############################################################################## # Example file to accompany the CIF dictionary for modulated structures # ############################################################################## # A more complicated example. The incommensurate composite (PbS)1.12 VS2 # # This is a CIF example corresponding to the modulated structure of # the incommensurate composite crystal (PbS)1.12VS2. # Data have been extracted from the already published paper: # # Structure of the Incommensurate Composiste Crystal (PbS)1.12VS2 # by Mitsuko Onoda, Katsuo Kato, Yoshito Gotoh & Yoshinao Oosawa # Acta Cryst. (1990), B46, 487-492 # # Any line starting with the symbol '#' is considered as a comment. ############################################################################## data_PbSVS2 _audit_block_code 1998-01-08|PbSVS2|G.M.| loop_ _audit_link_block_code _audit_link_block_description . 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' _audit_creation_date 1994-07-18 _audit_creation_method 'using a text processor from published results' _audit_conform_dict_name cif_ms.dic _audit_conform_dict_version 1.0 #----------------------------------------------------------------------------- # Chemical information #----------------------------------------------------------------------------- _chemical_formula_analytical 'Pb1.12 S3.12 V1' _chemical_formula_weight 384.20 #----------------------------------------------------------------------------- # 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 ; Weissenberg pothographs show monoclinic symmetry. The following extinction rules were detected: PbS subsystem hkl h+k = odd h+l = odd k+l = odd VS2 subsystem hkl h+k = odd l = odd extinction rules referred to a higher-dimensional reciprocal cell HKL0 H+K = odd H+L = odd K+L = odd H0LM H+M = odd L = odd Possible superspace groups: P:C2/m:1-1, P:C2:1, P:Cm:-1. Satellites were observed only by electron diffraction. ; #----------------------------------------------------------------------------- # The next items are neccessary, basically, to check the # consistency of the CIF. An extra Miller index is expected. #----------------------------------------------------------------------------- _exptl_crystal_type_of_structure 'comp' _cell_subsystems_number 2 _cell_modulation_dimension 1 _cell_reciprocal_basis_vect_number 4 #----------------------------------------------------------------------------- # Extended reciprocal cell. #----------------------------------------------------------------------------- _cell_reciprocal_basis_description ; a1*,b1*,c1* (reciprocal basis spanning the reciprocal basis of the PbS subsystem), a2* reciprocal axis corresponding to the VS2 subsystem. ; _space_group_ssg_name_WJJ 'P:C 2:1' _space_group_ssg_symops_number 8 loop_ _space_group_symop_ssg_id _space_group_symop_ssg_operation_algebraic 1 x1,x2,x3,x4 2 -x1,x2,-x3,x4 3 1/2+x1,1/2+x2,x3,1/2+x4 4 1/2-x1,1/2+x2,-x3,1/2+x4 5 x1,1/2+x2,1/2+x3,x4 6 -x1,1/2+x2,1/2-x3,x4 7 1/2+x1,x2,1/2+x3,1/2+x4 8 1/2-x1,x2,1/2-x3,1/2+x4 _exptl_crystal_description prism _exptl_crystal_size_max 0.132 _exptl_crystal_size_mid 0.043 _exptl_crystal_size_min 0.016 _exptl_crystal_density_diffrn 5.788 _exptl_crystal_density_meas ? _exptl_absorpt_coefficient_mu 46.45 _exptl_absorpt_correction_T_min 0.038 _exptl_absorpt_correction_T_max 0.257 _diffrn_special_details ; No satellites were measured. ; _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_measurement_device 'Enraf-Nonius CAD4' # In the next entry \q stands for theta. _diffrn_measurement_method '\q-2\q' _diffrn_reflns_theta_max 43.24 _diffrn_reflns_theta_min ? _diffrn_reflns_limit_h_max 11 _diffrn_reflns_limit_k_max 11 _diffrn_reflns_limit_l_max 45 _diffrn_reflns_limit_index_m_1_max 6 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_k_min 0 _diffrn_reflns_limit_l_min -45 _diffrn_reflns_limit_index_m_1_min 0 _diffrn_reflns_number 4832 loop_ _diffrn_reflns_class_description _diffrn_reflns_class_code _diffrn_reflns_class_av_R_eq 'Main reflections.Subsystem PbS' 'HKL0' 0.022 'Main reflections.Subsystem VS2' 'H0LM' 0.022 'Common Main reflections' 'H0L0' 0.029 # In the next entry \s stands for sigma. _reflns_observed_criterion 'I>3\s(I) for any reflection class' _reflns_number_total 3487 _reflns_number_observed 1780 loop_ _reflns_class_number_gt _reflns_class_code 1098 'HKL0' 499 'H0LM' 183 'H0L0' #----------------------------------------------------------------------------- # Common refinement conditions section. Some of the items present here could # be within the _REFRNCE (reference structure), _MOD (modulated structure), # _REFRNCE_SUB (reference structure of a subsystem) or _MOD_SUB (modulated # structure of a subsystem) data block depending on the specific compound. #----------------------------------------------------------------------------- _refine_ls_structure_factor_coef F _refine_ls_matrix_type full _refine_ls_weighting_scheme unit #----------------------------------------------------------------------------- # Computing section #----------------------------------------------------------------------------- _computing_structure_refinement 'FMLSM (Kato)' #----------------------------------------------------------------------------- # 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... #----------------------------------------------------------------------------- # Items concerning publication data #----------------------------------------------------------------------------- loop_ _citation_id _citation_title _citation_journal_abbrev _citation_journal_volume _citation_page_first _citation_page_last _citation_year primary 'Structure of the Incommensurate Composite Crystal (PbS)1.12VS2' 'Acta Cryst. B' 46 487 492 1990 loop_ _citation_author_citation_id _citation_author_name primary 'Mitsuko Onoda' primary 'Katsuo Kato' primary 'Yoshito Gotoh' primary 'Yoshinao Oosawa' ########################## End of common data ########################## ############################################################################## # Common items concerning the unmodulated (basic, average) structure ############################################################################## data_PbSVS2_REFRNCE _audit_block_code 1998-01-08|PbSVS2|G.M.|_REFRNCE loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' . 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' _refine_ls_R_factor_obs 0.083 loop_ _diffrn_reflns_class_description _diffrn_reflns_class_code 'Main reflections.Subsystem PbS' 'HKL0' 'Main reflections.Subsystem VS2' 'H0LM' 'Common Main reflections' 'H0L0' loop_ _refine_ls_class_R_factor_gt _refine_ls_class_code 0.072 'HKL0' 0.106 'H0LM' 0.098 'H0L0' ############### End of unmodulated structure common data ############### ############################################################################## # Items concerning the reference (basic, average) structure of the # first subsystem PbS ############################################################################## data_PbSVS2_REFRNCE_PbS _audit_block_code 1998-01-08|PbSVS2|G.M.|_REFRNCE_Pbs loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' . 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' _cell_length_a 5.7279(3) _cell_length_b 5.7886(7) _cell_length_c 23.939(2) _cell_angle_alpha 90.00 _cell_angle_beta 98.947(3) _cell_angle_gamma 90.00 _cell_measurement_theta_min 27.42 _cell_measurement_theta_max 31.44 _cell_measurement_reflns_used 23 _symmetry_cell_setting monoclinic loop_ _atom_type_symbol _atom_type_scat_source Pb International_Tables_Vol_IV S 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 Pb 1.0 0.79399(12) 0.0 0.06793(3) 0.0270(3) Uani S(1) 1.0 0.2811(9) -0.0203(10) 0.0485(2) 0.018(2) Uani _refine_special_details ; y-coordinate of Pb atom was not refined to fix the origin ; loop_ _geom_bond_atom_site_label_1 _geom_bond_site_ssg_symmetry_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance_min _geom_bond_distance_av _geom_bond_distance_max Pb 1 S(1) 1 ? 2.904(5) ? # .... Data omitted Pb 1 S(1) 3_5455 ? 3.046(5) ? Pb 1 S(2) 1 3.193(2) 3.329(3) 3.584(3) # .... Data omitted ######### End of reference structure first subsystem data ############ ############################################################################## # Items concerning the reference (basic, average) structure of the # second subsystem VS2 ############################################################################## data_PbSVS2_REFRNCE_VS2 _audit_block_code 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' . 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' _cell_length_a 5.7279(3) _cell_length_b 3.2560(7) _cell_length_c 23.939(2) _cell_angle_alpha 90.00 _cell_angle_beta 98.947(3) _cell_angle_gamma 90.00 _cell_measurement_theta_min ? _cell_measurement_theta_max ? _cell_measurement_reflns_used 16 _symmetry_cell_setting monoclinic loop_ _atom_type_symbol _atom_type_scat_source S International_Tables_Vol_IV V 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 V 1.0 0.0 0.0 0.25 0.015(1) Uani S S(2) 1.0 0.6284(4) -0.023(2) 0.18926(10) 0.0899(8) Uani . _refine_special_details ; y-coordinate of V atom was not refined to fix the origin ; loop_ _geom_bond_atom_site_label_1 _geom_bond_site_ssg_symmetry_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance_min _geom_bond_distance_av _geom_bond_distance_max V 1 S(2) 1_4555 ? 2.385(2) ? V 1 S(2) 3_4555 ? 2.324(4) ? # .... Data omitted ######### End of reference structure second subsystem data ############ ############################################################################## # Common items concerning the modulated structure ############################################################################## data_PbSVS2_MOD _audit_block_code 1998-01-08|PbSVS2|G.M.|_MOD loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' . 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' _refine_ls_mod_func_description ; Displacive modulation. Fourier series. ; loop_ _diffrn_reflns_class_description _diffrn_reflns_class_code 'Main reflections.Subsystem PbS' 'HKL0' 'Main reflections.Subsystem VS2' 'H0LM' 'Common Main reflections' 'H0L0' _refine_ls_number_parameters 156 _refine_ls_R_factor_obs 0.059 loop_ _refine_ls_class_R_factor_gt _refine_ls_class_code 0.051 'HKL0' 0.079 'H0LM' 0.071 'H0L0' ################ End of modulated structure common data ################ ############################################################################## # Items concerning the modulated structure of the first subsystem ############################################################################## data_PbSVS2_MOD_PbS _audit_block_code 1998-01-08|PbSVS2|G.M.|_MOD_PbS loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' . 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_VS2 'modulated structure (2-nd subsystem)' loop_ _atom_type_symbol _atom_type_scat_source Pb International_Tables_Vol_IV S 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_displace_modulation_flag _atom_site_U_modulation_flag Pb 1.0 0.7946(2) 0.0 0.06890(5) 0.0331(5) Uani yes yes S(1) 1.0 0.2822(12) -0.0100(14) 0.0482(3) 0.022(3) Uani yes yes _refine_special_details ; y-coordinate of Pb atom was not refined to fix the origin ; #----------------------------------------------------------------------------- # Modulation wave vector. Here is expressed the modulation wave vector # a2*, in the three-dimensional reciprocal basis of the first subsystem. #----------------------------------------------------------------------------- loop_ _cell_wave_vector_seq_id _cell_wave_vector_y 1 1.778 loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 1.778 'First harmonic' 2 3.556 'Second harmonic' #----------------------------------------------------------------------------- # Modulation parameters #----------------------------------------------------------------------------- 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 Pbx1 Pb x 1 Pby1 Pb y 1 Pbz1 Pb z 1 Pbx2 Pb x 2 Pby2 Pb y 2 Pbz2 Pb z 2 Sx1 S(1) x 1 Sy1 S(1) y 1 Sz1 S(1) z 1 Sx2 S(1) x 2 Sy2 S(1) y 2 Sz2 S(1) z 2 loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Pbx1 0.0062(7) 0.0067(7) Pby1 -0.0097(12) -0.0032(12) Pbz1 -0.0015(2) 0.0009(2) Pbx2 -0.0065(9) 0.0082(8) Pby2 0.0045(16) -0.0011(11) Pbz2 -0.0011(2) 0.0034(2) Sx1 -0.007(3) -0.021(3) Sy1 -0.019(3) -0.016(3) Sz1 -0.0033(6) 0.0037(8) Sx2 0.001(2) -0.012(3) Sy2 0.011(3) 0.022(2) Sz2 -0.0027(6) -0.0017(6) loop_ _atom_site_U_Fourier_id _atom_site_U_Fourier_atom_site_label _atom_site_U_Fourier_tens_elem _atom_site_U_Fourier_wave_vector_seq_id PbU1 Pb Uiso 1 PbU2 Pb Uiso 2 SU1 S(1) Uiso 1 SU2 S(1) Uiso 2 loop_ _atom_site_U_Fourier_param_id _atom_site_U_Fourier_param_cos _atom_site_U_Fourier_param_sin PbU1 0.001(2) -0.005(2) PbU2 0.003(2) 0.013(2) SU1 0.006(4) -0.015(5) SU2 -0.010(4) 0.023(4) loop_ _geom_bond_atom_site_label_1 _geom_bond_site_ssg_symmetry_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance_min _geom_bond_distance_av _geom_bond_distance_max Pb 1 S(1) 1 2.72(2) 2.91(2) 3.20(2) # .... Data omitted Pb 1 S(1) 3_5455 2.71(2) 3.00(2) 3.17(2) Pb 1 S(2) 1 3.162(15) 3.31(2) 3.55(2) # .... Data omitted ########## End of modulated structure first subsystem data ############ ############################################################################## #Items concerning the modulated structure of the second subsystem ############################################################################## data_PbSVS2_MOD_VS2 _audit_block_code 1998-01-08|PbSVS2|G.M.|_MOD_VS2 loop_ _audit_link_block_code _audit_link_block_description 1998-01-08|PbSVS2|G.M.| 'common experimental and publication data' 1998-01-08|PbSVS2|G.M.|_REFRNCE 'reference structure (global data)' 1998-01-08|PbSVS2|G.M.|_MOD 'modulated structure (global data)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_PbS 'reference structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_MOD_PbS 'modulated structure (1-st subsystem)' 1998-01-08|PbSVS2|G.M.|_REFRNCE_VS2 'reference structure (2-nd subsystem)' . 'modulated structure (2-nd subsystem)' loop_ _atom_type_symbol _atom_type_scat_source S International_Tables_Vol_IV V 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 _atom_site_displace_modulation_flag _atom_site_U_modulation_flag V 1.0 0.0 0.0 0.25 0.015(1) Uani S yes yes S(2) 1.0 0.6284(5) 0.002(3) 0.18943(12) 0.006(1) Uani . yes yes _refine_special_details ; y-coordinate of V atom was not refined to fix the origin. Ueq corresponding to V atom is unrealiable as the refined component U22 was negative. ; #----------------------------------------------------------------------------- # Modulation wave vector. Here is expressed the modulation wave vector # a1*, in the three-dimensional reciprocal basis of the second # subsystem. #----------------------------------------------------------------------------- loop_ _cell_wave_vector_seq_id _cell_wave_vector_y 1 0.562 loop_ _atom_site_Fourier_wave_vector_seq_id _atom_site_Fourier_wave_vector_x _atom_site_Fourier_wave_vector_description 1 0.562 'First harmonic' 2 1.124 'Second harmonic' #----------------------------------------------------------------------------- # Modulation parameters #----------------------------------------------------------------------------- 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 Vx1 V x 1 Vy1 V y 1 Vz1 V z 1 Vx2 V x 2 Vy2 V y 2 Vz2 V z 2 Sx1 S(2) x 1 Sy1 S(2) y 1 Sz1 S(2) z 1 Sx2 S(2) x 2 Sy2 S(2) y 2 Sz2 S(2) z 2 loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Vx1 -0.005(2) -0.007(3) Vy1 0.0 0.0 Vz1 0.0008(3) 0.0002(8) Vx2 0.0 0.0 Vy2 -0.044(4) -0.025(4) Vz2 0.0 0.0 Sx1 -0.0024(14) -0.005(3) Sy1 0.050(2) 0.005(6) Sz1 -0.0000(3) -0.0025(6) Sx2 0.001(3) -0.002(3) Sy2 -0.001(7) -0.003(5) Sz2 0.0003(7) 0.0011(8) loop_ _atom_site_U_Fourier_id _atom_site_U_Fourier_atom_site_label _atom_site_U_Fourier_tens_elem _atom_site_U_Fourier_wave_vector_seq_id VU1 V Uiso 1 VU2 V Uiso 2 SU1 S(2) Uiso 1 SU2 S(2) Uiso 2 loop_ _atom_site_U_Fourier_param_id _atom_site_U_Fourier_param_cos _atom_site_U_Fourier_param_sin VU1 0. 0. VU2 0.006(3) -0.003(5) SU1 0.003(3) -0.002(4) SU2 -0.002(3) -0.002(5) loop_ _geom_bond_atom_site_label_1 _geom_bond_site_ssg_symmetry_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance_min _geom_bond_distance_av _geom_bond_distance_max V 1 S(2) 1_4555 2.37(2) 2.39(2) 2.41(2) V 1 S(2) 3_4555 2.12(2) 2.38(2) 2.57(2) # .... Data omitted #########End of modulated structure second subsystem data###########