############################################################################## # Example file to accompany the CIF dictionary for modulated structures # ############################################################################## # A typical example: K2SeO4 # # This is a CIF example corresponding to the one-dimensional # incommensurately modulated structure of K2SeO4. Any line starting with # the symbol '#' is considered as a comment. ############################################################################## data_KSE _audit_block_code 1997-07-21|KSE|G.M.| loop_ _audit_link_block_code _audit_link_block_description . 'experimental data common to ref./mod. structures' 1997-07-21|KSE|G.M.|_REFRNCE 'reference structure' 1997-07-21|KSE|G.M.|_MOD 'modulated structure' _audit_creation_date 1997-07-21 _audit_update_record ; 1998-05-27 Modifications according to cifdic.ms 0.4 2001-04-20 Modifications according to cifdic.ms 0.47 ; _audit_creation_method 'using a text processor from unpublished results' _audit_conform_dict_name cif_ms.dic _audit_conform_dict_version 1.0 #----------------------------------------------------------------------------- # Chemical information #----------------------------------------------------------------------------- _chemical_formula_structural 'K2 O4 Se' _chemical_formula_weight 221.152 #----------------------------------------------------------------------------- # Common experimental section. Some of the items present here could be # within the _REFRNCE (reference structure) or _MOD (modulated structure) # data block depending on the specific experimental conditions. #----------------------------------------------------------------------------- _diffrn_symmetry_description ; The whole diffraction pattern shows orthorhombic symmetry. The following extinction rules were detected: 0kl0 k+l=odd h0lm h+m=odd hk0m m =odd h00m h,m=odd Superspace group: P:Pnam:-1ss ; # The next three items are neccessary, basically, to check the # consistency of the CIF. An extra Miller index is expected. _exptl_crystal_type_of_structure 'mod' _cell_modulation_dimension 1 _cell_reciprocal_basis_vect_number 4 # Extended reciprocal cell. _cell_reciprocal_basis_description ; a*,b*,c* (reciprocal basis spanning the lattice of main reflections), q modulation wave vector. ; _cell_wave_vectors_meas_details 'Determined from profiles along q' _exptl_crystal_description prism _exptl_crystal_colour colourless _exptl_crystal_size_max 0.20 _exptl_crystal_size_mid 0.19 _exptl_crystal_size_min 0.19 _exptl_crystal_density_diffrn 3.118 _exptl_crystal_density_meas ? _exptl_crystal_F_000 416 _exptl_absorpt_coefficient_mu 9.554 _exptl_absorpt_correction_type 'gaussian ORABS (XRAY72:Schwarzenbach)' #----------------------------------------------------------------------------- # Crystal faces. In this case four indices are required. Alternatively # _exptl_crystal_face_index_h, _exptl_crystal_face_index_k, # _exptl_crystal_face_index_l can be used in this case as no satellite # faces are reported. #----------------------------------------------------------------------------- loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist 1 -1 0 0.06 -1 1 0 0.09 # .................. More faces here 0 1 -1 0.04 _exptl_absorpt_correction_T_min 0.226 _exptl_absorpt_correction_T_max 0.382 # In the next entry \q stands for theta. _diffrn_special_details ; \q-2\q scan. Variable scan width. Data collection performed within the incommensurate phase.Satellites were measured together with their associated main reflection. ; _diffrn_ambient_temperature 113 _diffrn_radiation_wavelength 0.7107 # In the next entry \a stands for alpha. _diffrn_radiation_type 'Mo K\a' _diffrn_radiation_source 'X-ray tube' _diffrn_radiation_monochromator 'graphite' _diffrn_measurement_device 'Syntex P21' # In the next entry \q stands for theta. _diffrn_measurement_method '\q-2\q' _diffrn_standards_number 3 _diffrn_standards_interval_time 1600 _diffrn_standards_decay_% 5.5 #----------------------------------------------------------------------------- # Check reflections. In this case four indices are required. # Alternatively _diffrn_standard_refln_index_h, # _diffrn_standard_refln_index_k, _diffrn_standard_refln_index_l can be # used in this case as no satellites have used as standard reflections. #----------------------------------------------------------------------------- loop_ _diffrn_standard_refln_index_h _diffrn_standard_refln_index_k _diffrn_standard_refln_index_l 4 0 0 0 8 0 0 0 4 _diffrn_reflns_satellite_order_max 1 _diffrn_reflns_theta_max 40.14 _diffrn_reflns_theta_min 3.32 _diffrn_reflns_limit_h_max 8 _diffrn_reflns_limit_k_max 18 _diffrn_reflns_limit_l_max 10 _diffrn_reflns_limit_index_m_1_max 1 _diffrn_reflns_limit_h_min 0 _diffrn_reflns_limit_k_min 0 _diffrn_reflns_limit_l_min 0 _diffrn_reflns_limit_index_m_1_min -1 _diffrn_reflns_number 2625 _reflns_number_total 1791 _diffrn_reflns_av_R_equivalents 0.018 # In the next entry \s stands for sigma. _reflns_observed_criterion 'I>3\s(I) for any reflection class' _reflns_number_observed 1338 loop_ _diffrn_reflns_class_number _diffrn_reflns_class_d_res_low _diffrn_reflns_class_d_res_high _diffrn_reflns_class_av_R_eq _diffrn_reflns_class_code _diffrn_reflns_class_description 1580 6.136 0.551 0.015 'Main' 'm=0; main reflections' 1045 6.136 0.551 0.010 'Sat1' 'm=1; first-order satellites' loop_ _reflns_class_number_total _reflns_class_number_gt _reflns_class_code 1055 952 'Main' 736 386 'Sat1' #----------------------------------------------------------------------------- # Common refinement conditions section. Some of the items present here could # be within the _REFRNCE (reference structure), _MOD (modulated structure). #----------------------------------------------------------------------------- _refine_ls_structure_factor_coef F _refine_ls_matrix_type full _refine_ls_weighting_scheme sigma #----------------------------------------------------------------------------- # Computing section #----------------------------------------------------------------------------- _computing_data_reduction ; INTENS (XRAY72:Schwarzenbach. Local version for IC structures) DATRDN (XRAY72:Stewart) ; _computing_structure_refinement 'JANA93 (Petricek)' #----------------------------------------------------------------------------- # Items concerning publication data #----------------------------------------------------------------------------- _publ_author_name 'Madariaga G.' _publ_author_address ; Departamento de Fisica de la Materia Condensada. Facultad de Ciencias Universidad del Pais Vasco Apdo. 644 48080 Bilbao Spain ; _publ_contact_author_email wmpmameg@lg.ehu.es _publ_contact_author_fax '34 946012467' ########################## End of common data ########################## ############################################################################## # Items concerning the reference (basic, average) structure ############################################################################## data_KSE_REFRNCE _audit_block_code 1997-07-21|KSE|G.M.|_REFRNCE loop_ _audit_link_block_code _audit_link_block_description 1997-07-21|KSE|G.M.| 'experimental data common to ref./mod. structures' . 'reference structure' 1997-07-21|KSE|G.M.|_MOD 'modulated structure' _cell_length_a 7.597(4) _cell_length_b 10.375(4) _cell_length_c 5.975(2) _cell_angle_alpha 90.00 _cell_angle_beta 90.00 _cell_angle_gamma 90.00 _cell_volume 470.9(6) _cell_formula_units_Z 4 _cell_measurement_temperature 113 _symmetry_cell_setting orthorhombic _symmetry_space_group_name_H-M 'P n a m' loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 1/2+x,1/2-y,1/2-z 3 1/2-x,1/2+y,-z 4 -x,-y,1/2+z 5 -x,-y,-z 6 1/2-x,1/2+y,1/2+z 7 1/2+x,1/2-y,z 8 x,y,1/2-z loop_ _atom_type_symbol _atom_type_oxidation_number _atom_type_number_in_cell _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source K 0 8 0.179 0.250 International_Tables_Vol_IV Se 0 4 -.178 2.223 International_Tables_Vol_IV O 0 16 0.008 0.006 International_Tables_Vol_IV loop_ _atom_site_label _atom_site_occupancy _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_thermal_displace_type _atom_site_refinement_flags Se 0.5 0.22216(5) 0.41861(3) 0.250000 0.00499(9) Uani S K1 0.5 0.1670(1) 0.08069(7) 0.250000 0.0102(2) Uani S K2 0.5 -0.0013(1) 0.70765(7) 0.250000 0.009(1) Uani S O1 1.0 0.2891(3) 0.3413(2) 0.0277(3) 0.0194(5) Uani . O2 0.5 0.3131(4) 0.5621(2) 0.250000 0.0189(8) Uani S O3 0.5 0.0092(4) 0.4304(3) 0.250000 0.026(1) Uani S loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Se 0.0054(2) 0.0033(1) 0.0063(1) -0.0001(1) 0.0 0.0 K1 0.0082(4) 0.0093(2) 0.0130(3) 0.0005(3) 0.0 0.0 K2 0.0069(4) 0.0054(2) 0.0149(3) 0.0000(2) 0.0 0.0 O1 0.030(1) 0.0200(8) 0.0084(7) 0.0127(9) -0.0005(8) -0.0049(6) O2 0.011(1) 0.005(9) 0.041(2) -0.005(1) 0.0 0.0 O3 0.009(2) 0.015(1) 0.054(2) 0.000(1) 0.0 0.0 _refine_ls_extinction_method 'Becker-Coppens type 1 gaussian isotropic' _refine_ls_extinction_coef 2559(13) _refine_ls_number_reflns 861 _refine_ls_number_parameters 41 _refine_ls_R_factor_all 0.024 _refine_ls_R_factor_obs 0.024 _refine_ls_wR_factor_all 0.025 _refine_ls_goodness_of_fit_all 2.26 _refine_ls_goodness_of_fit_obs 2.26 _refine_ls_shift/esd_max 0.0002 _refine_ls_shift/esd_mean 0.0001 # Next two values are unknown _refine_diff_density_min ? _refine_diff_density_max ? _reflns_scale_group_code 1 _reflns_scale_meas_F 3.710(8) #----------------------------------------------------------------------------- # List of main reflections. #----------------------------------------------------------------------------- loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_meas _refln_F_calc _refln_F_sigma _refln_observed_status _refln_scale_group_code # Next question marks are included for consistency ? ? ? ? ? ? ? ? # More reflections here ... ################# End of reference structure data ##################### ############################################################################## # Items concerning the modulated structure ############################################################################## data_KSE_MOD _audit_block_code 1997-07-21|KSE|G.M.|_MOD loop_ _audit_link_block_code _audit_link_block_description 1997-07-21|KSE|G.M.| 'experimental data common to ref./mod. structures' 1997-07-21|KSE|G.M.|_REFRNCE 'reference structure' . 'modulated structure' _space_group_ssg_name_WJJ 'P:P n a m:-1 s s' _space_group_ssg_symops_number 8 loop_ _space_group_symop_ssg_id _space_group_symop_ssg_operation_algebraic 1 x1,x2,x3,x4 2 1/2+x1,1/2-x2,1/2-x3,x4 3 1/2-x1,1/2+x2,-x3,1/2-x4 4 -x1,-x2,1/2+x3,1/2-x4 5 -x1,-x2,-x3,-x4 6 1/2-x1,1/2+x2,1/2+x3,-x4 7 1/2+x1,1/2-x2,x3,1/2+x4 8 x1,x2,1/2-x3,1/2+x4 loop_ _atom_type_symbol _atom_type_oxidation_number _atom_type_number_in_cell _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source K 0 8 0.179 0.250 International_Tables_Vol_IV Se 0 4 -.178 2.223 International_Tables_Vol_IV O 0 16 0.008 0.006 International_Tables_Vol_IV # SeO4 group was constrained to be a rigid body loop_ _atom_site_description _atom_site_label _atom_site_occupancy _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_thermal_displace_type _atom_site_refinement_flags _atom_site_displace_modulation_flag ; SeO4 is a tetrahedral group formed by the atoms: Se O1 O2 O3 and O1p O1p is related to O1 by the mirror plane perpendicular to the c-axis. The coordinates given by _atom_site_fract_ correspond to the centre of mass. ; SeO4 0.5 0.22346 0.41868 0.250000 ? ? SG yes . Se 0.5 0.22216(4) 0.41861(3) 0.250000 0.00428(9) Uani S . . K1 0.5 0.1670(1) 0.08069(7) 0.250000 0.0102(2) Uani S yes . K2 0.5 -0.0013(1) 0.70766(4) 0.250000 0.0072(2) Uani S yes . O1 1.0 0.2890(3) 0.3413(2) 0.0277(3) 0.0130(6) Uani . . . O2 0.5 0.3130(4) 0.5621(2) 0.250000 0.0119(8) Uani S . . O3 0.5 0.0092(4) 0.4304(3) 0.250000 0.0164(9) Uani S . #----------------------------------------------------------------------------- # Modulation parameters #----------------------------------------------------------------------------- _refine_ls_mod_func_description ; Displacive modulation. Fourier series. Modulation of SeO4 group described in terms of rigid translations and rotations. ; #----------------------------------------------------------------------------- # Modulation wave vector #----------------------------------------------------------------------------- loop_ _cell_wave_vector_seq_id _cell_wave_vector_x 1 0.318(5) loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.318(5) 'Only the first harmonic was used' loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id K1_z_1 K1 z 1 K2_z_1 K2 z 1 SeO_z_1 SeO4 z 1 loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin K1_z_1 0.0080(4) -0.0106(5) K2_z_1 0.0159(4) 0.0071(6) SeO_z_1 -0.0089(2) -0.0058(2) loop_ _atom_site_rot_Fourier_id _atom_site_rot_Fourier_atom_site_label _atom_site_rot_Fourier_axis _atom_site_rot_Fourier_wave_vector_seq_id SeO_x_1 SeO4 x 1 SeO_y_1 SeO4 y 1 loop_ _atom_site_rot_Fourier_param_id _atom_site_rot_Fourier_param_cos _atom_site_rot_Fourier_param_sin SeO_x_1 -4.2(1) 0.91(3) SeO_y_1 4.3(1) 0. loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Se 0.0054(2) 0.0033(1) 0.0042(1) -0.0001(1) 0.0 0.0 K1 0.0082(4) 0.0093(2) 0.0097(4) 0.0005(3) 0.0 0.0 K2 0.0069(4) 0.0054(2) 0.0092(4) 0.0000(2) 0.0 0.0 O1 0.016(1) 0.0147(9) 0.0082(7) 0.006(1) 0.0001(8) -0.0054(6) O2 0.011(1) 0.0052(9) 0.019(2) -0.0047(9) 0.0 0.0 O3 0.009(1) 0.015(1) 0.025(2) 0.000(1) 0.0 0.0 _refine_ls_extinction_method 'Becker-Coppens type 1 gaussian isotropic' _refine_ls_extinction_coef 2158(10) _refine_ls_number_reflns 1326 _refine_ls_number_parameters 51 _refine_ls_F_calc_formula 'Petricek & Coppens;Acta Cryst. A44 (1988) 235' _refine_ls_F_calc_details ; Maximum number of Bessel functions used for infinite summation: 50. Accuracy of Bessel functions calculation: 0.00001. ; _refine_ls_F_calc_accuracy ? _refine_ls_R_factor_all 0.028 _refine_ls_R_factor_obs 0.028 _refine_ls_wR_factor_all 0.027 loop_ _diffrn_reflns_class_description _diffrn_reflns_class_code 'm=0; main reflections' 'Main' 'm=1; first-order satellites' 'Sat1' loop_ _refine_ls_class_code _refine_ls_class_R_factor_all _refine_ls_class_R_factor_gt _refine_ls_class_wR_factor_all 'Main' 0.024 0.024 0.025 'Sat1' 0.085 0.085 0.076 _refine_ls_goodness_of_fit_all 2.14 _refine_ls_goodness_of_fit_obs 2.14 _refine_ls_shift/esd_max 0.0003 _refine_ls_shift/esd_mean 0.0000 # Next two values are unknown _refine_diff_density_min ? _refine_diff_density_max ? _reflns_scale_group_code 1 _reflns_scale_meas_F 3.709(8) #----------------------------------------------------------------------------- # List of reflections. #----------------------------------------------------------------------------- loop_ _refln_index_h _refln_index_k _refln_index_l _refln_index_m_1 _refln_F_meas _refln_F_calc _refln_F_sigma _refln_observed_status _refln_scale_group_code # Next question marks are included for consistency ? ? ? ? ? ? ? ? ? # More reflections here... ################# End of modulated structure data #####################