.definition_id '_geom_special_details' + '_geom.details' + _definition.update 2012-11-22 + _description.text +; + Description of geometry information not covered by the existing data + names in the geometry categories, such as least-squares planes. +; + _description.common 'GeomSpecialDetails' + _name.category_id geom + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + +#---------------------------------------------------------------------------- + +save_GEOM_ANGLE + _definition.id GEOM_ANGLE + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the geometry angles in the + structural model as derived from the atomic sites. +; + _description.common 'BondAngleList' + _name.category_id GEOM + _name.object_id ANGLE + _category.key_id '_geom_angle.key' + loop_ + _method.purpose + _method.expression + Evaluation +; + dmin = _geom.bond_distance_min + + Loop m1 as model_site :i { # loop vertex model site + + rad1 = m1.radius_bond + _geom.bond_distance_incr + + Loop m2 as model_site :j { # loop first target site + + If (i==j or m1.mole_index != m2.mole_index) Next + v1 = m2.Cartn_xyz - m1.Cartn_xyz + d1 = Norm (v1) + + If (d1(rad1+m2.radius_bond)) Next + + rad2 = m2.radius_bond + _geom.bond_distance_incr + + Loop m3 as model_site :k>j { # loop second target site + + If (i==k or m1.mole_index != m3.mole_index) Next + v2 = m3.Cartn_xyz - m1.Cartn_xyz + d2 = Norm (v2) + + If (d2(rad2+m3.radius_bond)) Next + + angle = Acosd ( v1*v2 / (d1*d2) ) + + geom_angle( .id = List ( m2.id, m1.id, m3.id ), + .distances = List ( d1, d2 ), + .value = angle ) + } } } +; + + +save_geom_angle.key + _definition.id '_geom_angle.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of GEOM_ANGLE items + in a looped list. +; + _description.common 'Key to geometry angles' + _name.category_id angle + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(geom_angle.id) +; + Evaluation +; _geom_angle.key = _geom_angle.id +; + save_ + + +save_geom_angle.atom_site_label_1 + _definition.id '_geom_angle.atom_site_label_1' + loop_ + _alias.definition_id '_geom_angle_atom_site_label_1' + '_geom_angle.atom_site_id_1' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id angle + _name.object_id atom_site_label_1 + save_ + + +save_geom_angle.atom_site_label_2 + _definition.id '_geom_angle.atom_site_label_2' + loop_ + _alias.definition_id '_geom_angle_atom_site_label_2' + '_geom_angle.atom_site_id_2' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id angle + _name.object_id atom_site_label_2 + save_ + + +save_geom_angle.atom_site_label_3 + _definition.id '_geom_angle.atom_site_label_3' + loop_ + _alias.definition_id '_geom_angle_atom_site_label_3' + '_geom_angle.atom_site_id_3' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id angle + _name.object_id atom_site_label_3 + save_ + + +save_geom_angle.distances + _definition.id '_geom_angle.distances' + _definition.update 2012-11-22 + _description.text +; + The pair of distances between sites 1 - 2 and 2 - 3. +; + _name.category_id angle + _name.object_id distances + _type.purpose Measurand + _type.source Derived + _type.container List + _type.contents Real + _type.dimension [2] + _units.code angstroms + save_ + + +save_geom_angle.id + _definition.id '_geom_angle.id' + _definition.update 2012-11-22 + _description.text +; + Atom site labels and symmetry operators as pairs for each of the + three atom sites which identify the angle. The second label-symop + pair in the list identifies the site at the apex of the angle. +; + _description.common 'BondAngleId' + _name.category_id angle + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'List(Code,Symop)' + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_angle + + _geom_angle.id = [[ a.atom_site_label_1, a.site_symmetry_1 ], + [ a.atom_site_label_2, a.site_symmetry_2 ], + [ a.atom_site_label_3, a.site_symmetry_3 ]] +; + save_ + + +save_geom_angle.publ_flag + _definition.id '_geom_angle.publ_flag' + loop_ + _alias.definition_id '_geom_angle_publ_flag' + _definition.update 2012-11-22 + _description.text +; + Code signals if the angle is referred to in a publication or + should be placed in a table of significant angles. +; + _description.common 'BondAnglePublFlag' + _name.category_id angle + _name.object_id publ_flag + _type.purpose Quantity + _type.source Selected + _type.container Single + loop_ + _enumeration_set.state + _enumeration_set.detail + no 'do not include angle in special list' + n 'abbreviation for "no"' + yes 'do include angle in special list' + y 'abbreviation for "yes"' + _enumeration.default no + save_ + + +save_geom_angle.site_symmetry_1 + _definition.id '_geom_angle.site_symmetry_1' + loop_ + _alias.definition_id '_geom_angle_site_symmetry_1' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id angle + _name.object_id site_symmetry_1 + save_ + + +save_geom_angle.site_symmetry_2 + _definition.id '_geom_angle.site_symmetry_2' + loop_ + _alias.definition_id '_geom_angle_site_symmetry_2' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id angle + _name.object_id site_symmetry_2 + save_ + + +save_geom_angle.site_symmetry_3 + _definition.id '_geom_angle.site_symmetry_3' + loop_ + _alias.definition_id '_geom_angle_site_symmetry_3' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id angle + _name.object_id site_symmetry_3 + save_ + + +save_geom_angle.value + _definition.id '_geom_angle.value' + loop_ + _alias.definition_id '_geom_angle' + _definition.update 2012-12-14 + _description.text +; + Angle defined by the sites identified by _geom_angle.id +; + _description.common 'BondAngle' + _name.category_id angle + _name.object_id value + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_angle + + xc = List() + + For [label,symop] in a.id { + + xf = SymEquiv(symop, _atom_site[label].fract_xyz) + + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + v1,v2 = xc[0]-xc[1], xc[2]-xc[1] + + _geom_angle.value = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) ) +; + save_ + + save_ #----------- close of GEOM_ANGLE category + +#---------------------------------------------------------------------------- + + +save_GEOM_BOND + _definition.id GEOM_BOND + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the geometry bonds in the + structural model as derived from the atomic sites. +; + _description.common 'BondDistList' + _name.category_id GEOM + _name.object_id BOND + _category.key_id '_geom_bond.key' + loop_ + _method.purpose + _method.expression + Evaluation +; + dmin = _geom.bond_distance_min + + Loop m1 as model_site :i { + + rad = m1.radius_bond + _geom.bond_distance_incr + + Loop m2 as model_site :j { + + If (i==j or m1.mole_index != m2.mole_index) Next + + d = Norm (m1.Cartn_xyz - m2.Cartn_xyz) + + If (d(rad+m2.radius_bond)) Next + + geom_bond( .id = List ( m1.id, m2.id ), + .distance = d ) + } } +; + + +save_geom_bond.key + _definition.id '_geom_bond.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of GEOM_BOND items + in a looped list. +; + _description.common 'Key to geometry distances' + _name.category_id bond + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(geom_bond.id) +; + Evaluation +; _geom_bond.key = _geom_bond.id +; + save_ + + +save_geom_bond.atom_site_label_1 + _definition.id '_geom_bond.atom_site_label_1' + loop_ + _alias.definition_id '_geom_bond_atom_site_label_1' + '_geom_bond.atom_site_id_1' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id bond + _name.object_id atom_site_label_1 + save_ + + +save_geom_bond.atom_site_label_2 + _definition.id '_geom_bond.atom_site_label_2' + loop_ + _alias.definition_id '_geom_bond_atom_site_label_2' + '_geom_bond.atom_site_id_2' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id bond + _name.object_id atom_site_label_2 + save_ + + +save_geom_bond.distance + _definition.id '_geom_bond.distance' + loop_ + _alias.definition_id '_geom_bond_distance' + '_geom_bond.dist' + _definition.update 2012-12-14 + _description.text +; + Intramolecular bond distance between the sites identified + by _geom_bond.id +; + _description.common 'BondDist' + _name.category_id bond + _name.object_id distance + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + With b as geom_bond + + xc = List() + + For [label,symop] in b.id { + + xf = SymEquiv(symop, _atom_site[label].fract_xyz) + + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + _geom_bond.distance = Norm ( xc[0] - xc[1] ) +; + save_ + + +save_geom_bond.valence + _definition.id '_geom_bond.valence' + loop_ + _alias.definition_id '_geom_bond_valence' + _definition.update 2012-12-11 + _description.text +; + Bond valence calculated from the bond distance. +; + _name.category_id bond + _name.object_id valence + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_geom_bond.id + _definition.id '_geom_bond.id' + _definition.update 2012-11-22 + _description.text +; + Identity of bond distance in terms of the atom site labels and + symmetry operators as pairs for each of the two "bonded" atom sites. +; + _description.common 'BondDistId' + _name.category_id bond + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'List(Code,Symop)' + _type.dimension [2] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_bond + + _geom_bond.id = [[ a.atom_site_label_1, a.site_symmetry_1 ], + [ a.atom_site_label_2, a.site_symmetry_2 ]] +; + save_ + + +save_geom_bond.publ_flag + _definition.id '_geom_bond.publ_flag' + loop_ + _alias.definition_id '_geom_bond_publ_flag' + _definition.update 2012-11-22 + _description.text +; + This code signals whether the angle is referred to in a + publication or should be placed in a table of significant angles. +; + _description.common 'BondDistPublFlag' + _name.category_id bond + _name.object_id publ_flag + _type.purpose Quantity + _type.source Selected + _type.container Single + loop_ + _enumeration_set.state + _enumeration_set.detail + no 'do not include bond in special list' + n 'abbreviation for "no"' + yes 'do include bond in special list' + y 'abbreviation for "yes"' + _enumeration.default no + save_ + + +save_geom_bond.multiplicity + _definition.id '_geom_bond.multiplicity' + loop_ + _alias.definition_id '_geom_bond_multiplicity' + _definition.update 2013-01-22 + _description.text +; + The number of times the given bond appears in the environment + of the atoms labelled _geom_bond.atom_site_label_1. In cases + where the full list of bonds is given, one of the series of + equivalent bonds may be assigned the appropriate multiplicity + while the others are assigned a value of 0. +; + _name.category_id bond + _name.object_id multiplicity + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Count + save_ + + +save_geom_bond.site_symmetry_1 + _definition.id '_geom_bond.site_symmetry_1' + loop_ + _alias.definition_id '_geom_bond_site_symmetry_1' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id bond + _name.object_id site_symmetry_1 + save_ + + +save_geom_bond.site_symmetry_2 + _definition.id '_geom_bond.site_symmetry_2' + loop_ + _alias.definition_id '_geom_bond_site_symmetry_2' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id bond + _name.object_id site_symmetry_2 + save_ + + save_ #----------- close of GEOM_BOND category + +#---------------------------------------------------------------------------- + + +save_GEOM_CONTACT + _definition.id GEOM_CONTACT + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the interatomic + contact distances in the structural model. +; + _description.common 'Bond contact list' + _name.category_id GEOM + _name.object_id CONTACT + _category.key_id '_geom_contact.key' + loop_ + _method.purpose + _method.expression + Evaluation +; + Loop m1 as model_site { + + rb = m1.radius_bond + _geom.bond_distance_incr + rc = m1.radius_contact + _geom.contact_distance_incr + + Loop m2 as model_site { + + If (m2.id[1] != '1_555') Next + radb = rb + m2.radius_bond + radc = rc + m2.radius_contact + label = m2.id[0] + + Loop s as symmetry_equiv :ns { + + axyz = s.R * m2.fract_xyz + s.T + + Do i = -2,2 { Do j = -2,2 { Do k = -2,2 { # cell translations + + tran = List ([i,j,k]) + bxyz = axyz + tran + cxyz = _atom_sites_Cartn_transform.matrix * bxyz + d = Norm (cxyz - m1.Cartn_xyz) + + If (d < radb or d > radc) Next + + id = List( m1.id, List( label, Symop(ns+1,tran) ) ) + + geom_contact( .id = id, + .distance = d ) + } } } } } } +; + + +save_geom_contact.key + _definition.id '_geom_contact.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of GEOM_CONTACT items + in a looped list. +; + _description.common 'Key to geometry contact data' + _name.category_id contact + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(geom_contact.id) +; + Evaluation +; _geom_contact.key = _geom_contact.id +; + save_ + + +save_geom_contact.atom_site_label_1 + _definition.id '_geom_contact.atom_site_label_1' + loop_ + _alias.definition_id '_geom_contact_atom_site_label_1' + '_geom_contact.atom_site_id_1' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id contact + _name.object_id atom_site_label_1 + save_ + + +save_geom_contact.atom_site_label_2 + _definition.id '_geom_contact.atom_site_label_2' + loop_ + _alias.definition_id '_geom_contact_atom_site_label_2' + '_geom_contact.atom_site_id_2' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id contact + _name.object_id atom_site_label_2 + save_ + + +save_geom_contact.distance + _definition.id '_geom_contact.distance' + loop_ + _alias.definition_id '_geom_contact_distance' + '_geom_contact.dist' + _definition.update 2012-12-14 + _description.text +; + Intermolecular distance between the atomic sites identifyed + by _geom_contact.id +; + _description.common 'BondContactDist' + _name.category_id contact + _name.object_id distance + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as geom_contact + + xc = List() + + For [label,symop] in c.id { + + xf = SymEquiv(symop, _atom_site[label].fract_xyz) + + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + _geom_contact.distance = Norm ( xc[0] - xc[1] ) +; + save_ + + +save_geom_contact.id + _definition.id '_geom_contact.id' + _definition.update 2012-11-22 + _description.text +; + Atom site labels and symmetry operators as pairs for each of the + two atom sites which define the contact bond. +; + _description.common 'BondContactId' + _name.category_id contact + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'List(Code,Symop)' + _type.dimension [2] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_contact + + _geom_contact.id = [[ a.atom_site_label_1, a.site_symmetry_1 ], + [ a.atom_site_label_2, a.site_symmetry_2 ]] +; + save_ + + +save_geom_contact.publ_flag + _definition.id '_geom_contact.publ_flag' + loop_ + _alias.definition_id '_geom_contact_publ_flag' + _definition.update 2012-11-22 + _description.text +; + This code signals whether the contact distance is referred to + in a publication or should be placed in a list of significant + contact distances. +; + _description.common 'BondContactPublFlag' + _name.category_id contact + _name.object_id publ_flag + _type.purpose Quantity + _type.source Selected + _type.container Single + loop_ + _enumeration_set.state + _enumeration_set.detail + no 'do not include distance in special list' + n 'abbreviation for "no"' + yes 'do include distance in special list' + y 'abbreviation for "yes"' + _enumeration.default no + save_ + + +save_geom_contact.site_symmetry_1 + _definition.id '_geom_contact.site_symmetry_1' + loop_ + _alias.definition_id '_geom_contact_site_symmetry_1' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id contact + _name.object_id site_symmetry_1 + save_ + + +save_geom_contact.site_symmetry_2 + _definition.id '_geom_contact.site_symmetry_2' + loop_ + _alias.definition_id '_geom_contact_site_symmetry_2' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id contact + _name.object_id site_symmetry_2 + save_ + + save_ #----------- close of GEOM_CONTACT category + +#---------------------------------------------------------------------------- + + +save_GEOM_HBOND + _definition.id GEOM_HBOND + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the hydrogen bond + distances in the structural model as derived from atomic sites. +; + _description.common 'HbondList' + _name.category_id GEOM + _name.object_id HBOND + _category.key_id '_geom_hbond.key' + + +save_geom_hbond.key + _definition.id '_geom_hbond.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of GEOM_HBOND items + in a looped list. +; + _description.common 'Key to hydrogen bond data' + _name.category_id hbond + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(geom_hbond.id) +; + Evaluation +; _geom_hbond.key = _geom_hbond.id +; + save_ + + +save_geom_hbond.angle_DHA + _definition.id '_geom_hbond.angle_DHA' + loop_ + _alias.definition_id '_geom_hbond_angle_DHA' + _definition.update 2012-12-14 + _description.text +; + Angle subtended by the sites identifyed in _geom_hbond.id. + The hydrogen at site H is at the apex of the angle. +; + _description.common 'HbondAngleDHA' + _name.category_id hbond + _name.object_id angle_DHA + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + loop_ + _method.purpose + _method.expression + Evaluation +; + With h as geom_hbond + + xc = List() + + For [label,symop] in h.id { + + xf = SymEquiv(symop, _atom_site[label].fract_xyz) + + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + v1,v2 = xc[0]-xc[1], xc[2]-xc[1] + + _geom_hbond.angle_DHA = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) ) +; + save_ + + +save_geom_hbond.atom_site_label_A + _definition.id '_geom_hbond.atom_site_label_A' + loop_ + _alias.definition_id '_geom_hbond_atom_site_label_A' + '_geom_hbond.atom_site_id_A' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id hbond + _name.object_id atom_site_label_A + save_ + + +save_geom_hbond.atom_site_label_D + _definition.id '_geom_hbond.atom_site_label_D' + loop_ + _alias.definition_id '_geom_hbond_atom_site_label_D' + '_geom_hbond.atom_site_id_D' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id hbond + _name.object_id atom_site_label_D + save_ + + +save_geom_hbond.atom_site_label_H + _definition.id '_geom_hbond.atom_site_label_H' + loop_ + _alias.definition_id '_geom_hbond_atom_site_label_H' + '_geom_hbond.atom_site_id_H' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id hbond + _name.object_id atom_site_label_H + save_ + + +save_geom_hbond.distance_DH + _definition.id '_geom_hbond.distance_DH' + loop_ + _alias.definition_id '_geom_hbond_distance_DH' + '_geom_hbond.dist_DH' + _definition.update 2012-12-14 + _description.text +; + The set of data items which specify the distance between the + three atom sites identified by _geom_hbond.id. +; + _name.category_id hbond + _name.object_id distance_DH + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + xc = List() + + Do i=0,1 { + l,s = _geom_hbond.id [i] + xf = SymEquiv(s, _atom_site[l].fract_xyz) + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + _geom_hbond.distance_DH = Norm ( xc[0] - xc[1] ) +; + save_ + + +save_geom_hbond.distance_HA + _definition.id '_geom_hbond.distance_HA' + loop_ + _alias.definition_id '_geom_hbond_distance_HA' + '_geom_hbond.dist_HA' + _definition.update 2012-12-14 + _description.text +; + The set of data items which specify the distance between the + three atom sites identified by _geom_hbond.id. +; + _name.category_id hbond + _name.object_id distance_HA + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + xc = List() + + Do i=1,2 { + l,s = _geom_hbond.id [i] + xf = SymEquiv(s, _atom_site[l].fract_xyz) + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + _geom_hbond.distance_HA = Norm ( xc[0] - xc[1] ) +; + save_ + + +save_geom_hbond.distance_DA + _definition.id '_geom_hbond.distance_DA' + loop_ + _alias.definition_id '_geom_hbond_distance_DA' + '_geom_hbond.dist_DA' + _definition.update 2012-12-14 + _description.text +; + The set of data items which specify the distance between the + three atom sites identified by _geom_hbond.id. +; + _name.category_id hbond + _name.object_id distance_DA + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + xc = List() + + Do i=0,2,2 { + l,s = _geom_hbond.id [i] + xf = SymEquiv(s, _atom_site[l].fract_xyz) + xc ++= _atom_sites_Cartn_transform.matrix * xf + } + _geom_hbond.distance_DA = Norm ( xc[0] - xc[1] ) +; + save_ + + +save_geom_hbond.id + _definition.id '_geom_hbond.id' + _definition.update 2012-11-22 + _description.text +; + Atom site labels and symmetry operators as pairs for each of the + three atom sites which define the hydrogen angle and distances. + Site H is at the apex of the angle. +; + _description.common 'HbondId' + _name.category_id hbond + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'List(Code,Symop)' + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_hbond + + _geom_hbond.id = [[ a.atom_site_label_D, a.site_symmetry_D ], + [ a.atom_site_label_H, a.site_symmetry_H ], + [ a.atom_site_label_A, a.site_symmetry_A ]] +; + save_ + + +save_geom_hbond.publ_flag + _definition.id '_geom_hbond.publ_flag' + loop_ + _alias.definition_id '_geom_hbond_publ_flag' + _definition.update 2012-11-22 + _description.text +; + This code signals whether the hydrogen-bond information + is referred to in a publication or should be placed in a + table of significant hydrogen-bond geometry. +; + _description.common 'HbondPublFlag' + _name.category_id hbond + _name.object_id publ_flag + _type.purpose Quantity + _type.source Selected + _type.container Single + loop_ + _enumeration_set.state + _enumeration_set.detail + no 'do not include bond in special list' + n 'abbreviation for "no"' + yes 'do include bond in special list' + y 'abbreviation for "yes"' + _enumeration.default no + save_ + + +save_geom_hbond.site_symmetry_A + _definition.id '_geom_hbond.site_symmetry_A' + loop_ + _alias.definition_id '_geom_hbond_site_symmetry_A' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id hbond + _name.object_id site_symmetry_A + save_ + + +save_geom_hbond.site_symmetry_D + _definition.id '_geom_hbond.site_symmetry_D' + loop_ + _alias.definition_id '_geom_hbond_site_symmetry_D' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id hbond + _name.object_id site_symmetry_D + save_ + + +save_geom_hbond.site_symmetry_H + _definition.id '_geom_hbond.site_symmetry_H' + loop_ + _alias.definition_id '_geom_hbond_site_symmetry_H' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id hbond + _name.object_id site_symmetry_H + save_ + + save_ #----------- close of GEOM_HBOND category + +#---------------------------------------------------------------------------- + + +save_GEOM_TORSION + _definition.id GEOM_TORSION + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to specify the torsion angles in the + structural model as derived from the atomic sites. +; + _description.common 'Torsion angle list' + _name.category_id GEOM + _name.object_id TORSION + _category.key_id '_geom_torsion.key' + loop_ + _method.purpose + _method.expression + Evaluation +; + dmin = _geom.bond_distance_min + + Loop m1 as model_site :i { + + rad1 = m1.radius_bond + _geom.bond_distance_incr + + Loop m2 as model_site :j { + + If (i==j or m2.mole_index!=m1.mole_index) Next + v21 = m1.Cartn_xyz - m2.Cartn_xyz + d21 = Norm (v21) + + If (d21 < dmin or d21 > (rad1+m2.radius_bond)) Next + rad2 = m2.radius_bond + _geom.bond_distance_incr + + Loop m3 as model_site :k { + + If (k==i or k==j or m3.mole_index!=m2.mole_index) Next + v23 = m3.Cartn_xyz - m2.Cartn_xyz + d23 = Norm (v23) + + If (d23 < dmin or d23 > (rad2+m3.radius_bond)) Next + rad3 = m3.radius_bond + _geom.bond_distance_incr + + Loop m4 as model_site :l { + + If (l==k or l==j or l==i or m4.mole_index!=m3.mole_index) Next + v34 = m4.Cartn_xyz - m3.Cartn_xyz + d34 = Norm (v34) + + If (d34 < dmin or d34 > (rad3+m4.radius_bond)) Next + + u1 = v21 ^ v23 + u2 = v34 ^ v23 + + angle = Acosd ( u1 * u2 / ( Norm(u1) * Norm(u2) ) ) + If ( (u1^u2)*v23 < 0 ) angle = -angle + + geom_torsion( .id = List ( m1.id,m2.id,m3.id,m4.id ), + .distances = List ( d21,d23,d34 ), + .angle = angle ) + } } } } +; + + +save_geom_torsion.key + _definition.id '_geom_torsion.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of GEOM_TORSION items + in a looped list. +; + _description.common 'Key to geometry torsion data' + _name.category_id torsion + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(geom_torsion.id) +; + Evaluation +; _geom_torsion.key = _geom_torsion.id +; + save_ + + +save_geom_torsion.atom_site_label_1 + _definition.id '_geom_torsion.atom_site_label_1' + loop_ + _alias.definition_id '_geom_torsion_atom_site_label_1' + '_geom_torsion.atom_site_id_1' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id torsion + _name.object_id atom_site_label_1 + save_ + + +save_geom_torsion.atom_site_label_2 + _definition.id '_geom_torsion.atom_site_label_2' + loop_ + _alias.definition_id '_geom_torsion_atom_site_label_2' + '_geom_torsion.atom_site_id_2' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id torsion + _name.object_id atom_site_label_2 + save_ + + +save_geom_torsion.atom_site_label_3 + _definition.id '_geom_torsion.atom_site_label_3' + loop_ + _alias.definition_id '_geom_torsion_atom_site_label_3' + '_geom_torsion.atom_site_id_3' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id torsion + _name.object_id atom_site_label_3 + save_ + + +save_geom_torsion.atom_site_label_4 + _definition.id '_geom_torsion.atom_site_label_4' + loop_ + _alias.definition_id '_geom_torsion_atom_site_label_4' + '_geom_torsion.atom_site_id_4' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _name.category_id torsion + _name.object_id atom_site_label_4 + save_ + + +save_geom_torsion.distances + _definition.id '_geom_torsion.distances' + _definition.update 2012-11-22 + _description.text +; + Distances between sites 1 - 2, 2 - 3 and 3 - 4. +; + _name.category_id torsion + _name.object_id distances + _type.purpose Measurand + _type.source Derived + _type.container List + _type.contents Real + _type.dimension [3] + _units.code angstroms + save_ + + +save_geom_torsion.id + _definition.id '_geom_torsion.id' + _definition.update 2012-11-22 + _description.text +; + Atom site labels and symmetry operators as pairs for each of the + four atom sites which define the torsion angle. +; + _description.common 'TorsionAngleId' + _name.category_id torsion + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents 'List(Code,Symop)' + _type.dimension [4] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as geom_torsion + + _geom_torsion.id = [[ a.atom_site_label_1, a.site_symmetry_1 ], + [ a.atom_site_label_2, a.site_symmetry_2 ], + [ a.atom_site_label_3, a.site_symmetry_3 ], + [ a.atom_site_label_4, a.site_symmetry_4 ]] +; + save_ + + +save_geom_torsion.publ_flag + _definition.id '_geom_torsion.publ_flag' + loop_ + _alias.definition_id '_geom_torsion_publ_flag' + _definition.update 2012-11-22 + _description.text +; + Code signals if the torsion angle is required for publication. +; + _description.common 'TorsionAnglePublFlag' + _name.category_id torsion + _name.object_id publ_flag + _type.purpose Quantity + _type.source Selected + _type.container Single + loop_ + _enumeration_set.state + _enumeration_set.detail + Yes 'Publish' + No 'Do not publish' + _enumeration.default No + save_ + + +save_geom_torsion.angle + _definition.id '_geom_torsion.angle' + loop_ + _alias.definition_id '_geom_torsion' + '_geom_torsion.value' + _definition.update 2012-11-22 + _description.text +; + Angle defined by the sites identifyed in _geom_torsion.id. + The torsion-angle definition should be that of Klyne and Prelog. + The vector direction *_label_2 to *_label_3 is the viewing + direction, and the torsion angle is the angle of twist required + to superimpose the projection of the vector between site 2 and + site 1 onto the projection of the vector between site 3 and + site 4. Clockwise torsions are positive, anticlockwise torsions + are negative. + Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. +; + _description.common 'TorsionAngle' + _name.category_id torsion + _name.object_id angle + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees + save_ + + +save_geom_torsion.site_symmetry_1 + _definition.id '_geom_torsion.site_symmetry_1' + loop_ + _alias.definition_id '_geom_torsion_site_symmetry_1' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id torsion + _name.object_id site_symmetry_1 + save_ + + +save_geom_torsion.site_symmetry_2 + _definition.id '_geom_torsion.site_symmetry_2' + loop_ + _alias.definition_id '_geom_torsion_site_symmetry_2' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id torsion + _name.object_id site_symmetry_2 + save_ + + +save_geom_torsion.site_symmetry_3 + _definition.id '_geom_torsion.site_symmetry_3' + loop_ + _alias.definition_id '_geom_torsion_site_symmetry_3' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id torsion + _name.object_id site_symmetry_3 + save_ + + +save_geom_torsion.site_symmetry_4 + _definition.id '_geom_torsion.site_symmetry_4' + loop_ + _alias.definition_id '_geom_torsion_site_symmetry_4' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _name.category_id torsion + _name.object_id site_symmetry_4 + save_ + + save_ #----------- close of GEOM_TORSION category + + save_ #----------- close of GEOM category + + +#============================================================================ + +save_VALENCE + _definition.id VALENCE + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of items used to specify bond valence parameters + used to calculate bond valences from bond lengths. +; + _description.common 'BondValence' + _name.category_id MODEL + _name.object_id VALENCE + + +#---------------------------------------------------------------------------- + +save_VALENCE_PARAM + _definition.id VALENCE_PARAM + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of items for listing bond valences. +; + _name.category_id VALENCE + _name.object_id PARAM + _category.key_id '_valence_param.key' + + +save_valence_param.key + _definition.id '_valence_param.key' + _definition.update 2012-12-13 + _description.text +; + Unique key to looped list of VALENCE_PARAM items. +; + _description.common 'Key to bond valences' + _name.category_id param + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(valence_param.id) +; + Evaluation +; _valence_param.key = _valence_param.id +; + save_ + + +save_valence_param.id + _definition.id '_valence_param.id' + loop_ + _alias.definition_id '_valence_param_id' + _definition.update 2012-12-13 + _description.text +; + Unique index loop number of the valence parameter loop. +; + _name.category_id param + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Index + save_ + + +save_valence_param.ref_id + _definition.id '_valence_param.ref_id' + loop_ + _alias.definition_id '_valence_param_ref_id' + _definition.update 2012-12-13 + _description.text +; + Code linking parameters to the key valence_ref.id key + in the reference list in category VALENCE_REF. +; + _name.category_id param + _name.object_id ref_id + _name.linked_item_id '_valence_ref.id' + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_valence_param.atom_1 + _definition.id '_valence_param.atom_1' + loop_ + _alias.definition_id '_valence_param_atom_1' + _definition.update 2012-12-13 + _description.text +; + Atom type symbol for atom 1 forming a bond whose + valence parameters are given in this category. +; + _name.category_id param + _name.object_id atom_1 + _name.linked_item_id '_atom_type.symbol' + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_valence_param.atom_2 + _definition.id '_valence_param.atom_2' + loop_ + _alias.definition_id '_valence_param_atom_2' + _definition.update 2012-12-13 + _description.text +; + Atom type symbol for atom 2 forming a bond whose + valence parameters are given in this category. +; + _name.category_id param + _name.object_id atom_2 + _name.linked_item_id '_atom_type.symbol' + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_valence_param.atom_1_valence + _definition.id '_valence_param.atom_1_valence' + loop_ + _alias.definition_id '_valence_param_atom_1_valence' + _definition.update 2012-12-13 + _description.text +; + The valence (formal charge) of the atom 1 whose bond + valence parameters are given in this category. +; + _name.category_id param + _name.object_id atom_1_valence + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_valence_param.atom_2_valence + _definition.id '_valence_param.atom_2_valence' + loop_ + _alias.definition_id '_valence_param_atom_2_valence' + _definition.update 2012-12-13 + _description.text +; + The valence (formal charge) of the atom 2 whose bond + valence parameters are given in this category. +; + _name.category_id param + _name.object_id atom_2_valence + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_valence_param.B + _definition.id '_valence_param.B' + loop_ + _alias.definition_id '_valence_param_B' + _definition.update 2012-12-13 + _description.text +; + The bond valence parameter B used in the expression + s = exp[(Ro - R)/B] where s is the valence of bond length R. +; + _name.category_id param + _name.object_id B + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _units.code Angstroms + save_ + + +save_valence_param.Ro + _definition.id '_valence_param.Ro' + loop_ + _alias.definition_id '_valence_param_Ro' + _definition.update 2012-12-13 + _description.text +; + The bond valence parameter Ro used in the expression + s = exp[(Ro - R)/B] where s is the valence of bond length R. +; + _name.category_id param + _name.object_id Ro + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _units.code Angstroms + save_ + + +save_valence_param.details + _definition.id '_valence_param.details' + loop_ + _alias.definition_id '_valence_param_details' + _definition.update 2012-12-13 + _description.text +; + Details of valence parameters of stated bond. +; + _name.category_id param + _name.object_id details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #----------- close of VALENCE_PARAM category + + +#---------------------------------------------------------------------------- + +save_VALENCE_REF + _definition.id VALENCE_REF + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of items for listing valence references. +; + _name.category_id VALENCE + _name.object_id REF + _category.key_id '_valence_ref.key' + + +save_valence_ref.key + _definition.id '_valence_ref.key' + _definition.update 2012-12-13 + _description.text +; + Unique key to looped list of VALENCE_REF items. +; + _description.common 'Key to bond valences' + _name.category_id ref + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(valence_ref.id) +; + Evaluation +; _valence_ref.key = _valence_ref.id +; + save_ + + +save_valence_ref.id + _definition.id '_valence_ref.id' + loop_ + _alias.definition_id '_valence_ref_id' + _definition.update 2012-12-13 + _description.text +; + Unique loop code of the valence references. +; + _name.category_id ref + _name.object_id id + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_valence_ref.reference + _definition.id '_valence_ref.reference' + loop_ + _alias.definition_id '_valence_ref_reference' + _definition.update 2012-12-13 + _description.text +; + Literature reference from which the valence parameters + identified by _valence_param.id were taken +; + _name.category_id ref + _name.object_id reference + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #----------- close of VALENCE_REF category + + save_ #----------- close of VALENCE category + + +#============================================================================ + +save_MODEL_SITE + _definition.id MODEL_SITE + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-22 + _description.text +; + The CATEGORY of data items used to describe atomic sites and + connections in the proposed atomic model. +; + _description.common 'ModelSiteList' + _name.category_id MODEL + _name.object_id SITE + _category.key_id '_model_site.key' + loop_ + _method.purpose + _method.expression + Evaluation +; +# Store unique sites as a local list + + atomlist = List() + Loop a as atom_site { + axyz = a.fract_xyz + cxyz = _atom_sites_Cartn_transform.matrix * axyz + radb = _atom_type[a.type_symbol].radius_bond + radc = _atom_type[a.type_symbol].radius_contact + ls = List ( a.label, "1_555" ) + atomlist ++= [ls, axyz, cxyz, radb, radc, 0] + } + +# Store closest connected sites as a list + + molelist = List() + dmin = _geom.bond_distance_min + m = 0 + n = 0 + + For [ls1,a1,c1,rb1,rc1,m1] in atomlist { + If (m1 != 0) Next + m += 1 + n += 1 + molelist ++= [ls1,a1,c1,rb1,rc1,n,m] + atomlist --= [ls1,a1,c1,rb1,rc1,m] + + Repeat { + connect = "no" + + For [ls2,a2,c2,rb2,rc2,n2,m2] in molelist { + If (m2 != m) Next + + For [ls3,a3,c3,rb3,rc3,m3] in atomlist { + dmax = rb2 + rb3 + _geom.bond_distance_incr + + Loop s as symmetry_equiv :ns { + + axyz = s.R * a3 + s.T + bxyz,tran = Closest (axyz, a2) + cxyz = _atom_sites_Cartn_transform.matrix *bxyz + d = Norm (cxyz - c2) + + If (d > dmin and d < dmax) { + ls = List ( ls3[0], Symop(ns+1, tran) ) + + If (ls not in Strip(molelist,0)) { + n += 1 + molelist ++= [ls,bxyz,cxyz,rb3,rc3,n,m] + atomlist --= [ls3,a3,c3,rb3,rc3,m] + connect = "yes" + } } } } } + If (connect == "no") Break + } } + +# Store connected molecular sites as MODEL_SITE list + + For [ls,ax,cx,rb,rc,n,m] in molelist { + + model_site( .id = ls, + .fract_xyz = ax, + .Cartn_xyz = cx, + .radius_bond = rb, + .radius_contact = rc, + .index = n, + .mole_index = m ) + } +; + + +save_model_site.key + _definition.id '_model_site.key' + _definition.update 2012-11-22 + _description.text +; + Value is a unique key to a set of MODEL_SITE items + in a looped list. +; + _description.common 'Key to model atomic sites' + _name.category_id site + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(model_site.id) +; + Evaluation +; _model_site.key = _model_site.id +; + save_ + + +save_model_site.display_colour + _definition.id '_model_site.display_colour' + _definition.update 2013-01-23 + _description.text +; + Display colour code assigned to this atom site. Note that the + possible colours are enumerated in the colour_RBG list, and + the default code is enumerated in the colour_hue list. +; + _description.common 'AtomTypeColour' + _name.category_id site + _name.object_id display_colour + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'colour_RGB'}, + {"file":'templ_enum.cif',"save":'colour_hue'}] + _enumeration.def_index_id '_model_site.type_symbol' + save_ + + +save_model_site.radius_bond + _definition.id '_model_site.radius_bond' + _definition.update 2012-11-22 + _description.text +; + Atomic radius of atom located at this site. +; + _description.common 'ModelSiteBondRadius' + _name.category_id site + _name.object_id radius_bond + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + With m as model_site + + _model_site.radius_bond = _atom_type[m.type_symbol].radius_bond +; + save_ + + +save_model_site.adp_matrix_beta + _definition.id '_model_site.adp_matrix_beta' + _definition.update 2012-11-22 + _description.text +; + Matrix of dimensionless anisotropic atomic displacement parameters. +; + _description.common 'ModelSiteAdpMatrixBeta' + _name.category_id site + _name.object_id adp_matrix_beta + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + [label,symop] = _model_site.id + + a = atom_site[label] + s = symmetry_equiv[SymKey(symop)] + + _model_site.adp_matrix_beta = s.R * a.matrix_beta * s.RT +; + save_ + + +save_model_site.adp_eigen_system + _definition.id '_model_site.adp_eigen_system' + _definition.update 2012-11-22 + _description.text +; + The set of three adp eigenvales and associated eigenvectors + in the form of 4 element List. Each list has the form + + (val, vecX, vecY, vecZ) + + where the vector elements are direction cosines to the orthogonal + axes X,Y,Z. The lists are sorted in descending magnitude of val. + That is, the list with the largest val is first, and the smallest + val is last. +; + _description.common 'ModelSiteAdpEigenSystem' + _name.category_id site + _name.object_id adp_eigen_system + _type.purpose Measurand + _type.source Derived + _type.container List + _type.contents List(Real,Real,Real,Real) + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + A = _cell.orthogonal_matrix + U = A * _model_site.adp_matrix_beta * Transpose(A) /(2*Pi**2) + + _model_site.adp_eigen_system = Eigen( U ) + +; + save_ + + +save_model_site.radius_contact + _definition.id '_model_site.radius_contact' + _definition.update 2012-11-22 + _description.text +; + Atomic contact radius of atom specie located at this site. +; + _description.common 'ModelSiteContactRadius' + _name.category_id site + _name.object_id radius_contact + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + With m as model_site + + _model_site.radius_contact = _atom_type[m.type_symbol].radius_contact +; + save_ + + +save_model_site.Cartn_xyz + _definition.id '_model_site.Cartn_xyz' + _definition.update 2012-11-22 + _description.text +; + Vector of Cartesian (orthogonal angstrom) atom site coordinates. +; + _description.common 'ModelCartCoords' + _name.category_id site + _name.object_id Cartn_xyz + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With m as model_site + + _model_site.Cartn_xyz = _atom_sites_Cartn_transform.matrix * m.fract_xyz +; + save_ + + +save_model_site.fract_xyz + _definition.id '_model_site.fract_xyz' + _definition.update 2012-12-14 + _description.text +; + Vector of fractional atom site coordinates. +; + _description.common 'ModelFractCoords' + _name.category_id site + _name.object_id fract_xyz + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With m as model_site + + xyz = _atom_site[m.label].fract_xyz + + _model_site.fract_xyz = SymEquiv(m.symop, xyz) +; + save_ + + +save_model_site.id + _definition.id '_model_site.id' + _definition.update 2012-11-22 + _description.text +; + Identifier of model site in terms of the atom site label and + symmetry operator. +; + _description.common 'ModelSiteId' + _name.category_id site + _name.object_id id + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Code,Symop + _type.dimension [1] + loop_ + _method.purpose + _method.expression + Evaluation +; + With m as model_site + + _model_site.id = List ( m.label, m.symop ) +; + save_ + + +save_model_site.index + _definition.id '_model_site.index' + _definition.update 2012-11-22 + _description.text +; + Index number of an atomic site in the connected molecule. +; + _description.common 'ModelSiteIndex' + _name.category_id site + _name.object_id index + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Index + save_ + + +save_model_site.label + _definition.id '_model_site.label' + _definition.update 2012-11-22 + _description.text +; + Code identifies a site in the atom_site category of data. +; + _description.common 'ModelSiteLabel' + _name.category_id site + _name.object_id label + _name.linked_item_id '_atom_site.label' + _type.purpose Link + _type.source Assembled + _type.container Single + _type.contents Code + loop_ + _method.purpose + _method.expression + Evaluation +; + _model_site.label = _model_site.id [0] +; + save_ + + +save_model_site.mole_index + _definition.id '_model_site.mole_index' + _definition.update 2012-11-22 + _description.text +; + Index number of a distinct molecules in the cell, not related by + symmetry. +; + _description.common 'ModelSiteMoleIndex' + _name.category_id site + _name.object_id mole_index + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Index + save_ + + +save_model_site.symop + _definition.id '_model_site.symop' + _import.get [{"file":'templ_attr.cif',"save":'site_symmetry'}] + _description.common 'ModelSiteSymop' + _name.category_id site + _name.object_id symop + loop_ + _method.purpose + _method.expression + Evaluation +; + _model_site.symop = _model_site.id [1] +; + save_ + + +save_model_site.type_symbol + _definition.id '_model_site.type_symbol' + _definition.update 2012-11-22 + _description.text +; + Code to identify the atom specie(s) occupying this site. +; + _description.common 'ModelSiteAtomType' + _name.category_id site + _name.object_id type_symbol + _name.linked_item_id '_atom_type.symbol' + _type.purpose Link + _type.source Assembled + _type.container Single + _type.contents Code + loop_ + _method.purpose + _method.expression + Evaluation +; + _model_site.type_symbol = AtomType ( _model_site.label ) +; + save_ + + save_ #----------- close of MODEL_SITE category + + save_ #----------- close of MODEL category + + +#============================================================================= +# The dictionary's definition creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.1.01 2006-03-07 +; + Initial CORE_MODEL dictionary constructed from CORE_3 v3.5.02 +; + 1.1.02 2006-06-17 +; + Apply the DDL 3.6.01 changes. +; + 1.1.03 2006-06-17 +; + Apply changes to state values in _item.purpose enumeration list. +; + 1.1.04 2006-06-20 +; + Change Point to Link for _type.contents. + Change Point to Model for _type.contents. +; + 1.1.05 2006-06-30 +; + Apply the DDL 3.6.05 changes. +; + 1.1.06 2006-09-07 +; + Apply the DDL 3.6.08 changes. +; + 1.1.07 2006-11-13 +; + Apply DDL3 3.6.10 attributes. + Change method.id to method.purpose; EVAL to Evaluation +; + 1.1.08 2006-12-14 +; + Apply DDL3 3.7.01 attributes. +; + 1.2.01 2007-02-07 +; + Apply DDL3 3.7.04 attributes. +; + 1.2.02 2007-02-09 +; + In _model_site.mole_index changed type.purpose and + type.contents +; + 1.2.03 2007-10-13 +; + Placed tags in _category_key.primitive lists within quotes. +; + 1.2.04 2007-10-17 +; + Removed redundant '[' from method expression in _geom_bond.id +; + 1.2.05 2008-01-18 +; + Replaced import_list controls with leading uppercase character + Changed import_list [....] to [[....]] +; + 1.2.06 2008-01-22 +; + Change _import.scope in _import_list.id to 'Val' + Set _enumeration.def_index_id to '_model_site.type_symbol' + + Replaced import_list controls with leading uppercase character + Changed import_list [....] to [[....]] +; + 1.2.07 2008-03-28 +; + Replaced 'Limit' with 'Assigned' in a number of preset items. +; + 1.2.08 2008-06-18 +; + Change _import_list.id to be ((.....)) + For all *.key items change _type.contents from Code to Inherited + For other *.id items some _type.purpose from Key to Identify +; + 1.2.09 2008-06-24 +; + Change all _type.dimension values +; + 1.2.10 2008-08-14 +; + Replace the "<=" substitution digraph (previously "<<=") with a + new trigraph "--=" (the reverse of "++="). +; + 1.3.01 2011-06-07 +; + Replace category class "List" with "Loop" + Replace all "Tuple" with "List" + Replace all "Array" with "List" + Place all import lists into [[......]] +; + 1.3.01 2011-08-02 +; + Install nested save frames and import.get attributes. + Comply with the DDL 3.8 attributes. +; + 1.3.02 2011-08-03 +; + Change name of import file com_att.dic to templ_attr.cif + Change name of import file com_val.dic to templ_templcif +; + 1.3.03 2011-10-27 +; + Place "With" in all geom_* methods for idividual bonds & angles +; + 1.3.04 2011-12-01 +; + Change container type from List to Matrix for relevant item definitions +; + 1.3.05 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 1.4.01 2012-05-07 +; + Apply DDL 3.10.01 changes. +; + 1.4.02 2012-10-16 +; + Apply DDL 3.10.02 changes. + Remove type.contents "Inherited"; insert Definition method expression. +; + 1.4.03 2012-11-20 +; + Invoke container functions Matrix, List in methods scripts where needed. +; + 1.4.04 2012-11-22 +; + Add DDL1 tags as alias.definition_id values +; + 1.4.05 2012-12-13 +; + Add the VALENCE, VALENCE_PARAM and VALENCE_REF definitions. +; + 1.4.06 2013-01-22 +; + Add geom_bond.multiplicity and align some descriptions. +; diff --git a/core_publn.dic b/core_publn.dic new file mode 100755 index 0000000..af59775 --- /dev/null +++ b/core_publn.dic @@ -0,0 +1,4022 @@ +############################################################################## +# # +# CIF CORE PUBLICATION DICTIONARY # +# # +############################################################################## + +data_CORE_PUBLN + + _dictionary.title CORE_PUBLN + _dictionary.class Instance + _dictionary.version 1.4.09 + _dictionary.date 2013-01-23 + _dictionary.uri www.iucr.org/cif/dic/core_publn.dic + _dictionary.ddl_conformance 3.10.03 + _dictionary.namespace CorePubln + _description.text +; + This dictionary contains the definitions of data items that + are considered CORE to the description of PUBLICATION data. +; + + +save_PUBLICATION + _definition.id PUBLICATION + _definition.scope Category + _definition.class Head + _definition.update 2012-05-07 + _description.text +; + The DICTIONARY group encompassing the CORE PUBLICATION data items defined + and used with in the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_CORE + _name.object_id PUBLICATION + + +#============================================================================ + +save_PUBL + _definition.id PUBL + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + Data items in the PUBL category are used when submitting a + manuscript for publication. They refer either to the paper as + a whole, or to specific named elements within a paper (such as + the title and abstract, or the Comment and Experimental + sections of Acta Crystallographica Section C). The data items + in the PUBL_BODY category should be used for the textual + content of other submissions. Typically, each journal will + supply a list of the specific items it requires in its Notes + for Authors. +; + _name.category_id PUBLICATION + _name.object_id PUBL + + +save_publ.contact_letter + _definition.id '_publ.contact_letter' + loop_ + _alias.definition_id '_publ_contact_letter' + _definition.update 2012-11-29 + _description.text +; + A letter submitted to the journal editor by the contact author. +; + _name.category_id publ + _name.object_id contact_letter + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +#---------------------------------------------------------------------------- + +save_PUBL_MANUSCRIPT + _definition.id PUBL_MANUSCRIPT + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + Category of items describing the publication manuscript. +; + _name.category_id PUBL + _name.object_id MANUSCRIPT + + +save_publ_manuscript.creation + _definition.id '_publ_manuscript.creation' + loop_ + _alias.definition_id '_publ_manuscript_creation' + _definition.update 2012-11-29 + _description.text +; + A description of the wordprocessor package and computer used to + create the manuscript stored as publ_manuscript.processed. +; + _name.category_id manuscript + _name.object_id creation + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_manuscript.processed + _definition.id '_publ_manuscript.processed' + loop_ + _alias.definition_id '_publ_manuscript_processed' + _definition.update 2012-11-29 + _description.text +; + The full manuscript of a paper (excluding possibly the figures + and the tables) output in ASCII characters from a word processor. + Information about the generation of this data item must be + specified in the data item _publ_manuscript.creation. +; + _name.category_id manuscript + _name.object_id processed + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_manuscript.text + _definition.id '_publ_manuscript.text' + loop_ + _alias.definition_id '_publ_manuscript_text' + _definition.update 2012-11-29 + _description.text +; + The full manuscript of a paper (excluding figures and possibly + the tables) output as standard ASCII text. +; + _name.category_id manuscript + _name.object_id text + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +#============================================================================ + +save_PUBL_MANUSCRIPT_INCL_EXTRA + _definition.id PUBL_MANUSCRIPT_INCL_EXTRA + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-13 + _description.text +; + Category of data items that allow the authors of a manuscript to + submit for publication data names that should be added to the + standard request list employed by journal printing software. + Although these fields are primarily intended to identify CIF data + items that the author wishes to include in a published paper, they + can also be used to identify data names created so that non-CIF items + can be included in the publication. Note that *.item names MUST be + enclosed in single quotes. +; + _name.category_id PUBL_MANUSCRIPT + _name.object_id INCL_EXTRA + _category.key_id '_publ_manuscript_incl_extra.key' + + +save_publ_manuscript_incl_extra.key + _definition.id '_publ_manuscript_incl_extra.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of PUBL_MANUSCRIPT_INCL_EXTRA items + in a looped list. +; + _name.category_id publ_manuscript_incl_extra + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(publ_manuscript_incl_extra.item) +; + Evaluation +; _publ_manuscript_incl_extra.key = _publ_manuscript_incl_extra.item +; + save_ + + +save_publ_manuscript_incl_extra.item + _definition.id '_publ_manuscript_incl_extra.item' + loop_ + _alias.definition_id '_publ_manuscript_incl_extra_item' + _definition.update 2012-12-13 + _description.text +; + The data name (i.e. Tag) of a specific data item included in the + manuscript which is not normally requested by the journal. The values + of this item are the extra data names (which MUST be enclosed + in single quotes) that will be added to the journal request list. +; + _name.category_id incl_extra + _name.object_id item + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Tag + save_ + + +save_publ_manuscript_incl_extra.info + _definition.id '_publ_manuscript_incl_extra.info' + loop_ + _alias.definition_id '_publ_manuscript_incl_extra_info' + _definition.update 2012-12-13 + _description.text +; + A short note indicating the reason why the author wishes the + corresponding data item marked for inclusion in the journal + request list to be published. +; + _name.category_id incl_extra + _name.object_id info + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + +save_publ_manuscript_incl_extra.defn + _definition.id '_publ_manuscript_incl_extra.defn' + loop_ + _alias.definition_id '_publ_manuscript_incl_extra_defn' + _definition.update 2012-12-13 + _description.text +; + Yes/No flags whether the corresponding data item marked for inclusion + in a journal request list is a standard CIF definition or not. +; + _name.category_id incl_extra + _name.object_id defn + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail yes "yes include item in journal request list" + y "yes include item in journal request list" + no "exclude item in journal request list" + n "exclude item in journal request list" + _enumeration.default yes + save_ + + save_ #-------- close the PUBL_MANUSCRIPT_INCL_EXTRA category + + save_ #-------- close the PUBL_MANUSCRIPT category + + +#============================================================================ + +save_PUBL_REQUESTED + _definition.id PUBL_REQUESTED + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + CATEGORY of data items that enable the author to make + specific requests to the journal office for processing. +; + _name.category_id PUBL + _name.object_id REQUESTED + + +save_publ_requested.category + _definition.id '_publ_requested.category' + loop_ + _alias.definition_id '_publ_requested_category' + _definition.update 2012-12-13 + _description.text +; + The category of paper submitted. For submission to Acta + Crystallographica Section C or Acta Crystallographica + Section E, ONLY those codes indicated for use with those + journals should be used. +; + _name.category_id requested + _name.object_id category + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + FA 'Full article' + FI 'Full submission - inorganic (Acta C)' + FO 'Full submission - organic (Acta C)' + FM 'Full submission - metal-organic (Acta C)' + CI 'CIF-access paper - inorganic (Acta C)' + CO 'CIF-access paper - organic (Acta C)' + CM 'CIF-access paper - metal-organic (Acta C)' + EI 'Electronic submission - inorganic (Acta E)' + EO 'Electronic submission - organic (Acta E)' + EM 'Electronic submission - metal-organic (Acta E)' + AD 'Addenda & Errata (Acta C, Acta E)' + SC 'Short Communication' + _enumeration.default FA + save_ + + +save_publ_requested.coeditor_name + _definition.id '_publ_requested.coeditor_name' + loop_ + _alias.definition_id '_publ_requested_coeditor_name' + _definition.update 2012-12-13 + _description.text +; + The name of the Co-editor whom the authors would like to + process the submitted manuscript. +; + _name.category_id requested + _name.object_id coeditor_name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_requested.journal + _definition.id '_publ_requested.journal' + loop_ + _alias.definition_id '_publ_requested_journal' + _definition.update 2012-12-13 + _description.text +; + Name of the journal to which the manuscript is being submitted. +; + _name.category_id requested + _name.object_id journal + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #-------- close the PUBL_REQUESTED category + + +#============================================================================ + +save_PUBL_SECTION + _definition.id PUBL_SECTION + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + Manuscript section data if submitted in parts. see also + _publ_manuscript.text and _publ_manuscript.processed. + The _publ_section.exptl_prep, _publ_section.exptl_refinement + and _publ_section.exptl_solution items are preferred for + separating the chemical preparation, refinement and structure + solution aspects of the experimental description. +; + _name.category_id PUBL + _name.object_id SECTION + + +save_publ_section.title + _definition.id '_publ_section.title' + loop_ + _alias.definition_id '_publ_section_title' + _definition.update 2012-11-29 + _description.text +; + The full title of the submitted paper. +; + _name.category_id section + _name.object_id title + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.title_footnote + _definition.id '_publ_section.title_footnote' + loop_ + _alias.definition_id '_publ_section_title_footnote' + _definition.update 2012-11-29 + _description.text +; + Footnote (if any) to the title of the submitted paper. +; + _name.category_id section + _name.object_id title_footnote + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.synopsis + _definition.id '_publ_section.synopsis' + loop_ + _alias.definition_id '_publ_section_synopsis' + _definition.update 2012-11-29 + _description.text +; + The synopsis of the submitted paper. +; + _name.category_id section + _name.object_id synopsis + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.abstract + _definition.id '_publ_section.abstract' + loop_ + _alias.definition_id '_publ_section_abstract' + _definition.update 2012-11-29 + _description.text +; + The abstract of the submitted paper. +; + _name.category_id section + _name.object_id abstract + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.comment + _definition.id '_publ_section.comment' + loop_ + _alias.definition_id '_publ_section_comment' + _definition.update 2012-11-29 + _description.text +; + The comment section of the submitted paper. +; + _name.category_id section + _name.object_id abstract + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.introduction + _definition.id '_publ_section.introduction' + loop_ + _alias.definition_id '_publ_section_introduction' + _definition.update 2012-11-29 + _description.text +; + The introduction section of the submitted paper. +; + _name.category_id section + _name.object_id introduction + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.experimental + _definition.id '_publ_section.experimental' + loop_ + _alias.definition_id '_publ_section_experimental' + _definition.update 2012-11-29 + _description.text +; + The experimental section of the submitted paper. +; + _name.category_id section + _name.object_id experimental + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.exptl_prep + _definition.id '_publ_section.exptl_prep' + loop_ + _alias.definition_id '_publ_section_exptl_prep' + _definition.update 2012-11-29 + _description.text +; + The experimental preparation section of the submitted paper. +; + _name.category_id section + _name.object_id exptl_prep + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.exptl_refinement + _definition.id '_publ_section.exptl_refinement' + loop_ + _alias.definition_id '_publ_section_exptl_refinement' + _definition.update 2012-11-29 + _description.text +; + The experimental refinement section of the submitted paper. +; + _name.category_id section + _name.object_id exptl_refinement + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.exptl_solution + _definition.id '_publ_section.exptl_solution' + loop_ + _alias.definition_id '_publ_section_exptl_solution' + _definition.update 2012-11-29 + _description.text +; + The experimental solution section of the submitted paper. +; + _name.category_id section + _name.object_id exptl_solution + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.discussion + _definition.id '_publ_section.discussion' + loop_ + _alias.definition_id '_publ_section_discussion' + _definition.update 2012-11-29 + _description.text +; + The discussion section of the submitted paper. +; + _name.category_id section + _name.object_id discussion + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.acknowledgements + _definition.id '_publ_section.acknowledgements' + loop_ + _alias.definition_id '_publ_section_acknowledgements' + _definition.update 2012-11-29 + _description.text +; + The acknowledgements section of the submitted paper. +; + _name.category_id section + _name.object_id acknowledgements + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.references + _definition.id '_publ_section.references' + loop_ + _alias.definition_id '_publ_section_references' + _definition.update 2012-11-29 + _description.text +; + The references section of the submitted paper. +; + _name.category_id section + _name.object_id references + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.related_literature + _definition.id '_publ_section.related_literature' + loop_ + _alias.definition_id '_publ_section_related_literature' + _definition.update 2012-11-29 + _description.text +; + The related literature section of the submitted paper. +; + _name.category_id section + _name.object_id related_literature + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.figure_captions + _definition.id '_publ_section.figure_captions' + loop_ + _alias.definition_id '_publ_section_figure_captions' + _definition.update 2012-11-29 + _description.text +; + The figure captions of the submitted paper. +; + _name.category_id section + _name.object_id figure_captions + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.table_legends + _definition.id '_publ_section.table_legends' + loop_ + _alias.definition_id '_publ_section_table_legends' + _definition.update 2012-11-29 + _description.text +; + The table legends of the submitted paper. +; + _name.category_id section + _name.object_id table_legends + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_section.keywords + _definition.id '_publ_section.keywords' + loop_ + _alias.definition_id '_publ_section_keywords' + _definition.update 2012-11-29 + _description.text +; + The keywords of the submitted paper. +; + _name.category_id section + _name.object_id keywords + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #-------- close the PUBL_SECTION category + + +#============================================================================ + +save_PUBL_BODY + _definition.id PUBL_BODY + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-13 + _description.text +; + Data items in the PUBL_BODY category permit labelling of + different text sections within the body of a submitted paper. + Note that these should not be used in a paper which has + a standard format with sections tagged by specific data names + (such as in Acta Crystallographica Section C). Typically, + each journal will supply a list of the specific items it + requires in its Notes for Authors. +; + _name.category_id PUBL + _name.object_id BODY + _category.key_id '_publ_author.key' + + +save_publ_body.key + _definition.id '_publ_body.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of PUBL_BODY items + in a looped list. +; + _name.category_id publ_body + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(publ_body.label) +; + Evaluation +; _publ_body.key = _publ_body.label +; + save_ + + +save_publ_body.label + _definition.id '_publ_body.label' + loop_ + _alias.definition_id '_publ_body_label' + _definition.update 2012-12-13 + _description.text +; + Unigue identifier for each part of the body of the paper. +; + _name.category_id body + _name.object_id label + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _description_example.case 1 1.1 2.1.3 + save_ + + +save_publ_body.element + _definition.id '_publ_body.element' + loop_ + _alias.definition_id '_publ_body_element' + _definition.update 2012-12-13 + _description.text +; + The functional role of the associated text section. +; + _name.category_id body + _name.object_id element + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + loop_ _enumeration_set.state section + subsection + subsubsection + appendix + footnote + save_ + + +save_publ_body.contents + _definition.id '_publ_body.contents' + loop_ + _alias.definition_id '_publ_body_contents' + _definition.update 2012-12-13 + _description.text +; + A text section of a submitted paper. +; + _name.category_id body + _name.object_id contents + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_body.title + _definition.id '_publ_body.title' + loop_ + _alias.definition_id '_publ_body_title' + _definition.update 2012-12-13 + _description.text +; + Title of the associated section of text. +; + _name.category_id body + _name.object_id title + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_body.format + _definition.id '_publ_body.format' + loop_ + _alias.definition_id '_publ_body_format' + _definition.update 2012-12-13 + _description.text +; + Enumerated state indicating the appropriate typesetting + conventions for accented characters and special symbols + in the text section. +; + _name.category_id body + _name.object_id format + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail ascii 'no coding for special symbols' + cif 'CIF convention' + latex 'LaTeX' + rtf 'Rich Text Format' + sgml 'SGML (ISO 8879)' + tex 'TeX' + troff 'troff or nroff' + _enumeration.default cif + save_ + + save_ #-------- close the PUBL_BODY category + + +#============================================================================ + +save_PUBL_AUTHOR + _definition.id PUBL_AUTHOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-13 + _description.text +; + Category of data items recording the author information. +; + _name.category_id PUBL + _name.object_id AUTHOR + _category.key_id '_publ_author.key' + + +save_publ_author.key + _definition.id '_publ_author.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of PUBL_AUTHOR items + in a looped list. +; + _name.category_id publ_author + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(publ_author.name) +; + Evaluation +; _publ_author.key = _publ_author.name +; + save_ + + +save_publ_author.name + _definition.id '_publ_author.name' + loop_ + _alias.definition_id '_publ_author_name' + _definition.update 2012-12-13 + _description.text +; + The name of a publication author. If there are multiple authors, + this will be looped with _publ_author.address. The family + name(s), followed by a comma and including any dynastic + components, precedes the first names or initials. +; + _name.category_id author + _name.object_id name + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'Bleary, Percival R.' + "O'Neil, F.K." + 'Van den Bossche, G.' + 'Yang, D.-L.' + 'Simonov, Yu.A' + 'M\"uller, H.A.' + 'Ross II, C.R.' + save_ + + +save_publ_author.address + _definition.id '_publ_author.address' + loop_ + _alias.definition_id '_publ_author_address' + _definition.update 2012-12-13 + _description.text +; + The address of a publication author. If there is more than one + author, this will be looped with _publ_author_name. +; + _name.category_id author + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case +; Department + Institute + Street + City and postcode + COUNTRY +; + save_ + + +save_publ_author.email + _definition.id '_publ_author.email' + loop_ + _alias.definition_id '_publ_author_email' + _definition.update 2012-12-13 + _description.text +; + The e-mail address of a publication author. If there is more + than one author, this will be looped with _publ_author_name. + The format of e-mail addresses is given in Section 3.4, Address + Specification, of Internet Message Format, RFC 2822, P. Resnick + (Editor), Network Standards Group, April 2001. +; + _name.category_id author + _name.object_id email + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_author.footnote + _definition.id '_publ_author.footnote' + loop_ + _alias.definition_id '_publ_author_footnote' + _definition.update 2012-12-13 + _description.text +; + A footnote accompanying an author's name in the list of authors + of a paper. Typically indicates sabbatical address, additional + affiliations or date of decease. +; + _name.category_id author + _name.object_id footnote + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_author.id_iucr + _definition.id '_publ_author.id_iucr' + loop_ + _alias.definition_id '_publ_author_id_iucr' + _definition.update 2012-12-13 + _description.text +; + Identifier in the IUCr contact database of a publication + author. This identifier may be available from the World + Directory of Crystallographers (http://wdc.iucr.org). +; + _name.category_id author + _name.object_id id_iucr + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + save_ #-------- close the PUBL_AUTHOR category + + +#============================================================================ + +save_PUBL_CONTACT_AUTHOR + _definition.id PUBL_CONTACT_AUTHOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-05-07 + _description.text +; + Category of items describing contact author(s) details. +; + _name.category_id PUBL + _name.object_id CONTACT_AUTHOR + _category.key_id '_publ_contact_author.key' + + +save_publ_contact_author.key + _definition.id '_publ_contact_author.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of PUBL_CONTACT_AUTHOR items + in a looped list. +; + _name.category_id publ_contact_author + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(publ_contact_author.name) +; + Evaluation +; _publ_contact_author.key = _publ_contact_author.name +; + save_ + + +save_publ_contact_author.name + _definition.id '_publ_contact_author.name' + loop_ + _alias.definition_id '_publ_contact_author_name' + '_publ_contact_author' + _definition.update 2012-11-29 + _description.text +; + The name of the author(s) submitting the manuscript and + data block. This is the person contacted by the journal + editorial staff. +; + _name.category_id contact_author + _name.object_id name + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'Professor George Ferguson' + save_ + + +save_publ_contact_author.address + _definition.id '_publ_contact_author.address' + loop_ + _alias.definition_id '_publ_contact_author_address' + _definition.update 2012-11-29 + _description.text +; + The address of the author submitting the manuscript and + data block. This is the person contacted by the journal + editorial staff. +; + _name.category_id contact_author + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case +; Department of Chemistry and Biochemistry + University of Guelph + Ontario + Canada + N1G 2W1 +; + save_ + + +save_publ_contact_author.email + _definition.id '_publ_contact_author.email' + loop_ + _alias.definition_id '_publ_contact_author_email' + _definition.update 2012-11-29 + _description.text +; + E-mail address in a form recognizable to international networks. + The format of e-mail addresses is given in Section 3.4, Address + Specification, of Internet Message Format, RFC 2822, P. Resnick + (Editor), Network Standards Group, April 2001. +; + _name.category_id contact_author + _name.object_id email + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_contact_author.phone + _definition.id '_publ_contact_author.phone' + loop_ + _alias.definition_id '_publ_contact_author_phone' + _definition.update 2012-11-29 + _description.text +; + Telephone number of author submitting the manuscript and data block. + The recommended style is the international dialing prefix, + followed by the area code in parentheses, followed by the + local number and any extension number prefixed by 'x', with + no spaces. The earlier convention of including the international + dialing prefix in parentheses is no longer recommended. +; + _name.category_id contact_author + _name.object_id phone + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '12(34)9477330' + '12()349477330' + '12(34)9477330x5543' + save_ + + +save_publ_contact_author.fax + _definition.id '_publ_contact_author.fax' + loop_ + _alias.definition_id '_publ_contact_author_fax' + _definition.update 2012-11-29 + _description.text +; + Facsimile telephone number of the author submitting the manuscript + and data block. + The recommended style is the international dialing prefix, followed + by the area code in parentheses, followed by the local number with + no spaces. The earlier convention of including the international + dialing prefix in parentheses is no longer recommended. +; + _name.category_id contact_author + _name.object_id fax + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_publ_contact_author.id_iucr + _definition.id '_publ_contact_author.id_iucr' + loop_ + _alias.definition_id '_publ_contact_author_id_iucr' + _definition.update 2012-11-29 + _description.text +; + Identifier in the IUCr contact database of the author submitting + the manuscript and datablock. This identifier may be available + from the World Directory of Crystallographers (http://wdc.iucr.org). +; + _name.category_id contact_author + _name.object_id id_iucr + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #--------- close the PUBL_CONTACT_AUTHOR category + + save_ #--------- close the PUBL category + + +#============================================================================ + +save_JOURNAL + _definition.id JOURNAL + _definition.scope Category + _definition.class Set + _definition.update 2012-12-11 + _description.text +; + Category of items recording details about the book-keeping + by the journal staff when processing a CIF submitted for + publication. The creator of a CIF will not normally specify + these data items. The data names are not defined in the + dictionary because they are for journal use only. +; + _name.category_id PUBLICATION + _name.object_id JOURNAL + + +save_journal.coden_ASTM + _definition.id '_journal.coden_ASTM' + loop_ + _alias.definition_id '_journal_coden_ASTM' + _definition.update 2012-12-11 + _description.text +; + ASTM code assigned to journal. +; + _name.category_id journal + _name.object_id coden_ASTM + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.coden_Cambridge + _definition.id '_journal.coden_Cambridge' + loop_ + _alias.definition_id '_journal_coden_Cambridge' + _definition.update 2012-12-11 + _description.text +; + Cambridge Cryst. Data Centre code assigned to journal. +; + _name.category_id journal + _name.object_id coden_Cambridge + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.validation_number + _definition.id '_journal.validation_number' + loop_ + _alias.definition_id '_journal_data_validation_number' + _definition.update 2013-01-23 + _description.text +; + Data validation number assigned to journal. +; + _name.category_id journal + _name.object_id validation_number + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.issue + _definition.id '_journal.issue' + loop_ + _alias.definition_id '_journal_issue' + _definition.update 2012-12-11 + _description.text +; + Issue identifier within the journal. +; + _name.category_id journal + _name.object_id issue + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.language + _definition.id '_journal.language' + loop_ + _alias.definition_id '_journal_language' + _definition.update 2012-12-11 + _description.text +; + Language of the publication. +; + _name.category_id journal + _name.object_id language + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal.name_full + _definition.id '_journal.name_full' + loop_ + _alias.definition_id '_journal_name_full' + _definition.update 2012-12-11 + _description.text +; + Full name of the journal. +; + _name.category_id journal + _name.object_id name_full + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal.page_first + _definition.id '_journal.page_first' + loop_ + _alias.definition_id '_journal_page_first' + _definition.update 2012-12-11 + _description.text +; + First page of the publication in the journal. +; + _name.category_id journal + _name.object_id page_first + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal.page_last + _definition.id '_journal.page_last' + loop_ + _alias.definition_id '_journal_page_last' + _definition.update 2012-12-11 + _description.text +; + Last page of the publication in the journal. +; + _name.category_id journal + _name.object_id page_last + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal.paper_category + _definition.id '_journal.paper_category' + loop_ + _alias.definition_id '_journal_paper_category' + _definition.update 2012-12-11 + _description.text +; + Category of the publication in the journal. +; + _name.category_id journal + _name.object_id paper_category + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.paper_doi + _definition.id '_journal.paper_doi' + loop_ + _alias.definition_id '_journal_paper_doi' + _definition.update 2012-12-11 + _description.text +; + DOI of the publication in the journal. +; + _name.category_id journal + _name.object_id paper_doi + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.suppl_publ_number + _definition.id '_journal.suppl_publ_number' + loop_ + _alias.definition_id '_journal_suppl_publ_number' + _definition.update 2012-12-11 + _description.text +; + Number of supplementary publication. +; + _name.category_id journal + _name.object_id suppl_publ_number + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal.suppl_publ_pages + _definition.id '_journal.suppl_publ_pages' + loop_ + _alias.definition_id '_journal_suppl_publ_pages' + _definition.update 2012-12-11 + _description.text +; + Number of pages in the supplementary publication. +; + _name.category_id journal + _name.object_id suppl_publ_pages + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal.volume + _definition.id '_journal.volume' + loop_ + _alias.definition_id '_journal_volume' + _definition.update 2012-12-11 + _description.text +; + Volume number of the publication. +; + _name.category_id journal + _name.object_id volume + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal.year + _definition.id '_journal.year' + loop_ + _alias.definition_id '_journal_year' + _definition.update 2012-12-11 + _description.text +; + Year of the publication. +; + _name.category_id journal + _name.object_id year + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +#---------------------------------------------------------------------------- + +save_JOURNAL_COEDITOR + _definition.id JOURNAL_COEDITOR + _definition.scope Category + _definition.class Set + _definition.update 2012-12-11 + _description.text +; + Category of items recording co-editor details. +; + _name.category_id JOURNAL + _name.object_id COEDITOR + + +save_journal_coeditor.code + _definition.id '_journal_coeditor.code' + loop_ + _alias.definition_id '_journal_coeditor_code' + _definition.update 2012-12-11 + _description.text +; + The coeditor identifier. +; + _name.category_id coeditor + _name.object_id code + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal_coeditor.name + _definition.id '_journal_coeditor.name' + loop_ + _alias.definition_id '_journal_coeditor_name' + _definition.update 2012-12-11 + _description.text +; + The name of the coeditor. +; + _name.category_id coeditor + _name.object_id name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_coeditor.address + _definition.id '_journal_coeditor.address' + loop_ + _alias.definition_id '_journal_coeditor_address' + _definition.update 2012-12-11 + _description.text +; + The postal address of the coeditor. +; + _name.category_id coeditor + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_coeditor.email + _definition.id '_journal_coeditor.email' + loop_ + _alias.definition_id '_journal_coeditor_email' + _definition.update 2012-12-11 + _description.text +; + The email address of the coeditor. +; + _name.category_id coeditor + _name.object_id email + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_coeditor.phone + _definition.id '_journal_coeditor.phone' + loop_ + _alias.definition_id '_journal_coeditor_phone' + _definition.update 2012-12-11 + _description.text +; + The phone number of the coeditor. +; + _name.category_id coeditor + _name.object_id phone + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal_coeditor.fax + _definition.id '_journal_coeditor.fax' + loop_ + _alias.definition_id '_journal_coeditor_fax' + _definition.update 2012-12-11 + _description.text +; + The fax number of the coeditor. +; + _name.category_id coeditor + _name.object_id fax + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal_coeditor.notes + _definition.id '_journal_coeditor.notes' + loop_ + _alias.definition_id '_journal_coeditor_notes' + _definition.update 2012-12-11 + _description.text +; + Notes on coeditor interaction wrt this publication. +; + _name.category_id coeditor + _name.object_id notes + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #--------- close the JOURNAL_COEDITOR category + + +#---------------------------------------------------------------------------- + +save_JOURNAL_DATE + _definition.id JOURNAL_DATE + _definition.scope Category + _definition.class Set + _definition.update 2012-12-11 + _description.text +; + Category of items recording dates of publication processing. +; + _name.category_id JOURNAL + _name.object_id DATE + + +save_journal_date.accepted + _definition.id '_journal_date.accepted' + loop_ + _alias.definition_id '_journal_date_accepted' + _definition.update 2012-12-11 + _description.text +; + Date the publication was accepted. +; + _name.category_id date + _name.object_id accepted + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.from_coeditor + _definition.id '_journal_date.from_coeditor' + loop_ + _alias.definition_id '_journal_date_from_coeditor' + _definition.update 2012-12-11 + _description.text +; + Date the publication recieved from coeditor. +; + _name.category_id date + _name.object_id from_coeditor + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.to_coeditor + _definition.id '_journal_date.to_coeditor' + loop_ + _alias.definition_id '_journal_date_to_coeditor' + _definition.update 2012-12-11 + _description.text +; + Date the publication sent to the coeditor. +; + _name.category_id date + _name.object_id to_coeditor + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.printers_final + _definition.id '_journal_date.printers_final' + loop_ + _alias.definition_id '_journal_date_printers_final' + _definition.update 2012-12-11 + _description.text +; + Date the publication last sent to the printers. +; + _name.category_id date + _name.object_id printers_final + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.printers_first + _definition.id '_journal_date.printers_first' + loop_ + _alias.definition_id '_journal_date_printers_first' + _definition.update 2012-12-11 + _description.text +; + Date the publication first sent to the printers. +; + _name.category_id date + _name.object_id printers_first + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.proofs_in + _definition.id '_journal_date.proofs_in' + loop_ + _alias.definition_id '_journal_date_proofs_in' + _definition.update 2012-12-11 + _description.text +; + Date the publication proofs recieved. +; + _name.category_id date + _name.object_id proofs_in + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.proofs_out + _definition.id '_journal_date.proofs_out' + loop_ + _alias.definition_id '_journal_date_proofs_out' + _definition.update 2012-12-11 + _description.text +; + Date the publication proofs sent out. +; + _name.category_id date + _name.object_id proofs_out + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.recd_copyright + _definition.id '_journal_date.recd_copyright' + loop_ + _alias.definition_id '_journal_date_recd_copyright' + _definition.update 2012-12-11 + _description.text +; + Date completed copyright recieved. +; + _name.category_id date + _name.object_id recd_copyright + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.recd_electronic + _definition.id '_journal_date.recd_electronic' + loop_ + _alias.definition_id '_journal_date_recd_electronic' + _definition.update 2012-12-11 + _description.text +; + Date publication recieved electronically. +; + _name.category_id date + _name.object_id recd_electronic + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + +save_journal_date.recd_hard_copy + _definition.id '_journal_date.recd_hard_copy' + loop_ + _alias.definition_id '_journal_date_recd_hard_copy' + _definition.update 2012-12-11 + _description.text +; + Date publication recieved as hard copy. +; + _name.category_id date + _name.object_id recd_hard_copy + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + save_ + + save_ #--------- close the JOURNAL_DATE category + + +#---------------------------------------------------------------------------- + +save_JOURNAL_TECHEDITOR + _definition.id JOURNAL_TECHEDITOR + _definition.scope Category + _definition.class Set + _definition.update 2012-12-11 + _description.text +; + Category of items recording details of the technical editor + processing this publication. +; + _name.category_id JOURNAL + _name.object_id TECHEDITOR + + +save_journal_techeditor.code + _definition.id '_journal_techeditor.code' + loop_ + _alias.definition_id '_journal_techeditor_code' + _definition.update 2012-12-11 + _description.text +; + Code of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id code + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_journal_techeditor.name + _definition.id '_journal_techeditor.name' + loop_ + _alias.definition_id '_journal_techeditor_name' + _definition.update 2012-12-11 + _description.text +; + Name of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_techeditor.address + _definition.id '_journal_techeditor.address' + loop_ + _alias.definition_id '_journal_techeditor_address' + _definition.update 2012-12-11 + _description.text +; + Postal address of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_techeditor.email + _definition.id '_journal_techeditor.email' + loop_ + _alias.definition_id '_journal_techeditor_email' + _definition.update 2012-12-11 + _description.text +; + Email address of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id email + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_techeditor.phone + _definition.id '_journal_techeditor.phone' + loop_ + _alias.definition_id '_journal_techeditor_phone' + _definition.update 2012-12-11 + _description.text +; + Phone number of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id phone + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal_techeditor.fax + _definition.id '_journal_techeditor.fax' + loop_ + _alias.definition_id '_journal_techeditor_fax' + _definition.update 2012-12-11 + _description.text +; + Fax number of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id fax + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_journal_techeditor.notes + _definition.id '_journal_techeditor.notes' + loop_ + _alias.definition_id '_journal_techeditor_notes' + _definition.update 2012-12-11 + _description.text +; + Notes of the technical editor for this publication. +; + _name.category_id techeditor + _name.object_id notes + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + save_ #--------- close the JOURNAL_TECHEDITOR category + + +#---------------------------------------------------------------------------- + +save_JOURNAL_INDEX + _definition.id JOURNAL_INDEX + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-11 + _description.text +; + Category of items describing publication indices. +; + _name.category_id JOURNAL + _name.object_id INDEX + _category.key_id '_journal_index.key' + + +save_journal_index.key + _definition.id '_journal_index.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of JOURNAL_INDEX items + in a looped list. +; + _name.category_id index + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(journal_index.id) +; + Evaluation +; _journal_index.key = _journal_index.id +; + save_ + + +save_journal_index.id + _definition.id '_journal_index.id' + loop_ + _alias.definition_id '_journal_index_id' + _definition.update 2013-01-23 + _description.text +; + Index number identifier of the JOURNAL_INDEX category. +; + _name.category_id journal_index + _name.object_id id + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Index + save_ + + +save_journal_index.subterm + _definition.id '_journal_index.subterm' + loop_ + _alias.definition_id '_journal_index_subterm' + _definition.update 2012-12-11 + _description.text +; + Sub-term index assigned for the publication. +; + _name.category_id journal_index + _name.object_id subterm + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_index.term + _definition.id '_journal_index.term' + loop_ + _alias.definition_id '_journal_index_term' + _definition.update 2012-12-11 + _description.text +; + Term index assigned for the publication. +; + _name.category_id journal_index + _name.object_id term + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_journal_index.type + _definition.id '_journal_index.type' + loop_ + _alias.definition_id '_journal_index_type' + _definition.update 2012-12-11 + _description.text +; + Type of index assigned for the publication. +; + _name.category_id journal_index + _name.object_id type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + O '???????? formula ??????????????' + S '???????? structure description ???????' + save_ + + save_ #--------- close the JOURNAL_INDEX category + + save_ #--------- close the JOURNAL category + + +#============================================================================ + +save_CITATION + _definition.id CITATION + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-11 + _description.text +; + Category of items describing literature cited in the publication. +; + _name.category_id PUBLICATION + _name.object_id CITATION + _category.key_id '_citation.key' + + +save_citation.key + _definition.id '_citation.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of CITATION items + in a looped list. +; + _name.category_id citation + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(citation.id) +; + Evaluation +; _citation.key = _citation.id +; + save_ + + +save_citation.id + _definition.id '_citation.id' + loop_ + _alias.definition_id '_citation_id' + _definition.update 2012-12-11 + _description.text +; + Unique identifier to the CITATION list. A value of 'primary' + should be used to indicate the citation that the author(s) + consider to be the most pertinent to the contents of the data + block. Note that this item need not be a number; it can be + any unique identifier. +; + _name.category_id citation + _name.object_id id + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _description_example.case primary 1 2 3 + save_ + + +save_citation.abstract + _definition.id '_citation.abstract' + loop_ + _alias.definition_id '_citation_abstract' + _definition.update 2012-12-11 + _description.text +; + Abstract for the citation. This is used most when the + citation is extracted from a bibliographic database that + contains full text or abstract information. +; + _name.category_id citation + _name.object_id abstract + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.abstract_id_CAS + _definition.id '_citation.abstract_id_CAS' + loop_ + _alias.definition_id '_citation_abstract_id_CAS' + _definition.update 2012-12-11 + _description.text +; + Chemical Abstracts Service (CAS) abstract identifier. +; + _name.category_id citation + _name.object_id abstract_id_CAS + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + +save_citation.page_first + _definition.id '_citation.page_first' + loop_ + _alias.definition_id '_citation_page_first' + _definition.update 2012-12-11 + _description.text +; + First page of citation; relevant for articles and book chapters. +; + _name.category_id citation + _name.object_id page_first + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Index + save_ + + +save_citation.page_last + _definition.id '_citation.page_last' + loop_ + _alias.definition_id '_citation_page_last' + _definition.update 2012-12-11 + _description.text +; + Last page of citation; relevant for articles and book chapters. +; + _name.category_id citation + _name.object_id page_last + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Index + save_ + + +save_citation.special_details + _definition.id '_citation.special_details' + loop_ + _alias.definition_id '_citation_special_details' + _definition.update 2012-12-11 + _description.text +; + Special aspects of the relationship of the data block contents + to the literature item cited. +; + _name.category_id citation + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.title + _definition.id '_citation.title' + loop_ + _alias.definition_id '_citation_title' + _definition.update 2012-12-11 + _description.text +; + Title of citation; relevant for articles and book chapters. +; + _name.category_id citation + _name.object_id title + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.year + _definition.id '_citation.year' + loop_ + _alias.definition_id '_citation_year' + _definition.update 2012-12-11 + _description.text +; + Year of citation; relevant for articles and book chapters. +; + _name.category_id citation + _name.object_id year + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.coordinate_linkage + _definition.id '_citation.coordinate_linkage' + loop_ + _alias.definition_id '_citation_coordinate_linkage' + _definition.update 2012-12-11 + _description.text +; + Code specifies whether this citation is concerned with precisely + the set of coordinates given in the data block. If, for instance, + the publication described the same structure, but the coordinates + had undergone further refinement prior to creation of the data + block, the value of this data item would be 'no'. +; + _name.category_id citation + _name.object_id coordinate_linkage + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _enumeration_set.state + _enumeration_set.detail + no 'citation unrelated to current coordinates' + n 'abbreviation for "no"' + yes 'citation related to current coordinates' + y 'abbreviation for "yes"' + save_ + + +save_citation.country + _definition.id '_citation.country' + loop_ + _alias.definition_id '_citation_country' + _definition.update 2012-12-11 + _description.text +; + Country of publication; for journal articles and book chapters. +; + _name.category_id citation + _name.object_id country + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.database_id_CSD + _definition.id '_citation.database_id_CSD' + loop_ + _alias.definition_id '_citation_database_id_CSD' + _definition.update 2012-12-11 + _description.text +; + Identifier ('refcode') of the database record in the Cambridge + Structural Database containing details of the cited structure. +; + _name.category_id citation + _name.object_id database_id_CSD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation.database_id_Medline + _definition.id '_citation.database_id_Medline' + loop_ + _alias.definition_id '_citation_database_id_Medline' + _definition.update 2012-12-11 + _description.text +; +i Medline accession number categorizing a bibliographic entry. +; + _name.category_id citation + _name.object_id database_id_Medline + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_citation.book_id_ISBN + _definition.id '_citation.book_id_ISBN' + loop_ + _alias.definition_id '_citation_book_id_ISBN' + _definition.update 2012-12-11 + _description.text +; + International Standard Book Number (ISBN) for book chap. cited. +; + _name.category_id citation + _name.object_id book_id_ISBN + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.book_publisher + _definition.id '_citation.book_publisher' + loop_ + _alias.definition_id '_citation_book_publisher' + _definition.update 2012-12-11 + _description.text +; + Publisher of the citation; relevant for book chapters. +; + _name.category_id citation + _name.object_id book_publisher + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.book_publisher_city + _definition.id '_citation.book_publisher_city' + loop_ + _alias.definition_id '_citation_book_publisher_city' + _definition.update 2012-12-11 + _description.text +; + Location of publisher of the citation; relevant for book chapters. +; + _name.category_id citation + _name.object_id book_publisher_city + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.book_title + _definition.id '_citation.book_title' + loop_ + _alias.definition_id '_citation_book_title' + _definition.update 2012-12-11 + _description.text +; + Title of the book in which the citation appeared. +; + _name.category_id citation + _name.object_id book_title + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_citation.journal_abbrev + _definition.id '_citation.journal_abbrev' + loop_ + _alias.definition_id '_citation_journal_abbrev' + _definition.update 2012-12-11 + _description.text +; + Abbreviated name of the journal cited as given in the Chemical + Abstracts Service Source Index. +; + _name.category_id citation + _name.object_id journal_abbrev + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'J. Mol. Biol.' + save_ + + +save_citation.journal_full + _definition.id '_citation.journal_full' + loop_ + _alias.definition_id '_citation_journal_full' + _definition.update 2012-12-11 + _description.text +; + Full name of the journal cited; relevant for journal articles. +; + _name.category_id citation + _name.object_id journal_full + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'Journal of Molecular Biology' + save_ + + +save_citation.journal_id_ASTM + _definition.id '_citation.journal_id_ASTM' + loop_ + _alias.definition_id '_citation_journal_id_ASTM' + _definition.update 2012-12-11 + _description.text +; + American Society for the Testing of Materials (ASTM) code assigned + to the journal cited (also referred to as the CODEN designator of + the Chemical Abstracts Service); relevant for journal articles. +; + _name.category_id citation + _name.object_id journal_id_ASTM + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation.journal_id_CSD + _definition.id '_citation.journal_id_CSD' + loop_ + _alias.definition_id '_citation_journal_id_CSD' + _definition.update 2012-12-11 + _description.text +; + The Cambridge Structural Database (CSD) code assigned to the + journal cited; relevant for journal articles. This is also the + system used at the Protein Data Bank (PDB). +; + _name.category_id citation + _name.object_id journal_id_CSD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + loop_ _description_example.case '0070' + save_ + + +save_citation.journal_id_ISSN + _definition.id '_citation.journal_id_ISSN' + loop_ + _alias.definition_id '_citation_journal_id_ISSN' + _definition.update 2012-12-11 + _description.text +; + The International Standard Serial Number (ISSN) code assigned to + the journal cited; relevant for journal articles. +; + _name.category_id citation + _name.object_id journal_id_ISSN + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation.journal_issue + _definition.id '_citation.journal_issue' + loop_ + _alias.definition_id '_citation_journal_issue' + _definition.update 2012-12-11 + _description.text +; + Issue number of the journal cited; relevant for articles. +; + _name.category_id citation + _name.object_id journal_issue + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Index + loop_ _description_example.case 2 + save_ + + +save_citation.journal_volume + _definition.id '_citation.journal_volume' + loop_ + _alias.definition_id '_citation_journal_volume' + _definition.update 2012-12-11 + _description.text +; + Volume number of the journal cited; relevant for articles. +; + _name.category_id citation + _name.object_id journal_volume + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Index + loop_ _description_example.case 174 + save_ + + +save_citation.language + _definition.id '_citation.language' + loop_ + _alias.definition_id '_citation_language' + _definition.update 2012-12-11 + _description.text +; + Language in which the citation appears. +; + _name.category_id citation + _name.object_id language + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case German + save_ + + save_ #--------- close the CITATION category + +#============================================================================ + +save_CITATION_AUTHOR + _definition.id CITATION_AUTHOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-11 + _description.text +; + Category of items describing citation author(s) details. +; + _name.category_id PUBLICATION + _name.object_id CITATION_AUTHOR + _category.key_id '_citation_author.key' + + +save_citation_author.key + _definition.id '_citation_author.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of CITATION_AUTHOR items + in a looped list. +; + _name.category_id citation_author + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(citation_author.ordinal) +; + Evaluation +; _citation_author.key = _citation_author.ordinal +; + save_ + + +save_citation_author.ordinal + _definition.id '_citation_author.ordinal' + loop_ + _alias.definition_id '_citation_author_ordinal' + _definition.update 2012-12-11 + _description.text +; + Ordinal code specifies the order of the author's name in the list + of authors of the citation. +; + _name.category_id citation_author + _name.object_id ordinal + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation_author.citation_id + _definition.id '_citation_author.citation_id' + loop_ + _alias.definition_id '_citation_author_citation_id' + _definition.update 2012-12-11 + _description.text +; + Code identifier in the CITATION data list. The value of must match + an identifier specified in the CITATION list. +; + _name.category_id citation_author + _name.object_id citation_id + _name.linked_item_id '_citation.id' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation_author.name + _definition.id '_citation_author.name' + loop_ + _alias.definition_id '_citation_author_name' + _definition.update 2012-12-11 + _description.text +; + Name of citation author; relevant for articles and book chapters. + The family name(s), followed by a comma and including any + dynastic components, precedes the first name(s) or initial(s). +; + _name.category_id citation_author + _name.object_id name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'Bleary, Percival R.' + "O'Neil, F.K." + 'Van den Bossche, G.' + 'Yang, D.-L.' + 'Simonov, Yu.A' + 'M\"uller, H.A.' + 'Ross II, C.R.' + save_ + + save_ #--------- close the CITATION_AUTHOR category + + +#============================================================================ + +save_CITATION_EDITOR + _definition.id CITATION_EDITOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-12-11 + _description.text +; + Category of items describing citation editor(s) details. +; + _name.category_id PUBLICATION + _name.object_id CITATION_EDITOR + _category.key_id '_citation_editor.key' + + +save_citation_editor.key + _definition.id '_citation_editor.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of CITATION_EDITOR items + in a looped list. +; + _name.category_id citation_editor + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(citation_editor.id) +; + Evaluation +; _citation_editor.key = _citation_editor.id +; + save_ + + +save_citation_editor.id + _definition.id '_citation_editor.id' + loop_ + _alias.definition_id '_citation_editor_ordinal' + _definition.update 2012-12-11 + _description.text +; + Index number identifier of the CITATION_EDITOR category. +; + _name.category_id citation_editor + _name.object_id id + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Index + save_ + + +save_citation_editor.citation_id + _definition.id '_citation_editor.citation_id' + loop_ + _alias.definition_id '_citation_editor_citation_id' + _definition.update 2012-12-11 + _description.text +; + Code identifier in the CITATION list. The value must match an + identifier specified by _citation.id in the CITATION list. +; + _name.category_id citation_editor + _name.object_id citation_id + _name.linked_item_id '_citation.id' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_citation_editor.name + _definition.id '_citation_editor.name' + loop_ + _alias.definition_id '_citation_editor' + '_citation_editor_name' + _definition.update 2012-12-11 + _description.text +; + Name of citation editor; relevant for book chapters. + The family name(s), followed by a comma and including any + dynastic components, precedes the first name(s) or initial(s). +; + _name.category_id citation_editor + _name.object_id name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'Bleary, Percival R.' + "O'Neil, F.K." + 'Van den Bossche, G.' + 'Yang, D.-L.' + 'Simonov, Yu.A' + 'M\"uller, H.A.' + 'Ross II, C.R.' + save_ + + save_ #--------- close the CITATION_EDITOR category + + +#============================================================================ + +save_DATABASE + _definition.id DATABASE + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of data items recording database deposition. +; + _name.category_id PUBLICATION + _name.object_id DATABASE + + +save_database.CSD_history + _definition.id '_database.CSD_history' + loop_ + _alias.definition_id '_database_CSD_history' + _definition.update 2012-12-13 + _description.text +; + The history of changes made by the Cambridge Crystallographic Data + Centre and incorporated into the Cambridge Structural Database (CSD). +; + _name.category_id database + _name.object_id CSD_history + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_database.journal_CSD + _definition.id '_database.journal_CSD' + loop_ + _alias.definition_id '_database_journal_CSD' + _definition.update 2012-12-13 + _description.text +; + The journal code used in the Cambridge Structural Database. +; + _name.category_id database + _name.object_id journal_CSD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database.journal_ASTM + _definition.id '_database.journal_ASTM' + loop_ + _alias.definition_id '_database_journal_ASTM' + _definition.update 2012-12-13 + _description.text +; + ASTM CODEN designator for a journal as given in the Chemical + Source List maintained by the Chemical Abstracts Service. +; + _name.category_id database + _name.object_id journal_ASTM + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +#---------------------------------------------------------------------------- + +save_DATABASE_CODE + _definition.id DATABASE_CODE + _definition.scope Category + _definition.class Set + _definition.update 2012-12-13 + _description.text +; + The CATEGORY of data items recording database deposition. +; + _name.category_id DATABASE + _name.object_id CODE + + +save_database_code.CAS + _definition.id '_database_code.CAS' + loop_ + _alias.definition_id '_database_code_CAS' + _definition.update 2012-12-13 + _description.text +; + Code assigned by the Chemical Abstracts Service. +; + _name.category_id code + _name.object_id CAS + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.COD + _definition.id '_database_code.COD' + loop_ + _alias.definition_id '_database_code_COD' + _definition.update 2012-12-13 + _description.text +; + Code assigned by Crystallography Open Database (COD). +; + _name.category_id code + _name.object_id COD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.CSD + _definition.id '_database_code.CSD' + loop_ + _alias.definition_id '_database_code_CSD' + _definition.update 2012-12-13 + _description.text +; + Code assigned by the Cambridge Structural Database. +; + _name.category_id code + _name.object_id CSD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.ICSD + _definition.id '_database_code.ICSD' + loop_ + _alias.definition_id '_database_code_ICSD' + _definition.update 2012-12-13 + _description.text +; + Code assigned by the Inorganic Crystal Structure Database. +; + _name.category_id code + _name.object_id ICSD + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.MDF + _definition.id '_database_code.MDF' + loop_ + _alias.definition_id '_database_code_MDF' + _definition.update 2012-12-13 + _description.text +; + Code assigned in the Metals Data File. +; + _name.category_id code + _name.object_id MDF + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.NBS + _definition.id '_database_code.NBS' + loop_ + _alias.definition_id '_database_code_NBS' + _definition.update 2012-12-13 + _description.text +; + Code assigned by the NBS (NIST) Crystal Data Database. +; + _name.category_id code + _name.object_id NBS + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.PDB + _definition.id '_database_code.PDB' + loop_ + _alias.definition_id '_database_code_PDB' + _definition.update 2012-12-13 + _description.text +; + Code assigned by the Protein Data Base. +; + _name.category_id code + _name.object_id PDB + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.PDF + _definition.id '_database_code.PDF' + loop_ + _alias.definition_id '_database_code_PDF' + _definition.update 2012-12-13 + _description.text +; + Code assigned in the Powder Diffraction File. +; + _name.category_id code + _name.object_id PDF + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.depnum_ccdc_archive + _definition.id '_database_code.depnum_ccdc_archive' + loop_ + _alias.definition_id '_database_code_depnum_ccdc_archive' + _definition.update 20113-01-22 + _description.text +; + Deposition numbers assigned by the Cambridge Crystallographic + Data Centre (CCDC) to files containing structural information + archived by the CCDC. +; + _name.category_id code + _name.object_id depnum_ccdc_archive + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.depnum_ccdc_fiz + _definition.id '_database_code.depnum_ccdc_fiz' + loop_ + _alias.definition_id '_database_code_depnum_ccdc_fiz' + _definition.update 20113-01-22 + _description.text +; + Deposition numbers assigned by the Fachinformationszentrum + Karlsruhe (FIZ) to files containing structural information + archived by the Cambridge Crystallographic Data Centre (CCDC). +; + _name.category_id code + _name.object_id depnum_ccdc_fiz + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_database_code.depnum_ccdc_journal + _definition.id '_database_code.depnum_ccdc_journal' + loop_ + _alias.definition_id '_database_code_depnum_ccdc_journal' + _definition.update 2013-01-22 + _description.text +; + Deposition numbers assigned by various journals to files + containing structural information archived by the Cambridge + Crystallographic Data Centre (CCDC). +; + _name.category_id code + _name.object_id depnum_ccdc_journal + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + save_ #--------- close the DATABASE_CODE category + + save_ #--------- close the DATABASE category + + +#============================================================================ + +save_AUDIT + _definition.id AUDIT + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used to record details about the + creation and subsequent updating of the data block. +; + _name.category_id PUBLICATION + _name.object_id AUDIT + + +save_audit.creation_date + _definition.id '_audit.creation_date' + loop_ + _alias.definition_id '_audit_creation_date' + _definition.update 2012-11-29 + _description.text +; + The date dd-mm-yyyy of each revision to the data. +; + _name.category_id audit + _name.object_id creation_date + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Date + loop_ _description_example.case 1991-03-20 + save_ + + +save_audit.update_record + _definition.id '_audit.update_record' + loop_ + _alias.definition_id '_audit_update_record' + _definition.update 2012-11-29 + _description.text +; + A description of the revision applied to the data. +; + _name.category_id audit + _name.object_id update_record + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case '1990-07-15 Updated by Co-editor' + save_ + + +save_audit.block_code + _definition.id '_audit.block_code' + loop_ + _alias.definition_id '_audit_block_code' + _definition.update 2012-11-29 + _description.text +; + A unique block_code identifier for each revision. +; + _name.category_id audit + _name.object_id block_code + _type.purpose Describe + _type.source Selected + _type.container Single + _type.contents Code + loop_ _description_example.case TOZ_1991-03-20 + save_ + + +save_audit.creation_method + _definition.id '_audit.creation_method' + loop_ + _alias.definition_id '_audit_creation_method' + _definition.update 2012-11-29 + _description.text +; + A description of how the revision was applied to the data. +; + _name.category_id audit + _name.object_id creation_method + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'spawned by the program QBEE' + save_ + + +#============================================================================ + + +save_AUDIT_AUTHOR + _definition.id AUDIT_AUTHOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used for author(s) details. +; + _name.category_id AUDIT + _name.object_id AUTHOR + _category.key_id '_audit_author.key' + + +save_audit_author.key + _definition.id '_audit_author.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of AUDIT_AUTHOR items + in a looped list. +; + _name.category_id audit_author + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(audit_author.name) +; + Evaluation +; _audit_author.key = _audit_author.name +; + save_ + + +save_audit_author.name + _definition.id '_audit_author.name' + loop_ + _alias.definition_id '_audit_author_name' + _definition.update 2012-11-29 + _description.text +; + The name of an author of this data block. If there are multiple + authors, _audit_author.name is looped with _audit_author.address. + The family name(s), followed by a comma and including any + dynastic components, precedes the first name(s) or initial(s). + +; + _name.category_id author + _name.object_id name + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case + 'Bleary, Percival R.' + "O'Neil, F.K." + 'Van den Bossche, G.' + 'Yang, D.-L.' + 'Simonov, Yu.A.' + 'M\"uller, H.A.' + 'Ross II, C.R.' + save_ + + +save_audit_author.address + _definition.id '_audit_author.address' + loop_ + _alias.definition_id '_audit_author_address' + _definition.update 2012-11-29 + _description.text +; + The address of an author of this data block. If there are + multiple authors, _audit_author_address is looped with + _audit_author.name. +; + _name.category_id author + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case + '''Department + Institute + Street + City and postcode + COUNTRY ''' + save_ + + save_ #--------- close the AUDIT_AUTHOR category + + +#============================================================================ + + +save_AUDIT_CONFORM + _definition.id AUDIT_CONFORM + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used describe dictionary versions + by which data names in the current data block are conformant. +; + _name.category_id AUDIT + _name.object_id CONFORM + + +save_audit_conform.dict_name + _definition.id '_audit_conform.dict_name' + loop_ + _alias.definition_id '_audit_conform_dict_name' + _definition.update 2012-11-29 + _description.text +; + Name identifying highest-level data dictionary defining + data names used in this file. +; + _name.category_id conform + _name.object_id dict_name + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_audit_conform.dict_version + _definition.id '_audit_conform.dict_version' + loop_ + _alias.definition_id '_audit_conform_dict_version' + _definition.update 2012-11-29 + _description.text +; + Code for the version of data dictionary defining data names + used in this file. +; + _name.category_id conform + _name.object_id dict_version + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_audit_conform.dict_location + _definition.id '_audit_conform.dict_location' + loop_ + _alias.definition_id '_audit_conform_dict_location' + _definition.update 2012-11-29 + _description.text +; + File name or uniform resource locator (URL) where the + conformant data dictionary resides. +; + _name.category_id conform + _name.object_id dict_location + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #--------- close the AUDIT_CONFORM category + + +#============================================================================ + + +save_AUDIT_CONTACT_AUTHOR + _definition.id AUDIT_CONTACT_AUTHOR + _definition.scope Category + _definition.class Loop + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used for contact author(s) details. +; + _name.category_id AUDIT + _name.object_id CONTACT_AUTHOR + _category.key_id '_audit_contact_author.key' + + +save_audit_contact_author.key + _definition.id '_audit_contact_author.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of AUDIT_CONTACT_AUTHOR items + in a looped list. +; + _name.category_id audit_contact_author + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(audit_contact_author.name) +; + Evaluation +; _audit_contact_author.key = _audit_contact_author.name +; + save_ + + +save_audit_contact_author.name + _definition.id '_audit_contact_author.name' + loop_ + _alias.definition_id '_audit_contact_author_name' + '_audit_contact_author' + _definition.update 2012-11-29 + _description.text +; + The name of the author of the data block to whom correspondence + should be addressed. The family name(s), followed by a comma and + including any dynastic components, precedes the first name(s) or + initial(s). +; + _name.category_id contact_author + _name.object_id name + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Bleary, Percival R.' + "O'Neil, F.K." + 'Van den Bossche, G.' + save_ + + +save_audit_contact_author.address + _definition.id '_audit_contact_author.address' + loop_ + _alias.definition_id '_audit_contact_author_address' + _definition.update 2012-11-29 + _description.text +; + The mailing address of the author of the data block to whom + correspondence should be addressed. +; + _name.category_id contact_author + _name.object_id address + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case +; Department + Institute + Street + City and postcode + COUNTRY +; + save_ + + +save_audit_contact_author.email + _definition.id '_audit_contact_author.email' + loop_ + _alias.definition_id '_audit_contact_author_email' + _definition.update 2012-11-29 + _description.text +; + The electronic mail address of the author of the data block + to whom correspondence should be addressed, in a form + recognizable to international networks. The format of e-mail + addresses is given in Section 3.4, Address Specification, of + Internet Message Format, RFC 2822, P. Resnick (Editor), + Network Standards Group, April 2001. +; + _name.category_id contact_author + _name.object_id email + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case name@host.domain.country + bm@iucr.org + save_ + + +save_audit_contact_author.phone + _definition.id '_audit_contact_author.phone' + loop_ + _alias.definition_id '_audit_contact_author_phone' + _definition.update 2012-11-29 + _description.text +; + Telephone number of author submitting the manuscript and data block. + The recommended style is the international dialing prefix, + followed by the area code in parentheses, followed by the + local number and any extension number prefixed by 'x', with + no spaces. The earlier convention of including the international + dialing prefix in parentheses is no longer recommended. +; + _name.category_id contact_author + _name.object_id phone + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '12(34)9477330' + '12()349477330' + '12(34)9477330x5543' + save_ + + +save_audit_contact_author.fax + _definition.id '_audit_contact_author.fax' + loop_ + _alias.definition_id '_audit_contact_author_fax' + _definition.update 2012-11-29 + _description.text +; + Facsimile telephone number of the author submitting the manuscript + and data block. + The recommended style is the international dialing prefix, followed + by the area code in parentheses, followed by the local number with + no spaces. The earlier convention of including the international + dialing prefix in parentheses is no longer recommended. +; + _name.category_id contact_author + _name.object_id fax + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case '12(34)9477334' + '12()349477334' + save_ + + save_ #--------- close the AUDIT_CONTACT_AUTHOR category + + +#============================================================================ + + +save_AUDIT_LINK + _definition.id AUDIT_LINK + _definition.scope Category + _definition.class Loop + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used to record details about the + relationships between data blocks in the current CIF. +; + _name.category_id AUDIT + _name.object_id LINK + _category.key_id '_audit_link.key' + + +save_audit_link.key + _definition.id '_audit_link.key' + _definition.update 2012-12-13 + _description.text +; + Value is a unique key to a set of AUDIT_LINK items + in a looped list. +; + _name.category_id audit_link + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(audit_link.block_code) +; + Evaluation +; _audit_link.key = _audit_link.block_code +; + save_ + + +save_audit_link.block_code + _definition.id '_audit_link.block_code' + loop_ + _alias.definition_id '_audit_link_block_code' + _definition.update 2012-11-29 + _description.text +; + The value of _audit.block_code associated with a data block + in the current file related to the current data block. The + special value '.' may be used to refer to the current data + block for completeness. +; + _name.category_id link + _name.object_id block_code + _type.purpose Key + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_audit_link.block_description + _definition.id '_audit_link.block_description' + loop_ + _alias.definition_id '_audit_link_block_description' + _definition.update 2012-11-29 + _description.text +; + Description of the relationship of the referenced data block + to the current one. +; + _name.category_id link + _name.object_id block_description + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #--------- close the AUDIT_LINK category + + save_ #--------- close the AUDIT category + + +#============================================================================ + +save_COMPUTING + _definition.id COMPUTING + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used to record details of the + computer programs used in the crystal structure analysis. +; + _name.category_id PUBLICATION + _name.object_id COMPUTING + + +save_computing.diffrn_collection + _definition.id '_computing.diffrn_collection' + loop_ + _alias.definition_id '_computing_data_collection' + _definition.update 2012-12-11 + _description.text +; + Description of software used to measure diffraction data. +; + _name.category_id computing + _name.object_id diffrn_collection + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'CAD-4 (Enraf-Nonius, 1989)' + save_ + + +save_computing.diffrn_reduction + _definition.id '_computing.diffrn_reduction' + loop_ + _alias.definition_id '_computing_data_reduction' + _definition.update 2012-12-11 + _description.text +; + Description of software used to convert diffraction data + to measured structure factors. +; + _name.category_id computing + _name.object_id diffrn_reduction + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case + 'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)' + save_ + + +save_computing.cell_refinement + _definition.id '_computing.cell_refinement' + loop_ + _alias.definition_id '_computing_cell_refinement' + _definition.update 2012-11-29 + _description.text +; + Brief description of software used for cell_refinement. +; + _name.category_id computing + _name.object_id cell_refinement + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'CAD-4 (Enraf-Nonius, 1989)' + save_ + + +save_computing.structure_solution + _definition.id '_computing.structure_solution' + loop_ + _alias.definition_id '_computing_structure_solution' + _definition.update 2012-11-29 + _description.text +; + Brief description of software used for structure_solution. +; + _name.category_id computing + _name.object_id structure_solution + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'SHELXS86 (Sheldrick, 1990)' + save_ + + +save_computing.structure_refinement + _definition.id '_computing.structure_refinement' + loop_ + _alias.definition_id '_computing_structure_refinement' + _definition.update 2012-11-29 + _description.text +; + Brief description of software used for structure_refinement. +; + _name.category_id computing + _name.object_id structure_refinement + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ _description_example.case 'SHELXL93 (Sheldrick, 1993)' + save_ + + +save_computing.molecular_graphics + _definition.id '_computing.molecular_graphics' + loop_ + _alias.definition_id '_computing_molecular_graphics' + _definition.update 2012-11-29 + _description.text +; + Brief description of software used for molecular_graphics. +; + _name.category_id computing + _name.object_id molecular_graphics + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_computing.publication_material + _definition.id '_computing.publication_material' + loop_ + _alias.definition_id '_computing_publication_material' + _definition.update 2012-11-29 + _description.text +; + Brief description of software used for publication_material. +; + _name.category_id computing + _name.object_id publication_material + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + save_ #--------- close the COMPUTING category + +#============================================================================ + +save_DISPLAY + _definition.id DISPLAY + _definition.scope Category + _definition.class Set + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used to enumerate the display + parameters used in the discipline. +; + _name.category_id PUBLICATION + _name.object_id DISPLAY + +#---------------------------------------------------------------------------- + +save_DISPLAY_COLOUR + _definition.id DISPLAY_COLOUR + _definition.scope Category + _definition.class Loop + _definition.update 2012-05-07 + _description.text +; + The CATEGORY of data items used to enumerate the display + colour codes used in the discipline. +; + _name.category_id DISPLAY + _name.object_id COLOUR + _category.key_id '_display_colour.key' + + +save_display_colour.key + _definition.id '_display_colour.key' + _definition.update 2012-05-07 + _description.text +; + Value is a unique key to a set of DISPLAY_COLOUR items + in a looped list. +; + _description.common 'Key to display colours' + _name.category_id colour + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(display_colour.hue) +; + Evaluation +; _display_colour.key = _display_colour.hue +; + save_ + + +save_display_colour.hue + _definition.id '_display_colour.hue' + _definition.update 2012-05-07 + _description.text +; + Colour hue as an enumerated code. +; + _description.common 'DisplayHue' + _name.category_id colour + _name.object_id hue + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'colour_RGB'}] + _enumeration.default 'black' + save_ + + +save_display_colour.RGB + _definition.id '_display_colour.RGB' + _definition.update 2012-11-20 + _description.text +; + The red-green-blue intensities, bases 256, for each colour code. +; + _description.common 'DisplayColourRGB' + _name.category_id colour + _name.object_id RGB + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Integer + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With c as display_colour + + _display_colour.RGB = [ c.red, c.green, c.blue ] +; + save_ + + +save_display_colour.red + _definition.id '_display_colour.red' + _import.get [{"file":'templ_attr.cif',"save":'display_colour'}] + _name.category_id colour + _name.object_id red + save_ + + +save_display_colour.green + _definition.id '_display_colour.green' + _import.get [{"file":'templ_attr.cif',"save":'display_colour'}] + _name.category_id colour + _name.object_id green + save_ + + +save_display_colour.blue + _definition.id '_display_colour.blue' + _import.get [{"file":'templ_attr.cif',"save":'display_colour'}] + _name.category_id colour + _name.object_id blue + save_ + + save_ #----------- close of DISPLAY_COLOUR category + + save_ #----------- close of DISPLAY category + + save_ #----------- close of PUBLICATION category + + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.1.01 2006-03-07 +; + Initial CORE_PUBLICATION dictionary constructed from CORE_3 v3.5.02 +; + 1.1.02 2006-06-20 +; + Apply DDL 3.6.04 attributes. +; + 1.1.03 2006-06-30 +; + Apply DDL 3.6.05 attributes. +; + 1.1.04 2006-09-07 +; + Apply DDL 3.6.08 attributes. +; + 1.1.05 2006-11-13 +; + Apply DDL 3.6.10 attributes. +; + 1.1.06 2006-12-14 +; + Apply DDL 3.7.01 attributes. +; + 1.2.01 2007-02-07 +; + Apply DDL 3.7.04 attributes. +; + 1.2.02 2007-10-13 +; + Placed tags in _category_key.primitive lists within quotes. +; + 1.2.03 2008-01-18 +; + Replaced import_list controls with leading uppercase character. + Changed import_list [....] to [[....]] +; + 1.2.04 2008-01-22 +; + Changed _import.block in _import_list.id to 'colour_RBG' + Added _enumeration.default as 'black' +; + 1.2.05 2008-02-07 +; + Changed 'colour_RBG' to 'colour_RGB' +; + 1.2.06 2008-05-18 +; + Change _import_list.id to be ((.....)) + For all *.key items change _type.contents from Code to Inherited +; + 1.3.01 2011-06-07 +; + Replace category class "List" with "Loop" + Replace all "Tuple" with "List" + Place all import lists into [[......]] +; + 1.3.02 2011-08-02 +; + Instal the nested save frames and the import.get attributes. + Apply the DDL 3.8 attributes. +; + 1.3.03 2011-08-02 +; + Change name of import file com_att.dic to templ_attr.cif + Change name of import file com_val.dic to templ_templcif +; + 1.3.04 2011-12-01 +; + Update the DDL version. No Matrix types present. +; + 1.3.05 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 1.4.01 2012-05-07 +; + Apply DDL 3.10.01 changes. +; + 1.4.02 2012-10-16 +; + Apply DDL 3.10.02 changes. + Remove type.contents "Inherited"; insert Definition method expression. +; + 1.4.03 2012-11-20 +; + Invoke container functions Matrix, List in methods scripts where needed. +; + 1.4.04 2012-11-29 +; + Added AUDIT, PUBL and COMPUTING categories of definitions. +; + 1.4.05 2012-12-11 +; + Changed computing.data_collection to computing.diffrn_collection. + Changed computing.data_reduction to computing.diffrn_reduction. + Added the CITATION, CITATION_AUTHOR, CITATION_EDITOR definitions. +; + 1.4.06 2012-12-13 +; + Added DATABASE and DATABASE_CODE categories + Added PUBL_AUTHOR and PUBL_BODY categories + Reorganised PUBL_MANUSCRIPT categories. + Reorganised CITATION, CITATION_BOOK, CITATION_JOURNAL categories. +; + 1.4.07 2012-12-30 +; + Added *.key definitions for a number of Loop categories. +; + 1.4.08 2013-01-22 +; + Added several definitions/descriptions for alignment with latest DDL1 dic. +; + 1.4.09 2013-01-23 +; + Change _journal.data_validation_number to _journal.validation_number +; diff --git a/core_struc.dic b/core_struc.dic new file mode 100755 index 0000000..b2fd712 --- /dev/null +++ b/core_struc.dic @@ -0,0 +1,4583 @@ +############################################################################## +# # +# CIF CORE STRUCTURE DICTIONARY # +# # +############################################################################## + +data_CORE_STRUC + + _dictionary.title CORE_STRUC + _dictionary.class Instance + _dictionary.version 1.4.10 + _dictionary.date 2013-02-18 + _dictionary.uri www.iucr.org/cif/dic/core_struc.dic + _dictionary.ddl_conformance 3.10.03 + _dictionary.namespace CoreStruc + _description.text +; + This dictionary contains the definitions of data items that + are considered CORE to the description of STRUCTURE data. +; + + +save_STRUCTURE + _definition.id STRUCTURE + _definition.scope Category + _definition.class Head + _definition.update 2012-11-20 + _description.text +; + The DICTIONARY group encompassing the CORE STRUCTURE data items defined + and used with in the Crystallographic Information Framework (CIF). +; + _name.category_id CIF_CORE + _name.object_id STRUCTURE + +#=========================================================================== + +save_ATOM + + _definition.id ATOM + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe atomic information + used in crystallographic structure studies. +; + _description.common 'Atom' + _name.category_id STRUCTURE + _name.object_id ATOM + + +#=========================================================================== + +save_ATOM_SITE + + _definition.id ATOM_SITE + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe atom site information + used in crystallographic structure studies. +; + _description.common 'AtomSiteList' + _name.category_id ATOM + _name.object_id SITE + _category.key_id '_atom_site.key' + + +save_atom_site.key + _definition.id '_atom_site.key' + _definition.update 2012-11-20 + _description.text +; + Value is a unique key to a set of ATOM_SITE items + in a looped list. +; + _description.common 'Key to list of atomic sites' + _name.category_id site + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(atom_site.label) +; + Evaluation +; _atom_site.key = _atom_site.label +; + save_ + + +save_atom_site.adp_type + _definition.id '_atom_site.adp_type' + loop_ + _alias.definition_id '_atom_site_adp_type' + '_atom_site_thermal_displace_type' + '_atom_site.thermal_displace_type' + _definition.update 2012-11-20 + _description.text +; + Code for type of atomic displacement parameters used for the site. +; + _description.common 'AtomSiteAdpType' + _name.category_id site + _name.object_id adp_type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail Uani 'anisotropic Uij' + Uiso 'isotropic U' + Uovl 'overall U' + Umpe 'multipole expansion U' + Bani 'anisotropic Bij' + Biso 'isotropic B' + Bovl 'overall B' + _enumeration.default Uiso + save_ + + +save_atom_site.attached_hydrogens + _definition.id '_atom_site.attached_hydrogens' + loop_ + _alias.definition_id '_atom_site_attached_hydrogens' + _definition.update 2012-11-20 + _description.text +; + Number of hydrogen atoms attached to the atom at this site + excluding any H atoms for which coordinates (measured or calculated) + are given. +; + _description.common 'AtomSiteAttachedH' + _name.category_id site + _name.object_id attached_hydrogens + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0:8 + _enumeration.default 0 + loop_ + _description_example.case + _description_example.detail 2 'water oxygen' + 1 'hydroxyl oxygen' + 4 'ammonium nitrogen' + save_ + + +save_atom_site.B_equiv_geom_mean + _definition.id '_atom_site.B_equiv_geom_mean' + loop_ + _alias.definition_id '_atom_site_B_equiv_geom_mean' + _definition.update 2012-11-20 + _description.text +; + Equivalent isotropic atomic displacement parameter, B(equiv), + in angstroms squared, calculated as the geometric mean of + the anisotropic atomic displacement parameters. + + B(equiv) = (B~i~ B~j~ B~k~)^1/3^ + + B~n~ = the principal components of the orthogonalised B^ij^ + + The IUCr Commission on Nomenclature recommends against the use + of B for reporting atomic displacement parameters. U, being + directly proportional to B, is preferred. +; + _description.common 'AtomSiteBisoMean' + _name.category_id site + _name.object_id B_equiv_geom_mean + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms_squared + save_ + + +save_atom_site.B_iso_or_equiv + _definition.id '_atom_site.B_iso_or_equiv' + loop_ + _alias.definition_id '_atom_site_B_iso_or_equiv' + _definition.update 2012-11-20 + _description.text +; + Isotropic atomic displacement parameter, or equivalent isotropic + atomic displacement parameter, B(equiv), in angstroms squared, + calculated from anisotropic temperature factor parameters. + + B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)] + + a = the real-space cell lengths + a* = the reciprocal-space cell lengths + B^ij^ = 8 pi^2^ U^ij^ + Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. + + The IUCr Commission on Nomenclature recommends against the use + of B for reporting atomic displacement parameters. U, being + directly proportional to B, is preferred. +; + _description.common 'AtomSiteBisoEquiv' + _name.category_id site + _name.object_id B_iso_or_equiv + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms_squared + save_ + + +save_atom_site.calc_attached_atom + _definition.id '_atom_site.calc_attached_atom' + loop_ + _alias.definition_id '_atom_site_calc_attached_atom' + _definition.update 2012-11-20 + _description.text +; + The _atom_site.label of the atom site to which the 'geometry- + calculated' atom site is attached. +; + _description.common 'AtomSiteParentAtom' + _name.category_id site + _name.object_id calc_attached_atom + _name.linked_item_id '_atom_site.label' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_atom_site.calc_flag + _definition.id '_atom_site.calc_flag' + loop_ + _alias.definition_id '_atom_site_calc_flag' + _definition.update 2012-11-20 + _description.text +; + A standard code to signal if the site coordinates have been + determined from the intensities or calculated from the geometry + of surrounding sites, or have been assigned dummy coordinates. +; + _description.common 'AtomSiteCalcStatus' + _name.category_id site + _name.object_id calc_flag + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail d 'determined from diffraction measurements' + calc 'calculated from molecular geometry' + c 'abbreviation for "calc"' + dum 'dummy site with meaningless coordinates' + _enumeration.default d + save_ + + +save_atom_site.Cartn_xyz + _definition.id '_atom_site.Cartn_xyz' + _definition.update 2012-11-20 + _description.text +; + Vector of Cartesian (orthogonal angstrom) atom site coordinates. +; + _description.common 'AtomSiteCartnXyz' + _name.category_id site + _name.object_id Cartn_xyz + _type.purpose Measurand + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site + + _atom_site.Cartn_xyz = [a.Cartn_x, a.Cartn_y, a.Cartn_z] +; + save_ + + +save_atom_site.Cartn_x + _definition.id '_atom_site.Cartn_x' + loop_ + _alias.definition_id '_atom_site_Cartn_x' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_coord'}] + _name.category_id site + _name.object_id Cartn_x + save_ + + +save_atom_site.Cartn_y + _definition.id '_atom_site.Cartn_y' + loop_ + _alias.definition_id '_atom_site_Cartn_y' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_coord'}] + _name.category_id site + _name.object_id Cartn_y + save_ + + +save_atom_site.Cartn_z + _definition.id '_atom_site.Cartn_z' + loop_ + _alias.definition_id '_atom_site_Cartn_z' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_coord'}] + _name.category_id site + _name.object_id Cartn_z + save_ + + +save_atom_site.chemical_conn_number + _definition.id '_atom_site.chemical_conn_number' + loop_ + _alias.definition_id '_atom_site_chemical_conn_number' + _definition.update 2012-11-20 + _description.text +; + This number links an atom site to the chemical connectivity list. + It must match a number specified by _chemical_conn_atom.number. +; + _description.common 'AtomSiteChemConnLink' + _name.category_id site + _name.object_id chemical_conn_number + _name.linked_item_id '_chemical_conn_atom.number' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Index + _enumeration.range 1: + save_ + + +save_atom_site.constraints + _definition.id '_atom_site.constraints' + loop_ + _alias.definition_id '_atom_site_constraints' + _definition.update 2012-11-20 + _description.text +; + A description of the constraints applied to parameters at this + site during refinement. See also _atom_site.refinement_flags + and _refine_ls.number_constraints. +; + _description.common 'AtomSiteConstraints' + _name.category_id site + _name.object_id constraints + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'pop=1.0-pop(Zn3)' + save_ + + +save_atom_site.description + _definition.id '_atom_site.description' + loop_ + _alias.definition_id '_atom_site_description' + '_atom_site.details' + _definition.update 2012-11-20 + _description.text +; + A description of special aspects of this site. See also + _atom_site.refinement_flags. +; + _description.common 'AtomSiteDetails' + _name.category_id site + _name.object_id description + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Ag/Si disordered' + save_ + + +save_atom_site.disorder_assembly + _definition.id '_atom_site.disorder_assembly' + loop_ + _alias.definition_id '_atom_site_disorder_assembly' + _definition.update 2012-11-20 + _description.text +; + A code which identifies a cluster of atoms that show long range + positional disorder but are locally ordered. Within each such + cluster of atoms, _atom_site.disorder_group is used to identify + the sites that are simultaneously occupied. This field is only + needed if there is more than one cluster of disordered atoms + showing independent local order. +; + _description.common 'AtomSiteDisorderCode' + _name.category_id site + _name.object_id disorder_assembly + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case + _description_example.detail + A 'disordered methyl assembly with groups 1 and 2' + B 'disordered sites related by a mirror' + S 'disordered sites independent of symmetry' + save_ + + +save_atom_site.disorder_group + _definition.id '_atom_site.disorder_group' + loop_ + _alias.definition_id '_atom_site_disorder_group' + _definition.update 2012-11-20 + _description.text +; + A code that identifies a group of positionally disordered atom + sites that are locally simultaneously occupied. Atoms that are + positionally disordered over two or more sites (e.g. the H + atoms of a methyl group that exists in two orientations) can + be assigned to two or more groups. Sites belonging to the same + group are simultaneously occupied, but those belonging to + different groups are not. A minus prefix (e.g. "-1") is used to + indicate sites disordered about a special position. +; + _description.common 'AtomSiteDisorderGroup' + _name.category_id site + _name.object_id disorder_group + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _description_example.case + _description_example.detail + 1 'unique disordered site in group 1' + 2 'unique disordered site in group 2' + -1 'symmetry-independent disordered site' + save_ + + +save_atom_site.fract_xyz + + _definition.id '_atom_site.fract_xyz' + _definition.update 2012-11-20 + _description.text +; + Vector of atom site coordinates projected onto the crystal unit + cell as fractions of the cell lengths. +; + _description.common 'AtomSiteFractXyz' + _name.category_id site + _name.object_id fract_xyz + _type.purpose Measurand + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site + + atom_site.fract_xyz = [a.fract_x, a.fract_y, a.fract_z] +; + save_ + + +save_atom_site.fract_x + _definition.id '_atom_site.fract_x' + loop_ + _alias.definition_id '_atom_site_fract_x' + _import.get [{"file":'templ_attr.cif',"save":'fract_coord'}] + _name.category_id site + _name.object_id fract_x + save_ + + +save_atom_site.fract_y + _definition.id '_atom_site.fract_y' + loop_ + _alias.definition_id '_atom_site_fract_y' + _import.get [{"file":'templ_attr.cif',"save":'fract_coord'}] + _name.category_id site + _name.object_id fract_y + save_ + + +save_atom_site.fract_z + _definition.id '_atom_site.fract_z' + loop_ + _alias.definition_id '_atom_site_fract_z' + _import.get [{"file":'templ_attr.cif',"save":'fract_coord'}] + _name.category_id site + _name.object_id fract_z + save_ + + +save_atom_site.label + _definition.id '_atom_site.label' + loop_ + _alias.definition_id '_atom_site_label' + _import.get [{"file":'templ_attr.cif',"save":'atom_site_label'}] + _description.common 'AtomSiteLabel' + _name.category_id site + _name.object_id label + save_ + + +save_atom_site.label_component_0 + _definition.id '_atom_site.label_component_0' + loop_ + _alias.definition_id '_atom_site_label_component_0' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_0 + save_ + + +save_atom_site.label_component_1 + _definition.id '_atom_site.label_component_1' + loop_ + _alias.definition_id '_atom_site_label_component_1' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_1 + save_ + + +save_atom_site.label_component_2 + _definition.id '_atom_site.label_component_2' + loop_ + _alias.definition_id '_atom_site_label_component_2' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_2 + save_ + + +save_atom_site.label_component_3 + _definition.id '_atom_site.label_component_3' + loop_ + _alias.definition_id '_atom_site_label_component_3' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_3 + save_ + + +save_atom_site.label_component_4 + _definition.id '_atom_site.label_component_4' + loop_ + _alias.definition_id '_atom_site_label_component_4' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_4 + save_ + + +save_atom_site.label_component_5 + _definition.id '_atom_site.label_component_5' + loop_ + _alias.definition_id '_atom_site_label_component_5' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_5 + save_ + + +save_atom_site.label_component_6 + _definition.id '_atom_site.label_component_6' + loop_ + _alias.definition_id '_atom_site_label_component_6' + _import.get [{"file":'templ_attr.cif',"save":'label_component'}] + _name.category_id site + _name.object_id label_component_6 + save_ + + +save_atom_site.occupancy + _definition.id '_atom_site.occupancy' + loop_ + _alias.definition_id '_atom_site_occupancy' + _definition.update 2012-11-20 + _description.text +; + The fraction of the atom type present at this site. + The sum of the occupancies of all the atom types at this site + may not significantly exceed 1.0 unless it is a dummy site. The + value must lie in the 99.97% Gaussian confidence interval + -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus + correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). +; + _description.common 'AtomSiteOccupancy' + _name.category_id site + _name.object_id occupancy + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + _enumeration.default 1.0 + save_ + + +save_atom_site.refinement_flags + _definition.id '_atom_site.refinement_flags' + loop_ + _alias.definition_id '_atom_site_refinement_flags' + _definition.update 2012-11-20 + _description.text +; + A concatenated series of single-letter codes which indicate the + refinement restraints or constraints applied to this site. +; + _description.common 'AtomSiteRefineFlags' + _name.category_id site + _name.object_id refinement_flags + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + S 'special position constraint on site' + G 'rigid group refinement of site' + R 'riding-atom site attached to non-riding atom' + D 'distance or angle restraint on site' + T 'thermal displacement constraints' + U 'Uiso or Uij restraint (rigid bond)' + P 'partial occupancy constraint' + . 'no refinement constraints' + save_ + + +save_atom_site.refinement_flags_adp + _definition.id '_atom_site.refinement_flags_adp' + loop_ + _alias.definition_id '_atom_site_refinement_flags_adp' + _definition.update 2012-11-20 + _description.text +; + A code which indicates the refinement restraints or constraints + applied to the atomic displacement parameters of this site. +; + _name.category_id site + _name.object_id refinement_flags_adp + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + . 'no constraints on atomic displacement parameters' + T 'special-position constraints on atomic displacement parameters' + U 'Uiso or Uij restraint (rigid bond)' + TU 'both constraints applied' + save_ + + +save_atom_site.refinement_flags_occupancy + _definition.id '_atom_site.refinement_flags_occupancy' + loop_ + _alias.definition_id '_atom_site_refinement_flags_occupancy' + _definition.update 2012-11-20 + _description.text +; + A code which indicates the refinement restraints or constraints + applied to the occupancy of this site. +; + _name.category_id site + _name.object_id refinement_flags_occupancy + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + . 'no constraints on atomic displacement parameters' + T 'special-position constraints on atomic displacement parameters' + U 'Uiso or Uij restraint (rigid bond)' + TU 'both constraints applied' + save_ + + +save_atom_site.refinement_flags_posn + _definition.id '_atom_site.refinement_flags_posn' + loop_ + _alias.definition_id '_atom_site_refinement_flags_posn' + _definition.update 2012-11-20 + _description.text +; + A code which indicates the refinement restraints or constraints + applied to the positional coordinates of this site. +; + _name.category_id site + _name.object_id refinement_flags_posn + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + . 'no constraints on positional coordinates' + D 'distance or angle restraint on positional coordinates' + G 'rigid-group refinement of positional coordinates' + R 'riding-atom site attached to non-riding atom' + S 'special-position constraint on positional coordinates' + DG 'combination of the above constraints' + DR 'combination of the above constraints' + DS 'combination of the above constraints' + GR 'combination of the above constraints' + GS 'combination of the above constraints' + RS 'combination of the above constraints' + DGR 'combination of the above constraints' + DGS 'combination of the above constraints' + DRS 'combination of the above constraints' + GRS 'combination of the above constraints' + DGRS 'combination of the above constraints' + save_ + + +save_atom_site.restraints + _definition.id '_atom_site.restraints' + loop_ + _alias.definition_id '_atom_site_restraints' + _definition.update 2012-11-20 + _description.text +; + A description of restraints applied to specific parameters at + this site during refinement. See also _atom_site.refinement_flags + and _refine_ls.number_restraints. +; + _description.common 'AtomSiteRestraints' + _name.category_id site + _name.object_id restraints + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'restrained to planar ring' + save_ + + +save_atom_site.site_symmetry_multiplicity + _definition.id '_atom_site.site_symmetry_multiplicity' + loop_ + _alias.definition_id '_atom_site_site_symmetry_multiplicity' + '_atom_site_symmetry_multiplicity' + _definition.update 2012-11-20 + _description.text +; + The number of different sites that are generated by the + application of the space-group symmetry to the coordinates + given for this site. It is equal to the multiplicity given + for this Wyckoff site in International Tables for Cryst. + Vol. A (2002). It is equal to the multiplicity of the general + position divided by the order of the site symmetry given in + _atom_site.site_symmetry_order. +; + _description.common 'AtomSiteMultiplicity' + _name.category_id site + _name.object_id site_symmetry_multiplicity + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Index + _enumeration.range 1:192 + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site + + mul = 1 + xyz = a.fract_xyz + + Loop s as symmetry_equiv { + + sxyz = s.R * xyz + s.T + diff = Mod( 99.5 + xyz - sxyz, 1.0) - 0.5 + + If ( Norm ( diff ) > 0.1 ) mul += 1 + } + _atom_site.site_symmetry_multiplicity = mul +; + save_ + + +save_atom_site.site_symmetry_order + _definition.id '_atom_site.site_symmetry_order' + loop_ + _alias.definition_id '_atom_site_site_symmetry_order' + _definition.update 2012-11-20 + _description.text +; + The number of times application of the crystallographic symmetry + to the coordinates for this site generates the same coordinates. + That is: + multiplicity of the general position + ------------------------------------ + _atom_site.site_symmetry_multiplicity +; + _description.common 'AtomSiteMultiplicity' + _name.category_id site + _name.object_id site_symmetry_order + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Index + _enumeration.range 1:48 + save_ + + +save_atom_site.type_symbol + _definition.id '_atom_site.type_symbol' + loop_ + _alias.definition_id '_atom_site_type_symbol' + _definition.update 2012-11-20 + _description.text +; + A code to identify the atom specie(s) occupying this site. + This code must match a corresponding _atom_type.symbol. The + specification of this code is optional if component_0 of the + _atom_site.label is used for this purpose. See _atom_type.symbol. +; + _description.common 'AtomSiteTypeSymbol' + _name.category_id site + _name.object_id type_symbol + _name.linked_item_id '_atom_type.symbol' + _type.purpose Link + _type.source Assembled + _type.container Single + _type.contents Code + loop_ + _description_example.case Cu Cu2+ S O1- + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_site.type_symbol = AtomType ( _atom_site.label ) +; + save_ + + +save_atom_site.U_equiv_geom_mean + _definition.id '_atom_site.U_equiv_geom_mean' + loop_ + _alias.definition_id '_atom_site_U_equiv_geom_mean' + _definition.update 2012-11-20 + _description.text +; + Equivalent isotropic atomic displacement parameter, U(equiv), + in angstroms squared, calculated as the geometric mean of + the anisotropic atomic displacement parameters. + + U(equiv) = (U~i~ U~j~ U~k~)^1/3^ + + U~n~ = the principal components of the orthogonalised U^ij^ +; + _description.common 'AtomSiteUisoMean' + _name.category_id site + _name.object_id U_equiv_geom_mean + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms_squared + save_ + + +save_atom_site.U_iso_or_equiv + _definition.id '_atom_site.U_iso_or_equiv' + loop_ + _alias.definition_id '_atom_site_U_iso_or_equiv' + _definition.update 2012-11-20 + _description.text +; + Isotropic atomic displacement parameter, or equivalent isotropic + atomic displacement parameter, U(equiv), in angstroms squared, + calculated from anisotropic atomic displacement parameters. + + U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)] + + a = the real-space cell lengths + a* = the reciprocal-space cell lengths + Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. +; + _description.common 'AtomSiteUisoEquiv' + _name.category_id site + _name.object_id U_iso_or_equiv + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms_squared + save_ + + +save_atom_site.Wyckoff_symbol + _definition.id '_atom_site.Wyckoff_symbol' + loop_ + _alias.definition_id '_atom_site_Wyckoff_symbol' + _definition.update 2012-11-20 + _description.text +; + The Wyckoff symbol (letter) as listed in the space-group section + of International Tables for Crystallography, Vol. A (1987). +; + _description.common 'AtomSiteWyckoff' + _name.category_id site + _name.object_id Wyckoff_symbol + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + save_ + +#---------------------------------------------------------------------------- + + +save_ATOM_SITE_ANISO + + _definition.id ATOM_SITE_ANISO + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe the anisotropic + thermal parameters of the atomic sites in a crystal structure. +; + _description.common 'Anisotropic thermal parameters' + _name.category_id ATOM_SITE + _name.object_id ANISO + _category.key_id '_atom_site_aniso.key' + + +save_atom_site_aniso.key + _definition.id '_atom_site_aniso.key' + _definition.update 2012-11-20 + _description.text +; + Value is a unique key to a set of ATOM_SITE_ANISO items + in a looped list. +; + _description.common 'Key to list of atomic sites' + _name.category_id aniso + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(atom_site_aniso.label) +; + Evaluation +; _atom_site_aniso.key = _atom_site_aniso.label +; + save_ + + +save_atom_site_aniso.label + _definition.id '_atom_site_aniso.label' + loop_ + _alias.definition_id '_atom_site_aniso_label' + _definition.update 2013-01-23 + _description.text +; + Anisotropic atomic displacement parameters are usually looped in + a separate list. If this is the case, this code must match the + _atom_site_label of the associated atom in the atom coordinate + list and conform with the same rules described in _atom_site.label. +; + _description.common 'AtomSiteAnisoLabel' + _name.category_id aniso + _name.object_id label + _type.purpose Quantity + _type.source Selected + _type.container Single + _type.contents Code + save_ + + +save_atom_site_aniso.ratio + _definition.id '_atom_site_aniso.ratio' + loop_ + _alias.definition_id '_atom_site_aniso_ratio' + '_atom_site_anisotrop.ratio' + _definition.update 2012-11-20 + _description.text +; + Ratio of the maximum to minimum eigenvalues of the atomic + displacement (thermal) ellipsoids. +; + _description.common 'AtomSiteAnisoRatio' + _name.category_id aniso + _name.object_id ratio + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 1.0: + save_ + + +save_atom_site_aniso.type_symbol + _definition.id '_atom_site_aniso.type_symbol' + loop_ + _alias.definition_id '_atom_site_aniso_type_symbol' + '_atom_site_anisotrop.type_symbol' + _definition.update 2012-11-20 + _description.text +; + This _atom_type.symbol code links the anisotropic atom parameters to + the atom type data associated with this site and must match one of + the _atom_type.symbol codes in this list. +; + _description.common 'AtomSiteAnisoTypeSymbol' + _name.category_id aniso + _name.object_id type_symbol + _name.linked_item_id '_atom_type.symbol' + _type.purpose Link + _type.source Assembled + _type.container Single + _type.contents Code + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_site_aniso.type_symbol = AtomType ( _atom_site_aniso.label ) +; + save_ + + +save_atom_site_aniso.matrix_beta + _definition.id '_atom_site_aniso.matrix_beta' + _definition.update 2012-11-20 + _description.text +; + The symmetric anisotropic atomic displacement matrix beta(IJ) + appears in a structure factor expression as: + + t = exp - ( beta11 h h + ............ 2 beta23 k l ) + + It is related to the adp matrices U(IJ) and B(IJ) as follows: + + t = exp -2pi**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* ) +; + _description.common 'AtomSiteAnisoBetaIJ' + _name.category_id aniso + _name.object_id matrix_beta + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site_aniso + + If (a.adp_type == 'uani') { + + C = _cell_reciprocal.convert_U_to_beta + B = C * _atom_site_aniso.matrix_U * C + } + Else If (a.adp_type == 'bani') { + + C = _cell_reciprocal.convert_U_to_beta / (2.828427 * Pi) + B = C * _atom_site_aniso.matrix_B * C + } + Else { + If (a.adp_type == 'uiso') b = a.U_iso_or_equiv + Else b = a.B_iso_or_equiv / (8 * Pi**2) + + C = _cell_reciprocal.convert_U_to_beta + B = C * Matrix([[b,0,0],[0,b,0],[0,0,b]]) * C + } + _atom_site_aniso.matrix_beta = B +; + save_ + + +save_atom_site_aniso.matrix_B + _definition.id '_atom_site_aniso.matrix_B' + _definition.update 2012-11-20 + _description.text +; + The symmetric anisotropic atomic displacement matrix B. +; + _description.common 'AtomSiteAnisoBIJ' + _name.category_id aniso + _name.object_id matrix_B + _type.purpose Measurand + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site_aniso + + a.matrix_B = [[ a.B_11, a.B_12, a.B_13 ], + [ a.B_12, a.B_22, a.B_23 ], + [ a.B_13, a.B_23, a.B_33 ]] +; + save_ + + +save_atom_site_aniso.B_11 + _definition.id '_atom_site_aniso.B_11' + loop_ + _alias.definition_id '_atom_site_aniso_B_11' + '_atom_site.aniso_B[1][1]' + '_atom_site_anisotrop.B[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_11 + save_ + + +save_atom_site_aniso.B_12 + _definition.id '_atom_site_aniso.B_12' + loop_ + _alias.definition_id '_atom_site_aniso_B_12' + '_atom_site.aniso_B[1][2]' + '_atom_site_anisotrop.B[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_12 + save_ + + +save_atom_site_aniso.B_13 + _definition.id '_atom_site_aniso.B_13' + loop_ + _alias.definition_id '_atom_site_aniso_B_13' + '_atom_site.aniso_B[1][3]' + '_atom_site_anisotrop.B[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_13 + save_ + + +save_atom_site_aniso.B_22 + _definition.id '_atom_site_aniso.B_22' + loop_ + _alias.definition_id '_atom_site_aniso_B_22' + '_atom_site.aniso_B[2][2]' + '_atom_site_anisotrop.B[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_22 + save_ + + +save_atom_site_aniso.B_23 + _definition.id '_atom_site_aniso.B_23' + loop_ + _alias.definition_id '_atom_site_aniso_B_23' + '_atom_site.aniso_B[2][3]' + '_atom_site_anisotrop.B[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_23 + save_ + + +save_atom_site_aniso.B_33 + _definition.id '_atom_site_aniso.B_33' + loop_ + _alias.definition_id '_atom_site_aniso_B_33' + '_atom_site.aniso_B[3][3]' + '_atom_site_anisotrop.B[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_BIJ'}] + _name.category_id aniso + _name.object_id B_33 + save_ + + +save_atom_site_aniso.matrix_U + _definition.id '_atom_site_aniso.matrix_U' + _definition.update 2012-11-20 + _description.text +; + The symmetric anisotropic atomic displacement matrix U. +; + _description.common 'AtomSiteAnisoUIJ' + _name.category_id aniso + _name.object_id matrix_U + _type.purpose Measurand + _type.source Assembled + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_site_aniso + + a.matrix_U = [[ a.U_11, a.U_12, a.U_13 ], + [ a.U_12, a.U_22, a.U_23 ], + [ a.U_13, a.U_23, a.U_33 ]] +; + save_ + + +save_atom_site_aniso.U_11 + _definition.id '_atom_site_aniso.U_11' + loop_ + _alias.definition_id '_atom_site_aniso_U_11' + '_atom_site.aniso_U[1][1]' + '_atom_site_anisotrop.U[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_11 + save_ + + +save_atom_site_aniso.U_12 + _definition.id '_atom_site_aniso.U_12' + loop_ + _alias.definition_id '_atom_site_aniso_U_12' + '_atom_site.aniso_U[1][2]' + '_atom_site_anisotrop.U[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_12 + save_ + + +save_atom_site_aniso.U_13 + _definition.id '_atom_site_aniso.U_13' + loop_ + _alias.definition_id '_atom_site_aniso_U_13' + '_atom_site.aniso_U[1][3]' + '_atom_site_anisotrop.U[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_13 + save_ + + +save_atom_site_aniso.U_22 + _definition.id '_atom_site_aniso.U_22' + loop_ + _alias.definition_id '_atom_site_aniso_U_22' + '_atom_site.aniso_U[2][2]' + '_atom_site_anisotrop.U[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_22 + save_ + + +save_atom_site_aniso.U_23 + _definition.id '_atom_site_aniso.U_23' + loop_ + _alias.definition_id '_atom_site_aniso_U_23' + '_atom_site.aniso_U[2][3]' + '_atom_site_anisotrop.U[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_23 + save_ + + +save_atom_site_aniso.U_33 + _definition.id '_atom_site_aniso.U_33' + loop_ + _alias.definition_id '_atom_site_aniso_U_33' + '_atom_site.aniso_U[3][3]' + '_atom_site_anisotrop.U[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'aniso_UIJ'}] + _name.category_id aniso + _name.object_id U_33 + save_ + + save_ #------ close ATOM_SITE category + + save_ #------ close ATOM_SITE_ANISO category + +#============================================================================ + + +save_ATOM_SITES + + _definition.id ATOM_SITES + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe information which applies + to all atom sites in a crystal structure. +; + _name.category_id ATOM + _name.object_id SITES + + +save_atom_sites.solution_primary + _definition.id '_atom_sites.solution_primary' + loop_ + _alias.definition_id '_atom_sites_solution_primary' + _definition.update 2012-11-20 + _description.text +; + Codes which identify the methods used to locate the initial + atom sites. The *_primary code identifies how the first + atom sites were determined; the *_secondary code identifies + how the remaining non-hydrogen sites were located; and the + *_hydrogens code identifies how the hydrogen sites were located. + + Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., + Miller, R. and Us\'on, I. (2001). Ab initio phasing. + In International Tables for Crystallography, + Vol. F. Crystallography of biological macromolecules, + edited by M. G. Rossmann and E. Arnold, ch. 16.1. + Dordrecht: Kluwer Academic Publishers. +; + _description.common 'MethodologySolnPrimary' + _name.category_id sites + _name.object_id solution_primary + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + difmap 'difference Fourier map' + vecmap 'real-space vector search' + heavy 'heavy-atom method' + direct 'structure-invariant direct methods' + geom 'inferred from neighbouring sites' + disper 'anomalous-dispersion techniques' + isomor 'isomorphous structure methods' + notdet 'coordinates were not determined' + dual 'dual-space method (Sheldrick et al., 2001)' + iterative '''iterative e.g. charge flipping [Oszl\'anyi, G. + and S\"uto, A. (2004). Acta Cryst. A60, 134-141]''' + other 'a method not included elsewhere in this list' + + _enumeration.default direct + save_ + + +save_atom_sites.solution_secondary + _definition.id '_atom_sites.solution_secondary' + loop_ + _alias.definition_id '_atom_sites_solution_secondary' + _definition.update 2012-11-20 + _description.text +; + Codes which identify the methods used to locate the initial + atom sites. The *_primary code identifies how the first + atom sites were determined; the *_secondary code identifies + how the remaining non-hydrogen sites were located; and the + *_hydrogens code identifies how the hydrogen sites were located. + + Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., + Miller, R. and Us\'on, I. (2001). Ab initio phasing. + In International Tables for Crystallography, + Vol. F. Crystallography of biological macromolecules, + edited by M. G. Rossmann and E. Arnold, ch. 16.1. + Dordrecht: Kluwer Academic Publishers. +; + _description.common 'MethodologySolnSecondary' + _name.category_id sites + _name.object_id solution_secondary + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + difmap 'difference Fourier map' + vecmap 'real-space vector search' + heavy 'heavy-atom method' + direct 'structure-invariant direct methods' + geom 'inferred from neighbouring sites' + disper 'anomalous-dispersion techniques' + isomor 'isomorphous structure methods' + notdet 'coordinates were not determined' + dual 'dual-space method (Sheldrick et al., 2001)' + iterative '''iterative e.g. charge flipping [Oszl\'anyi, G. + and S\"uto, A. (2004). Acta Cryst. A60, 134-141]''' + other 'a method not included elsewhere in this list' + + _enumeration.default difmap + save_ + + +save_atom_sites.solution_hydrogens + _definition.id '_atom_sites.solution_hydrogens' + loop_ + _alias.definition_id '_atom_sites_solution_hydrogens' + _definition.update 2012-11-20 + _description.text +; + Codes which identify the methods used to locate the initial + atom sites. The *_primary code identifies how the first + atom sites were determined; the *_secondary code identifies + how the remaining non-hydrogen sites were located; and the + *_hydrogens code identifies how the hydrogen sites were located. + + Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., + Miller, R. and Us\'on, I. (2001). Ab initio phasing. + In International Tables for Crystallography, + Vol. F. Crystallography of biological macromolecules, + edited by M. G. Rossmann and E. Arnold, ch. 16.1. + Dordrecht: Kluwer Academic Publishers. +; + _description.common 'methodologySolnHatoms' + _name.category_id sites + _name.object_id solution_hydrogens + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + difmap 'difference Fourier map' + vecmap 'real-space vector search' + heavy 'heavy-atom method' + direct 'structure-invariant direct methods' + geom 'inferred from neighbouring sites' + disper 'anomalous-dispersion techniques' + isomor 'isomorphous structure methods' + notdet 'coordinates were not determined' + dual 'dual-space method (Sheldrick et al., 2001)' + iterative '''iterative e.g. charge flipping [Oszl\'anyi, G. + and S\"uto, A. (2004). Acta Cryst. A60, 134-141]''' + other 'a method not included elsewhere in this list' + + _enumeration.default difmap + save_ + + +save_atom_sites.special_details + _definition.id '_atom_sites.special_details' + loop_ + _alias.definition_id '_atom_sites_special_details' + _definition.update 2012-11-20 + _description.text +; + Information about atomic coordinates not coded elsewhere in the CIF. +; + _name.category_id sites + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +#---------------------------------------------------------------------------- + + +save_ATOM_SITES_CARTN_TRANSFORM + + _definition.id ATOM_SITES_CARTN_TRANSFORM + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe the matrix elements + used to transform Cartesion coordinates into fractional coordinates + of all atom sites in a crystal structure. +; + _name.category_id ATOM_SITES + _name.object_id CARTN_TRANSFORM + + +save_atom_sites_Cartn_transform.axes + _definition.id '_atom_sites_Cartn_transform.axes' + loop_ + _alias.definition_id '_atom_sites_Cartn_transform_axes' + '_atom_sites.Cartn_transform_axes' + _definition.update 2012-12-11 + _description.text +; + Description of the relative alignment of the crystal cell axes to the + Cartesian orthogonal axes as applied in the transformation matrix + _atom_sites_Cartn_transform.matrix. +; + _description.common 'AtomSitesCartnTransfAxes' + _name.category_id Cartn_transform + _name.object_id axes + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'a parallel to x; b in the plane of y & z' + save_ + + +save_atom_sites_Cartn_transform.matrix + _definition.id '_atom_sites_Cartn_transform.matrix' + _definition.update 2012-12-11 + _description.text +; + Matrix used to transform fractional coordinates in the ATOM_SITE + category to Cartesian coordinates. The axial alignments of this + transformation are described in _atom_sites_Cartn_transform.axes. + The 3 x 1 translation is defined in _atom_sites_Cartn_transform.vector. + + x' |11 12 13| x | 1 | + ( y' ) Cartesian = |21 22 23| * ( y ) fractional + v| 2 | + z' |31 32 33| z | 3 | + + The default transformation matrix 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. +; + _description.common 'AtomSitesCartnTransfMatrix' + _name.category_id Cartn_transform + _name.object_id matrix + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_sites_Cartn_transform + + _atom_sites_Cartn_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13], + [a.mat_21, a.mat_22, a.mat_23], + [a.mat_31, a.mat_32, a.mat_33]] +; + save_ + + +save_atom_sites_Cartn_transform.mat_11 + _definition.id '_atom_sites_Cartn_transform.mat_11' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_11' + '_atom_sites_Cartn_tran_matrix_[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_11 + loop_ + _method.purpose + _method.expression + Evaluation +; + With l as cell_length + With a as cell_angle + With r as cell_reciprocal_angle + + _atom_sites_Cartn_transform.mat_11 = l.a*Sind(a.beta)*Sind(r.gamma) +; + save_ + + +save_atom_sites_Cartn_transform.mat_12 + _definition.id '_atom_sites_Cartn_transform.mat_12' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_12' + '_atom_sites_Cartn_tran_matrix_[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_12 + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_sites_Cartn_transform.mat_12 = 0. +; + save_ + + +save_atom_sites_Cartn_transform.mat_13 + _definition.id '_atom_sites_Cartn_transform.mat_13' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_13' + '_atom_sites_Cartn_tran_matrix_[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_13 + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_sites_Cartn_transform.mat_13 = 0. +; + save_ + + +save_atom_sites_Cartn_transform.mat_21 + _definition.id '_atom_sites_Cartn_transform.mat_21' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_21' + '_atom_sites_Cartn_tran_matrix_[2][1]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_21 + loop_ + _method.purpose + _method.expression + Evaluation +; + With l as cell_length + With a as cell_angle + With r as cell_reciprocal_angle + + _atom_sites_Cartn_transform.mat_21 = -l.a*Sind(a.beta)*Cosd(r.gamma) +; + save_ + + +save_atom_sites_Cartn_transform.mat_22 + _definition.id '_atom_sites_Cartn_transform.mat_22' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_22' + '_atom_sites_Cartn_tran_matrix_[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_22 + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as cell_angle + + _atom_sites_Cartn_transform.mat_22 = _cell_length.b * Sind(a.alpha) +; + save_ + + +save_atom_sites_Cartn_transform.mat_23 + _definition.id '_atom_sites_Cartn_transform.mat_23' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_23' + '_atom_sites_Cartn_tran_matrix_[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_23 + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_sites_Cartn_transform.mat_23 = 0. +; + save_ + + +save_atom_sites_Cartn_transform.mat_31 + _definition.id '_atom_sites_Cartn_transform.mat_31' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_31' + '_atom_sites_Cartn_tran_matrix_[3][1]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_31 + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as cell_angle + + _atom_sites_Cartn_transform.mat_31 = _cell_length.a * Cosd(a.beta) +; + save_ + + +save_atom_sites_Cartn_transform.mat_32 + _definition.id '_atom_sites_Cartn_transform.mat_32' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_32' + '_atom_sites_Cartn_tran_matrix_[3][2]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_32 + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as cell_angle + + _atom_sites_Cartn_transform.mat_32 = _cell_length.b * Cosd(a.alpha) +; + save_ + + +save_atom_sites_Cartn_transform.mat_33 + _definition.id '_atom_sites_Cartn_transform.mat_33' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_matrix_33' + '_atom_sites_Cartn_tran_matrix_[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id mat_33 + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_sites_Cartn_transform.mat_33 = _cell_length.c +; + save_ + + +save_atom_sites_Cartn_transform.vector + _definition.id '_atom_sites_Cartn_transform.vector' + _definition.update 2012-11-20 + _description.text +; + The 3x1 translation is used with _atom_sites_Cartn_transform.matrix + used to transform fractional coordinates to Cartesian coordinates. + The axial alignments of this transformation are described in + _atom_sites_Cartn_transform.axes. +; + _description.common 'AtomSitesCartnTransfVector' + _name.category_id atom_sites_Cartn_transform + _name.object_id vector + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as atom_sites_Cartn_transform + + _atom_sites_Cartn_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ] +; + save_ + + +save_atom_sites_Cartn_transform.vec_1 + _definition.id '_atom_sites_Cartn_transform.vec_1' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_vector_1' + '_atom_sites_Cartn_tran_vector_[1]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id vec_1 + save_ + + +save_atom_sites_Cartn_transform.vec_2 + _definition.id '_atom_sites_Cartn_transform.vec_2' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_vector_2' + '_atom_sites_Cartn_tran_vector_[2]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id vec_2 + save_ + + +save_atom_sites_Cartn_transform.vec_3 + _definition.id '_atom_sites_Cartn_transform.vec_3' + loop_ + _alias.definition_id '_atom_sites_Cartn_tran_vector_3' + '_atom_sites_Cartn_tran_vector_[3]' + _import.get [{"file":'templ_attr.cif',"save":'Cartn_matrix'}] + _name.category_id Cartn_transform + _name.object_id vec_3 + save_ + + save_ #------ close ATOM_SITES_CARTN_TRANSFORM category + + +#---------------------------------------------------------------------------- + + +save_ATOM_SITES_FRACT_TRANSFORM + + _definition.id ATOM_SITES_FRACT_TRANSFORM + _definition.scope Category + _definition.class Set + _definition.update 2012-12-11 + _description.text +; + The CATEGORY of data items used to describe the matrix elements + used to transform Cartesion coordinates into fractional coordinates + of all atom sites in a crystal structure. +; + _name.category_id ATOM_SITES + _name.object_id FRACT_TRANSFORM + + +save_atom_sites_fract_transform.axes + _definition.id '_atom_sites_fract_transform.axes' + loop_ + _alias.definition_id '_atom_sites_fract_transform_axes' + '_atom_sites.fract_transform_axes' + _definition.update 2012-12-11 + _description.text +; + Description of the relative alignment of the crystal cell axes to the + Cartesian orthogonal axes as applied in the transformation matrix + _atom_sites_fract_transform.matrix. +; + _description.common 'AtomSitesfractTransfAxes' + _name.category_id fract_transform + _name.object_id axes + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'a parallel to x; b in the plane of y & z' + save_ + + +save_atom_sites_fract_transform.matrix + _definition.id '_atom_sites_fract_transform.matrix' + _definition.update 2012-12-11 + _description.text +; + Matrix used to transform fractional coordinates in the ATOM_SITE + category to Cartesian coordinates. The axial alignments of this + transformation are described in _atom_sites_fract_transform.axes. + The 3 x 1 translation is defined in _atom_sites_fract_transform.vector. + + x' |11 12 13| x | 1 | + ( y' )fractional = mat |21 22 23| * ( y ) Cartesian + vec| 2 | + z' |31 32 33| z | 3 | + + The default transformation matrix 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. +; + _description.common 'AtomSitesfractTransfMatrix' + _name.category_id fract_transform + _name.object_id matrix + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3,3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With a as atom_sites_fract_transform + + _atom_sites_fract_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13], + [a.mat_21, a.mat_22, a.mat_23], + [a.mat_31, a.mat_32, a.mat_33]] +; + save_ + + +save_atom_sites_fract_transform.mat_11 + _definition.id '_atom_sites_fract_transform.mat_11' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_11' + '_atom_sites_fract_tran_matrix_[1][1]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_11 + save_ + + +save_atom_sites_fract_transform.mat_12 + _definition.id '_atom_sites_fract_transform.mat_12' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_12' + '_atom_sites_fract_tran_matrix_[1][2]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_12 + save_ + + +save_atom_sites_fract_transform.mat_13 + _definition.id '_atom_sites_fract_transform.mat_13' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_13' + '_atom_sites_fract_tran_matrix_[1][3]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_13 + save_ + + +save_atom_sites_fract_transform.mat_21 + _definition.id '_atom_sites_fract_transform.mat_21' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_21' + '_atom_sites_fract_tran_matrix_[2][1]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_21 + save_ + + +save_atom_sites_fract_transform.mat_22 + _definition.id '_atom_sites_fract_transform.mat_22' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_22' + '_atom_sites_fract_tran_matrix_[2][2]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_22 + save_ + + +save_atom_sites_fract_transform.mat_23 + _definition.id '_atom_sites_fract_transform.mat_23' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_23' + '_atom_sites_fract_tran_matrix_[2][3]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_23 + save_ + + +save_atom_sites_fract_transform.mat_31 + _definition.id '_atom_sites_fract_transform.mat_31' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_31' + '_atom_sites_fract_tran_matrix_[3][1]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_31 + save_ + + +save_atom_sites_fract_transform.mat_32 + _definition.id '_atom_sites_fract_transform.mat_32' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_32' + '_atom_sites_fract_tran_matrix_[3][2]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_32 + save_ + + +save_atom_sites_fract_transform.mat_33 + _definition.id '_atom_sites_fract_transform.mat_33' + loop_ + _alias.definition_id '_atom_sites_fract_tran_matrix_33' + '_atom_sites_fract_tran_matrix_[3][3]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id mat_33 + save_ + + +save_atom_sites_fract_transform.vector + _definition.id '_atom_sites_fract_transform.vector' + _definition.update 2012-11-20 + _description.text +; + The 3x1 translation is used with _atom_sites_fract_transform.matrix + used to transform Cartesian coordinates to fractional coordinates. + The axial alignments of this transformation are described in + _atom_sites_fract_transform.axes. +; + _description.common 'AtomSitesfractTransfVector' + _name.category_id atom_sites_fract_transform + _name.object_id vector + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.contents Real + _type.dimension [3] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as atom_sites_fract_transform + + _atom_sites_fract_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ] +; + save_ + + +save_atom_sites_fract_transform.vec_1 + _definition.id '_atom_sites_fract_transform.vec_1' + loop_ + _alias.definition_id '_atom_sites_fract_tran_vector_1' + '_atom_sites_fract_tran_vector_[1]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id vec_1 + save_ + + +save_atom_sites_fract_transform.vec_2 + _definition.id '_atom_sites_fract_transform.vec_2' + loop_ + _alias.definition_id '_atom_sites_fract_tran_vector_2' + '_atom_sites_fract_tran_vector_[2]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id vec_2 + save_ + + +save_atom_sites_fract_transform.vec_3 + _definition.id '_atom_sites_fract_transform.vec_3' + loop_ + _alias.definition_id '_atom_sites_fract_tran_vector_3' + '_atom_sites_fract_tran_vector_[3]' + _import.get [{"file":'templ_attr.cif',"save":'fract_matrix'}] + _name.category_id fract_transform + _name.object_id vec_3 + save_ + + save_ #------ close ATOM_SITES_FRACT_TRANSFORM category + + save_ #------ close ATOM_SITES category + + +#============================================================================ + +save_ATOM_TYPE + + _definition.id ATOM_TYPE + _definition.scope Category + _definition.class Loop + _definition.update 2013-02-18 + _description.text +; + The CATEGORY of data items used to describe atomic type information + used in crystallographic structure studies. +; + _description.common 'AtomTypeList' + _name.category_id ATOM + _name.object_id TYPE + _category.key_id '_atom_type.key' + loop_ + _method.purpose + _method.expression + Evaluation +; + typelist = List() + + Loop a as atom_site { + type = AtomType ( a.label ) + If( type not in typelist ) typelist ++= type + } + For type in typelist { + atom_type(.symbol = type, + .number_in_cell = '?' ) + } +; + + +save_atom_type.key + _definition.id '_atom_type.key' + _definition.update 2012-11-20 + _description.text +; + Value is a unique key to a set of ATOM_TYPE items + in a looped list. +; + _description.common 'Key to list of atomic types' + _name.category_id type + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(atom_type.symbol) +; + Evaluation +; _atom_type.key = _atom_type.symbol +; + save_ + + +save_atom_type.analytical_mass_percent + _definition.id '_atom_type.analytical_mass_percent' + loop_ + _alias.definition_id '_atom_type_analytical_mass_%' + _definition.update 2012-11-20 + loop_ + _alias.definition_id '_atom_type.analytical_mass_%' + _description.text +; + Mass percentage of this atom type derived from chemical analysis. +; + _description.common 'AtomTypeComposition%' + _name.category_id type + _name.object_id analytical_mass_percent + _type.purpose Measurand + _type.source Observed + _type.container Single + _type.contents Real + _enumeration.range 0.0:100. + save_ + + +save_atom_type.atomic_mass + _definition.id '_atom_type.atomic_mass' + _definition.update 2012-11-20 + _description.text +; + Mass of this atom type. +; + _description.common 'AtomTypeMass' + _name.category_id type + _name.object_id atomic_mass + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'atomic_mass'}] + _enumeration.def_index_id '_atom_type.symbol' + _units.code daltons + save_ + + +save_atom_type.atomic_number + _definition.id '_atom_type.atomic_number' + _definition.update 2012-11-20 + _description.text +; + Atomic number of this atom type. +; + _description.common 'AtomTypeNumber' + _name.category_id type + _name.object_id atomic_number + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + _import.get [{"file":'templ_enum.cif',"save":'atomic_number'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type.description + _definition.id '_atom_type.description' + loop_ + _alias.definition_id '_atom_type_description' + _definition.update 2012-11-20 + _description.text +; + A description of the atom(s) designated by this atom type. In + most cases this will be the element name and oxidation state of + a single atom species. For disordered or nonstoichiometric + structures it will describe a combination of atom species. +; + _description.common 'AtomTypeDetails' + _name.category_id type + _name.object_id description + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case deuterium '0.34Fe+0.66Ni' + save_ + + +save_atom_type.display_colour + _definition.id '_atom_type.display_colour' + _definition.update 2012-11-20 + _description.text +; + The display colour assigned to this atom type. Note that the + possible colours are enumerated in the display_colour list + category of items. +; + _description.common 'AtomTypeColour' + _name.category_id type + _name.object_id display_colour + _type.purpose State + _type.source Selected + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'colour_rgb'}, + {"file":'templ_enum.cif',"save":'colour_hue'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type.electron_count + _definition.id '_atom_type.electron_count' + _definition.update 2012-11-20 + _description.text +; + Number of electrons in this atom type. +; + _description.common 'AtomTypeElectrons' + _name.category_id type + _name.object_id electron_count + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Index + _import.get [{"file":'templ_enum.cif',"save":'electron_count'}] + _enumeration.def_index_id '_atom_type.symbol' + _enumeration.range 1: + save_ + + +save_atom_type.element_symbol + _definition.id '_atom_type.element_symbol' + _definition.update 2012-11-20 + _description.text +; + Element symbol for of this atom type. The default value is extracted + from the ion-to-element enumeration_default list using the index + value of atom_type.symbol. +; + _description.common 'AtomTypeElement' + _name.category_id type + _name.object_id element_symbol + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + _import.get [{"file":'templ_enum.cif',"save":'element_symbol'}, + {"file":'templ_enum.cif',"save":'ion_to_element'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type.number_in_cell + _definition.id '_atom_type.number_in_cell' + loop_ + _alias.definition_id '_atom_type_number_in_cell' + _definition.update 2013-01-28 + _description.text +; + Total number of atoms of this atom type in the unit cell. +; + _description.common 'AtomTypeCellCount' + _name.category_id type + _name.object_id number_in_cell + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0: + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as atom_type + + cnt = 0. + + Loop a as atom_site { + + if ( a.type_symbol == t.symbol ) { + + cnt += a.occupancy * a.site_symmetry_multiplicity + } } + _atom_type.number_in_cell = cnt +; + save_ + + +save_atom_type.oxidation_number + _definition.id '_atom_type.oxidation_number' + loop_ + _alias.definition_id '_atom_type_oxidation_number' + _definition.update 2012-11-20 + _description.text +; + Formal oxidation state of this atom type in the structure. +; + _description.common 'AtomTypeOxidation' + _name.category_id type + _name.object_id oxidation_number + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range -8:8 + _enumeration.default 0 + save_ + + +save_atom_type.radius_bond + _definition.id '_atom_type.radius_bond' + loop_ + _alias.definition_id '_atom_type_radius_bond' + _definition.update 2012-11-20 + _description.text +; + The effective intra-molecular bonding radius of this atom type. +; + _description.common 'AtomTypeBondRad' + _name.category_id type + _name.object_id radius_bond + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'radius_bond'}] + _enumeration.def_index_id '_atom_type.symbol' + _enumeration.range 0.0:5.0 + _units.code angstroms + save_ + + +save_atom_type.radius_contact + _definition.id '_atom_type.radius_contact' + loop_ + _alias.definition_id '_atom_type_radius_contact' + _definition.update 2012-11-20 + _description.text +; + The effective inter-molecular bonding radius of this atom type. +; + _description.common 'AtomTypeContactRad' + _name.category_id type + _name.object_id radius_contact + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0:5.0 + _units.code angstroms + loop_ + _method.purpose + _method.expression + Evaluation +; + _atom_type.radius_contact = atom_type.radius_bond + 1.25 +; + save_ + + +save_atom_type.symbol + _definition.id '_atom_type.symbol' + loop_ + _alias.definition_id '_atom_type_symbol' + _definition.update 2012-12-21 + _description.text +; + The identity of the atom specie(s) representing this atom type. + Normally this code is the element symbol followed by the charge + if there is one. The symbol may be composed of any character except + an underline or a blank, with the proviso that digits designate an + oxidation state and must be followed by a + or - character. +; + _description.common 'AtomTypeSymbol' + _name.category_id type + _name.object_id symbol + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _description_example.case Mg Cu2+ dummy FeNi + save_ + + +#============================================================================ + + +save_ATOM_TYPE_SCAT + + _definition.id ATOM_TYPE_SCAT + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to describe atomic scattering + information used in crystallographic structure studies. +; + _name.category_id ATOM_TYPE + _name.object_id SCAT + _category.key_id '_atom_type_scat.key' + + +save_atom_type_scat.key + _definition.id '_atom_type_scat.key' + _definition.update 2012-11-20 + _description.text +; + Value is a unique key to a set of ATOM_TYPE_SCAT items in a + looped list. This list may be joined with the ATOM_TYPE list. +; + _description.common 'Key to atomic scattering list' + _name.category_id scat + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(atom_type_scat.symbol) +; + Evaluation +; _atom_type_scat.key = _atom_type_scat.symbol +; + save_ + + +save_atom_type_scat.Cromer_Mann_coeffs + _definition.id '_atom_type_scat.Cromer_Mann_coeffs' + _definition.update 2012-11-20 + _description.text +; + The set of Cromer-Mann coefficients for generating X-ray scattering + factors. [ a1, b1, a2, b2, a3, b3, a4, b4, c] + Ref: International Tables for Crystallography, Vol. C + (1991) Table 6.1.1.4 +; + _description.common 'AtomTypeCMCoeffs' + _name.category_id scat + _name.object_id Cromer_Mann_coeffs + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Real + _type.dimension [9] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as atom_type_scat + + _atom_type_scat.Cromer_Mann_coeffs = [ t.Cromer_Mann_c, + t.Cromer_Mann_a1, t.Cromer_Mann_b1, + t.Cromer_Mann_a2, t.Cromer_Mann_b2, + t.Cromer_Mann_a3, t.Cromer_Mann_b3, + t.Cromer_Mann_a4, t.Cromer_Mann_b4 ] +; + save_ + + +save_atom_type_scat.Cromer_Mann_a1 + _definition.id '_atom_type_scat.Cromer_Mann_a1' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_a1' + '_atom_type.scat_Cromer_Mann_a1' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_a1'}] + _name.category_id scat + _name.object_id Cromer_Mann_a1 + save_ + + +save_atom_type_scat.Cromer_Mann_a2 + _definition.id '_atom_type_scat.Cromer_Mann_a2' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_a2' + '_atom_type.scat_Cromer_Mann_a2' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_a2'}] + _name.category_id scat + _name.object_id Cromer_Mann_a2 + save_ + + +save_atom_type_scat.Cromer_Mann_a3 + _definition.id '_atom_type_scat.Cromer_Mann_a3' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_a3' + '_atom_type.scat_Cromer_Mann_a3' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_a3'}] + _name.category_id scat + _name.object_id Cromer_Mann_a3 + save_ + + +save_atom_type_scat.Cromer_Mann_a4 + _definition.id '_atom_type_scat.Cromer_Mann_a4' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_a4' + '_atom_type.scat_Cromer_Mann_a4' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_a4'}] + _name.category_id scat + _name.object_id Cromer_Mann_a4 + save_ + + +save_atom_type_scat.Cromer_Mann_b1 + _definition.id '_atom_type_scat.Cromer_Mann_b1' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_b1' + '_atom_type.scat_Cromer_Mann_b1' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_b1'}] + _name.category_id scat + _name.object_id Cromer_Mann_b1 + save_ + + +save_atom_type_scat.Cromer_Mann_b2 + _definition.id '_atom_type_scat.Cromer_Mann_b2' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_b2' + '_atom_type.scat_Cromer_Mann_b2' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_b2'}] + _name.category_id scat + _name.object_id Cromer_Mann_b2 + save_ + + +save_atom_type_scat.Cromer_Mann_b3 + _definition.id '_atom_type_scat.Cromer_Mann_b3' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_b3' + '_atom_type.scat_Cromer_Mann_b3' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_b3'}] + _name.category_id scat + _name.object_id Cromer_Mann_b3 + save_ + + +save_atom_type_scat.Cromer_Mann_b4 + _definition.id '_atom_type_scat.Cromer_Mann_b4' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_b4' + '_atom_type.scat_Cromer_Mann_b4' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_b4'}] + _name.category_id scat + _name.object_id Cromer_Mann_b4 + save_ + + +save_atom_type_scat.Cromer_Mann_c + _definition.id '_atom_type_scat.Cromer_Mann_c' + loop_ + _alias.definition_id '_atom_type_scat_Cromer_Mann_c' + '_atom_type.scat_Cromer_Mann_c' + _import.get [{"file":'templ_attr.cif',"save":'Cromer_Mann_coeff'}, + {"file":'templ_enum.cif',"save":'Cromer_Mann_c'}] + _name.category_id scat + _name.object_id Cromer_Mann_c + save_ + + +save_atom_type_scat.dispersion_imag + _definition.id '_atom_type_scat.dispersion_imag' + loop_ + _alias.definition_id '_atom_type_scat_dispersion_imag' + '_atom_type.scat_dispersion_imag' + _definition.update 2012-11-20 + _description.text +; + The imaginary component of the anomalous dispersion scattering factors + for this atom type and radiation by _diffrn_radiation_wavelength.value +; + _description.common 'AnomDispImag' + _name.category_id scat + _name.object_id dispersion_imag + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.default 0.0 + loop_ + _method.purpose + _method.expression + Evaluation +; + With q as atom_type_scat + + If ( _diffrn_radiation.type == 'Cu' ) a = q.dispersion_imag_cu + If ( _diffrn_radiation.type == 'Mo' ) a = q.dispersion_imag_mo + + _atom_type_scat.dispersion_imag = a +; + save_ + + +save_atom_type_scat.dispersion_imag_cu + _definition.id '_atom_type_scat.dispersion_imag_cu' + _definition.update 2012-11-20 + _description.text +; + The imaginary component of the anomalous dispersion scattering factors + for this atom type and Cu K alpha radiation +; + _description.common 'AnomDispImagCu' + _name.category_id scat + _name.object_id dispersion_imag_cu + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'dispersion_imag_cu'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type_scat.dispersion_imag_mo + _definition.id '_atom_type_scat.dispersion_imag_mo' + _definition.update 2012-11-20 + _description.text +; + The imaginary component of the anomalous dispersion scattering factors + for this atom type and Mo K alpha radiation +; + _description.common 'AnomDispImagMo' + _name.category_id scat + _name.object_id dispersion_imag_mo + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'dispersion_imag_mo'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type_scat.dispersion_real + _definition.id '_atom_type_scat.dispersion_real' + loop_ + _alias.definition_id '_atom_type_scat_dispersion_real' + '_atom_type.scat_dispersion_real' + _definition.update 2012-11-20 + _description.text +; + The real component of the anomalous dispersion scattering factors + for this atom type and radiation by _diffrn_radiation_wavelength.value +; + _description.common 'AtomTypeAnomDispReal' + _name.category_id scat + _name.object_id dispersion_real + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Evaluation +; + With q as atom_type_scat + + If ( _diffrn_radiation.type == 'Cu' ) a = q.dispersion_real_cu + If ( _diffrn_radiation.type == 'Mo' ) a = q.dispersion_real_mo + + _atom_type_scat.dispersion_real = a +; + _enumeration.default 0.0 + save_ + + +save_atom_type_scat.dispersion_real_cu + _definition.id '_atom_type_scat.dispersion_real_cu' + _definition.update 2012-11-20 + _description.text +; + The real component of the anomalous dispersion scattering factors + for this atom type and Cu K alpha radiation +; + _description.common 'AnomDispRealCu' + _name.category_id scat + _name.object_id dispersion_real_cu + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'dispersion_real_cu'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type_scat.dispersion_real_mo + _definition.id '_atom_type_scat.dispersion_real_mo' + _definition.update 2012-11-20 + _description.text +; + The real component of the anomalous dispersion scattering factors + for this atom type and Mo K alpha radiation +; + _description.common 'AnomDispRealMo' + _name.category_id scat + _name.object_id dispersion_real_mo + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _import.get [{"file":'templ_enum.cif',"save":'dispersion_real_mo'}] + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_atom_type_scat.dispersion_source + _definition.id '_atom_type_scat.dispersion_source' + loop_ + _alias.definition_id '_atom_type_scat_dispersion_source' + _definition.update 2012-11-20 + _description.text +; + Reference to source of real and imaginary dispersion + corrections for scattering factors used for this atom type. +; + _description.common 'AtomTypeAnomDispDetails' + _name.category_id scat + _name.object_id dispersion_source + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'International Tables Vol. IV Table 2.3.1' + save_ + + +save_atom_type_scat.hi_ang_Fox_coeffs + _definition.id '_atom_type_scat.hi_ang_Fox_coeffs' + _definition.update 2012-11-30 + _description.text +; + The set of Fox et al. coefficients for generating high angle + X-ray scattering factors. [ c0, c1, c2, c3 ] + Ref: International Tables for Crystallography, Vol. C + (1991) Table 6.1.1.5 +; + _description.common 'AtomTypeFoxCoeffs' + _name.category_id scat + _name.object_id hi_ang_Fox_coeffs + _type.purpose Quantity + _type.source Assembled + _type.container List + _type.contents Real + _type.dimension [4] + loop_ + _method.purpose + _method.expression + Evaluation +; + With t as atom_type_scat + + _atom_type_scat.hi_ang_Fox_coeffs = \ + [t.hi_ang_Fox_c0,t.hi_ang_Fox_c1,t.hi_ang_Fox_c2,t.hi_ang_Fox_c3] +; + save_ + + +save_atom_type_scat.hi_ang_Fox_c0 + _definition.id '_atom_type_scat.hi_ang_Fox_c0' + _import.get [{"file":'templ_attr.cif',"save":'hi_ang_Fox_coeffs'}, + {"file":'templ_enum.cif',"save":'hi_ang_Fox_c0'}] + _name.category_id scat + _name.object_id hi_ang_Fox_c0 + save_ + + +save_atom_type_scat.hi_ang_Fox_c1 + _definition.id '_atom_type_scat.hi_ang_Fox_c1' + _import.get [{"file":'templ_attr.cif',"save":'hi_ang_Fox_coeffs'}, + {"file":'templ_enum.cif',"save":'hi_ang_Fox_c1'}] + _name.category_id scat + _name.object_id hi_ang_Fox_c1 + save_ + + +save_atom_type_scat.hi_ang_Fox_c2 + _definition.id '_atom_type_scat.hi_ang_Fox_c2' + _import.get [{"file":'templ_attr.cif',"save":'hi_ang_Fox_coeffs'}, + {"file":'templ_enum.cif',"save":'hi_ang_Fox_c2'}] + _name.category_id scat + _name.object_id hi_ang_Fox_c2 + save_ + + +save_atom_type_scat.hi_ang_Fox_c3 + _definition.id '_atom_type_scat.hi_ang_Fox_c3' + _import.get [{"file":'templ_attr.cif',"save":'hi_ang_Fox_coeffs'}, + {"file":'templ_enum.cif',"save":'hi_ang_Fox_c3'}] + _name.category_id scat + _name.object_id hi_ang_Fox_c3 + save_ + + +save_atom_type_scat.length_neutron + _definition.id '_atom_type_scat.length_neutron' + loop_ + _alias.definition_id '_atom_type_scat_length_neutron' + _definition.update 2012-11-20 + _description.text +; + The bound coherent scattering length for the atom type at the + isotopic composition used for the diffraction experiment. +; + _description.common 'AtomTypeScatNeutronB' + _name.category_id scat + _name.object_id length_neutron + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.default 0.0 + _units.code femtometres + save_ + + +save_atom_type_scat.source + _definition.id '_atom_type_scat.source' + loop_ + _alias.definition_id '_atom_type_scat_source' + '_atom_type.scat_source' + _definition.update 2012-11-20 + _description.text +; + Reference to source of scattering factors used for this atom type. +; + _description.common 'AtomTypeScatDetails' + _name.category_id scat + _name.object_id source + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'International Tables Vol. IV Table 2.4.6B' + save_ + + +save_atom_type_scat.symbol + _definition.id '_atom_type_scat.symbol' + loop_ + _alias.definition_id '_atom_type_scat_symbol' + _definition.update 2013-01-23 + _description.text +; + The identity of the atom specie(s) representing this atom type. + See _atom_type.symbol for further details. +; + _description.common 'AtomTypeScatSymbol' + _name.category_id scat + _name.object_id symbol + _name.linked_item_id '_atom_type.symbol' + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_atom_type_scat.versus_stol_list + _definition.id '_atom_type_scat.versus_stol_list' + loop_ + _alias.definition_id '_atom_type_scat_versus_stol_list' + '_atom_type.scat_versus_stol_list' + _definition.update 2013-01-21 + _description.text +; + Table of scattering factors as a function of sin theta on lambda. + Table has the form ['':'', ....] + in increments of 0.01, increasing from 0.0. +; + _description.common 'AtomTypeScatTable' + _name.category_id scat + _name.object_id versus_stol_list + _type.purpose Quantity + _type.source Assigned + _type.container List + _type.contents List([Real,Real]) + save_ + + save_ #------ close ATOM_TYPE_SCAT category + + save_ #------ close ATOM_TYPE category + + save_ #------ close ATOM category + +#============================================================================ + +save_REFINE + + _definition.id REFINE + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to specify information about the + refinement of the structural model. +; + _name.category_id STRUCTURE + _name.object_id REFINE + +save_refine.special_details + _definition.id '_refine.special_details' + loop_ + _alias.definition_id '_refine_special_details' + _definition.update 2012-11-20 + _description.text +; + Details of the refinement not specified by other data items. +; + _description.common 'RefinementDetails' + _name.category_id refine + _name.object_id special_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + +#---------------------------------------------------------------------------- + +save_REFINE_DIFF + + _definition.id REFINE_DIFF + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items which specify the electron density limits + in a difference Fourier map after the structure has been refined. The + rms value is with respect to the arithmetic mean density, and is derived + from summations over each grid point in the asymmetric unit of the cell. +; + _name.category_id REFINE + _name.object_id DIFF + + +save_refine_diff.density_max + _definition.id '_refine_diff.density_max' + loop_ + _alias.definition_id '_refine_diff_density_max' + '_refine.diff_density_max' + _definition.update 2012-11-20 + _description.text +; + Maximum density value in a difference Fourier map. +; + _description.common 'RefineDiffDensMax' + _name.category_id refine_diff + _name.object_id density_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ + + +save_refine_diff.density_min + _definition.id '_refine_diff.density_min' + loop_ + _alias.definition_id '_refine_diff_density_min' + '_refine.diff_density_min' + _definition.update 2012-11-20 + _description.text +; + Miniumum density value in a difference Fourier map. +; + _description.common 'RefineDiffDensMin' + _name.category_id refine_diff + _name.object_id density_min + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ + + +save_refine_diff.density_rms + _definition.id '_refine_diff.density_rms' + loop_ + _alias.definition_id '_refine_diff_density_rms' + '_refine.diff_density_rms' + _definition.update 2012-11-20 + _description.text +; + Root mean square density value in a difference Fourier map. + This value is measured with respect to the arithmetic mean + density and is derived from summations over each grid point + in the asymmetric unit of the cell. This quantity is useful + for assessing the significance of *_min and *_max values, + and also for defining suitable contour levels. +; + _description.common 'RefineDiffDensRms' + _name.category_id refine_diff + _name.object_id density_rms + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ + + save_ #------ close REFINE_DIFF category + +#---------------------------------------------------------------------------- + +save_REFINE_LS + + _definition.id REFINE_LS + _definition.scope Category + _definition.class Set + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to specify information about the + refinement of the structural model. +; + _name.category_id REFINE + _name.object_id LS + + +save_refine_ls.abs_structure_details + _definition.id '_refine_ls.abs_structure_details' + loop_ + _alias.definition_id '_refine_ls_abs_structure_details' + '_refine.ls_abs_structure_details' + _definition.update 2012-11-20 + _description.text +; + Details on the absolute structure and how it was determined. +; + _description.common 'RefineAbsStructDetails' + _name.category_id refine_ls + _name.object_id abs_structure_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_refine_ls.abs_structure_Flack + _definition.id '_refine_ls.abs_structure_Flack' + loop_ + _alias.definition_id '_refine_ls_abs_structure_Flack' + '_refine.ls_abs_structure_Flack' + _definition.update 2012-11-20 + _description.text +; + The measure of absolute structure as defined by Flack (1983). + For centrosymmetric structures, the only permitted value, if the + data name is present, is 'inapplicable', represented by '.' . + For noncentrosymmetric structures, the value must lie in the + 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a + standard uncertainty (e.s.d.) u must be supplied. The + _enumeration.range of 0.0:1.0 is correctly interpreted as + meaning (0.0 - 3u) =< x =< (1.0 + 3u). + Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. +; + _description.common 'RefineAbsStructFlack' + _name.category_id refine_ls + _name.object_id abs_structure_Flack + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + save_ + + +save_refine_ls.abs_structure_Rogers + _definition.id '_refine_ls.abs_structure_Rogers' + loop_ + _alias.definition_id '_refine_ls_abs_structure_Rogers' + '_refine.ls_abs_structure_Rogers' + _definition.update 2012-11-20 + _description.text +; + The measure of absolute structure as defined by Rogers (1981). + The value must lie in the 99.97% Gaussian confidence interval + -1 -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must + be supplied. The _enumeration.range of -1.0:1.0 is correctly + interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). + Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. +; + _description.common 'RefineAbsStructRogers' + _name.category_id refine_ls + _name.object_id abs_structure_Rogers + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range -1.0:1.0 + save_ + + +save_refine_ls.d_res_high + _definition.id '_refine_ls.d_res_high' + loop_ + _alias.definition_id '_refine_ls_d_res_high' + '_refine.ls_d_res_high' + _definition.update 2012-11-20 + _description.text +; + Highest resolution for the reflections used in refinement. + This corresponds to the smallest interpanar d value. +; + _description.common 'RefineResolutionHigh' + _name.category_id refine_ls + _name.object_id d_res_high + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_refine_ls.d_res_low + _definition.id '_refine_ls.d_res_low' + loop_ + _alias.definition_id '_refine_ls_d_res_low' + '_refine.ls_d_res_low' + _definition.update 2012-11-20 + _description.text +; + Lowest resolution for the reflections used in refinement. + This corresponds to the largest interpanar d value. +; + _description.common 'RefineResolutionLow' + _name.category_id refine_ls + _name.object_id d_res_low + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_refine_ls.extinction_coef + _definition.id '_refine_ls.extinction_coef' + loop_ + _alias.definition_id '_refine_ls_extinction_coef' + '_refine.ls_extinction_coef' + _definition.update 2012-11-20 + _description.text +; + The extinction coefficient used to calculate the correction + factor applied to the structure-factor data. The nature of the + extinction coefficient is given in the definitions of + _refine_ls.extinction_expression and _refine_ls.extinction_method. + For the 'Zachariasen' method it is the r* value; for the + 'Becker-Coppens type 1 isotropic' method it is the 'g' value. + For 'Becker-Coppens type 2 isotropic' corrections it is + the 'rho' value. Note that the magnitude of these values is + usually of the order of 10000. + Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, + 129-147, 148-153. + Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. + Larson, A. C. (1967). Acta Cryst. 23, 664-665. +; + _description.common 'RefineExtinctionCoeff' + _name.category_id refine_ls + _name.object_id extinction_coef + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + loop_ + _description_example.case + _description_example.detail + 3472(52) 'Zachariasen coefficient r* = 0.347(5) E04' + save_ + + +save_refine_ls.extinction_expression + _definition.id '_refine_ls.extinction_expression' + loop_ + _alias.definition_id '_refine_ls_extinction_expression' + '_refine.ls_extinction_expression' + _definition.update 2012-11-20 + _description.text +; + Description of or reference to the extinction-correction equation + used to apply the data item _refine_ls.extinction_coef. This + information should be sufficient to reproduce the extinction- + correction factors applied to the structure factors. +; + _description.common 'RefineExtinctionExpression' + _name.category_id refine_ls + _name.object_id extinction_expression + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case + _description_example.detail 'Larson approach' +; Larson, A. C. (1970). "Crystallographic Computing", edited by + F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard. +; + save_ + + +save_refine_ls.extinction_method + _definition.id '_refine_ls.extinction_method' + loop_ + _alias.definition_id '_refine_ls_extinction_method' + '_refine.ls_extinction_method' + _definition.update 2012-11-20 + _description.text +; + Description of the extinction correction method applied with the + data item _refine_ls.extinction_coef. This description should + include information about the correction method, either 'Becker- + Coppens' or 'Zachariasen'. The latter is sometimes referred to as + the 'Larson' method even though it employs Zachariasen's formula. + + The Becker-Coppens procedure is referred to as 'type 1' when + correcting secondary extinction dominated by the mosaic spread; + as 'type 2' when secondary extinction is dominated by particle + size and includes a primary extinction component; and as 'mixed' + when there are types 1 and 2. + + For the Becker-Coppens method it is also necessary to set the + mosaic distribution as either 'Gaussian' or 'Lorentzian'; and the + nature of the extinction as 'isotropic' or 'anisotropic'. Note + that if either the 'mixed' or 'anisotropic' corrections are applied + the multiple coefficients cannot be contained in the + _refine_ls.extinction_coef and must be listed in *.special_details. + + Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-153. + Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. + Larson, A. C. (1967). Acta Cryst. 23, 664-665. +; + _description.common 'RefineExtinctionMethod' + _name.category_id refine_ls + _name.object_id extinction_method + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case Zachariasen + 'B-C type 2 Gaussian isotropic' + save_ + + +save_refine_ls.F_calc_details + _definition.id '_refine_ls.F_calc_details' + loop_ + _alias.definition_id '_refine_ls_F_calc_details' + _definition.update 2013-01-21 + _description.text +; + Details concerning the evaluation of the structure factors + using the expression given in _refine_ls.F_calc_formula. +; + _name.category_id refine_ls + _name.object_id F_calc_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case 'Gaussian integration using 16 points' + ''' Bessel functions expansion up to 5th + order. estimated accuracy of Bessel + function better than 0.001 electrons''' + save_ + + +save_refine_ls.F_calc_formula + _definition.id '_refine_ls.F_calc_formula' + loop_ + _alias.definition_id '_refine_ls_F_calc_formula' + _definition.update 2013-01-23 + _description.text +; + Analytical expression used to calculate the structure factors. +; + _name.category_id refine_ls + _name.object_id F_calc_formula + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + save_ + + +save_refine_ls.F_calc_precision + _definition.id '_refine_ls.F_calc_precision' + loop_ + _alias.definition_id '_refine_ls_F_calc_precision' + _definition.update 2013-01-21 + _description.text +; + Estimate of the precision resulting from the numerical + approximations made during the evaluation of the structure + factors using the expression _refine_ls.F_calc_formula + following the method outlined in _refine_ls.F_calc_details. +; + _name.category_id refine_ls + _name.object_id F_calc_precision + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + loop_ + _method.purpose + _method.expression + Definition +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ + + +save_refine_ls.goodness_of_fit_all + _definition.id '_refine_ls.goodness_of_fit_all' + loop_ + _alias.definition_id '_refine_ls_goodness_of_fit_all' + '_refine.ls_goodness_of_fit_all' + _definition.update 2012-11-20 + _description.text +; + Least-squares goodness-of-fit parameter S for all reflections after + the final cycle of refinement. Ideally, account should be taken of + parameters restrained in the least squares. + + { sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ + S = { ------------------------------------ } + { Nref - Nparam } + + Y(meas) = the measured coefficients + (see _refine_ls.structure_factor_coef) + Y(calc) = the calculated coefficients + (see _refine_ls.structure_factor_coef) + w = the least-squares reflection weight + [1/(u^2^)] + u = standard uncertainty + Nref = the number of reflections used in the refinement + Nparam = the number of refined parameters + and the sum is taken over the specified reflections +; + _description.common 'RefineLsGofAllReflns' + _name.category_id refine_ls + _name.object_id goodness_of_fit_all + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.goodness_of_fit_gt + _definition.id '_refine_ls.goodness_of_fit_gt' + loop_ + _alias.definition_id '_refine_ls_goodness_of_fit_gt' + '_refine_ls_goodness_of_fit_obs' + '_refine.ls_goodness_of_fit_obs' + _definition.update 2012-11-20 + _description.text +; + Least-squares goodness-of-fit parameter S for significantly + intense reflections, (i.e. 'observed' reflections with values + greater-than the threshold set in _reflns.threshold_expression), + after the final cycle. Ideally, account should be taken of + parameters restrained in the least-squares refinement. + + { sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^ + S = { --------------------------------------- } + { Nref - Nparam } + + Y(meas_gt) = the 'observed' coefficients + (see _refine_ls.structure_factor_coef) + Y(calc) = the calculated coefficients + (see _refine_ls.structure_factor_coef) + w = the least-squares reflection weight + [1/(u^2^)] + u = standard uncertainty + Nref = the number of reflections used in the refinement + Nparam = the number of refined parameters + and the sum is taken over the specified reflections +; + _description.common 'RefineLsGofGtReflns' + _name.category_id refine_ls + _name.object_id goodness_of_fit_gt + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.goodness_of_fit_ref + _definition.id '_refine_ls.goodness_of_fit_ref' + loop_ + _alias.definition_id '_refine_ls_goodness_of_fit_ref' + _definition.update 2012-11-20 + _description.text +; + Least-squares goodness-of-fit parameter S for those reflections + included in the final cycle of refinement. Account should be + taken of restrained parameters. + + { sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ + S = { ------------------------------------ } + { Nref - Nparam } + + Y(meas) = the measured coefficients + (see _refine_ls.structure_factor_coef) + Y(calc) = the calculated coefficients + (see _refine_ls.structure_factor_coef) + w = the least-squares reflection weight + [1/(u^2^)] + u = standard uncertainty + Nref = the number of reflections used in the refinement + Nparam = the number of refined parameters + and the sum is taken over the specified reflections +; + _description.common 'RefineLsGofRefineReflns' + _name.category_id refine_ls + _name.object_id goodness_of_fit_ref + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.hydrogen_treatment + _definition.id '_refine_ls.hydrogen_treatment' + loop_ + _alias.definition_id '_refine_ls_hydrogen_treatment' + '_refine.ls_hydrogen_treatment' + _definition.update 2012-11-20 + _description.text +; + Code identifying how hydrogen atoms were treated in the refinement. +; + _description.common 'RefineLsHatomTreatment' + _name.category_id refine_ls + _name.object_id hydrogen_treatment + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail + refall 'refined all H-atom parameters' + refxyz 'refined H-atom coordinates only' + refU 'refined H-atom U's only' + noref 'no refinement of H-atom parameters' + constr 'H-atom parameters constrained' + hetero + '''H-atom parameters constrained for H on C, all + H-atom parameters refined for H on heteroatoms''' + heteroxyz + '''H-atom parameters constrained for H on C, refined + H-atom coordinates only for H on heteroatoms''' + heteroU + '''H-atom parameters constrained for H on C, refined + H-atom U's only for H on heteroatoms''' + heteronoref + '''H-atom parameters constrained for H on C, no + refinement of H-atom parameters for H on heteroatoms''' + hetero-mixed + '''H-atom parameters constrained for H on C and some + heteroatoms, all H-atom parameters refined + for H on remaining heteroatoms''' + heteroxyz-mixed + '''H-atom parameters constrained for H on C and some + heteroatoms, refined H-atom coordinates only + for H on remaining heteroatoms''' + heteroU-mixed + '''H-atom parameters constrained for H on C and some + heteroatoms, refined H-atom U's only for H on + remaining heteroatoms''' + heteronoref-mixed + '''H-atom parameters constrained for H on C and some + heteroatoms, no refinement of H-atom parameters + for H on remaining heteroatoms''' + mixed 'some constrained, some independent' + undef 'H-atom parameters not defined' + _enumeration.default undef + save_ + + +save_refine_ls.matrix_type + _definition.id '_refine_ls.matrix_type' + loop_ + _alias.definition_id '_refine_ls_matrix_type' + '_refine.ls_matrix_type' + _definition.update 2012-11-20 + _description.text +; + Code identifying the matrix type used for least-squares derivatives. +; + _description.common 'RefineLsMatrixType' + _name.category_id refine_ls + _name.object_id matrix_type + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail full 'full' + fullcycle 'full with fixed elements per cycle' + atomblock 'block diagonal per atom' + userblock 'user-defined blocks' + diagonal 'diagonal elements only' + sparse 'selected elements only' + _enumeration.default full + save_ + + +save_refine_ls.number_constraints + _definition.id '_refine_ls.number_constraints' + loop_ + _alias.definition_id '_refine_ls_number_constraints' + '_refine.ls_number_constraints' + _definition.update 2012-11-20 + _description.text +; + Number of constrained (non-refined or dependent) parameters + in the least-squares process. These may be due to symmetry or any + other constraint process (e.g. rigid-body refinement). See also + _atom_site.constraints and _atom_site.refinement_flags. A general + description of constraints may appear in _refine.special_details. +; + _description.common 'RefineLsConstraintsCount' + _name.category_id refine_ls + _name.object_id number_constraints + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + _enumeration.default 0 + save_ + + +save_refine_ls.number_parameters + _definition.id '_refine_ls.number_parameters' + loop_ + _alias.definition_id '_refine_ls_number_parameters' + '_refine.ls_number_parameters' + _definition.update 2012-11-20 + _description.text +; + Number of parameters refined in the least-squares process. If + possible this number should include the restrained parameters. + The restrained parameters are distinct from the constrained + parameters (where one or more parameters are linearly dependent + on the refined value of another). Least-squares restraints + often depend on geometry or energy considerations and this + makes their direct contribution to this number, and to the + goodness-of-fit calculation, difficult to assess. +; + _description.common 'RefineLsParametersCount' + _name.category_id refine_ls + _name.object_id number_parameters + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_refine_ls.number_reflns + _definition.id '_refine_ls.number_reflns' + loop_ + _alias.definition_id '_refine_ls_number_reflns' + '_refine.ls_number_reflns_all' + _definition.update 2012-11-20 + _description.text +; + Number of unique reflections used in the least-squares refinement. +; + _description.common 'RefineLsReflectionsCount' + _name.category_id refine_ls + _name.object_id number_reflns + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 1: + save_ + + +save_refine_ls.number_restraints + _definition.id '_refine_ls.number_restraints' + loop_ + _alias.definition_id '_refine_ls_number_restraints' + '_refine.ls_number_restraints' + _definition.update 2012-11-20 + _description.text +; + Number of restrained parameters in the least-squares refinement. These + parameters do not directly dependent on another refined parameter. Often + restrained parameters involve geometry or energy dependencies. See also + _atom_site.constraints and _atom_site.refinement_flags. A description + of refinement constraints may appear in _refine.special_details. +; + _description.common 'RefineLsConstraintsCount' + _name.category_id refine_ls + _name.object_id number_restraints + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_refine_ls.R_factor_all + _definition.id '_refine_ls.R_factor_all' + loop_ + _alias.definition_id '_refine_ls_R_factor_all' + '_refine.ls_R_factor_all' + _definition.update 2012-11-20 + _description.text +; + Residual factor for all reflections satisfying the resolution limits + specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is + the conventional R factor. See also wR factor definitions. + + sum | F(meas) - F(calc) | + R = ------------------------ + sum | F(meas) | + + F(meas) = the measured structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + and the sum is taken over the specified reflections +; + _description.common 'RefineLsResid(F)AllReflns' + _name.category_id refine_ls + _name.object_id R_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.R_factor_gt + _definition.id '_refine_ls.R_factor_gt' + loop_ + _alias.definition_id '_refine_ls_R_factor_obs' + '_refine_ls_R_factor_gt' + '_refine.ls_R_factor_obs' + _definition.update 2012-11-20 + _description.text +; + Residual factor for the reflections judged significantly intense + (see _reflns.number_gt and _reflns.threshold_expression) and included + in the refinement. The reflections also satisfy the resolution limits + specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is + the conventional R factor. + + sum | F(meas_gt) - F(calc) | + R = ----------------------------- + sum | F(meas_gt) | + + F(meas_gt) = the 'observed' structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + and the sum is taken over the specified reflections +; + _description.common 'RefineLsResid(F)GtReflns' + _name.category_id refine_ls + _name.object_id R_factor_gt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.R_Fsqd_factor + _definition.id '_refine_ls.R_Fsqd_factor' + loop_ + _alias.definition_id '_refine_ls_R_Fsqd_factor' + '_refine.ls_R_Fsqd_factor_obs' + _definition.update 2012-11-20 + _description.text +; + Residual factor R(Fsqd), calculated on the squared amplitudes of the + measured and calculated structure factors, for significantly intense + reflections (satisfying _reflns.threshold_expression) and included in + the refinement. The reflections also satisfy the resolution limits + specified by _refine_ls.d_res_high and _refine_ls.d_res_low. + + sum | F(meas_gt)^2^ - F(calc)^2^ | + R(Fsqd) = ------------------------------------ + sum F(meas_gt)^2^ + + F(meas_gt)^2^ = squares of the 'observed' structure-factor + F(calc)^2^ = squares of the calculated structure-factor + and the sum is taken over the specified reflections +; + _description.common 'RefineLsResid(Fsqd)GtReflns' + _name.category_id refine_ls + _name.object_id R_Fsqd_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.R_I_factor + _definition.id '_refine_ls.R_I_factor' + loop_ + _alias.definition_id '_refine_ls_R_I_factor' + '_refine.ls_R_I_factor_obs' + _definition.update 2012-11-20 + _description.text +; + Residual factor R(I) for significantly intense reflections (satisfying + _reflns.threshold_expression) and included in the refinement. This is + most often calculated in Rietveld refinements of powder data, where it + is referred to as R~B~ or R~Bragg~. + + sum | I(meas_gt) - I(calc) | + R(I) = ----------------------------- + sum | I(meas_gt) | + + I(meas_gt) = the net 'observed' intensities + I(calc) = the net calculated intensities + and the sum is taken over the specified reflections +; + _description.common 'RefineLsResid(I)GtReflns' + _name.category_id refine_ls + _name.object_id R_I_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.restrained_S_all + _definition.id '_refine_ls.restrained_S_all' + loop_ + _alias.definition_id '_refine_ls_restrained_S_all' + '_refine.ls_restrained_S_all' + _definition.update 2012-11-20 + _description.text +; + Least-squares goodness-of-fit parameter S' for all reflections after + the final cycle of least squares. This parameter explicitly includes + the restraints applied in the least-squares process. See also + _refine_ls.goodness_of_fit_all definition. + + {sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ + { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } + S' = { -------------------------------------------------- } + { N~ref~ + N~restr~ - N~param~ } + + Y(meas) = the measured coefficients + (see _refine_ls.structure_factor_coef) + Y(calc) = the calculated coefficients + (see _refine_ls.structure_factor_coef) + w = the least-squares reflection weight + [1/square of standard uncertainty (e.s.d.)] + P(calc) = the calculated restraint values + P(targ) = the target restraint values + w~r~ = the restraint weight + + N~ref~ = the number of reflections used in the refinement + (see _refine_ls.number_reflns) + N~restr~ = the number of restraints + (see _refine_ls.number_restraints) + N~param~ = the number of refined parameters + (see _refine_ls.number_parameters) + + sum is taken over the specified reflections + sum~r~ is taken over the restraints +; + _description.common 'RefineLsGofRestrainedAllReflns' + _name.category_id refine_ls + _name.object_id restrained_S_all + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.restrained_S_gt + _definition.id '_refine_ls.restrained_S_gt' + loop_ + _alias.definition_id '_refine_ls_restrained_S_obs' + '_refine_ls_restrained_S_gt' + '_refine.ls_restrained_S_obs' + _definition.update 2012-11-20 + _description.text +; + Least-squares goodness-of-fit parameter S' for significantly intense + reflections (satisfying _reflns.threshold_expression) after the final + cycle of least squares. This parameter explicitly includes the restraints + applied. The expression for S' is given in _refine_ls.restrained_S_all. + + {sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^ + { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } + S' = { -------------------------------------------------- } + { N~ref~ + N~restr~ - N~param~ } + + Y(meas_gt) = the 'observed' coefficients + (see _refine_ls.structure_factor_coef) + Y(calc) = the calculated coefficients + (see _refine_ls.structure_factor_coef) + w = the least-squares reflection weight + [1/square of standard uncertainty (e.s.d.)] + P(calc) = the calculated restraint values + P(targ) = the target restraint values + w~r~ = the restraint weight + + N~ref~ = the number of reflections used in the refinement + (see _refine_ls.number_reflns) + N~restr~ = the number of restraints + (see _refine_ls.number_restraints) + N~param~ = the number of refined parameters + (see _refine_ls.number_parameters) + + sum is taken over the specified reflections + sum~r~ is taken over the restraints +; + _description.common 'RefineLsGofRestrainedGtReflns' + _name.category_id refine_ls + _name.object_id restrained_S_gt + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.shift_over_su_max + _definition.id '_refine_ls.shift_over_su_max' + loop_ + _alias.definition_id '_refine_ls_shift_over_su_max' + '_refine.ls_shift_over_esd_max' + '_refine_ls_shift/su_max' + '_refine_ls_shift/esd_max' + _definition.update 2012-11-20 + _description.text +; + The largest ratio of the final least-squares parameter shift + to the final standard uncertainty (s.u., formerly described + as estimated standard deviation, e.s.d.). +; + _description.common 'RefineLsMaxShift/Su' + _name.category_id refine_ls + _name.object_id shift_over_su_max + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.shift_over_su_max_lt + _definition.id '_refine_ls.shift_over_su_max_lt' + loop_ + _alias.definition_id '_refine_ls_shift/su_max_lt' + _definition.update 2012-12-11 + _description.text +; + Upper limit for the largest ratio of the final l-s parameter + shift divided by the final standard uncertainty. This item is + used when the largest value of the shift divided by the final + standard uncertainty is too small to measure. +; + _name.category_id refine_ls + _name.object_id shift_over_su_max_lt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.shift_over_su_mean + _definition.id '_refine_ls.shift_over_su_mean' + loop_ + _alias.definition_id '_refine_ls_shift_over_su_mean' + '_refine.ls_shift_over_esd_mean' + '_refine_ls_shift/su_mean' + '_refine_ls_shift/esd_mean' + _definition.update 2012-11-20 + _description.text +; + The average ratio of the final least-squares parameter shift + to the final standard uncertainty (s.u., formerly described + as estimated standard deviation, e.s.d.). +; + _description.common 'RefineLsMeanShift/Su' + _name.category_id refine_ls + _name.object_id shift_over_su_mean + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.shift_over_su_mean_lt + _definition.id '_refine_ls.shift_over_su_mean_lt' + loop_ + _alias.definition_id '_refine_ls_shift/su_mean_lt' + _definition.update 2012-12-11 + _description.text +; + Upper limit for the average ratio of the final l-s parameter + shift divided by the final standard uncertainty. This item is + used when the average value of the shift divided by the final + standard uncertainty is too small to measure. +; + _name.category_id refine_ls + _name.object_id shift_over_su_mean_lt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.structure_factor_coef + _definition.id '_refine_ls.structure_factor_coef' + loop_ + _alias.definition_id '_refine_ls_structure_factor_coef' + '_refine.ls_structure_factor_coef' + _definition.update 2012-11-20 + _description.text +; + Structure-factor coefficient used in the least-squares process. +; + _description.common 'RefineLsStructFactorCoeff' + _name.category_id refine_ls + _name.object_id structure_factor_coef + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail F 'structure factor magnitude' + Fsqd 'structure factor squared' + Inet 'net intensity' + _enumeration.default F + save_ + + +save_refine_ls.weighting_details + _definition.id '_refine_ls.weighting_details' + loop_ + _alias.definition_id '_refine_ls_weighting_details' + '_refine.ls_weighting_details' + _definition.update 2012-11-20 + _description.text +; + Description of special aspects of the weighting scheme used in the + least-squares refinement. Used to describe the weighting when the + value of _refine_ls.weighting_scheme is specified as 'calc'. +; + _description.common 'RefineLsWeightDetails' + _name.category_id refine_ls + _name.object_id weighting_details + _type.purpose Describe + _type.source Assigned + _type.container Single + _type.contents Text + loop_ + _description_example.case +; + Sigdel model of Konnert-Hendrickson: + Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6) + Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. + Afsig = 16.0, Bfsig = 60.0 at the end of refinement. +; + save_ + + +save_refine_ls.weighting_scheme + _definition.id '_refine_ls.weighting_scheme' + loop_ + _alias.definition_id '_refine_ls_weighting_scheme' + '_refine.ls_weighting_scheme' + _definition.update 2012-11-20 + _description.text +; + General description of the weighting scheme used in the least-squares. + An enumerated code should be contained in this description. +; + _description.common 'RefineLsWeightCode' + _name.category_id refine_ls + _name.object_id weighting_scheme + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _enumeration_set.state + _enumeration_set.detail sigma "based on measured s.u.'s" + unit 'unit or no weights applied' + calc 'calculated weights applied' + _enumeration.default sigma + save_ + + +save_refine_ls.wR_factor_all + _definition.id '_refine_ls.wR_factor_all' + loop_ + _alias.definition_id '_refine_ls_wR_factor_all' + '_refine.ls_wR_factor_all' + _definition.update 2012-11-20 + _description.text +; + Weighted residual factors for all reflections satisfying the resolution + limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. + See also the _refine_ls.R_factor_all definition. + + ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ + wR = ( ------------------------------ ) + ( sum w Y(meas)^2^ ) + + Y(meas) = the measured amplitude _refine_ls.structure_factor_coef + Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef + w = the least-squares weight + and the sum is taken over the specified reflections +; + _description.common 'RefineLsWResidAllReflns' + _name.category_id refine_ls + _name.object_id wR_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.wR_factor_gt + _definition.id '_refine_ls.wR_factor_gt' + loop_ + _alias.definition_id '_refine_ls_wR_factor_obs' + '_refine.ls_wR_factor_obs' + '_refine_ls_wR_factor_gt' + _definition.update 2012-11-20 + _description.text +; + Weighted residual factors for significantly intense reflections + (satisfying @reflns_threshold_expression) included in the refinement. + The reflections must also satisfy the resolution limits established by + _refine_ls.d_res_high and _refine_ls.d_res_low. + + ( sum w [ Y(meas_gt) - Y(calc) ]^2^ )^1/2^ + wR = ( ---------------------------------- ) + ( sum w Y(meas_gt)^2^ ) + + Y(meas_gt) = the 'observed' amplitude _refine_ls.structure_factor_coef + Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef + w = the least-squares weight + and the sum is taken over the specified reflections +; + _description.common 'RefineLsWResidGtReflns' + _name.category_id refine_ls + _name.object_id wR_factor_gt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls.wR_factor_ref + _definition.id '_refine_ls.wR_factor_ref' + loop_ + _alias.definition_id '_refine_ls_wR_factor_ref' + _definition.update 2012-11-20 + _description.text +; + Weighted residual factors for reflections included in the refinement + which satisfy the limits specified by _refine_ls.d_res_high and + _refine_ls.d_res_low. + + ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ + wR = ( ------------------------------ ) + ( sum w Y(meas)^2^ ) + + Y(meas) = the measured amplitude _refine_ls.structure_factor_coef + Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef + w = the least-squares weight + and the sum is taken over the specified reflections +; + _description.common 'RefineLsWResidRefineReflns' + _name.category_id refine_ls + _name.object_id wR_factor_ref + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + +#---------------------------------------------------------------------------- + +save_REFINE_LS_CLASS + + _definition.id REFINE_LS_CLASS + _definition.scope Category + _definition.class Loop + _definition.update 2012-11-20 + _description.text +; + The CATEGORY of data items used to specify information about the + refinement of the structural model. +; + _name.category_id REFINE_LS + _name.object_id CLASS + _category.key_id '_refine_ls_class.key' + + +save_refine_ls_class.key + _definition.id '_refine_ls_class.key' + _definition.update 2012-11-20 + _description.text +; + Value is a unique key to a set of REFINE_LS_CLASS items + in a looped list. +; + _description.common 'Key to ls refinement data' + _name.category_id refine_ls_class + _name.object_id key + _type.purpose Key + _type.source Assembled + _type.container Single + loop_ + _method.purpose + _method.expression + Definition +; _type.contents = Type_Contents(refine_ls_class.code) +; + Evaluation +; _refine_ls_class.key = _refine_ls_class.code +; + save_ + + +save_refine_ls_class.code + _definition.id '_refine_ls_class.code' + loop_ + _alias.definition_id '_refine_ls_class_code' + _definition.update 2012-11-20 + _description.text +; + Code identifying a certain reflection class. +; + _description.common 'LsShellCode' + _name.category_id refine_ls_class + _name.object_id code + _name.linked_item_id '_reflns_class.code' + _type.purpose Link + _type.source Selected + _type.container Single + _type.contents Code + loop_ + _description_example.case '1' 'm1' 's2' + save_ + + +save_refine_ls_class.d_res_high + _definition.id '_refine_ls_class.d_res_high' + loop_ + _alias.definition_id '_refine_ls_class_d_res_high' + _definition.update 2012-11-20 + _description.text +; + Highest resolution for the reflections in this class. + This corresponds to the smallest interpanar d value. +; + _description.common 'LsShellResolHigh' + _name.category_id refine_ls_class + _name.object_id d_res_high + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_refine_ls_class.d_res_low + _definition.id '_refine_ls_class.d_res_low' + loop_ + _alias.definition_id '_refine_ls_class_d_res_low' + _definition.update 2012-11-20 + _description.text +; + Lowest resolution for the reflections in this class. + This corresponds to the largest interpanar d value. +; + _description.common 'LsShellResolLow' + _name.category_id refine_ls_class + _name.object_id d_res_low + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms + save_ + + +save_refine_ls_class.R_factor_all + _definition.id '_refine_ls_class.R_factor_all' + loop_ + _alias.definition_id '_refine_ls_class_R_factor_all' + _definition.update 2012-11-20 + _description.text +; + Residual factor for reflections in this class included in the + refinement. See _refine_ls.R_factor_all definition for details. +; + _description.common 'LsShellResid(F)AllReflns' + _name.category_id refine_ls_class + _name.object_id R_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls_class.R_factor_gt + _definition.id '_refine_ls_class.R_factor_gt' + loop_ + _alias.definition_id '_refine_ls_class_R_factor_gt' + '_refine_ls_class_R_factor_obs' + _definition.update 2012-11-20 + _description.text +; + Residual factor for the reflections in this class judged + significantly intense (see _reflns.threshold_expression) and + included in refinement. See _refine_ls.R_factor_gt for details. +; + _description.common 'LsShellResid(F)GtReflns' + _name.category_id refine_ls_class + _name.object_id R_factor_gt + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls_class.R_Fsqd_factor + _definition.id '_refine_ls_class.R_Fsqd_factor' + loop_ + _alias.definition_id '_refine_ls_class_R_Fsqd_factor' + _definition.update 2012-11-20 + _description.text +; + Residual factor R(F^2^) for reflections in this class judged + significantly intense (see _reflns.threshold_expression) and + included in refinement. See _refine_ls.R_Fsqd_factor for details. +; + _description.common 'LsShellResid(Fsqd)GtReflns' + _name.category_id refine_ls_class + _name.object_id R_Fsqd_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls_class.R_I_factor + _definition.id '_refine_ls_class.R_I_factor' + loop_ + _alias.definition_id '_refine_ls_class_R_I_factor' + _definition.update 2012-11-20 + _description.text +; + Residual factor R(I) for reflections in this class judged + significantly intense (see _reflns.threshold_expression) and + included in refinement. See _refine_ls.R_I_factor for details. +; + _description.common 'LsShellResid(I)GtReflns' + _name.category_id refine_ls_class + _name.object_id R_I_factor + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + +save_refine_ls_class.wR_factor_all + _definition.id '_refine_ls_class.wR_factor_all' + loop_ + _alias.definition_id '_refine_ls_class_wR_factor_all' + _definition.update 2012-11-20 + _description.text +; + Weight residual for all reflections in this class judged + significantly intense (see _reflns.threshold_expression) and + included in refinement. See _refine_ls.wR_factor_all for details. +; + _description.common 'LsShellWResid(F)GtReflns' + _name.category_id refine_ls_class + _name.object_id wR_factor_all + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + save_ + + save_ #------ close REFINE_LS_CLASS category + + save_ #------ close REFINE_LS category + + save_ #------ close REFINE category + + save_ #------ close STRUCTURE category + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.1.01 2006-03-07 +; + Initial CORE_STRUCTURE dictionary constructed from CORE_3 v3.5.02 +; + 1.1.02 2006-03-22 +; + Insert the _enumeration.def_index_id names and remove the + _enumeration.default values where present. +; + 1.1.03 2006-06-20 +; + Apply DDL3 3.6.01 attributes. +; + 1.1.04 2006-06-29 +; + Apply DDL3 3.6.05 attributes. +; + 1.1.05 2006-09-07 +; + Apply DDL3 3.6.08 attributes. +; + 1.1.06 2006-11-13 +; + Apply DDL3 3.6.10 attributes. + Change method.id to method.purpose; EVAL to Evaluation +; + 1.1.07 2006-12-14 +; + Apply DDL3 3.7.01 attributes. +; + 1.2.01 2007-02-07 +; + Apply DDL3 3.7.04 attributes. +; + 1.2.02 2007-02-09 +; + Correct TYPE in _refine_ls.number_parameters and + _refine_ls.number_reflns +; + 1.2.03 2007-10-13 +; + Placed tags in _category_key.primitive lists within quotes. +; + 1.2.04 2008-01-18 +; + Replaced import_list controls with leading uppercase character. + Changed import_list [....] to [[....]] +; + 1.2.05 2008-06-18 +; + Change _import_list.id to be ((.....),(....)) + For all *.key items change _type.contents from Code to Inherited + For other *.id items some _type.purpose from Key to Identify +; + 1.2.06 2008-06-19 +; + Ensure that all items with _type.contents Code are enumerated + otherwise they are Text. +; + 1.2.07 2008-06-24 +; + Change all _type.dimension values +; + 1.3.01 2011-06-07 +; + Replace category class "List" with "Loop" + Replace all "Tuple" with "List" + Replace all "Array" with "List" + Place all import lists into [[......]] +; + 1.3.02 2011-07-31 +; + Make all the changes needed with DDL 3.8 and import.get +; + 1.3.03 2011-08-03 +; + Change name of import file com_att.dic to templ_attr.cif + Change name of import file com_val.dic to templ_templcif +; + 1.3.04 2011-12-01 +; + Change container type from List to Matrix for relevant item definitions +; + 1.3.05 2012-01-25 +; + For import.get change the key "fram" to "save". +; + 1.4.01 2012-05-07 +; + Apply DDL 3.10.01 changes. +; + 1.4.02 2012-10-16 +; + Apply DDL 3.10.02 changes. + Corrected atom_type.element_symbol -- default link is atom_type.symbol + Corrected many other definitions -- default link is atom_type.symbol + Remove type.contents "Inherited"; insert Definition method expression. +; + 1.4.03 2012-11-20 +; + Invoke container functions Matrix, List in methods scripts where needed. + Add DDL1 tags as alias.definition_id values +; + 1.4.04 2012-11-30 +; + Add "\" to method expression for _atom_type_scat.hi_ang_Fox_coeffs + Doug's TEMPORARY FIX!!!!! +; + 1.4.05 2012-12-11 +; + Add method to atom_type_scat.symbol definition. + Add the Cartn_transform matrix elements & modify matrix method. + Add the Cartn_transform vector elements. + Add the fract_transform matrix and the elements. + Add the fract_transform vector elements. + Add refine_ls.shift_over_su_max_lt + Add refine_ls.shift_over_su_mean_lt +; + 1.4.06 2012-12-21 +; + Add alias tag atom_site_aniso_label to atom_site_label definition. + Add alias tag atom_site_label to atom_site_aniso_label definition. + Add alias tag atom_type_scat_symbol to atom_type_symbol definition. + Add alias tag atom_type_symbol to atom_type_scat_symbol definition. +; + 1.4.07 2013-01-21 +; + Additional definitions added for alignment with latest DDL1 core dic. +; + 1.4.08 2013-01-23 +; + Remove cross-aliases between ATOM_SITE and ATOM_SITE_ANISO labels + Remove incorrect alias for refine_ls.F_calc_formula +; + 1.4.09 2013-01-28 +; + Changed atom_site.symmetry_multiplicity to *.site_symmetry_multiplicity +; + 1.4.10 2013-02-18 +; + Added evaluation method for ATOM_TYPE in case type symbols are missing +; \ No newline at end of file diff --git a/templ_attr.cif b/templ_attr.cif new file mode 100755 index 0000000..9fea13c --- /dev/null +++ b/templ_attr.cif @@ -0,0 +1,452 @@ +############################################################################## +# # +# TEMPLATE DEFINITION ATTRIBUTES DICTIONARY # +# # +############################################################################## + +data_TEMPL_ATTR + + _dictionary.title TEMPL_ATTR + _dictionary.class Template + _dictionary.version 1.3.06 + _dictionary.date 2012-12-11 + _dictionary.uri www.iucr.org/cif/dic/com_att.dic + _dictionary.ddl_conformance 3.10.03 + _description.text +; + This dictionary contains definition attribute sets that are common + to other CIF dictionaries and is imported by them. +; + +#--------------------------------------------------------------------------- + +save_atom_site_label + _definition.update 2012-10-16 + _description.text +; + This label is a unique identifier for a particular site in the + asymmetric unit of the crystal unit cell. It is made up of + components, _atom_site.label_component_0 to *_6, which may be + specified as separate data items. Component 0 usually matches one + of the specified _atom_type.symbol codes. This is not mandatory + if an _atom_site.type_symbol item is included in the atom site + list. The _atom_site.type_symbol always takes precedence over + an _atom_site.label in the identification of the atom type. The + label components 1 to 6 are optional, and normally only + components 0 and 1 are used. Note that components 0 and 1 are + concatenated, while all other components, if specified, are + separated by an underline character. Underline separators are + only used if higher-order components exist. If an intermediate + component is not used it may be omitted provided the underline + separators are inserted. For example the label 'C233__ggg' is + acceptable and represents the components C, 233, '', and ggg. + Each label may have a different number of components. +; + _description.common 'Atom Site Label' + _name.linked_item_id '_atom_site.label' + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + loop_ + _description_example.case C12 Ca3g28 Fe3+17 H*251 + C_a_phe_83_a_0 Zn_Zn_301_A_0 + save_ + + +save_site_symmetry + _definition.update 2012-05-07 + _description.text +; + The set of data items which specify the symmetry operation codes + which must be applied to the atom sites involved in the geometry angle. + + The symmetry code of each atom site as the symmetry-equivalent position + number 'n' and the cell translation number 'klm'. These numbers are + combined to form the code 'n klm' or n_klm. + + The character string n_klm is composed as follows: + + n refers to the symmetry operation that is applied to the + coordinates stored in _atom_site.fract_xyz. It must match a + number given in _symmetry_equiv.pos_site_id. + + k, l and m refer to the translations that are subsequently + applied to the symmetry transformed coordinates to generate + the atom used in calculating the angle. These translations + (x,y,z) are related to (k,l,m) by the relations + k = 5 + x + l = 5 + y + m = 5 + z +; + _type.purpose Quantity + _type.source Derived + _type.container Single + _type.contents Symop + loop_ + _description_example.case + _description_example.detail 4 '4th symmetry operation applied' + 7_645 '7th symm. posn.; +a on x; -b on y' + _enumeration.default '1_555' + save_ + + +save_Cartn_coord + _definition.update 2012-05-07 + _description.text +; + The atom site coordinates in angstroms specified according to a + set of orthogonal Cartesian axes related to the cell axes as + specified by the _atom_sites_Cartn_transform.axes description. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstroms + save_ + + +save_fract_coord + _definition.update 2012-05-07 + _description.text +; + Atom site coordinates as fractions of the cell length values. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_label_component + _definition.update 2012-05-07 + _description.text +; + Component_0 is normally a code which matches identically with + one of the _atom_type.symbol codes. If this is the case then the + rules governing the _atom_type.symbol code apply. If, however, + the data item _atom_site.type_symbol is also specified in the + atom site list, component 0 need not match this symbol or adhere + to any of the _atom_type.symbol rules. + Component_1 is referred to as the "atom number". When component 0 + is the atom type code, it is used to number the sites with the + same atom type. This component code must start with at least one + digit which is not followed by a + or - sign (to distinguish it + from the component 0 rules). + Components_2 to 6 contain the identifier, residue, sequence, + asymmetry identifier and alternate codes, respectively. These + codes may be composed of any characters except an underline. +; + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Code + save_ + + +save_Cartn_matrix + _definition.update 2012-12-11 + _description.text +; + Matrix used to transform fractional coordinates in the ATOM_SITE + category to Cartesian coordinates. The axial alignments of this + transformation are described in _atom_sites_Cartn_transform.axes. + The 3x1 translation is defined in _atom_sites_Cartn_transform.vector. + + x' |11 12 13| x | 1 | + ( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 | + z' |31 32 33| z | 3 | + + The default transformation matrix 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. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_fract_matrix + _definition.update 2012-12-11 + _description.text +; + Matrix used to transform Cartesian coordinates in the ATOM_SITE + category to fractional coordinates. The axial alignments of this + transformation are described in _atom_sites_fract_transform.axes. + The 3x1 translation is defined in _atom_sites_fract_transform.vector. + + x' |11 12 13| x | 1 | + ( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 | + z' |31 32 33| z | 3 | + + The default transformation matrix 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. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + save_ + + +save_aniso_BIJ + _definition.update 2012-05-07 + _description.text +; + These are the standard anisotropic atomic displacement components + in angstroms squared which appear in the structure factor term: + + T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } + + h = the Miller indices + a* = the reciprocal-space cell lengths + The unique elements of the real symmetric matrix are entered by row. + + The IUCr Commission on Nomenclature recommends against the use + of B for reporting atomic displacement parameters. U, being + directly proportional to B, is preferred. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstroms_squared + save_ + + +save_aniso_UIJ + _definition.update 2012-05-07 + _description.text +; + These are the standard anisotropic atomic displacement + components in angstroms squared which appear in the + structure factor term: + + T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } + + h = the Miller indices + a* = the reciprocal-space cell lengths + + The unique elements of the real symmetric matrix are entered by row. +; + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _units.code angstroms_squared + save_ + + +save_Cromer_Mann_coeff + _definition.update 2012-11-29 + _description.text +; + The set of data items used to define Cromer-Mann coefficients + for generation of X-ray scattering factors. + + Ref: International Tables for X-ray Crystallography, Vol. IV + (1974) Table 2.2B + or International Tables for Crystallography, Vol. C + (1991) Tables 6.1.1.4 and 6.1.1.5 +; + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_hi_ang_Fox_coeffs + _definition.update 2012-11-29 + _description.text +; + The set of data items used to define Fox et al. coefficients + for generation of high angle (s >2.0) X-ray scattering factors. + + Ref: International Tables for Crystallography, Vol. C + (1991) Table 6.1.1.5 +; + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.def_index_id '_atom_type.symbol' + save_ + + +save_Miller_index + _definition.update 2012-05-07 + _description.text +; + The index of a reciprocal space vector. +; + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Integer + save_ + + +save_orient_matrix + _definition.update 2012-05-07 + _description.text +; + The set of data items which specify the elements of the matrix of + the orientation of the crystal axes to the diffractometer goniometer. +; + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Real + save_ + + +save_transf_matrix + _definition.update 2012-05-07 + _description.text +; + The set of data items which specify the elements of the matrix + used to transform the reflection indices _diffrn_refln.hkl + into _refln.hkl. +; + _type.purpose Quantity + _type.source Assigned + _type.container Single + _type.contents Real + save_ + + +save_diffr_angle + _definition.update 2012-05-07 + _description.text +; + A diffractometer angle value. +; + _type.purpose Quantity + _type.source Measured + _type.container Single + _type.contents Real + _units.code degrees + _enumeration.range -180.:180. + save_ + + +save_diffr_counts + _definition.update 2012-10-16 + _description.text +; + The set of data items which specify the diffractometer counts. + Background counts before the peak, background after the peak, + net counts after background removed, counts for peak scan or position, + and the total counts (background plus peak). +; + _type.purpose Measurand + _type.source Measured + _type.container Single + _type.contents Count + _enumeration.range 0: + save_ + + +save_display_colour + _definition.update 2012-10-16 + _description.text +; + Integer value between 0 and 255 giving the intensity of a + specific colour component (red, green or blue) for the RBG + display colour code. + +; + _type.purpose Quantity + _type.source Observed + _type.container Single + _type.contents Index + _enumeration.range 0:255 + save_ + + + +#============================================================================= +# The dictionary's attribute creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.0.0 2005-12-12 +; + Initial version of the TEMPLATES dictionary created from the + definitions used in CORE_3 dictionary version 3.5.02 +; + 1.0.1 2006-02-12 +; + Remove dictionary attributes from a save frame. + Change category core_templates to template +; + 1.2.01 2006-02-21 +; + File structure to conform with prototype version dictionaries. +; + 1.2.02 2006-03-07 +; + Added the template _template.relational_id for the ddl3 dictionary. +; + 1.2.03 2006-06-17 +; + Apply DDL 3.6.01 changes +; + 1.2.04 2006-06-29 +; + Remove "_template" from the definition names. + Apply DDL 3.6.05 changes. + Change file name from templates.dic to com_att.dic +; + 1.2.05 2006-09-07 +; + Apply DDL 3.6.08 changes +; + 1.2.06 2006-11-13 +; + Apply DDL 3.6.10 changes +; + 1.2.07 2006-12-14 +; + Apply DDL 3.7.01 changes +; + 1.2.08 2008-06-18 +; + Change _type.purpose for Miller_index from Observed to Identify +; + 1.3.01 2011-08-03 +; + Remove definition.id lines in keeping with nested imports. +; + 1.3.02 2011-12-01 +; + Update the DDL version. No Matrix types present. +; + 1.3.03 2012-05-07 +; + Apply changes of 3.10.01 DDL version. +; + 1.3.04 2012-10-16 +; + Apply changes of 3.10.02 DDL version. "Label" becomes "Code". +; + 1.3.05 2012-11-29 +; + Add "_enumeration.def_index_id '_atom_type.symbol' " + to Cromer_Mann_coeff and hi_ang_Fox_coeffs. +; + 1.3.06 2012-12-11 +; + Add the templates Cartn_matrix and fract_matrix +; diff --git a/templ_enum.cif b/templ_enum.cif new file mode 100755 index 0000000..135dac2 --- /dev/null +++ b/templ_enum.cif @@ -0,0 +1,1531 @@ +############################################################################## +# # +# TEMPLATE DICTIONARY OF COMMONLY USER ENUMERATIONS # +# # +############################################################################## + +data_COM_VAL + + _dictionary.title COM_VAL + _dictionary.class Template + _dictionary.version 1.3.05 + _dictionary.date 2012-10-16 + _dictionary.uri www.iucr.org/cif/dic/com_val.dic + _dictionary.ddl_conformance 3.10.02 + _description.text +; + This dictionary contains commonly used enumeration value sets that + are imported into CIF dictionaries. +; + +#--------------------------------------------------------------------------- + +save_colour_RGB + loop_ + _enumeration_set.state + _enumeration_set.detail + black [ 000, 000, 000 ] + white [ 255, 255, 255 ] + grey [ 192, 192, 192 ] + grey_light [ 211, 211, 211 ] + grey_slate [ 112, 128, 144 ] + blue [ 000, 000, 255 ] + blue_light [ 176, 224, 230 ] + blue_medium [ 000, 000, 205 ] + blue_dark [ 025, 025, 112 ] + blue_navy [ 000, 000, 128 ] + blue_royal [ 065, 105, 225 ] + blue_sky [ 135, 206, 235 ] + blue_steel [ 070, 130, 180 ] + turquoise [ 064, 224, 208 ] + cyan [ 000, 255, 255 ] + cyan_light [ 224, 255, 255 ] + green [ 000, 255, 000 ] + green_light [ 152, 251, 152 ] + green_dark [ 000, 100, 000 ] + green_sea [ 046, 139, 087 ] + green_lime [ 050, 205, 050 ] + green_olive [ 107, 142, 035 ] + green_khaki [ 240, 230, 140 ] + yellow [ 255, 255, 000 ] + yellow_light [ 255, 255, 224 ] + yellow_gold [ 255, 215, 000 ] + brown [ 165, 042, 042 ] + brown_sienna [ 160, 082, 045 ] + brown_beige [ 245, 245, 220 ] + brown_tan [ 210, 180, 140 ] + salmon [ 250, 128, 114 ] + salmon_light [ 255, 160, 122 ] + salmon_dark [ 233, 150, 122 ] + orange [ 255, 165, 000 ] + orange_dark [ 255, 140, 000 ] + red [ 255, 000, 000 ] + red_coral [ 255, 127, 080 ] + red_tomato [ 255, 099, 071 ] + red_orange [ 255, 069, 000 ] + red_violet [ 219, 112, 147 ] + red_maroon [ 176, 048, 096 ] + pink [ 255, 192, 203 ] + pink_light [ 255, 182, 193 ] + pink_deep [ 255, 020, 147 ] + pink_hot [ 255, 105, 180 ] + violet [ 238, 130, 238 ] + violet_red [ 208, 032, 144 ] + violet_magenta [ 255, 000, 255 ] + violet_dark [ 148, 000, 211 ] + violet_blue [ 138, 043, 226 ] + save_ + + +save_element_symbol + loop_ + _enumeration_set.state + _enumeration_set.detail + Ac Actinium + Ag Silver + Al Aluminum + Am Americium + Ar Argon + As Arsenic + At Astatine + Au Gold + B Boron + Ba Barium + Be Beryllium + Bh Bohrium + Bi Bismuth + Bk Berkelium + Br Bromine + C Carbon + Ca Calcium + Cd Cadmium + Ce Cerium + Cf Californium + Cl Chlorine + Cm Curium + Co Cobalt + Cr Chromium + Cs Cesium + Cu Copper + Db Dubnium + Ds Darmstadtium + Dy Dysprosium + Er Erbium + Es Einsteinium + Eu Europium + F Fluorine + Fe Iron + Fm Fermium + Fr Francium + Ga Gallium + Gd Gadolinium + Ge Germanium + H Hydrogen + He Helium + Hf Hafnium + Hg Mercury + Ho Holmium + Hs Hassium + I Iodine + In Indium + Ir Iridium + K Potassium + Kr Krypton + La Lanthanum + Li Lithium + Lr Lawrencium + Lu Lutetium + Md Mendelevium + Mg Magnesium + Mn Manganese + Mo Molybdenum + Mt Meitnerium + N Nitrogen + Na Sodium + Ne Neon + Nb Niobium + Nd Neodymium + Ni Nickel + No Nobelium + Np Neptunium + O Oxygen + Os Osmium + P Phosphorus + Pd Palladium + Po Polonium + Pb Lead + Pt Platinum + Pr Praseodymium + Pm Promethium + Pu Plutonium + Pa Protactinium + Ra Radium + Rb Rubidium + Re Rhenium + Rf Rutherfordium + Rh Rhodium + Rn Radon + Ru Ruthenium + S Sulfur + Sb Antimony + Sc Scandium + Se Selenium + Sg Seaborgium + Si Silicon + Sm Samarium + Sn Tin + Sr Strontium + Ta Tantalum + Tb Terbium + Tc Technetium + Te Tellurium + Th Thorium + Ti Titanium + Tl Thallium + Tm Thulium + U Uranium + Uub Ununbium + Uun Ununnilium + Uuu Ununumium + V Vanadium + W Tungsten + Xe Xenon + Y Yttrium + Yb Ytterbium + Zn Zinc + Zr Zirconium + save_ + + +save_units_code + loop_ + _enumeration_set.state + _enumeration_set.detail + + 'centimetres' "length 'centimetres (meters * 10^( -2))'" + 'millimetres' "length 'millimetres (meters * 10^( -3))'" + 'nanometres' "length 'nanometres (meters * 10^( -9))'" + 'angstroms' "length 'angstroms (meters * 10^(-10))'" + 'picometres' "length 'picometres (meters * 10^(-12))'" + 'femtometres' "length 'femtometres (meters * 10^(-15))'" + + 'reciprocal_centimetres' + "per_length 'reciprocal centimetres (meters * 10^( -2)^-1)'" + 'reciprocal_millimetres' + "per_length 'reciprocal millimetres (meters * 10^( -3)^-1)'" + 'reciprocal_nanometres' + "per-length 'reciprocal nanometres (meters * 10^( -9)^-1)'" + 'reciprocal_angstroms' + "per-length 'reciprocal angstroms (meters * 10^(-10)^-1)'" + 'reciprocal_picometres' + "per-length 'reciprocal picometres (meters * 10^(-12)^-1)'" + + 'nanometre_squared' + "length_squared 'nanometres squared (meters * 10^( -9))^2'" + 'angstrom_squared' + "length_squared 'angstroms squared (meters * 10^(-10))^2'" + '8pi_angstroms_squared' + "length_squared '8pi^2 * angstroms squared (meters * 10^(-10))^2'" + 'picometre_squared' + "length_squared 'picometres squared (meters * 10^(-12))^2'" + + 'nanometre_cubed' + "length_cubed 'nanometres cubed (meters * 10^( -9))^3'" + 'angstrom_cubed' + "length_cubed 'angstroms cubed (meters * 10^(-10))^3'" + 'picometre_cubed' + "length_cubed 'picometres cubed (meters * 10^(-12))^3'" + + 'kilopascals' "pressure 'kilopascals'" + 'gigapascals' "pressure 'gigapascals'" + + 'hours' "time 'hours'" + 'minutes' "time 'minutes'" + 'seconds' "time 'seconds'" + 'microseconds' "time 'microseconds'" + + 'degrees' "angle 'degrees (of arc)'" + + 'degree_per_minute' "rotation_per_time 'degrees (of arc) per minute'" + + 'celsius' "temperature 'degrees (of temperature) Celsius'" + 'kelvins' "temperature 'degrees (of temperature) Kelvin'" + + 'electrons' "electrons 'electrons'" + + 'electron_squared' "electrons-squared 'electrons squared'" + + 'electrons_per_nanometre_cubed' + "electron-density 'electrons per nanometres cubed (meters * 10^( -9))^3'" + 'electrons_per_angstrom_cubed' + "electron-density 'electrons per angstroms cubed (meters * 10^(-10))^3'" + 'electrons_per_picometre_cubed' + "electron-density 'electrons per picometres cubed (meters * 10^(-12))^3'" + + 'kilowatts' "power 'kilowatts'" + 'milliamperes' "current 'milliamperes'" + 'kilovolts' "emf 'kilovolts'" + + 'arbitrary' "arbitary 'arbitrary system of units'" + + save_ + + +#--------------------------------------------------------------------------- + + +save_atomic_number + loop_ + _enumeration_default.index + _enumeration_default.value + H 01 D 01 H1- 01 He 02 Li 03 + Li1+ 03 Be 04 Be2+ 04 B 05 C 06 + N 07 O 08 O1- 08 F 09 F1- 09 + Ne 10 Na 11 Na1+ 11 Mg 12 Mg2+ 12 + Al 13 Al3+ 13 Si 14 Si4+ 14 P 15 + S 16 Cl 17 Cl1- 17 Ar 18 K 19 + K1+ 19 Ca 20 Ca2+ 20 Sc 21 Sc3+ 21 + Ti 22 Ti2+ 22 Ti3+ 22 Ti4+ 22 V 23 + V2+ 23 V3+ 23 V5+ 23 Cr 24 Cr2+ 24 + Cr3+ 24 Mn 25 Mn2+ 25 Mn3+ 25 Mn4+ 25 + Fe 26 Fe2+ 26 Fe3+ 26 Co 27 Co2+ 27 + Co3+ 27 Ni 28 Ni2+ 28 Ni3+ 28 Cu 29 + Cu1+ 29 Cu2+ 29 Zn 30 Zn2+ 30 Ga 31 + Ga3+ 31 Ge 32 Ge4+ 32 As 33 Se 34 + Br 35 Br1- 35 Kr 36 Rb 37 Rb1+ 37 + Sr 38 Sr2+ 38 Y 39 Y3+ 39 Zr 40 + Zr4+ 40 Nb 41 Nb3+ 41 Nb5+ 41 Mo 42 + Mo3+ 42 Mo5+ 42 Mo6+ 42 Tc 43 Ru 44 + Ru3+ 44 Ru4+ 44 Rh 45 Rh3+ 45 Rh4+ 45 + Pd 46 Pd2+ 46 Pd4+ 46 Ag 47 Ag1+ 47 + Ag2+ 47 Cd 48 Cd2+ 48 In 49 In3+ 49 + Sn 50 Sn2+ 50 Sn4+ 50 Sb 51 Sb3+ 51 + Sb5+ 51 Te 52 I 53 I1- 53 Xe 54 + Cs 55 Cs1+ 55 Ba 56 Ba2+ 56 La 57 + La3+ 57 Ce 58 Ce3+ 58 Ce4+ 58 Pr 59 + Pr3+ 59 Pr4+ 59 Nd 60 Nd3+ 60 Pm 61 + Sm 62 Sm3+ 62 Eu 63 Eu2+ 63 Eu3+ 63 + Gd 64 Gd3+ 64 Tb 65 Tb3+ 65 Dy 66 + Dy3+ 66 Ho 67 Ho3+ 67 Er 68 Er3+ 68 + Tm 69 Tm3+ 69 Yb 70 Yb2+ 70 Yb3+ 70 + Lu 71 Lu3+ 71 Hf 72 Hf4+ 72 Ta 73 + Ta5+ 73 W 74 W6+ 74 Re 75 Os 76 + Os4+ 76 Ir 77 Ir3+ 77 Ir4+ 77 Pt 78 + Pt2+ 78 Pt4+ 78 Au 79 Au1+ 79 Au3+ 79 + Hg 80 Hg1+ 80 Hg2+ 80 Tl 81 TL1+ 81 + Tl3+ 81 Pb 82 Pb2+ 82 Pb4+ 82 Bi 83 + Bi3+ 83 Bi5+ 83 Po 84 At 85 Rn 86 + Fr 87 Ra 88 Ra2+ 88 Ac 89 Ac3+ 89 + Th 90 Th4+ 90 Pa 91 U 92 U3+ 92 + U4+ 92 U6+ 92 Np 93 Np3+ 93 Np4+ 93 + Np6+ 93 Pu 94 Pu3+ 94 Pu4+ 94 Pu6+ 94 + Am 95 Cm 96 Bk 97 Cf 98 + save_ + + +save_electron_count + loop_ + _enumeration_default.index + _enumeration_default.value + H 01 D 01 H1- 02 He 02 Li 03 + Li1+ 02 Be 04 Be2+ 02 B 05 C 06 + N 07 O 08 O1- 09 F 09 F1- 10 + Ne 10 Na 11 Na1+ 10 Mg 12 Mg2+ 10 + Al 13 Al3+ 10 Si 14 Si4+ 10 P 15 + S 16 Cl 17 Cl1- 18 Ar 18 K 19 + K1+ 18 Ca 20 Ca2+ 18 Sc 21 Sc3+ 18 + Ti 22 Ti2+ 20 Ti3+ 19 Ti4+ 18 V 23 + V2+ 21 V3+ 20 V5+ 18 Cr 24 Cr2+ 22 + Cr3+ 21 Mn 25 Mn2+ 23 Mn3+ 22 Mn4+ 21 + Fe 26 Fe2+ 24 Fe3+ 23 Co 27 Co2+ 25 + Co3+ 24 Ni 28 Ni2+ 26 Ni3+ 25 Cu 29 + Cu1+ 28 Cu2+ 27 Zn 30 Zn2+ 28 Ga 31 + Ga3+ 28 Ge 32 Ge4+ 28 As 33 Se 34 + Br 35 Br1- 36 Kr 36 Rb 37 Rb1+ 36 + Sr 38 Sr2+ 36 Y 39 Y3+ 36 Zr 40 + Zr4+ 36 Nb 41 Nb3+ 38 Nb5+ 36 Mo 42 + Mo3+ 39 Mo5+ 37 Mo6+ 36 Tc 43 Ru 44 + Ru3+ 41 Ru4+ 40 Rh 45 Rh3+ 42 Rh4+ 41 + Pd 46 Pd2+ 44 Pd4+ 42 Ag 47 Ag1+ 46 + Ag2+ 45 Cd 48 Cd2+ 46 In 49 In3+ 46 + Sn 50 Sn2+ 48 Sn4+ 46 Sb 51 Sb3+ 48 + Sb5+ 46 Te 52 I 53 I1- 54 Xe 54 + Cs 55 Cs1+ 54 Ba 56 Ba2+ 54 La 57 + La3+ 54 Ce 58 Ce3+ 55 Ce4+ 54 Pr 59 + Pr3+ 56 Pr4+ 55 Nd 60 Nd3+ 57 Pm 61 + Sm 62 Sm3+ 59 Eu 63 Eu2+ 61 Eu3+ 60 + Gd 64 Gd3+ 61 Tb 65 Tb3+ 62 Dy 66 + Dy3+ 63 Ho 67 Ho3+ 64 Er 68 Er3+ 65 + Tm 69 Tm3+ 66 Yb 70 Yb2+ 68 Yb3+ 67 + Lu 71 Lu3+ 68 Hf 72 Hf4+ 68 Ta 73 + Ta5+ 68 W 74 W6+ 68 Re 75 Os 76 + Os4+ 72 Ir 77 Ir3+ 74 Ir4+ 73 Pt 78 + Pt2+ 76 Pt4+ 74 Au 79 Au1+ 78 Au3+ 76 + Hg 80 Hg1+ 79 Hg2+ 78 Tl 81 TL1+ 80 + Tl3+ 78 Pb 82 Pb2+ 80 Pb4+ 78 Bi 83 + Bi3+ 80 Bi5+ 78 Po 84 At 85 Rn 86 + Fr 87 Ra 88 Ra2+ 86 Ac 89 Ac3+ 86 + Th 90 Th4+ 86 Pa 91 U 92 U3+ 89 + U4+ 88 U6+ 84 Np 93 Np3+ 90 Np4+ 89 + Np6+ 87 Pu 94 Pu3+ 91 Pu4+ 90 Pu6+ 88 + Am 95 Cm 96 Bk 97 Cf 98 + save_ + + +save_ion_to_element + loop_ + _enumeration_default.index + _enumeration_default.value + H H D D H1- H He He Li Li + Li1+ Li Be Be Be2+ Be B B C C + N N O O O1- O F F F1- F + Ne Ne Na Na Na1+ Na Mg Mg Mg2+ Mg + Al Al Al3+ Al Si Si Si4+ Si P P + S S Cl Cl Cl1- Cl Ar Ar K K + K1+ K Ca Ca Ca2+ Ca Sc Sc Sc3+ Sc + Ti Ti Ti2+ Ti Ti3+ Ti Ti4+ Ti V V + V2+ V V3+ V V5+ V Cr Cr Cr2+ Cr + Cr3+ Cr Mn Mn Mn2+ Mn Mn3+ Mn Mn4+ Mn + Fe Fe Fe2+ Fe Fe3+ Fe Co Co Co2+ Co + Co3+ Co Ni Ni Ni2+ Ni Ni3+ Ni Cu Cu + Cu1+ Cu Cu2+ Cu Zn Zn Zn2+ Zn Ga Ga + Ga3+ Ga Ge Ge Ge4+ Ge As As Se Se + Br Br Br1- Br Kr Kr Rb Rb Rb1+ Rb + Sr Sr Sr2+ Sr Y Y Y3+ Y Zr Zr + Zr4+ Zr Nb Nb Nb3+ Nb Nb5+ Nb Mo Mo + Mo3+ Mo Mo5+ Mo Mo6+ Mo Tc Tc Ru Ru + Ru3+ Ru Ru4+ Ru Rh Rh Rh3+ Rh Rh4+ Rh + Pd Pd Pd2+ Pd Pd4+ Pd Ag Ag Ag1+ Ag + Ag2+ Ag Cd Cd Cd2+ Cd In In In3+ In + Sn Sn Sn2+ Sn Sn4+ Sn Sb Sb Sb3+ Sb + Sb5+ Sb Te Te I I I1- I Xe Xe + Cs Cs Cs1+ Cs Ba Ba Ba2+ Ba La La + La3+ La Ce Ce Ce3+ Ce Ce4+ Ce Pr Pr + Pr3+ Pr Pr4+ Pr Nd Nd Nd3+ Nd Pm Pm + Sm Sm Sm3+ Sm Eu Eu Eu2+ Eu Eu3+ Eu + Gd Gd Gd3+ Gd Tb Tb Tb3+ Tb Dy Dy + Dy3+ Dy Ho Ho Ho3+ Ho Er Er Er3+ Er + Tm Tm Tm3+ Tm Yb Yb Yb2+ Yb Yb3+ Yb + Lu Lu Lu3+ Lu Hf Hf Hf4+ Hf Ta Ta + Ta5+ Ta W W W6+ W Re Re Os Os + Os4+ Os Ir Ir Ir3+ Ir Ir4+ Ir Pt Pt + Pt2+ Pt Pt4+ Pt Au Au Au1+ Au Au3+ Au + Hg Hg Hg1+ Hg Hg2+ Hg Tl Tl TL1+ Tl + Tl3+ Tl Pb Pb Pb2+ Pb Pb4+ Pb Bi Bi + Bi3+ Bi Bi5+ Bi Po Po At At Rn Rn + Fr Fr Ra Ra Ra2+ Ra Ac Ac Ac3+ Ac + Th Th Th4+ Th Pa Pa U U U3+ U + U4+ U U6+ U Np Np Np3+ Np Np4+ Np + Np6+ Np Pu Pu Pu3+ Pu Pu4+ Pu Pu6+ Pu + Am Am Cm Cm Bk Bk Cf Cf + save_ + + +save_atomic_mass + loop_ + _enumeration_default.index + _enumeration_default.value + H 1.008 D 2.008 H1- 1.008 He 4.003 Li 6.941 + Li1+ 6.941 Be 9.012 Be2+ 9.012 B 10.811 C 12.011 + N 14.007 O 15.999 O1- 15.999 F 18.998 F1- 18.998 + Ne 20.179 Na 22.990 Na1+ 22.990 Mg 24.305 Mg2+ 24.305 + Al 26.982 Al3+ 26.982 Si 28.086 Si4+ 28.086 P 30.974 + S 32.066 Cl 35.453 Cl1- 35.453 Ar 39.948 K 39.098 + K1+ 39.098 Ca 40.078 Ca2+ 40.078 Sc 44.956 Sc3+ 44.956 + Ti 47.88 Ti2+ 47.88 Ti3+ 47.88 Ti4+ 47.88 V 50.942 + V2+ 50.942 V3+ 50.942 V5+ 50.942 Cr 51.996 Cr2+ 51.996 + Cr3+ 51.996 Mn 54.938 Mn2+ 54.938 Mn3+ 54.938 Mn4+ 54.938 + Fe 55.847 Fe2+ 55.847 Fe3+ 55.847 Co 58.933 Co2+ 58.933 + Co3+ 58.933 Ni 58.69 Ni2+ 58.69 Ni3+ 58.69 Cu 63.546 + Cu1+ 63.546 Cu2+ 63.546 Zn 65.39 Zn2+ 65.39 Ga 69.723 + Ga3+ 69.723 Ge 72.59 Ge4+ 72.59 As 74.922 Se 78.96 + Br 79.904 Br1- 79.904 Kr 83.80 Rb 85.468 Rb1+ 85.468 + Sr 87.62 Sr2+ 87.62 Y 88.906 Y3+ 88.906 Zr 91.224 + Zr4+ 91.224 Nb 92.906 Nb3+ 92.906 Nb5+ 92.906 Mo 95.94 + Mo3+ 95.94 Mo5+ 95.94 Mo6+ 95.94 Tc 98.906 Ru 101.07 + Ru3+ 101.07 Ru4+ 101.07 Rh 102.906 Rh3+ 102.906 Rh4+ 102.906 + Pd 106.42 Pd2+ 106.42 Pd4+ 106.42 Ag 107.868 Ag1+ 107.868 + Ag2+ 107.868 Cd 112.41 Cd2+ 112.41 In 114.82 In3+ 114.82 + Sn 118.71 Sn2+ 118.71 Sn4+ 118.71 Sb 121.75 Sb3+ 121.75 + Sb5+ 121.75 Te 127.60 I 126.905 I1- 126.905 Xe 131.29 + Cs 132.905 Cs1+ 132.905 Ba 137.33 Ba2+ 137.33 La 138.906 + La3+ 138.906 Ce 140.12 Ce3+ 140.12 Ce4+ 140.12 Pr 140.908 + Pr3+ 140.908 Pr4+ 140.908 Nd 144.24 Nd3+ 144.24 Pm 147. + Sm 150.36 Sm3+ 150.36 Eu 151.96 Eu2+ 151.96 Eu3+ 151.96 + Gd 157.25 Gd3+ 157.25 Tb 158.926 Tb3+ 158.926 Dy 162.5 + Dy3+ 162.5 Ho 164.93 Ho3+ 164.93 Er 167.26 Er3+ 167.26 + Tm 168.934 Tm3+ 168.934 Yb 173.04 Yb2+ 173.04 Yb3+ 173.04 + Lu 174.967 Lu3+ 174.967 Hf 178.49 Hf4+ 178.49 Ta 180.948 + Ta5+ 180.948 W 183.85 W6+ 183.85 Re 186.207 Os 190.2 + Os4+ 190.2 Ir 192.22 Ir3+ 192.22 Ir4+ 192.22 Pt 195.08 + Pt2+ 195.08 Pt4+ 195.08 Au 196.966 Au1+ 196.966 Au3+ 196.966 + Hg 200.59 Hg1+ 200.59 Hg2+ 200.59 Tl 204.383 TL1+ 204.383 + Tl3+ 204.383 Pb 207.2 Pb2+ 207.2 Pb4+ 207.2 Bi 208.980 + Bi3+ 208.980 Bi5+ 208.980 Po 209. At 210. Rn 222. + Fr 223. Ra 226.025 Ra2+ 226.025 Ac 227. Ac3+ 227. + Th 232.038 Th4+ 232.038 Pa 231.036 U 238.029 U3+ 238.029 + U4+ 238.029 U6+ 238.029 Np 237.048 Np3+ 237.048 Np4+ 237.048 + Np6+ 237.048 Pu 242. Pu3+ 242. Pu4+ 242. Pu6+ 242. + Am 243. Cm 247. Bk 247. Cf 249. + save_ + + +save_radius_bond + loop_ + _enumeration_default.index + _enumeration_default.value + H 0.37 D 0.37 H1- 0.37 He 0.40 Li 1.23 + Li1+ 1.23 Be 0.89 Be2+ 0.89 B 0.80 C 0.77 + N 0.74 O 0.74 O1- 0.74 F 0.72 F1- 0.72 + Ne 0.72 Na 1.57 Na1+ 1.57 Mg 1.36 Mg2+ 1.36 + Al 1.25 Al3+ 1.25 Si 1.17 Si4+ 1.17 P 1.10 + S 1.04 Cl 0.99 Cl1- 0.99 Ar 1.00 K 2.03 + K1+ 2.03 Ca 1.74 Ca2+ 1.74 Sc 1.44 Sc3+ 1.44 + Ti 1.35 Ti2+ 1.35 Ti3+ 1.35 Ti4+ 1.35 V 1.22 + V2+ 1.22 V3+ 1.22 V5+ 1.22 Cr 1.17 Cr2+ 1.17 + Cr3+ 1.17 Mn 1.17 Mn2+ 1.17 Mn3+ 1.17 Mn4+ 1.17 + Fe 1.17 Fe2+ 1.17 Fe3+ 1.17 Co 1.16 Co2+ 1.16 + Co3+ 1.16 Ni 1.15 Ni2+ 1.15 Ni3+ 1.15 Cu 1.17 + Cu1+ 1.17 Cu2+ 1.17 Zn 1.25 Zn2+ 1.25 Ga 1.25 + Ga3+ 1.25 Ge 1.22 Ge4+ 1.22 As 1.21 Se 1.17 + Br 1.14 Br1- 1.14 Kr 1.14 Rb 2.16 Rb1+ 2.16 + Sr 1.91 Sr2+ 1.91 Y 1.62 Y3+ 1.62 Zr 1.45 + Zr4+ 1.45 Nb 1.34 Nb3+ 1.34 Nb5+ 1.34 Mo 1.29 + Mo3+ 1.29 Mo5+ 1.29 Mo6+ 1.29 Tc 1.27 Ru 1.24 + Ru3+ 1.24 Ru4+ 1.24 Rh 1.25 Rh3+ 1.25 Rh4+ 1.25 + Pd 1.28 Pd2+ 1.28 Pd4+ 1.28 Ag 1.34 Ag1+ 1.34 + Ag2+ 1.34 Cd 1.41 Cd2+ 1.41 In 1.50 In3+ 1.50 + Sn 1.41 Sn2+ 1.41 Sn4+ 1.41 Sb 1.41 Sb3+ 1.41 + Sb5+ 1.41 Te 1.37 I 1.33 I1- 1.33 Xe 1.33 + Cs 2.35 Cs1+ 2.35 Ba 1.98 Ba2+ 1.98 La 1.69 + La3+ 1.69 Ce 1.65 Ce3+ 1.65 Ce4+ 1.65 Pr 1.65 + Pr3+ 1.65 Pr4+ 1.65 Nd 1.64 Nd3+ 1.64 Pm 1.63 + Sm 1.66 Sm3+ 1.66 Eu 1.85 Eu2+ 1.85 Eu3+ 1.85 + Gd 1.61 Gd3+ 1.61 Tb 1.59 Tb3+ 1.59 Dy 1.59 + Dy3+ 1.59 Ho 1.58 Ho3+ 1.58 Er 1.57 Er3+ 1.57 + Tm 1.56 Tm3+ 1.56 Yb 1.70 Yb2+ 1.70 Yb3+ 1.70 + Lu 1.56 Lu3+ 1.56 Hf 1.44 Hf4+ 1.44 Ta 1.34 + Ta5+ 1.34 W 1.30 W6+ 1.30 Re 1.28 Os 1.26 + Os4+ 1.26 Ir 1.26 Ir3+ 1.26 Ir4+ 1.26 Pt 1.29 + Pt2+ 1.29 Pt4+ 1.29 Au 1.34 Au1+ 1.34 Au3+ 1.34 + Hg 1.44 Hg1+ 1.44 Hg2+ 1.44 Tl 1.55 TL1+ 1.55 + Tl3+ 1.55 Pb 1.54 Pb2+ 1.54 Pb4+ 1.54 Bi 1.52 + Bi3+ 1.52 Bi5+ 1.52 Po 1.53 At 1.53 Rn 1.53 + Fr 1.53 Ra 1.53 Ra2+ 1.53 Ac 1.53 Ac3+ 1.53 + Th 1.65 Th4+ 1.65 Pa 1.53 U 1.42 U3+ 1.42 + U4+ 1.42 U6+ 1.42 Np 1.42 Np3+ 1.42 Np4+ 1.42 + Np6+ 1.42 Pu 1.42 Pu3+ 1.42 Pu4+ 1.42 Pu6+ 1.42 + Am 1.42 Cm 1.42 Bk 1.42 Cf 1.42 + save_ + + +save_length_neutron + loop_ + _enumeration_default.index + _enumeration_default.value + H -3.739 D 6.671 H1- -3.739 He 3.26 Li -1.90 + Li1+ -1.90 Be 7.79 Be2+ 7.79 B 5.30 C 6.646 + N 9.36 O 5.803 O1- 5.803 F 5.654 F1- 5.654 + Ne 4.547 Na 3.63 Na1+ 3.63 Mg 5.375 Mg2+ 5.375 + Al 3.449 Al3+ 3.449 Si 4.149 Si4+ 4.149 P 5.13 + S 2.847 Cl 9.577 Cl1- 9.577 Ar 1.909 K 3.71 + K1+ 3.71 Ca 4.90 Ca2+ 4.90 Sc 12.29 Sc3+ 12.29 + Ti -3.438 Ti2+ -3.438 Ti3+ -3.438 Ti4+ -3.438 V -0.3824 + V2+ -0.382 V3+ -0.382 V5+ -0.382 Cr 3.635 Cr2+ 3.635 + Cr3+ 3.635 Mn -3.73 Mn2+ -3.73 Mn3+ -3.73 Mn4+ -3.73 + Fe 9.54 Fe2+ 9.54 Fe3+ 9.54 Co 2.50 Co2+ 2.50 + Co3+ 2.50 Ni 10.3 Ni2+ 10.3 Ni3+ 10.3 Cu 7.718 + Cu1+ 7.718 Cu2+ 7.718 Zn 5.689 Zn2+ 5.689 Ga 7.287 + Ga3+ 7.287 Ge 8.192 Ge4+ 8.192 As 6.58 Se 7.970 + Br 6.795 Br1- 6.795 Kr 7.80 Rb 7.08 Rb1+ 7.08 + Sr 7.02 Sr2+ 7.02 Y 7.75 Y3+ 7.75 Zr 7.16 + Zr4+ 7.16 Nb 7.054 Nb3+ 7.054 Nb5+ 7.054 Mo 6.95 + Mo3+ 6.95 Mo5+ 6.95 Mo6+ 6.95 Tc 6.8 Ru 7.21 + Ru3+ 7.21 Ru4+ 7.21 Rh 5.88 Rh3+ 5.88 Rh4+ 5.88 + Pd 5.91 Pd2+ 5.91 Pd4+ 5.91 Ag 5.922 Ag1+ 5.922 + Ag2+ 5.922 Cd 5.1 Cd2+ 5.1 In 4.065 In3+ 4.065 + Sn 6.225 Sn2+ 6.225 Sn4+ 6.225 Sb 5.57 Sb3+ 5.57 + Sb5+ 5.57 Te 5.80 I 5.28 I1- 5.28 Xe 4.85 + Cs 5.42 Cs1+ 5.42 Ba 5.06 Ba2+ 5.06 La 8.24 + La3+ 8.24 Ce 4.84 Ce3+ 4.84 Ce4+ 4.84 Pr 4.45 + Pr3+ 4.45 Pr4+ 4.45 Nd 7.69 Nd3+ 7.69 Pm 12.6 + Sm 4.2 Sm3+ 4.2 Eu 6.73 Eu2+ 6.73 Eu3+ 6.73 + Gd 9.5 Gd3+ 9.5 Tb 7.38 Tb3+ 7.38 Dy 16.9 + Dy3+ 16.9 Ho 8.08 Ho3+ 8.08 Er 8.03 Er3+ 8.03 + Tm 7.07 Tm3+ 7.07 Yb 12.41 Yb2+ 12.41 Yb3+ 12.41 + Lu 7.21 Lu3+ 7.21 Hf 7.77 Hf4+ 7.77 Ta 6.91 + Ta5+ 6.91 W 4.77 W6+ 4.77 Re 9.2 Os 11.0 + Os4+ 11.0 Ir 10.6 Ir3+ 10.6 Ir4+ 10.6 Pt 9.60 + Pt2+ 9.60 Pt4+ 9.60 Au 7.63 Au1+ 7.63 Au3+ 7.63 + Hg 12.692 Hg1+ 12.692 Hg2+ 12.692 Tl 8.776 TL1+ 8.776 + Tl3+ 8.776 Pb 9.401 Pb2+ 9.401 Pb4+ 9.401 Bi 8.530 + Bi3+ 8.530 Bi5+ 8.530 Po 0. At 0. Rn 0. + Fr 0. Ra 10.0 Ra2+ 10.0 Ac 0. Ac3+ 0. + Th 10.63 Th4+ 10.63 Pa 9.1 U 8.417 U3+ 8.417 + U4+ 8.417 U6+ 8.417 Np 10.55 Np3+ 10.55 Np4+ 10.55 + Np6+ 10.55 Pu 14.1 Pu3+ 14.1 Pu4+ 14.1 Pu6+ 14.1 + Am 8.3 Cm 9.5 Bk 9.5 Cf 0. + save_ + + +save_dispersion_real_cu + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He .0 Li .001 + Li1+ .001 Be .003 Be2+ .003 B .008 C .017 + N .029 O .047 O1- .047 F .069 F1- .069 + Ne .097 Na 0.129 Na1+ 0.129 Mg .165 Mg2+ .165 + Al .204 Al3+ .204 Si .244 Si4+ .244 P .283 + S .319 Cl .348 Cl1- .348 Ar .366 K .365 + K1+ .365 Ca .341 Ca2+ .341 Sc 0.285 Sc3+ 0.285 + Ti .189 Ti2+ .189 Ti3+ .189 Ti4+ .189 V .035 + V2+ .035 V3+ .035 V5+ .035 Cr -.198 Cr2+ -.198 + Cr3+ -.198 Mn -.568 Mn2+ -.568 Mn3+ -.568 Mn4+ -.568 + Fe -1.179 Fe2+ -1.179 Fe3+ -1.179 Co -2.464 Co2+ -2.464 + Co3+ -2.464 Ni -2.956 Ni2+ -2.956 Ni3+ -2.956 Cu -2.019 + Cu1+ -2.019 Cu2+ -2.019 Zn -1.612 Zn2+ -1.612 Ga -1.354 + Ga3+ -1.354 Ge -1.163 Ge4+ -1.163 As -1.011 Se -.879 + Br -.767 Br1- -.767 Kr -.665 Rb -.574 Rb1+ -.574 + Sr -.465 Sr2+ -.465 Y -.386 Y3+ -.386 Zr -.314 + Zr4+ -.314 Nb -.248 Nb3+ -.248 Nb5+ -.248 Mo -.191 + Mo3+ -.191 Mo5+ -.191 Mo6+ -.191 Tc -.145 Ru -.105 + Ru3+ -.105 Ru4+ -.105 Rh -.077 Rh3+ -.077 Rh4+ -.077 + Pd -.059 Pd2+ -.059 Pd4+ -.059 Ag -.06 Ag1+ -.06 + Ag2+ -.06 Cd -.079 Cd2+ -.079 In -.126 In3+ -.126 + Sn -.194 Sn2+ -.194 Sn4+ -.194 Sb -.287 Sb3+ -.287 + Sb5+ -.287 Te -.418 I -.579 I1- -.579 Xe -.783 + Cs -1.022 Cs1+ -1.022 Ba -1.334 Ba2+ -1.334 La -1.716 + La3+ -1.716 Ce -2.17 Ce3+ -2.17 Ce4+ -2.17 Pr -2.939 + Pr3+ -2.939 Pr4+ -2.939 Nd -3.431 Nd3+ -3.431 Pm -4.357 + Sm -5.696 Sm3+ -5.696 Eu -7.718 Eu2+ -7.718 Eu3+ -7.718 + Gd -9.242 Gd3+ -9.242 Tb -9.498 Tb3+ -9.498 Dy -10.423 + Dy3+ -10.423 Ho -12.255 Ho3+ -12.255 Er -9.733 Er3+ -9.733 + Tm -8.488 Tm3+ -8.488 Yb -7.701 Yb2+ -7.701 Yb3+ -7.701 + Lu -7.133 Lu3+ -7.133 Hf -6.715 Hf4+ -6.715 Ta -6.351 + Ta5+ -6.351 W -6.048 W6+ -6.048 Re -5.79 Os -5.581 + Os4+ -5.581 Ir -5.391 Ir3+ -5.391 Ir4+ -5.391 Pt -5.233 + Pt2+ -5.233 Pt4+ -5.233 Au -5.096 Au1+ -5.096 Au3+ -5.096 + Hg -4.99 Hg1+ -4.99 Hg2+ -4.99 Tl -4.883 TL1+ -4.883 + Tl3+ -4.883 Pb -4.818 Pb2+ -4.818 Pb4+ -4.818 Bi -4.776 + Bi3+ -4.776 Bi5+ -4.776 Po -4.756 At -4.772 Rn -4.787 + Fr -4.833 Ra -4.898 Ra2+ -4.898 Ac -4.994 Ac3+ -4.994 + Th -5.091 Th4+ -5.091 Pa -5.216 U -5.359 U3+ -5.359 + U4+ -5.359 U6+ -5.359 Np -5.529 Np3+ -5.529 Np4+ -5.529 + Np6+ -5.529 Pu -5.712 Pu3+ -5.712 Pu4+ -5.712 Pu6+ -5.712 + Am -5.93 Cm -6.176 Bk -6.498 Cf -6.798 + save_ + + +save_dispersion_imag_cu + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He .0 Li .0 + Li1+ .0 Be .001 Be2+ .001 B .004 C .009 + N .018 O .032 O1- .032 F .053 F1- .053 + Ne .083 Na .124 Na1+ .124 Mg .177 Mg2+ .177 + Al .246 Al3+ .246 Si .33 Si4+ .33 P .434 + S .557 Cl .702 Cl1- .702 Ar .872 K 1.066 + K1+ 1.066 Ca 1.286 Ca2+ 1.286 Sc 1.533 Sc3+ 1.533 + Ti 1.807 Ti2+ 1.807 Ti3+ 1.807 Ti4+ 1.807 V 2.11 + V2+ 2.11 V3+ 2.11 V5+ 2.11 Cr 2.443 Cr2+ 2.443 + Cr3+ 2.443 Mn 2.808 Mn2+ 2.808 Mn3+ 2.808 Mn4+ 2.808 + Fe 3.204 Fe2+ 3.204 Fe3+ 3.204 Co 3.608 Co2+ 3.608 + Co3+ 3.608 Ni .509 Ni2+ .509 Ni3+ .509 Cu .589 + Cu1+ .589 Cu2+ .589 Zn .678 Zn2+ .678 Ga 0.777 + Ga3+ 0.777 Ge .886 Ge4+ .886 As 1.006 Se 1.139 + Br 1.283 Br1- 1.283 Kr 1.439 Rb 1.608 Rb1+ 1.608 + Sr 1.82 Sr2+ 1.82 Y 2.025 Y3+ 2.025 Zr 2.245 + Zr4+ 2.245 Nb 2.482 Nb3+ 2.482 Nb5+ 2.482 Mo 2.735 + Mo3+ 2.735 Mo5+ 2.735 Mo6+ 2.735 Tc 3.005 Ru 3.296 + Ru3+ 3.296 Ru4+ 3.296 Rh 3.605 Rh3+ 3.605 Rh4+ 3.605 + Pd 3.934 Pd2+ 3.934 Pd4+ 3.934 Ag 4.282 Ag1+ 4.282 + Ag2+ 4.282 Cd 4.653 Cd2+ 4.653 In 5.045 In3+ 5.045 + Sn 5.459 Sn2+ 5.459 Sn4+ 5.459 Sb 5.894 Sb3+ 5.894 + Sb5+ 5.894 Te 6.352 I 6.835 I1- 6.835 Xe 7.348 + Cs 7.904 Cs1+ 7.904 Ba 8.46 Ba2+ 8.46 La 9.036 + La3+ 9.036 Ce 9.648 Ce3+ 9.648 Ce4+ 9.648 Pr 10.535 + Pr3+ 10.535 Pr4+ 10.535 Nd 10.933 Nd3+ 10.933 Pm 11.614 + Sm 12.32 Sm3+ 12.32 Eu 11.276 Eu2+ 11.276 Eu3+ 11.276 + Gd 11.946 Gd3+ 11.946 Tb 9.242 Tb3+ 9.242 Dy 9.748 + Dy3+ 9.748 Ho 3.704 Ho3+ 3.704 Er 3.937 Er3+ 3.937 + Tm 4.181 Tm3+ 4.181 Yb 4.432 Yb2+ 4.432 Yb3+ 4.432 + Lu 4.693 Lu3+ 4.693 Hf 4.977 Hf4+ 4.977 Ta 5.271 + Ta5+ 5.271 W 5.577 W6+ 5.577 Re 5.891 Os 6.221 + Os4+ 6.221 Ir 6.566 Ir3+ 6.566 Ir4+ 6.566 Pt 6.925 + Pt2+ 6.925 Pt4+ 6.925 Au 7.297 Au1+ 7.297 Au3+ 7.297 + Hg 7.686 Hg1+ 7.686 Hg2+ 7.686 Tl 8.089 TL1+ 8.089 + Tl3+ 8.089 Pb 8.505 Pb2+ 8.505 Pb4+ 8.505 Bi 8.93 + Bi3+ 8.93 Bi5+ 8.93 Po 9.383 At 9.843 Rn 10.317 + Fr 10.803 Ra 11.296 Ra2+ 11.296 Ac 11.799 Ac3+ 11.799 + Th 12.33 Th4+ 12.33 Pa 12.868 U 13.409 U3+ 13.409 + U4+ 13.409 U6+ 13.409 Np 13.967 Np3+ 13.967 Np4+ 13.967 + Np6+ 13.967 Pu 14.536 Pu3+ 14.536 Pu4+ 14.536 Pu6+ 14.536 + Am 15.087 Cm 15.634 Bk 16.317 Cf 16.93 + save_ + + +save_dispersion_real_mo + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He .0 Li .0 + Li1+ .0 Be .0 Be2+ .0 B .0 C .002 + N .004 O .008 O1- .008 F .014 F1- .014 + Ne .021 Na 0.03 Na1+ 0.03 Mg .042 Mg2+ .042 + Al .056 Al3+ .056 Si .072 Si4+ .072 P .09 + S .11 Cl .132 Cl1- .132 Ar .155 K .179 + K1+ .179 Ca .203 Ca2+ .203 Sc 0.226 Sc3+ 0.226 + Ti .248 Ti2+ .248 Ti3+ .248 Ti4+ .248 V .267 + V2+ .267 V3+ .267 V5+ .267 Cr .284 Cr2+ .284 + Cr3+ .284 Mn .295 Mn2+ .295 Mn3+ .295 Mn4+ .295 + Fe .301 Fe2+ .301 Fe3+ .301 Co .299 Co2+ .299 + Co3+ .299 Ni .285 Ni2+ .285 Ni3+ .285 Cu .263 + Cu1+ .263 Cu2+ .263 Zn .222 Zn2+ .222 Ga 0.163 + Ga3+ 0.163 Ge .081 Ge4+ .081 As -.03 Se -.178 + Br -.374 Br1- -.374 Kr -.652 Rb -1.044 Rb1+ -1.044 + Sr -1.657 Sr2+ -1.657 Y -2.951 Y3+ -2.951 Zr -2.965 + Zr4+ -2.965 Nb -2.197 Nb3+ -2.197 Nb5+ -2.197 Mo -1.825 + Mo3+ -1.825 Mo5+ -1.825 Mo6+ -1.825 Tc -1.59 Ru -1.42 + Ru3+ -1.42 Ru4+ -1.42 Rh -1.287 Rh3+ -1.287 Rh4+ -1.287 + Pd -1.177 Pd2+ -1.177 Pd4+ -1.177 Ag -1.085 Ag1+ -1.085 + Ag2+ -1.085 Cd -1.005 Cd2+ -1.005 In -.936 In3+ -.936 + Sn -.873 Sn2+ -.873 Sn4+ -.873 Sb -.816 Sb3+ -.816 + Sb5+ -.816 Te -.772 I -.726 I1- -.726 Xe -.684 + Cs -.644 Cs1+ -.644 Ba -.613 Ba2+ -.613 La -.588 + La3+ -.588 Ce -.564 Ce3+ -.564 Ce4+ -.564 Pr -.53 + Pr3+ -.53 Pr4+ -.53 Nd -.535 Nd3+ -.535 Pm -.53 + Sm -.533 Sm3+ -.533 Eu -.542 Eu2+ -.542 Eu3+ -.542 + Gd -.564 Gd3+ -.564 Tb -.591 Tb3+ -.591 Dy -.619 + Dy3+ -.619 Ho -.666 Ho3+ -.666 Er -.723 Er3+ -.723 + Tm -.795 Tm3+ -.795 Yb -.884 Yb2+ -.884 Yb3+ -.884 + Lu -.988 Lu3+ -.988 Hf -1.118 Hf4+ -1.118 Ta -1.258 + Ta5+ -1.258 W -1.421 W6+ -1.421 Re -1.598 Os -1.816 + Os4+ -1.816 Ir -2.066 Ir3+ -2.066 Ir4+ -2.066 Pt -2.352 + Pt2+ -2.352 Pt4+ -2.352 Au -2.688 Au1+ -2.688 Au3+ -2.688 + Hg -3.084 Hg1+ -3.084 Hg2+ -3.084 Tl -3.556 TL1+ -3.556 + Tl3+ -3.556 Pb -4.133 Pb2+ -4.133 Pb4+ -4.133 Bi -4.861 + Bi3+ -4.861 Bi5+ -4.861 Po -5.924 At -7.444 Rn -8.862 + Fr -7.912 Ra -7.62 Ra2+ -7.62 Ac -7.725 Ac3+ -7.725 + Th -8.127 Th4+ -8.127 Pa -8.96 U -10.673 U3+ -10.673 + U4+ -10.673 U6+ -10.673 Np -11.158 Np3+ -11.158 Np4+ -11.158 + Np6+ -11.158 Pu -9.725 Pu3+ -9.725 Pu4+ -9.725 Pu6+ -9.725 + Am -8.926 Cm -8.416 Bk -7.99 Cf -7.683 + save_ + + +save_dispersion_imag_mo + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He .0 Li .0 + Li1+ .0 Be .0 Be2+ .0 B .001 C .002 + N .003 O .006 O1- .006 F .01 F1- .01 + Ne .016 Na .025 Na1+ .025 Mg .036 Mg2+ .036 + Al .052 Al3+ .052 Si .071 Si4+ .071 P .095 + S .124 Cl .159 Cl1- .159 Ar .201 K .25 + K1+ .25 Ca .306 Ca2+ .306 Sc 0.372 Sc3+ 0.372 + Ti .446 Ti2+ .446 Ti3+ .446 Ti4+ .446 V .53 + V2+ .53 V3+ .53 V5+ .53 Cr .624 Cr2+ .624 + Cr3+ .624 Mn .729 Mn2+ .729 Mn3+ .729 Mn4+ .729 + Fe .845 Fe2+ .845 Fe3+ .845 Co .973 Co2+ .973 + Co3+ .973 Ni 1.113 Ni2+ 1.113 Ni3+ 1.113 Cu 1.266 + Cu1+ 1.266 Cu2+ 1.266 Zn 1.431 Zn2+ 1.431 Ga 1.609 + Ga3+ 1.609 Ge 1.801 Ge4+ 1.801 As 2.007 Se 2.223 + Br 2.456 Br1- 2.456 Kr 2.713 Rb 2.973 Rb1+ 2.973 + Sr 3.264 Sr2+ 3.264 Y 3.542 Y3+ 3.542 Zr .56 + Zr4+ .56 Nb 0.621 Nb3+ 0.621 Nb5+ 0.621 Mo .688 + Mo3+ .688 Mo5+ .688 Mo6+ .688 Tc .759 Ru .836 + Ru3+ .836 Ru4+ .836 Rh .919 Rh3+ .919 Rh4+ .919 + Pd 1.007 Pd2+ 1.007 Pd4+ 1.007 Ag 1.101 Ag1+ 1.101 + Ag2+ 1.101 Cd 1.202 Cd2+ 1.202 In 1.31 In3+ 1.31 + Sn 1.424 Sn2+ 1.424 Sn4+ 1.424 Sb 1.546 Sb3+ 1.546 + Sb5+ 1.546 Te 1.675 I 1.812 I1- 1.812 Xe 1.958 + Cs 2.119 Cs1+ 2.119 Ba 2.282 Ba2+ 2.282 La 2.452 + La3+ 2.452 Ce 2.632 Ce3+ 2.632 Ce4+ 2.632 Pr 2.845 + Pr3+ 2.845 Pr4+ 2.845 Nd 3.018 Nd3+ 3.018 Pm 3.225 + Sm 3.442 Sm3+ 3.442 Eu 3.669 Eu2+ 3.669 Eu3+ 3.669 + Gd 3.904 Gd3+ 3.904 Tb 4.151 Tb3+ 4.151 Dy 4.41 + Dy3+ 4.41 Ho 4.678 Ho3+ 4.678 Er 4.958 Er3+ 4.958 + Tm 5.248 Tm3+ 5.248 Yb 5.548 Yb2+ 5.548 Yb3+ 5.548 + Lu 5.858 Lu3+ 5.858 Hf 6.185 Hf4+ 6.185 Ta 6.523 + Ta5+ 6.523 W 6.872 W6+ 6.872 Re 7.232 Os 7.605 + Os4+ 7.605 Ir 7.99 Ir3+ 7.99 Ir4+ 7.99 Pt 8.388 + Pt2+ 8.388 Pt4+ 8.388 Au 8.798 Au1+ 8.798 Au3+ 8.798 + Hg 9.223 Hg1+ 9.223 Hg2+ 9.223 Tl 9.659 TL1+ 9.659 + Tl3+ 9.659 Pb 10.102 Pb2+ 10.102 Pb4+ 10.102 Bi 10.559 + Bi3+ 10.559 Bi5+ 10.559 Po 11.042 At 9.961 Rn 10.403 + Fr 7.754 Ra 8.105 Ra2+ 8.105 Ac 8.472 Ac3+ 8.472 + Th 8.87 Th4+ 8.87 Pa 9.284 U 9.654 U3+ 9.654 + U4+ 9.654 U6+ 9.654 Np 4.148 Np3+ 4.148 Np4+ 4.148 + Np6+ 4.148 Pu 4.33 Pu3+ 4.33 Pu4+ 4.33 Pu6+ 4.33 + Am 4.511 Cm 4.697 Bk 4.908 Cf 5.107 + save_ + + +save_Cromer_Mann_a1 + loop_ + _enumeration_default.index + _enumeration_default.value + H .493002 D .493002 H1- .897661 He 0.8734 Li 1.1282 + Li1+ .6968 Be 1.5919 Be2+ 6.2603 B 2.0545 C 2.31 + N 12.2126 O 3.0485 O1- 4.1916 F 3.5392 F1- 3.6322 + Ne 3.9553 Na 4.7626 Na1+ 3.2565 Mg 5.4204 Mg2+ 3.4988 + Al 6.4202 Al3+ 4.17448 Si 6.2915 Si4+ 4.43918 P 6.4345 + S 6.9053 Cl 11.4604 Cl1- 18.2915 Ar 7.4845 K 8.2186 + K1+ 7.9578 Ca 8.6266 Ca2+ 15.6348 Sc 9.189 Sc3+ 13.4008 + Ti 9.7595 Ti2+ 9.11423 Ti3+ 17.7344 Ti4+ 19.5114 V 10.2971 + V2+ 10.106 V3+ 9.43141 V5+ 15.6887 Cr 10.6406 Cr2+ 9.54034 + Cr3+ 9.6809 Mn 11.2819 Mn2+ 10.8061 Mn3+ 9.84521 Mn4+ 9.96253 + Fe 11.7695 Fe2+ 11.0424 Fe3+ 11.1764 Co 12.2841 Co2+ 11.2296 + Co3+ 10.338 Ni 12.8376 Ni2+ 11.4166 Ni3+ 10.7806 Cu 13.338 + Cu1+ 11.9475 Cu2+ 11.8168 Zn 14.0743 Zn2+ 11.9719 Ga 15.2354 + Ga3+ 12.692 Ge 16.0816 Ge4+ 12.9172 As 16.6723 Se 17.0006 + Br 17.1789 Br1- 17.1718 Kr 17.3555 Rb 17.1784 Rb1+ 17.5816 + Sr 17.5663 Sr2+ 18.0874 Y 17.776 Y3+ 17.9268 Zr 17.8765 + Zr4+ 18.1668 Nb 17.6142 Nb3+ 19.8812 Nb5+ 17.9163 Mo 3.7025 + Mo3+ 21.1664 Mo5+ 21.0149 Mo6+ 17.8871 Tc 19.1301 Ru 19.2674 + Ru3+ 18.5638 Ru4+ 18.5003 Rh 19.2957 Rh3+ 18.8785 Rh4+ 18.8545 + Pd 19.3319 Pd2+ 19.1701 Pd4+ 19.2493 Ag 19.2808 Ag1+ 19.1812 + Ag2+ 19.1643 Cd 19.2214 Cd2+ 19.1514 In 19.1624 In3+ 19.1045 + Sn 19.1889 Sn2+ 19.1094 Sn4+ 18.9333 Sb 19.6418 Sb3+ 18.9755 + Sb5+ 19.8685 Te 19.9644 I 20.1472 I1- 20.2332 Xe 20.2933 + Cs 20.3892 Cs1+ 20.3524 Ba 20.3361 Ba2+ 20.1807 La 20.578 + La3+ 20.2489 Ce 21.1671 Ce3+ 20.8036 Ce4+ 20.3235 Pr 22.044 + Pr3+ 21.3727 Pr4+ 20.9413 Nd 22.6845 Nd3+ 21.961 Pm 23.3405 + Sm 24.0042 Sm3+ 23.1504 Eu 24.6274 Eu2+ 24.0063 Eu3+ 23.7497 + Gd 25.0709 Gd3+ 24.3466 Tb 25.8976 Tb3+ 24.9559 Dy 26.507 + Dy3+ 25.5395 Ho 26.9049 Ho3+ 26.1296 Er 27.6563 Er3+ 26.722 + Tm 28.1819 Tm3+ 27.3083 Yb 28.6641 Yb2+ 28.1209 Yb3+ 27.8917 + Lu 28.9476 Lu3+ 28.4628 Hf 29.144 Hf4+ 28.8131 Ta 29.2024 + Ta5+ 29.1587 W 29.0818 W6+ 29.4936 Re 28.7621 Os 28.1894 + Os4+ 30.419 Ir 27.3049 Ir3+ 30.4156 Ir4+ 30.7058 Pt 27.0059 + Pt2+ 29.8429 Pt4+ 30.9612 Au 16.8819 Au1+ 28.0109 Au3+ 30.6886 + Hg 20.6809 Hg1+ 25.0853 Hg2+ 29.5641 Tl 27.5446 TL1+ 21.3985 + Tl3+ 30.8695 Pb 31.0617 Pb2+ 21.7886 Pb4+ 32.1244 Bi 33.3689 + Bi3+ 21.8053 Bi5+ 33.5364 Po 34.6726 At 35.3163 Rn 35.5631 + Fr 35.9299 Ra 35.7630 Ra2+ 35.2150 Ac 35.6597 Ac3+ 35.1736 + Th 35.5645 Th4+ 35.1007 Pa 35.8847 U 36.0228 U3+ 35.5747 + U4+ 35.3715 U6+ 34.8509 Np 36.1874 Np3+ 35.7074 Np4+ 35.5103 + Np6+ 35.0136 Pu 36.5254 Pu3+ 35.8400 Pu4+ 35.6493 Pu6+ 35.1736 + Am 36.6706 Cm 36.6488 Bk 36.7881 Cf 36.9185 + save_ + + +save_Cromer_Mann_b1 + loop_ + _enumeration_default.index + _enumeration_default.value + H 10.5109 D 10.5109 H1- 53.1368 He 9.1037 Li 3.9546 + Li1+ 4.6237 Be 43.6427 Be2+ .0027 B 23.2185 C 20.8439 + N .0057 O 13.2771 O1- 12.8573 F 10.2825 F1- 5.27756 + Ne 8.4042 Na 3.285 Na1+ 2.6671 Mg 2.8275 Mg2+ 2.1676 + Al 3.0387 Al3+ 1.93816 Si 2.4386 Si4+ 1.64167 P 1.9067 + S 1.4679 Cl .0104 Cl1- .0066 Ar 0.9072 K 12.7949 + K1+ 12.6331 Ca 10.4421 Ca2+ -.0074 Sc 9.0213 Sc3+ .29854 + Ti 7.8508 Ti2+ 7.5243 Ti3+ .22061 Ti4+ .178847 V 6.8657 + V2+ 6.8818 V3+ 6.39535 V5+ .679003 Cr 6.1038 Cr2+ 5.66078 + Cr3+ 5.59463 Mn 5.3409 Mn2+ 5.2796 Mn3+ 4.91797 Mn4+ 4.8485 + Fe 4.7611 Fe2+ 4.6538 Fe3+ 4.6147 Co 4.2791 Co2+ 4.1231 + Co3+ 3.90969 Ni 3.8785 Ni2+ 3.6766 Ni3+ 3.5477 Cu 3.5828 + Cu1+ 3.3669 Cu2+ 3.37484 Zn 3.2655 Zn2+ 2.9946 Ga 3.0669 + Ga3+ 2.81262 Ge 2.8509 Ge4+ 2.53718 As 2.6345 Se 2.4098 + Br 2.1723 Br1- 2.2059 Kr 1.9384 Rb 1.7888 Rb1+ 1.7139 + Sr 1.5564 Sr2+ 1.4907 Y 1.4029 Y3+ 1.35417 Zr 1.27618 + Zr4+ 1.2148 Nb 1.18865 Nb3+ .019175 Nb5+ 1.12446 Mo .2772 + Mo3+ .014734 Mo5+ .014345 Mo6+ 1.03649 Tc .864132 Ru .80852 + Ru3+ .847329 Ru4+ .844582 Rh .751536 Rh3+ .764252 Rh4+ .760825 + Pd .698655 Pd2+ .696219 Pd4+ .683839 Ag .6446 Ag1+ .646179 + Ag2+ .645643 Cd .5946 Cd2+ .597922 In .5476 In3+ .551522 + Sn 5.8303 Sn2+ .5036 Sn4+ 5.764 Sb 5.3034 Sb3+ .467196 + Sb5+ 5.44853 Te 4.81742 I 4.347 I1- 4.3579 Xe 3.9282 + Cs 3.569 Cs1+ 3.552 Ba 3.216 Ba2+ 3.21367 La 2.94817 + La3+ 2.9207 Ce 2.81219 Ce3+ 2.77691 Ce4+ 2.65941 Pr 2.77393 + Pr3+ 2.6452 Pr4+ 2.54467 Nd 2.66248 Nd3+ 2.52722 Pm 2.5627 + Sm 2.47274 Sm3+ 2.31641 Eu 2.3879 Eu2+ 2.27783 Eu3+ 2.22258 + Gd 2.25341 Gd3+ 2.13553 Tb 2.24256 Tb3+ 2.05601 Dy 2.1802 + Dy3+ 1.9804 Ho 2.07051 Ho3+ 1.91072 Er 2.07356 Er3+ 1.84659 + Tm 2.02859 Tm3+ 1.78711 Yb 1.9889 Yb2+ 1.78503 Yb3+ 1.73272 + Lu 1.90182 Lu3+ 1.68216 Hf 1.83262 Hf4+ 1.59136 Ta 1.77333 + Ta5+ 1.50711 W 1.72029 W6+ 1.42755 Re 1.67191 Os 1.62903 + Os4+ 1.37113 Ir 1.59279 Ir3+ 1.34323 Ir4+ 1.30923 Pt 1.51293 + Pt2+ 1.32927 Pt4+ 1.24813 Au .4611 Au1+ 1.35321 Au3+ 1.2199 + Hg .545 Hg1+ 1.39507 Hg2+ 1.21152 Tl .65515 TL1+ 1.4711 + Tl3+ 1.1008 Pb .6902 Pb2+ 1.3366 Pb4+ 1.00566 Bi .704 + Bi3+ 1.2356 Bi5+ .91654 Po .700999 At .685870 Rn .6631 + Fr .646453 Ra .616341 Ra2+ .604909 Ac .589092 Ac3+ .579689 + Th .563359 Th4+ .555054 Pa .547751 U .5293 U3+ .520480 + U4+ .516598 U6+ .507079 Np .511929 Np3+ .502322 Np4+ .498626 + Np6+ .489810 Pu .499384 Pu3+ .484938 Pu4+ .481422 Pu6+ .473204 + Am .483629 Cm .465154 Bk .451018 Cf .437533 + save_ + + +save_Cromer_Mann_a2 + loop_ + _enumeration_default.index + _enumeration_default.value + H .322912 D .322912 H1- .565616 He 0.6309 Li .7508 + Li1+ .7888 Be 1.1278 Be2+ .8849 B 1.3326 C 1.02 + N 3.1322 O 2.2868 O1- 1.63969 F 2.6412 F1- 3.51057 + Ne 3.1125 Na 3.1736 Na1+ 3.9362 Mg 2.1735 Mg2+ 3.8378 + Al 1.9002 Al3+ 3.3876 Si 3.0353 Si4+ 3.20345 P 4.1791 + S 5.2034 Cl 7.1964 Cl1- 7.2084 Ar 6.6623 K 7.4398 + K1+ 7.4917 Ca 7.3873 Ca2+ 7.9518 Sc 7.3679 Sc3+ 8.0273 + Ti 7.3558 Ti2+ 7.62174 Ti3+ 8.73816 Ti4+ 8.23473 V 7.3511 + V2+ 7.3541 V3+ 7.7419 V5+ 8.14208 Cr 7.3537 Cr2+ 7.7509 + Cr3+ 7.81136 Mn 7.3573 Mn2+ 7.362 Mn3+ 7.87194 Mn4+ 7.97057 + Fe 7.3573 Fe2+ 7.374 Fe3+ 7.3863 Co 7.3409 Co2+ 7.3883 + Co3+ 7.88173 Ni 7.292 Ni2+ 7.4005 Ni3+ 7.75868 Cu 7.1676 + Cu1+ 7.3573 Cu2+ 7.11181 Zn 7.0318 Zn2+ 7.3862 Ga 6.7006 + Ga3+ 6.69883 Ge 6.3747 Ge4+ 6.70003 As 6.0701 Se 5.8196 + Br 5.2358 Br1- 6.3338 Kr 6.7286 Rb 9.6435 Rb1+ 7.6598 + Sr 9.8184 Sr2+ 8.1373 Y 10.2946 Y3+ 9.1531 Zr 10.948 + Zr4+ 10.0562 Nb 12.0144 Nb3+ 18.0653 Nb5+ 13.3417 Mo 17.2356 + Mo3+ 18.2017 Mo5+ 18.0992 Mo6+ 11.175 Tc 11.0948 Ru 12.9182 + Ru3+ 13.2885 Ru4+ 13.1787 Rh 14.3501 Rh3+ 14.1259 Rh4+ 13.9806 + Pd 15.5017 Pd2+ 15.2096 Pd4+ 14.79 Ag 16.6885 Ag1+ 15.9719 + Ag2+ 16.2456 Cd 17.6444 Cd2+ 17.2535 In 18.5596 In3+ 18.1108 + Sn 19.1005 Sn2+ 19.0548 Sn4+ 19.7131 Sb 19.0455 Sb3+ 18.933 + Sb5+ 19.0302 Te 19.0138 I 18.9949 I1- 18.997 Xe 19.0298 + Cs 19.1062 Cs1+ 19.1278 Ba 19.297 Ba2+ 19.1136 La 19.599 + La3+ 19.3763 Ce 19.7695 Ce3+ 19.559 Ce4+ 19.8186 Pr 19.6697 + Pr3+ 19.7491 Pr4+ 20.0539 Nd 19.6847 Nd3+ 19.9339 Pm 19.6095 + Sm 19.4258 Sm3+ 20.2599 Eu 19.0886 Eu2+ 19.9504 Eu3+ 20.3745 + Gd 19.0798 Gd3+ 20.4208 Tb 18.2185 Tb3+ 20.3271 Dy 17.6383 + Dy3+ 20.2861 Ho 17.294 Ho3+ 20.0994 Er 16.4285 Er3+ 19.7748 + Tm 15.8851 Tm3+ 19.332 Yb 15.4345 Yb2+ 17.6817 Yb3+ 18.7614 + Lu 15.2208 Lu3+ 18.121 Hf 15.1726 Hf4+ 18.4601 Ta 15.2293 + Ta5+ 18.8407 W 15.43 W6+ 19.3763 Re 15.7189 Os 16.155 + Os4+ 15.2637 Ir 16.7296 Ir3+ 15.862 Ir4+ 15.5512 Pt 17.7639 + Pt2+ 16.7224 Pt4+ 15.9829 Au 18.5913 Au1+ 17.8204 Au3+ 16.9029 + Hg 19.0417 Hg1+ 18.4973 Hg2+ 18.06 Tl 19.1584 TL1+ 20.4723 + Tl3+ 18.3841 Pb 13.0637 Pb2+ 19.5682 Pb4+ 18.8003 Bi 12.951 + Bi3+ 19.5026 Bi5+ 25.0946 Po 15.4733 At 19.0211 Rn 21.2816 + Fr 23.0547 Ra 22.9064 Ra2+ 21.6700 Ac 23.1032 Ac3+ 22.1112 + Th 23.4219 Th4+ 22.4418 Pa 23.2948 U 23.4128 U3+ 22.5259 + U4+ 22.5326 U6+ 22.7584 Np 23.5964 Np3+ 22.6130 Np4+ 22.5787 + Np6+ 22.7286 Pu 23.8083 Pu3+ 22.7169 Pu4+ 22.6460 Pu6+ 22.7181 + Am 24.0992 Cm 24.4096 Bk 24.7736 Cf 25.1995 + save_ + + +save_Cromer_Mann_b2 + loop_ + _enumeration_default.index + _enumeration_default.value + H 26.1257 D 26.1257 H1- 15.187 He 3.3568 Li 1.0524 + Li1+ 1.9557 Be 1.8623 Be2+ .8313 B 1.021 C 10.2075 + N 9.8933 O 5.7011 O1- 4.17236 F 4.2944 F1- 14.7353 + Ne 3.4262 Na 8.8422 Na1+ 6.1153 Mg 79.2611 Mg2+ 4.7542 + Al .7426 Al3+ 4.14553 Si 32.3337 Si4+ 3.43757 P 27.157 + S 22.2151 Cl 1.1662 Cl1- 1.1717 Ar 14.8407 K .7748 + K1+ .7674 Ca .6599 Ca2+ .6089 Sc .5729 Sc3+ 7.9629 + Ti .5 Ti2+ .457585 Ti3+ 7.04716 Ti4+ 6.67018 V .4385 + V2+ .4409 V3+ .383349 V5+ 5.40135 Cr .392 Cr2+ .344261 + Cr3+ .334393 Mn .3432 Mn2+ .3435 Mn3+ .294393 Mn4+ .283303 + Fe .3072 Fe2+ .3053 Fe3+ .3005 Co .2784 Co2+ .2726 + Co3+ .238668 Ni .2565 Ni2+ .2449 Ni3+ .22314 Cu .247 + Cu1+ .2274 Cu2+ .244078 Zn .2333 Zn2+ .2031 Ga .2412 + Ga3+ .22789 Ge .2516 Ge4+ .205855 As .2647 Se .2726 + Br 16.5796 Br1- 19.3345 Kr 16.5623 Rb 17.3151 Rb1+ 14.7957 + Sr 14.0988 Sr2+ 12.6963 Y 12.8006 Y3+ 11.2145 Zr 11.916 + Zr4+ 10.1483 Nb 11.766 Nb3+ 1.13305 Nb5+ .028781 Mo 1.0958 + Mo3+ 1.03031 Mo5+ 1.02238 Mo6+ 8.48061 Tc 8.14487 Ru 8.43467 + Ru3+ 8.37164 Ru4+ 8.12534 Rh 8.21758 Rh3+ 7.84438 Rh4+ 7.62436 + Pd 7.98929 Pd2+ 7.55573 Pd4+ 7.14833 Ag 7.4726 Ag1+ 7.19123 + Ag2+ 7.18544 Cd 6.9089 Cd2+ 6.80639 In 6.3776 In3+ 6.3247 + Sn .5031 Sn2+ 5.8378 Sn4+ .4655 Sb .4607 Sb3+ 5.22126 + Sb5+ .467973 Te .420885 I .3814 I1- .3815 Xe 0.344 + Cs .3107 Cs1+ .3086 Ba .2756 Ba2+ .28331 La .244475 + La3+ .250698 Ce .226836 Ce3+ .23154 Ce4+ .21885 Pr .222087 + Pr3+ .214299 Pr4+ .202481 Nd .210628 Nd3+ .199237 Pm 0.202088 + Sm .196451 Sm3+ .174081 Eu .1942 Eu2+ .17353 Eu3+ .16394 + Gd .181951 Gd3+ .155525 Tb .196143 Tb3+ .149525 Dy .202172 + Dy3+ .143384 Ho .19794 Ho3+ .139358 Er .223545 Er3+ .13729 + Tm .238849 Tm3+ .136974 Yb .25711 Yb2+ .15997 Yb3+ .13879 + Lu 9.98519 Lu3+ .142292 Hf 9.5999 Hf4+ .128903 Ta 9.37046 + Ta5+ .116741 W 9.2259 W6+ .104621 Re 9.09227 Os 8.97948 + Os4+ 6.84706 Ir 8.86553 Ir3+ 7.10909 Ir4+ 6.71983 Pt 8.81174 + Pt2+ 7.38979 Pt4+ 6.60834 Au 8.6216 Au1+ 7.7395 Au3+ 6.82872 + Hg 8.4484 Hg1+ 7.65105 Hg2+ 7.05639 Tl 8.70751 TL1+ .517394 + Tl3+ 6.53852 Pb 2.3576 Pb2+ .488383 Pb4+ 6.10926 Bi 2.9238 + Bi3+ 6.24149 Bi5+ .039042 Po 3.55078 At 3.97458 Rn 4.0691 + Fr 4.17619 Ra 3.87135 Ra2+ 3.57670 Ac 3.65155 Ac3+ 3.41437 + Th 3.46204 Th4+ 3.24498 Pa 3.41519 U 3.3253 U3+ 3.12293 + U4+ 3.05053 U6+ 2.89030 Np 3.25396 Np3+ 3.03807 Np4+ 2.96627 + Np6+ 2.81099 Pu 3.26371 Pu3+ 2.96118 Pu4+ 2.89020 Pu6+ 2.73848 + Am 3.20647 Cm 3.08997 Bk 3.04619 Cf 3.00775 + save_ + + +save_Cromer_Mann_a3 + loop_ + _enumeration_default.index + _enumeration_default.value + H .140191 D .140191 H1- .415815 He 0.3112 Li .6175 + Li1+ .3414 Be .5391 Be2+ .7993 B 1.0979 C 1.5886 + N 2.0125 O 1.5463 O1- 1.52673 F 1.517 F1- 1.26064 + Ne 1.4546 Na 1.2674 Na1+ 1.3998 Mg 1.2269 Mg2+ 1.3284 + Al 1.5936 Al3+ 1.20296 Si 1.9891 Si4+ 1.19453 P 1.78 + S 1.4379 Cl 6.2556 Cl1- 6.5337 Ar 0.6539 K 1.0519 + K1+ 6.359 Ca 1.5899 Ca2+ 8.4372 Sc 1.6409 Sc3+ 1.65943 + Ti 1.6991 Ti2+ 2.2793 Ti3+ 5.25691 Ti4+ 2.01341 V 2.0703 + V2+ 2.2884 V3+ 2.15343 V5+ 2.03081 Cr 3.324 Cr2+ 3.58274 + Cr3+ 2.87603 Mn 3.0193 Mn2+ 3.5268 Mn3+ 3.56531 Mn4+ 2.76067 + Fe 3.5222 Fe2+ 4.1346 Fe3+ 3.3948 Co 4.0034 Co2+ 4.7393 + Co3+ 4.76795 Ni 4.4438 Ni2+ 5.3442 Ni3+ 5.22746 Cu 5.6158 + Cu1+ 6.2455 Cu2+ 5.78135 Zn 5.1652 Zn2+ 6.4668 Ga 4.3591 + Ga3+ 6.06692 Ge 3.7068 Ge4+ 6.06791 As 3.4313 Se 3.9731 + Br 5.6377 Br1- 5.5754 Kr 5.5493 Rb 5.1399 Rb1+ 5.8981 + Sr 5.422 Sr2+ 2.5654 Y 5.72629 Y3+ 1.76795 Zr 5.41732 + Zr4+ 1.01118 Nb 4.04183 Nb3+ 11.0177 Nb5+ 10.799 Mo 12.8876 + Mo3+ 11.7423 Mo5+ 11.4632 Mo6+ 6.57891 Tc 4.64901 Ru 4.86337 + Ru3+ 9.32602 Ru4+ 4.71304 Rh 4.73425 Rh3+ 3.32515 Rh4+ 2.53464 + Pd 5.29537 Pd2+ 4.32234 Pd4+ 2.89289 Ag 4.8045 Ag1+ 5.27475 + Ag2+ 4.3709 Cd 4.461 Cd2+ 4.47128 In 4.2948 In3+ 3.78897 + Sn 4.4585 Sn2+ 4.5648 Sn4+ 3.4182 Sb 5.0371 Sb3+ 5.10789 + Sb5+ 2.41253 Te 6.14487 I 7.5138 I1- 7.8069 Xe 8.9767 + Cs 10.662 Cs1+ 10.2821 Ba 10.888 Ba2+ 10.9054 La 11.3727 + La3+ 11.6323 Ce 11.8513 Ce3+ 11.9369 Ce4+ 12.1233 Pr 12.3856 + Pr3+ 12.1329 Pr4+ 12.4668 Nd 12.774 Nd3+ 12.12 Pm 13.1235 + Sm 13.4396 Sm3+ 11.9202 Eu 13.7603 Eu2+ 11.8034 Eu3+ 11.8509 + Gd 13.8518 Gd3+ 11.8708 Tb 14.3167 Tb3+ 12.2471 Dy 14.5596 + Dy3+ 11.9812 Ho 14.5583 Ho3+ 11.9788 Er 14.9779 Er3+ 12.1506 + Tm 15.1542 Tm3+ 12.3339 Yb 15.3087 Yb2+ 13.3335 Yb3+ 12.6072 + Lu 15.1 Lu3+ 12.8429 Hf 14.7586 Hf4+ 12.7285 Ta 14.5135 + Ta5+ 12.8268 W 14.4327 W6+ 13.0544 Re 14.5564 Os 14.9305 + Os4+ 14.7458 Ir 15.6115 Ir3+ 13.6145 Ir4+ 14.2326 Pt 15.7131 + Pt2+ 13.2153 Pt4+ 13.7348 Au 25.5582 Au1+ 14.3359 Au3+ 12.7801 + Hg 21.6575 Hg1+ 16.8883 Hg2+ 12.8374 Tl 15.538 TL1+ 18.7478 + Tl3+ 11.9328 Pb 18.442 Pb2+ 19.1406 Pb4+ 12.0175 Bi 16.5877 + Bi3+ 19.1053 Bi5+ 19.2497 Po 13.1138 At 9.49887 Rn 8.0037 + Fr 12.1439 Ra 12.4739 Ra2+ 7.91342 Ac 12.5977 Ac3+ 8.19216 + Th 12.7473 Th4+ 9.78554 Pa 14.1891 U 14.9491 U3+ 12.2165 + U4+ 12.0291 U6+ 14.0099 Np 15.6402 Np3+ 12.9898 Np4+ 12.7766 + Np6+ 14.3884 Pu 16.7707 Pu3+ 13.5807 Pu4+ 13.3595 Pu6+ 14.7635 + Am 17.3415 Cm 17.3990 Bk 17.8919 Cf 18.3317 + save_ + + +save_Cromer_Mann_b3 + loop_ + _enumeration_default.index + _enumeration_default.value + H 3.14236 D 3.14236 H1- 186.576 He 22.9276 Li 85.3905 + Li1+ .6316 Be 103.483 Be2+ 2.2758 B 60.3498 C .5687 + N 28.9975 O .3239 O1- 47.0179 F .2615 F1- .442258 + Ne 0.2306 Na .3136 Na1+ .2001 Mg .3808 Mg2+ .185 + Al 31.5472 Al3+ .228753 Si .6785 Si4+ .2149 P .526 + S .2536 Cl 18.5194 Cl1- 19.5424 Ar 43.8983 K 213.187 + K1+ -.002 Ca 85.7484 Ca2+ 10.3116 Sc 136.108 Sc3+ -.28604 + Ti 35.6338 Ti2+ 19.5361 Ti3+ -.15762 Ti4+ -.29263 V 26.8938 + V2+ 20.3004 V3+ 15.1908 V5+ 9.97278 Cr 20.2626 Cr2+ 13.3075 + Cr3+ 12.8288 Mn 17.8674 Mn2+ 14.343 Mn3+ 10.8171 Mn4+ 10.4852 + Fe 15.3535 Fe2+ 12.0546 Fe3+ 11.6729 Co 13.5359 Co2+ 10.2443 + Co3+ 8.35583 Ni 12.1763 Ni2+ 8.873 Ni3+ 7.64468 Cu 11.3966 + Cu1+ 8.6625 Cu2+ 7.9876 Zn 10.3163 Zn2+ 7.0826 Ga 10.7805 + Ga3+ 6.36441 Ge 11.4468 Ge4+ 5.47913 As 12.9479 Se 15.2372 + Br .2609 Br1- .2871 Kr 0.2261 Rb .2748 Rb1+ .1603 + Sr .1664 Sr2+ 24.5651 Y .125599 Y3+ 22.6599 Zr .117622 + Zr4+ 21.6054 Nb .204785 Nb3+ 10.1621 Nb5+ 9.28206 Mo 11.004 + Mo3+ 9.53659 Mo5+ 8.78809 Mo6+ .058881 Tc 21.5707 Ru 24.7997 + Ru3+ .017662 Ru4+ .036495 Rh 25.8749 Rh3+ 21.2487 Rh4+ 19.3317 + Pd 25.2052 Pd2+ 22.5057 Pd4+ 17.9144 Ag 24.6605 Ag1+ 21.7326 + Ag2+ 21.4072 Cd 24.7008 Cd2+ 20.2521 In 25.8499 In3+ 17.3595 + Sn 26.8909 Sn2+ 23.3752 Sn4+ 14.0049 Sb 27.9074 Sb3+ 19.5902 + Sb5+ 14.1259 Te 28.5284 I 27.766 I1- 29.5259 Xe 26.4659 + Cs 24.3879 Cs1+ 23.7128 Ba 20.2073 Ba2+ 20.0558 La 18.7726 + La3+ 17.8211 Ce 17.6083 Ce3+ 16.5408 Ce4+ 15.7992 Pr 16.7669 + Pr3+ 15.323 Pr4+ 14.8137 Nd 15.885 Nd3+ 14.1783 Pm 15.1009 + Sm 14.3996 Sm3+ 12.1571 Eu 13.7546 Eu2+ 11.6096 Eu3+ 11.311 + Gd 12.9331 Gd3+ 10.5782 Tb 12.6648 Tb3+ 10.0499 Dy 12.1899 + Dy3+ 9.34972 Ho 11.4407 Ho3+ 8.80018 Er 11.3604 Er3+ 8.36225 + Tm 10.9975 Tm3+ 7.96778 Yb 10.6647 Yb2+ 8.18304 Yb3+ 7.64412 + Lu .261033 Lu3+ 7.33727 Hf .275116 Hf4+ 6.76232 Ta .295977 + Ta5+ 6.31524 W .321703 W6+ 5.93667 Re .3505 Os .382661 + Os4+ .165191 Ir .417916 Ir3+ .204633 Ir4+ .167252 Pt .424593 + Pt2+ .263297 Pt4+ .16864 Au 1.4826 Au1+ .356752 Au3+ .212867 + Hg 1.5729 Hg1+ .443378 Hg2+ .284738 Tl 1.96347 TL1+ 7.43463 + Tl3+ .219074 Pb 8.618 Pb2+ 6.7727 Pb4+ .147041 Bi 8.7937 + Bi3+ .469999 Bi5+ 5.71414 Po 9.55642 At 11.3824 Rn 14.0422 + Fr 23.1052 Ra 19.9887 Ra2+ 12.6010 Ac 18.5990 Ac3+ 12.9187 + Th 17.8309 Th4+ 13.4661 Pa 16.9235 U 16.0927 U3+ 12.7148 + U4+ 12.5723 U6+ 13.1767 Np 15.3622 Np3+ 12.1449 Np4+ 11.9484 + Np6+ 12.3300 Pu 14.9455 Pu3+ 11.5331 Pu4+ 11.3160 Pu6+ 11.5530 + Am 14.3136 Cm 13.4346 Bk 12.8946 Cf 12.4044 + save_ + + +save_Cromer_Mann_a4 + loop_ + _enumeration_default.index + _enumeration_default.value + H .04081 D .04081 H1- .116973 He 0.178 Li .4653 + Li1+ .1563 Be .7029 Be2+ .1647 B .7068 C .865 + N 1.1663 O .867 O1- -20.307 F 1.0243 F1- .940706 + Ne 1.1251 Na 1.1128 Na1+ 1.0032 Mg 2.3073 Mg2+ .8497 + Al 1.9646 Al3+ .528137 Si 1.541 Si4+ .41653 P 1.4908 + S 1.5863 Cl 1.6455 Cl1- 2.3386 Ar 1.6442 K .8659 + K1+ 1.1915 Ca 1.0211 Ca2+ .8537 Sc 1.468 Sc3+ 1.57936 + Ti 1.9021 Ti2+ .087899 Ti3+ 1.92134 Ti4+ 1.5208 V 2.0571 + V2+ .0223 V3+ .016865 V5+ -9.576 Cr 1.4922 Cr2+ .509107 + Cr3+ .113575 Mn 2.2441 Mn2+ .2184 Mn3+ .323613 Mn4+ .054447 + Fe 2.3045 Fe2+ .4399 Fe3+ .0724 Co 2.3488 Co2+ .7108 + Co3+ .725591 Ni 2.38 Ni2+ .9773 Ni3+ .847114 Cu 1.6735 + Cu1+ 1.5578 Cu+ 1.14523 Zn 2.41 Zn2+ 1.394 Ga 2.9623 + Ga3+ 1.0066 Ge 3.683 Ge4+ .859041 As 4.2779 Se 4.3543 + Br 3.9851 Br1- 3.7272 Kr 3.5375 Rb 1.5292 Rb1+ 2.7817 + Sr 2.6694 Sr2+ -34.193 Y 3.26588 Y3+ -33.108 Zr 3.65721 + Zr4+ -2.6479 Nb 3.53346 Nb3+ 1.94715 Nb5+ .337905 Mo 3.7429 + Mo3+ 2.30951 Mo5+ .740625 Mo6+ 0. Tc 2.71263 Ru 1.56756 + Ru3+ 3.00964 Ru4+ 2.18535 Rh 1.28918 Rh3+ -6.1989 Rh4+ -5.6526 + Pd .605844 Pd2+ 0. Pd4+ -7.9492 Ag 1.0463 Ag1+ .357534 + Ag2+ 0. Cd 1.6029 Cd2+ 0. In 2.0396 In3+ 0. + Sn 2.4663 Sn2+ .487 Sn4+ .0193 Sb 2.6827 Sb3+ .288753 + Sb5+ 0. Te 2.5239 I 2.2735 I1- 2.8868 Xe 1.99 + Cs 1.4953 Cs1+ .9615 Ba 2.6959 Ba2+ .773634 La 3.28719 + La3+ .336048 Ce 3.33049 Ce3+ .612376 Ce4+ .144583 Pr 2.82428 + Pr3+ .97518 Pr4+ .296689 Nd 2.85137 Nd3+ 1.51031 Pm 2.87516 + Sm 2.89604 Sm3+ 2.71488 Eu 2.9227 Eu2+ 3.87243 Eu3+ 3.26503 + Gd 3.54545 Gd3+ 3.7149 Tb 2.95354 Tb3+ 3.773 Dy 2.96577 + Dy3+ 4.50073 Ho 3.63837 Ho3+ 4.93676 Er 2.98233 Er3+ 5.17379 + Tm 2.98706 Tm3+ 5.38348 Yb 2.98963 Yb2+ 5.14657 Yb3+ 5.47647 + Lu 3.71601 Lu3+ 5.59415 Hf 4.30013 Hf4+ 5.59927 Ta 4.76492 + Ta5+ 5.38695 W 5.11982 W6+ 5.06412 Re 5.44174 Os 5.67589 + Os4+ 5.06795 Ir 5.83377 Ir3+ 5.82008 Ir4+ 5.53672 Pt 5.7837 + Pt2+ 6.35234 Pt4+ 5.92034 Au 5.86 Au1+ 6.58077 Au3+ 6.52354 + Hg 5.9676 Hg1+ 6.48216 Hg2+ 6.89912 Tl 5.52593 TL1+ 6.82847 + Tl3+ 7.00574 Pb 5.9696 Pb2+ 7.01107 Pb4+ 6.96886 Bi 6.4692 + Bi3+ 7.10295 Bi5+ 6.91555 Po 7.02588 At 7.42518 Rn 7.4433 + Fr 2.11253 Ra 3.21097 Ra2+ 7.65078 Ac 4.08655 Ac3+ 7.05545 + Th 4.80703 Th4+ 5.29444 Pa 4.17287 U 4.1880 U3+ 5.37073 + U4+ 4.79840 U6+ 1.21457 Np 4.18550 Np3+ 5.43227 Np4+ 4.92159 + Np6+ 1.75669 Pu 3.47947 Pu3+ 5.66016 Pu4+ 5.18831 Pu6+ 2.28678 + Am 3.49331 Cm 4.21665 Bk 4.23284 Cf 4.24391 + save_ + + +save_Cromer_Mann_b4 + loop_ + _enumeration_default.index + _enumeration_default.value + H 57.7997 D 57.7997 H1- 3.56709 He 0.9821 Li 168.261 + Li1+ 10.0953 Be .542 Be2+ 5.1146 B .1403 C 51.6512 + N .5826 O 32.9089 O1- -.01404 F 26.1476 F1- 47.3437 + Ne 21.7814 Na 129.424 Na1+ 14.039 Mg 7.1937 Mg2+ 10.1411 + Al 85.0886 Al3+ 8.28524 Si 81.6937 Si4+ 6.65365 P 68.1645 + S 56.172 Cl 47.7784 Cl1- 60.4486 Ar 33.3929 K 41.6841 + K1+ 31.9128 Ca 178.437 Ca2+ 25.9905 Sc 51.3531 Sc3+ 16.0662 + Ti 116.105 Ti2+ 61.6558 Ti3+ 15.9768 Ti4+ 12.9464 V 102.478 + V2+ 115.122 V3+ 63.969 V5+ .940464 Cr 98.7399 Cr2+ 32.4224 + Cr3+ 32.8761 Mn 83.7543 Mn2+ 41.3235 Mn3+ 24.1281 Mn4+ 27.573 + Fe 76.8805 Fe2+ 31.2809 Fe3+ 38.5566 Co 71.1692 Co2+ 25.6466 + Co3+ 18.3491 Ni 66.3421 Ni2+ 22.1626 Ni3+ 16.9673 Cu 64.8126 + Cu1+ 25.8487 Cu2+ 19.897 Zn 58.7097 Zn2+ 18.0995 Ga 61.4135 + Ga3+ 14.4122 Ge 54.7625 Ge4+ 11.603 As 47.7972 Se 43.8163 + Br 41.4328 Br1- 58.1535 Kr 39.3972 Rb 164.934 Rb1+ 31.2087 + Sr 132.376 Sr2+ -.0138 Y 104.354 Y3+ -.01319 Zr 87.6627 + Zr4+ -.10276 Nb 69.7957 Nb3+ 28.3389 Nb5+ 25.7228 Mo 61.6584 + Mo3+ 26.6307 Mo5+ 23.3452 Mo6+ 0. Tc 86.8472 Ru 94.2928 + Ru3+ 22.887 Ru4+ 20.8504 Rh 98.6062 Rh3+ -.01036 Rh4+ -.0102 + Pd 76.8986 Pd2+ 0. Pd4+ .005127 Ag 99.8156 Ag1+ 66.1147 + Ag2+ 0. Cd 87.4825 Cd2+ 0. In 92.8029 In3+ 0. + Sn 83.9571 Sn2+ 62.2061 Sn4+ -.7583 Sb 75.2825 Sb3+ 55.5113 + Sb5+ 0. Te 70.8403 I 66.8776 I1- 84.9304 Xe 64.2658 + Cs 213.904 Cs1+ 59.4565 Ba 167.202 Ba2+ 51.746 La 133.124 + La3+ 54.9453 Ce 127.113 Ce3+ 43.1692 Ce4+ 62.2355 Pr 143.644 + Pr3+ 36.4065 Pr4+ 45.4643 Nd 137.903 Nd3+ 30.8717 Pm 132.721 + Sm 128.007 Sm3+ 24.8242 Eu 123.174 Eu2+ 26.5156 Eu3+ 22.9966 + Gd 101.398 Gd3+ 21.7029 Tb 115.362 Tb3+ 21.2773 Dy 111.874 + Dy3+ 19.581 Ho 92.6566 Ho3+ 18.5908 Er 105.703 Er3+ 17.8974 + Tm 102.961 Tm3+ 17.2922 Yb 100.417 Yb2+ 20.39 Yb3+ 16.8153 + Lu 84.3298 Lu3+ 16.3535 Hf 72.029 Hf4+ 14.0366 Ta 63.3644 + Ta5+ 12.4244 W 57.056 W6+ 11.1972 Re 52.0861 Os 48.1647 + Os4+ 18.003 Ir 45.0011 Ir3+ 20.3254 Ir4+ 17.4911 Pt 38.6103 + Pt2+ 22.9426 Pt4+ 16.9392 Au 36.3956 Au1+ 26.4043 Au3+ 18.659 + Hg 38.3246 Hg1+ 28.2262 Hg2+ 20.7482 Tl 45.8149 TL1+ 28.8482 + Tl3+ 17.2114 Pb 47.2579 Pb2+ 23.8132 Pb4+ 14.714 Bi 48.0093 + Bi3+ 20.3185 Bi5+ 12.8285 Po 47.0045 At 45.4715 Rn 44.2473 + Fr 150.645 Ra 142.325 Ra2+ 29.8436 Ac 117.020 Ac3+ 25.9443 + Th 99.1722 Th4+ 23.9533 Pa 105.251 U 100.613 U3+ 26.3394 + U4+ 23.4582 U6+ 25.2017 Np 97.4908 Np3+ 25.4928 Np4+ 22.7502 + Np6+ 22.6581 Pu 105.980 Pu3+ 24.3992 Pu4+ 21.8301 Pu6+ 20.9303 + Am 102.273 Cm 88.4834 Bk 86.0030 Cf 83.7881 + save_ + + +save_Cromer_Mann_c + loop_ + _enumeration_default.index + _enumeration_default.value + H .003038 D .003038 H1- .002389 He 0.0064 Li .0377 + Li1+ .0167 Be .0385 Be2+ -6.1092 B -.1932 C .2156 + N -11.529 O .2508 O1- 21.9412 F .2776 F1- .653396 + Ne 0.3515 Na .6760 Na1+ .4040 Mg .8584 Mg2+ .4853 + Al 1.1151 Al3+ .706786 Si 1.1407 Si4+ .746297 P 1.1149 + S .8669 Cl -9.5574 Cl1- -16.378 Ar 1.44450 K 1.4228 + K1+ -4.9978 Ca 1.3751 Ca2+ -14.875 Sc 1.3329 Sc3+ -6.6667 + Ti 1.2807 Ti2+ .897155 Ti3+ -14.652 Ti4+ -13.280 V 1.2199 + V2+ 1.2298 V3+ .656565 V5+ 1.71430 Cr 1.1832 Cr2+ .616898 + Cr3+ .518275 Mn 1.0896 Mn2+ 1.0874 Mn3+ .393974 Mn4+ .251877 + Fe 1.0369 Fe2+ 1.0097 Fe3+ .9707 Co 1.0118 Co2+ .9324 + Co3+ .286667 Ni 1.0341 Ni2+ .8614 Ni3+ .386044 Cu 1.1910 + Cu1+ .8900 Cu2+ 1.14431 Zn 1.3041 Zn2+ .7807 Ga 1.7189 + Ga3+ 1.53545 Ge 2.1313 Ge4+ 1.45572 As 2.5310 Se 2.8409 + Br 2.9557 Br1- 3.1776 Kr 2.825 Rb 3.4873 Rb1+ 2.0782 + Sr 2.5064 Sr2+ 41.4025 Y 1.91213 Y3+ 40.2602 Zr 2.06929 + Zr4+ 9.41454 Nb 3.75591 Nb3+ -12.912 Nb5+ -6.3934 Mo 4.3875 + Mo3+ -14.421 Mo5+ -14.316 Mo6+ .344941 Tc 5.40428 Ru 5.37874 + Ru3+ -3.1892 Ru4+ 1.42357 Rh 5.32800 Rh3+ 11.8678 Rh4+ 11.2835 + Pd 5.26593 Pd2+ 5.29160 Pd4+ 13.0174 Ag 5.1790 Ag1+ 5.21572 + Ag2+ 5.21404 Cd 5.0694 Cd2+ 5.11937 In 4.9391 In3+ 4.99635 + Sn 4.7821 Sn2+ 4.7861 Sn4+ 3.9182 Sb 4.5909 Sb3+ 4.69626 + Sb5+ 4.69263 Te 4.35200 I 4.0712 I1- 4.0714 Xe 3.7118 + Cs 3.3352 Cs1+ 3.2791 Ba 2.7731 Ba2+ 3.02902 La 2.14678 + La3+ 2.40860 Ce 1.86264 Ce3+ 2.09013 Ce4+ 1.59180 Pr 2.05830 + Pr3+ 1.77132 Pr4+ 1.24285 Nd 1.98486 Nd3+ 1.47588 Pm 2.02876 + Sm 2.20963 Sm3+ .954586 Eu 2.5745 Eu2+ 1.36389 Eu3+ .759344 + Gd 2.41960 Gd3+ .645089 Tb 3.58324 Tb3+ .691967 Dy 4.29728 + Dy3+ .689690 Ho 4.56796 Ho3+ .852795 Er 5.92046 Er3+ 1.17613 + Tm 6.75621 Tm3+ 1.63929 Yb 7.56672 Yb2+ 3.70983 Yb3+ 2.26001 + Lu 7.97628 Lu3+ 2.97573 Hf 8.58154 Hf4+ 2.39699 Ta 9.24354 + Ta5+ 1.78555 W 9.88750 W6+ 1.01074 Re 10.4720 Os 11.0005 + Os4+ 6.49804 Ir 11.4722 Ir3+ 8.27903 Ir4+ 6.96824 Pt 11.6883 + Pt2+ 9.85329 Pt4+ 7.39534 Au 12.0658 Au1+ 11.2299 Au3+ 9.09680 + Hg 12.6089 Hg1+ 12.0205 Hg2+ 10.6268 Tl 13.1746 TL1+ 12.5258 + Tl3+ 9.80270 Pb 13.4118 Pb2+ 12.4734 Pb4+ 8.08428 Bi 13.5782 + Bi3+ 12.4711 Bi5+ -6.7994 Po 13.6770 At 13.7108 Rn 13.6905 + Fr 13.7247 Ra 13.6211 Ra2+ 13.5431 Ac 13.5266 Ac3+ 13.4637 + Th 13.4314 Th4+ 13.3760 Pa 13.4287 U 13.3966 U3+ 13.3092 + U4+ 13.2671 U6+ 13.1665 Np 13.3573 Np3+ 13.2544 Np4+ 13.2116 + Np6+ 13.1130 Pu 13.3812 Pu3+ 13.1991 Pu4+ 13.1555 Pu6+ 13.0582 + Am 13.3592 Cm 13.2887 Bk 13.2754 Cf 13.2674 + save_ + + +save_hi_ang_Fox_c0 + loop_ + _enumeration_default.index + _enumeration_default.value + H -4.8 D -4.8 H1- -4.8 He 0.52543 Li 0.89463 + Li1+ 0.89463 Be 1.2584 Be2+ 1.2584 B 1.6672 C 1.70560 + N 1.54940 O 1.30530 O1- 1.30530 F 1.16710 F1- 1.16710 + Ne 1.09310 Na 0.84558 Na1+ 0.84558 Mg 0.71877 Mg2+ 0.71877 + Al 0.67975 Al3+ 0.67975 Si 0.70683 Si4+ 0.70683 P 0.85532 + S 1.10400 Cl 1.42320 Cl1- 1.42320 Ar 1.82020 K 2.26550 + K1+ 2.26550 Ca 2.71740 Ca2+ 2.71740 Sc 3.11730 Sc3+ 3.11730 + Ti 3.45360 Ti2+ 3.45360 Ti3+ 3.45360 Ti4+ 3.45360 V 3.71270 + V2+ 3.71270 V3+ 3.71270 V5+ 3.71270 Cr 3.87870 Cr2+ 3.87870 + Cr3+ 3.87870 Mn 3.98550 Mn2+ 3.98550 Mn3+ 3.98550 Mn4+ 3.98550 + Fe 3.99790 Fe2+ 3.99790 Fe3+ 3.99790 Co 3.95900 Co2+ 3.95900 + Co3+ 3.95900 Ni 3.86070 Ni2+ 3.86070 Ni3+ 3.86070 Cu 3.72510 + Cu1+ 3.72510 Cu2+ 3.72510 Zn 3.55950 Zn2+ 3.55950 Ga 3.37560 + Ga3+ 3.37560 Ge 3.17800 Ge4+ 3.17800 As 2.97740 Se 2.78340 + Br 2.60610 Br1- 2.60610 Kr 2.44280 Rb 2.30990 Rb1+ 2.30990 + Sr 2.21070 Sr2+ 2.21070 Y 2.14220 Y3+ 2.14220 Zr 2.12690 + Zr4+ 2.12690 Nb 2.12120 Nb3+ 2.12120 Nb5+ 2.12120 Mo 2.18870 + Mo3+ 2.18870 Mo5+ 2.18870 Mo6+ 2.18870 Tc 2.25730 Ru 2.37300 + Ru3+ 2.37300 Ru4+ 2.37300 Rh 2.50990 Rh3+ 2.50990 Rh4+ 2.50990 + Pd 2.67520 Pd2+ 2.67520 Pd4+ 2.67520 Ag 2.88690 Ag1+ 2.88690 + Ag2+ 2.88690 Cd 3.08430 Cd2+ 3.08430 In 3.31400 In3+ 3.31400 + Sn 3.49840 Sn2+ 3.49840 Sn4+ 3.49840 Sb 3.70410 Sb3+ 3.70410 + Sb5+ 3.70410 Te 3.88240 I 4.08010 I1- 4.08010 Xe 4.24610 + Cs 4.38910 Cs1+ 4.38910 Ba 4.51070 Ba2+ 4.51070 La 4.60250 + La3+ 4.60250 Ce 4.69060 Ce3+ 4.69060 Ce4+ 4.69060 Pr 4.72150 + Pr3+ 4.72150 Pr4+ 4.72150 Nd 4.75090 Nd3+ 4.75090 Pm 4.74070 + Sm 4.71700 Sm3+ 4.71700 Eu 4.66940 Eu2+ 4.66940 Eu3+ 4.66940 + Gd 4.61010 Gd3+ 4.61010 Tb 4.52550 Tb3+ 4.52550 Dy 4.45230 + Dy3+ 4.45230 Ho 4.37660 Ho3+ 4.37660 Er 4.29460 Er3+ 4.29460 + Tm 4.21330 Tm3+ 4.21330 Yb 4.13430 Yb2+ 4.13430 Yb3+ 4.13430 + Lu 4.04230 Lu3+ 4.04230 Hf 3.95160 Hf4+ 3.95160 Ta 3.85000 + Ta5+ 3.85000 W 3.76510 W6+ 3.76510 Re 3.67600 Os 3.60530 + Os4+ 3.60530 Ir 3.53130 Ir3+ 3.53130 Ir4+ 3.53130 Pt 3.47070 + Pt2+ 3.47070 Pt4+ 3.47070 Au 3.41630 Au1+ 3.41630 Au3+ 3.41630 + Hg 3.37350 Hg1+ 3.37350 Hg2+ 3.37350 Tl 3.34590 TL1+ 3.34590 + Tl3+ 3.34590 Pb 3.32330 Pb2+ 3.32330 Pb4+ 3.32330 Bi 3.31880 + Bi3+ 3.31880 Bi5+ 3.31880 Po 3.32030 At 3.34250 Rn 3.37780 + Fr 3.41990 Ra 3.47530 Ra2+ 3.47530 Ac 3.49020 Ac3+ 3.49020 + Th 3.61060 Th4+ 3.61060 Pa 3.68630 U 3.76650 U3+ 3.76650 + U4+ 3.76650 U6+ 3.76650 Np 3.82870 Np3+ 3.82870 Np4+ 3.82870 + Np6+ 3.82870 Pu 3.88970 Pu3+ 3.88970 Pu4+ 3.88970 Pu6+ 3.88970 + Am 3.95060 Cm 4.01470 Bk 4.07780 Cf 4.14210 + save_ + + +save_hi_ang_Fox_c1 + loop_ + _enumeration_default.index + _enumeration_default.value + H -.5 D -.5 H1- -.5 He -3.433 Li -2.4366 + Li1+ -2.4366 Be -1.9459 Be2+ -1.9459 B -1.8556 C -1.56760 + N -1.20190 O -0.83742 O1- -0.83742 F -0.63203 F1- -0.63203 + Ne -0.50221 Na -0.26294 Na1+ -0.26294 Mg -0.13144 Mg2+ -0.13144 + Al -0.08756 Al3+ -0.08756 Si -0.09888 Si4+ -0.09888 P -0.21262 + S -0.40325 Cl -0.63936 Cl1- -0.63936 Ar -0.92776 K -1.24530 + K1+ -1.24530 Ca -1.55670 Ca2+ -1.55670 Sc -1.81380 Sc3+ -1.81380 + Ti -2.01150 Ti2+ -2.01150 Ti3+ -2.01150 Ti4+ -2.01150 V -2.13920 + V2+ -2.13920 V3+ -2.13920 V5+ -2.13920 Cr -2.19000 Cr2+ -2.19000 + Cr3+ -2.19000 Mn -2.18850 Mn2+ -2.18850 Mn3+ -2.18850 Mn4+ -2.18850 + Fe -2.11080 Fe2+ -2.11080 Fe3+ -2.11080 Co -1.99650 Co2+ -1.99650 + Co3+ -1.99650 Ni -1.88690 Ni2+ -1.88690 Ni3+ -1.88690 Cu -1.65500 + Cu1+ -1.65500 Cu2+ -1.65500 Zn -1.45100 Zn2+ -1.45100 Ga -1.23910 + Ga3+ -1.23910 Ge -1.02230 Ge4+ -1.02230 As -0.81038 Se -0.61110 + Br -0.43308 Br1- -0.43308 Kr -0.27244 Rb -0.14328 Rb1+ -0.14328 + Sr -0.04770 Sr2+ -0.04770 Y 0.01935 Y3+ 0.01935 Zr 0.08618 + Zr4+ 0.08618 Nb 0.05381 Nb3+ 0.05381 Nb5+ 0.05381 Mo -0.00655 + Mo3+ -0.00655 Mo5+ -0.00655 Mo6+ -0.00655 Tc -0.05737 Ru -0.15040 + Ru3+ -0.15040 Ru4+ -0.15040 Rh -0.25906 Rh3+ -0.25906 Rh4+ -0.25906 + Pd -0.39137 Pd2+ -0.39137 Pd4+ -0.39137 Ag -0.56119 Ag1+ -0.56119 + Ag2+ -0.56119 Cd -0.71450 Cd2+ -0.71450 In -0.89697 In3+ -0.89697 + Sn -1.02990 Sn2+ -1.02990 Sn4+ -1.02990 Sb -1.18270 Sb3+ -1.18270 + Sb5+ -1.18270 Te -1.30980 I -1.45080 I1- -1.45080 Xe -1.56330 + Cs -1.65420 Cs1+ -1.65420 Ba -1.72570 Ba2+ -1.72570 La -1.77070 + La3+ -1.77070 Ce -1.81790 Ce3+ -1.81790 Ce4+ -1.81790 Pr -1.81390 + Pr3+ -1.81390 Pr4+ -1.81390 Nd -1.80800 Nd3+ -1.80800 Pm -1.76600 + Sm -1.71410 Sm3+ -1.71410 Eu -1.64140 Eu2+ -1.64140 Eu3+ -1.64140 + Gd -1.55750 Gd3+ -1.55750 Tb -1.45520 Tb3+ -1.45520 Dy -1.36440 + Dy3+ -1.36440 Ho -1.27460 Ho3+ -1.27460 Er -1.18170 Er3+ -1.18170 + Tm -1.09060 Tm3+ -1.09060 Yb -1.00310 Yb2+ -1.00310 Yb3+ -1.00310 + Lu -0.90518 Lu3+ -0.90518 Hf -0.80978 Hf4+ -0.80978 Ta -0.70599 + Ta5+ -0.70599 W -0.61807 W6+ -0.61807 Re -0.52688 Os -0.45420 + Os4+ -0.45420 Ir -0.37856 Ir3+ -0.37856 Ir4+ -0.37856 Pt -0.31534 + Pt2+ -0.31534 Pt4+ -0.31534 Au -0.25987 Au1+ -0.25987 Au3+ -0.25987 + Hg -0.21428 Hg1+ -0.21428 Hg2+ -0.21428 Tl -0.18322 TL1+ -0.18322 + Tl3+ -0.18322 Pb -0.15596 Pb2+ -0.15596 Pb4+ -0.15596 Bi -0.14554 + Bi3+ -0.14554 Bi5+ -0.14554 Po -0.13999 At -0.15317 Rn -0.17800 + Fr -0.20823 Ra -0.25005 Ra2+ -0.25005 Ac -0.25109 Ac3+ -0.25109 + Th -0.35409 Th4+ -0.35409 Pa -0.41329 U -0.47542 U3+ -0.47542 + U4+ -0.47542 U6+ -0.47542 Np -0.51955 Np3+ -0.51955 Np4+ -0.51955 + Np6+ -0.51955 Pu -0.56296 Pu3+ -0.56296 Pu4+ -0.56296 Pu6+ -0.56296 + Am -0.60554 Cm -0.65062 Bk -0.69476 Cf -0.73977 + save_ + + +save_hi_ang_Fox_c2 + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He 4.8007 Li 2.325 + Li1+ 2.325 Be 1.3046 Be2+ 1.3046 B 1.6044 C 1.18930 + N 0.51064 O -0.16738 O1- -0.16738 F -0.40207 F1- -0.40207 + Ne -0.53648 Na -0.87884 Na1+ -0.87884 Mg -1.20900 Mg2+ -1.20900 + Al -0.95431 Al3+ -0.95431 Si -0.98356 Si4+ -0.98356 P -0.37390 + S 0.20094 Cl 0.84722 Cl1- 0.84722 Ar 1.59220 K 2.38330 + K1+ 2.38330 Ca 3.13170 Ca2+ 3.13170 Sc 3.71390 Sc3+ 3.71390 + Ti 4.13170 Ti2+ 4.13170 Ti3+ 4.13170 Ti4+ 4.13170 V 4.35610 + V2+ 4.35610 V3+ 4.35610 V5+ 4.35610 Cr 4.38670 Cr2+ 4.38670 + Cr3+ 4.38670 Mn 4.27960 Mn2+ 4.27960 Mn3+ 4.27960 Mn4+ 4.27960 + Fe 3.98170 Fe2+ 3.98170 Fe3+ 3.98170 Co 3.60630 Co2+ 3.60630 + Co3+ 3.60630 Ni 3.12390 Ni2+ 3.12390 Ni3+ 3.12390 Cu 2.60290 + Cu1+ 2.60290 Cu2+ 2.60290 Zn 2.03390 Zn2+ 2.03390 Ga 1.46160 + Ga3+ 1.46160 Ge 0.89119 Ge4+ 0.89119 As 0.34861 Se -0.14731 + Br -0.57381 Br1- -0.57381 Kr -0.95570 Rb -1.22600 Rb1+ -1.22600 + Sr -1.41100 Sr2+ -1.41100 Y -1.52240 Y3+ -1.52240 Zr -1.49190 + Zr4+ -1.49190 Nb -1.50070 Nb3+ -1.50070 Nb5+ -1.50070 Mo -1.25340 + Mo3+ -1.25340 Mo5+ -1.25340 Mo6+ -1.25340 Tc -1.07450 Ru -0.77694 + Ru3+ -0.77694 Ru4+ -0.77694 Rh -0.44719 Rh3+ -0.44719 Rh4+ -0.44719 + Pd -0.05894 Pd2+ -0.05894 Pd4+ -0.05894 Ag 0.42189 Ag1+ 0.42189 + Ag2+ 0.42189 Cd 0.84482 Cd2+ 0.84482 In 1.35030 In3+ 1.35030 + Sn 1.68990 Sn2+ 1.68990 Sn4+ 1.68990 Sb 2.08920 Sb3+ 2.08920 + Sb5+ 2.08920 Te 2.41170 I 2.76730 I1- 2.76730 Xe 3.04200 + Cs 3.25450 Cs1+ 3.25450 Ba 3.41320 Ba2+ 3.41320 La 3.49970 + La3+ 3.49970 Ce 3.60280 Ce3+ 3.60280 Ce4+ 3.60280 Pr 3.56480 + Pr3+ 3.56480 Pr4+ 3.56480 Nd 3.51970 Nd3+ 3.51970 Pm 3.37430 + Sm 3.20800 Sm3+ 3.20800 Eu 2.98580 Eu2+ 2.98580 Eu3+ 2.98580 + Gd 2.73190 Gd3+ 2.73190 Tb 2.43770 Tb3+ 2.43770 Dy 2.17540 + Dy3+ 2.17540 Ho 1.92540 Ho3+ 1.92540 Er 1.67060 Er3+ 1.67060 + Tm 1.42390 Tm3+ 1.42390 Yb 1.18810 Yb2+ 1.18810 Yb3+ 1.18810 + Lu 0.92889 Lu3+ 0.92889 Hf 0.67951 Hf4+ 0.67951 Ta 0.41103 + Ta5+ 0.41103 W 0.18568 W6+ 0.18568 Re -0.04706 Os -0.22529 + Os4+ -0.22529 Ir -0.41174 Ir3+ -0.41174 Ir4+ -0.41174 Pt -0.56487 + Pt2+ -0.56487 Pt4+ -0.56487 Au -0.69030 Au1+ -0.69030 Au3+ -0.69030 + Hg -0.79013 Hg1+ -0.79013 Hg2+ -0.79013 Tl -0.84911 TL1+ -0.84911 + Tl3+ -0.84911 Pb -0.89878 Pb2+ -0.89878 Pb4+ -0.89878 Bi -0.90198 + Bi3+ -0.90198 Bi5+ -0.90198 Po -0.89333 At -0.83350 Rn -0.74320 + Fr -0.64000 Ra -0.50660 Ra2+ -0.50660 Ac -0.49651 Ac3+ -0.49651 + Th -0.18926 Th4+ -0.18926 Pa -0.01192 U 0.16850 U3+ 0.16850 + U4+ 0.16850 U6+ 0.16850 Np 0.29804 Np3+ 0.29804 Np4+ 0.29804 + Np6+ 0.29804 Pu 0.42597 Pu3+ 0.42597 Pu4+ 0.42597 Pu6+ 0.42597 + Am 0.54967 Cm 0.67922 Bk 0.80547 Cf 0.93342 + save_ + + +save_hi_ang_Fox_c3 + loop_ + _enumeration_default.index + _enumeration_default.value + H .0 D .0 H1- .0 He -2.5476 Li -.71949 + Li1+ -.71949 Be -0.04297 Be2+ -0.04297 B -0.65981 C -0.42715 + N 0.02472 O 0.47500 O1- 0.47500 F 0.54352 F1- 0.54352 + Ne 0.60957 Na 0.76974 Na1+ 0.76974 Mg 0.82738 Mg2+ 0.82738 + Al 0.72294 Al3+ 0.72294 Si 0.55631 Si4+ 0.55631 P 0.20731 + S -0.26058 Cl -0.76135 Cl1- -0.76135 Ar -1.32510 K -1.91290 + K1+ -1.91290 Ca -2.45670 Ca2+ -2.45670 Sc -2.85330 Sc3+ -2.85330 + Ti -3.11710 Ti2+ -3.11710 Ti3+ -3.11710 Ti4+ -3.11710 V -3.22040 + V2+ -3.22040 V3+ -3.22040 V5+ -3.22040 Cr -3.17520 Cr2+ -3.17520 + Cr3+ -3.17520 Mn -3.02150 Mn2+ -3.02150 Mn3+ -3.02150 Mn4+ -3.02150 + Fe -2.71990 Fe2+ -2.71990 Fe3+ -2.71990 Co -2.37050 Co2+ -2.37050 + Co3+ -2.37050 Ni -1.94290 Ni2+ -1.94290 Ni3+ -1.94290 Cu -1.49760 + Cu1+ -1.49760 Cu2+ -1.49760 Zn -1.02160 Zn2+ -1.02160 Ga -0.55471 + Ga3+ -0.55471 Ge -0.09984 Ge4+ -0.09984 As 0.32231 Se 0.69837 + Br 1.00950 Br1- 1.00950 Kr 1.27070 Rb 1.45320 Rb1+ 1.45320 + Sr 1.55410 Sr2+ 1.55410 Y 1.59630 Y3+ 1.59630 Zr 1.51820 + Zr4+ 1.51820 Nb 1.50150 Nb3+ 1.50150 Nb5+ 1.50150 Mo 1.24010 + Mo3+ 1.24010 Mo5+ 1.24010 Mo6+ 1.24010 Tc 1.06630 Ru 0.79060 + Ru3+ 0.79060 Ru4+ 0.79060 Rh 0.49443 Rh3+ 0.49443 Rh4+ 0.49443 + Pd 0.15404 Pd2+ 0.15404 Pd4+ 0.15404 Ag -0.25659 Ag1+ -0.25659 + Ag2+ -0.25659 Cd -0.60990 Cd2+ -0.60990 In -1.03910 In3+ -1.03910 + Sn -1.29860 Sn2+ -1.29860 Sn4+ -1.29860 Sb -1.61640 Sb3+ -1.61640 + Sb5+ -1.61640 Te -1.86420 I -2.13920 I1- -2.13920 Xe -2.34290 + Cs -2.49220 Cs1+ -2.49220 Ba -2.59590 Ba2+ -2.59590 La -2.64050 + La3+ -2.64050 Ce -2.70670 Ce3+ -2.70670 Ce4+ -2.70670 Pr -2.65180 + Pr3+ -2.65180 Pr4+ -2.65180 Nd -2.59010 Nd3+ -2.59010 Pm -2.44210 + Sm -2.28170 Sm3+ -2.28170 Eu -2.07460 Eu2+ -2.07460 Eu3+ -2.07460 + Gd -1.84040 Gd3+ -1.84040 Tb -1.57950 Tb3+ -1.57950 Dy -1.34550 + Dy3+ -1.34550 Ho -1.13090 Ho3+ -1.13090 Er -0.91467 Er3+ -0.91467 + Tm -0.70804 Tm3+ -0.70804 Yb -0.51120 Yb2+ -0.51120 Yb3+ -0.51120 + Lu -0.29820 Lu3+ -0.29820 Hf -0.09620 Hf4+ -0.09620 Ta 0.11842 + Ta5+ 0.11842 W 0.29787 W6+ 0.29787 Re 0.48180 Os 0.61700 + Os4+ 0.61700 Ir 0.75967 Ir3+ 0.75967 Ir4+ 0.75967 Pt 0.87492 + Pt2+ 0.87492 Pt4+ 0.87492 Au 0.96224 Au1+ 0.96224 Au3+ 0.96224 + Hg 1.02850 Hg1+ 1.02850 Hg2+ 1.02850 Tl 1.05970 TL1+ 1.05970 + Tl3+ 1.05970 Pb 1.08380 Pb2+ 1.08380 Pb4+ 1.08380 Bi 1.06850 + Bi3+ 1.06850 Bi5+ 1.06850 Po 1.04380 At 0.97641 Rn 0.88510 + Fr 0.78354 Ra 0.65836 Ra2+ 0.65836 Ac 0.64340 Ac3+ 0.64340 + Th 0.36849 Th4+ 0.36849 Pa 0.20878 U 0.05060 U3+ 0.05060 + U4+ 0.05060 U6+ 0.05060 Np -0.06566 Np3+ -0.06566 Np4+ -0.06566 + Np6+ -0.06566 Pu -0.18080 Pu3+ -0.18080 Pu4+ -0.18080 Pu6+ -0.18080 + Am -0.29112 Cm -0.40588 Bk -0.51729 Cf -0.62981 + save_ + + +save_colour_hue + loop_ + _enumeration_default.index + _enumeration_default.value + H white D blue_light H1- white He unknown Li unknown + Li1+ unknown Be unknown Be2+ unknown B unknown C steel_grey + N blue O red O1- red F green F1- green + Ne unknown Na magenta Na1+ magenta Mg magenta Mg2+ magenta + Al magenta Al3+ magenta Si unknown Si4+ unknown P magenta + S yellow Cl green Cl1- green Ar unknown K magenta + K1+ magenta Ca magenta Ca2+ magenta Sc unknown Sc3+ unknown + Ti magenta Ti2+ magenta Ti3+ magenta Ti4+ magenta V magenta + V2+ magenta V3+ magenta V5+ magenta Cr magenta Cr2+ magenta + Cr3+ magenta Mn magenta Mn2+ magenta Mn3+ magenta Mn4+ magenta + Fe magenta Fe2+ magenta Fe3+ magenta Co magenta Co2+ magenta + Co3+ magenta Ni magenta Ni2+ magenta Ni3+ magenta Cu magenta + Cu1+ magenta Cu2+ magenta Zn magenta Zn2+ magenta Ga magenta + Ga3+ magenta Ge magenta Ge4+ magenta As magenta Se yellow + Br green Br1- green Kr unknown Rb unknown Rb1+ unknown + Sr unknown Sr2+ unknown Y unknown Y3+ unknown Zr unknown + Zr4+ unknown Nb unknown Nb3+ unknown Nb5+ unknown Mo unknown + Mo3+ magenta Mo5+ magenta Mo6+ magenta Tc unknown Ru unknown + Ru3+ unknown Ru4+ unknown Rh unknown Rh3+ unknown Rh4+ unknown + Pd unknown Pd2+ unknown Pd4+ unknown Ag magenta Ag1+ magenta + Ag2+ magenta Cd magenta Cd2+ magenta In unknown In3+ unknown + Sn magenta Sn2+ magenta Sn4+ magenta Sb magenta Sb3+ magenta + Sb5+ magenta Te unknown I green I1- green Xe unknown + Cs unknown Cs1+ unknown Ba unknown Ba2+ unknown La unknown + La3+ unknown Ce unknown Ce3+ unknown Ce4+ unknown Pr unknown + Pr3+ unknown Pr4+ unknown Nd unknown Nd3+ unknown Pm unknown + Sm unknown Sm3+ unknown Eu unknown Eu2+ unknown Eu3+ unknown + Gd unknown Gd3+ unknown Tb unknown Tb3+ unknown Dy unknown + Dy3+ unknown Ho unknown Ho3+ unknown Er unknown Er3+ unknown + Tm unknown Tm3+ unknown Yb unknown Yb2+ unknown Yb3+ unknown + Lu unknown Lu3+ unknown Hf unknown Hf4+ unknown Ta unknown + Ta5+ unknown W unknown W6+ unknown Re unknown Os unknown + Os4+ unknown Ir unknown Ir3+ unknown Ir4+ unknown Pt magenta + Pt2+ magenta Pt4+ magenta Au magenta Au1+ magenta Au3+ magenta + Hg magenta Hg1+ magenta Hg2+ magenta Tl unknown TL1+ unknown + Tl3+ unknown Pb magenta Pb2+ magenta Pb4+ magenta Bi magenta + Bi3+ magenta Bi5+ magenta Po unknown At unknown Rn unknown + Fr unknown Ra unknown Ra2+ unknown Ac unknown Ac3+ unknown + Th unknown Th4+ unknown Pa unknown U unknown U3+ unknown + U4+ unknown U6+ unknown Np unknown Np3+ unknown Np4+ unknown + Np6+ unknown Pu unknown Pu3+ unknown Pu4+ unknown Pu6+ unknown + Am unknown Cm unknown Bk unknown Cf unknown + save_ + + +#============================================================================= +# The dictionary's creation history. +#============================================================================ + + loop_ + _dictionary_audit.version + _dictionary_audit.date + _dictionary_audit.revision + + 1.0.01 2005-12-12 +; + Initial version of the TEMPLATES dictionary created from the + definitions used in CORE_3 dictionary version 3.5.02 +; + 1.0.1 2006-02-12 +; + Remove dictionary attributes from a save frame. + Change category core_templates to template +; + 1.2.01 2006-02-21 +; + File structure to conform with prototype version dictionaries. +; + 1.2.02 2006-03-07 +; + Added the template _template.relational_id for the ddl3 dictionary. +; + 1.2.03 2006-06-20 +; + Apply DDL 3.6.04 attributes. +; + 1.2.04 2006-06-27 +; + Change filename to com_val.dic. + apply DDL 3.6.05 changes. + add 'context' and 'method' enumerated lists + add 'enumeration_default' blocks to this file +; + 1.2.05 2006-08-30 +; + In type.contents change constrction of Otag to 'ANchar [_]' +; + 1.2.06 2006-11-13 +; + Remove method and context frames +; + 1.2.07 2006-12-14 +; + Apply DDL3 3.7.01 attributes. +; + 1.2.08 2007-10-11 +; + Correct definitions of Ctag and Otag in _type.contents +; + 1.2.09 2011-03-25 +; + Change the syntax of "Filename" in type_contents enumeration set. +; + 1.3.01 2011-08-03 +; + Remove definition.id lines in keeping with nested imports. +; + 1.3.02 2011-12-01 +; + Update the DDL version. No Matrix types present. +; + 1.3.03 2012-05-07 +; + Update the DDL version. Change dictionary class to Template +; + 1.3.04 2012-07-08 +; + Remove type.contents enumeration list +; + 1.3.05 2012-10-16 +; + Change all element symbols in the ion-to-elemnt default list to Upper + and lower case characters (from all upper). +;