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CIF files can used when [[processing:synthetic_dataset|creating synthetic datasets]] with [[software:polyxsim|PolyXSim]] for testing and learning Multigrain XRD. | CIF files can used when [[processing:synthetic_dataset|creating synthetic datasets]] with [[software:polyxsim|PolyXSim]] for testing and learning Multigrain XRD. | ||
- | ==== Example of CIF file for Olivine ==== | + | Specific examples: |
- | + | * [[fileformat:olivinecif|Olivine in Pnma]] | |
- | We made a CIF file for olivine in the Pnma space group. | + | |
- | + | ||
- | <code> | + | |
- | data_Olivine | + | |
- | _audit_creation_method 'manual editing' | + | |
- | _chemical_name_systematic | + | |
- | ; | + | |
- | Forsterite | + | |
- | ; | + | |
- | _chemical_formula_sum '(Mg2) Si O4' | + | |
- | _cell_length_a 10.1902 | + | |
- | _cell_length_b 5.9783 | + | |
- | _cell_length_c 4.7534 | + | |
- | _cell_angle_alpha 90 | + | |
- | _cell_angle_beta 90 | + | |
- | _cell_angle_gamma 90 | + | |
- | _cell_volume 289.58 | + | |
- | _symmetry_cell_setting 'Orthorhombic' | + | |
- | _symmetry_space_group_name_H-M 'P n m a' | + | |
- | + | ||
- | loop_ | + | |
- | _space_group_symop_operation_xyz | + | |
- | 'x,y,z' | + | |
- | 'x,y,1/2-z' | + | |
- | '-x,-y,1/2+z' | + | |
- | '1/2+x,1/2-y,1/2+z' | + | |
- | '1/2-x,1/2+y,1/2-z' | + | |
- | '1/2-x,1/2+y,z' | + | |
- | '1/2+x,1/2-y,-z' | + | |
- | '-x,-y,-z' | + | |
- | + | ||
- | loop_ | + | |
- | _atom_type_symbol | + | |
- | _atom_type_description | + | |
- | 'Mg' 'Mg' | + | |
- | 'Si' 'Si' | + | |
- | 'O' 'O' | + | |
- | + | ||
- | loop_ | + | |
- | _atom_site_label | + | |
- | _atom_site_type_symbol | + | |
- | _atom_site_fract_z | + | |
- | _atom_site_fract_x | + | |
- | _atom_site_fract_y | + | |
- | _atom_site_occupancy | + | |
- | Mg1 'Mg' 0.00000 0.00000 0.00000 1.00000 | + | |
- | Mg2 'Mg' 0.99090 0.27650 0.25000 1.00000 | + | |
- | Si 'Si' 0.42780 0.09480 0.25000 1.00000 | + | |
- | O1 'O' 0.76700 0.09250 0.25000 1.00000 | + | |
- | O2 'O' 0.21540 0.44810 0.25000 1.00000 | + | |
- | O3 'O' 0.28100 0.16400 0.03350 1.00000 | + | |
- | </code> | + | |
- | + | ||
- | But it do not work right. Some atoms are in double in the unit cell. | + | |
- | + | ||
- | Here is the correction : | + | |
- | + | ||
- | <code> | + | |
- | data_global | + | |
- | _chemical_name_mineral 'Forsterite' | + | |
- | loop_ | + | |
- | _publ_author_name | + | |
- | 'Miyake M' | + | |
- | 'Nakamura H' | + | |
- | 'Kojima H' | + | |
- | 'Marumo F' | + | |
- | _journal_name_full 'American Mineralogist' | + | |
- | _journal_volume 72 | + | |
- | _journal_year 1987 | + | |
- | _journal_page_first 594 | + | |
- | _journal_page_last 598 | + | |
- | _publ_section_title | + | |
- | ; | + | |
- | + | ||
- | ; | + | |
- | _database_code_amcsd 0001089 | + | |
- | _chemical_formula_sum 'Mg2 Si O4' | + | |
- | _cell_length_c 4.779 | + | |
- | _cell_length_a 10.277 | + | |
- | _cell_length_b 5.995 | + | |
- | _cell_angle_alpha 90 | + | |
- | _cell_angle_beta 90 | + | |
- | _cell_angle_gamma 90 | + | |
- | _cell_volume 294.437 | + | |
- | _exptl_crystal_density_diffrn 4.271 | + | |
- | _symmetry_space_group_name_H-M 'P n m a' | + | |
- | loop_ | + | |
- | _space_group_symop_operation_xyz | + | |
- | 'x,y,z' | + | |
- | 'x,1/2-y,z' | + | |
- | '-x,1/2+y,-z | + | |
- | '1/2-x,1/2+y,1/2+z' | + | |
- | '1/2+x,1/2-y,1/2-z' | + | |
- | '1/2+x,y,1/2-z' | + | |
- | '1/2-x,-y,1/2+z' | + | |
- | '-x,-y,-z' | + | |
- | loop_ | + | |
- | _atom_site_label | + | |
- | _atom_site_fract_z | + | |
- | _atom_site_fract_x | + | |
- | _atom_site_fract_y | + | |
- | _atom_site_occupancy | + | |
- | Mg1 0.00000 0.00000 0.00000 1.0000 | + | |
- | Mg2 0.99090 0.27650 0.25000 1.0000 | + | |
- | Si 0.42780 0.09480 0.25000 1.00000 | + | |
- | O1 0.76700 0.09250 0.25000 1.00000 | + | |
- | O2 0.21540 0.44810 0.25000 1.00000 | + | |
- | O3 0.28100 0.16400 0.03350 1.00000 | + | |
- | </code> | + | |
- | + | ||
- | But it has problem to run on PolyXSim. Here is the last correction, which give a correct crystal structure and can be read by PolyXSim. | + | |
- | + | ||
- | <code> | + | |
- | data_Olivine | + | |
- | _audit_creation_method 'manual editing' | + | |
- | _chemical_name_systematic | + | |
- | ; | + | |
- | Forsterite | + | |
- | ; | + | |
- | _chemical_formula_sum '(Mg2) Si O4' | + | |
- | _cell_length_a 10.1902 | + | |
- | _cell_length_b 5.9783 | + | |
- | _cell_length_c 4.7534 | + | |
- | _cell_angle_alpha 90 | + | |
- | _cell_angle_beta 90 | + | |
- | _cell_angle_gamma 90 | + | |
- | _cell_volume 289.58 | + | |
- | _symmetry_cell_setting 'Orthorhombic' | + | |
- | _symmetry_space_group_name_H-M 'P n m a' | + | |
- | _space_group_IT_number 62 | + | |
- | + | ||
- | loop_ | + | |
- | _space_group_symop_operation_xyz | + | |
- | 'x, y, z' | + | |
- | '-x, -y, -z' | + | |
- | '-x+1/2, -y, z+1/2' | + | |
- | 'x+1/2, y, -z+1/2' | + | |
- | '-x, y+1/2, -z' | + | |
- | 'x, -y+1/2, z' | + | |
- | 'x+1/2, -y+1/2, -z+1/2' | + | |
- | '-x+1/2, y+1/2, z+1/2' | + | |
- | + | ||
- | loop_ | + | |
- | _atom_type_symbol | + | |
- | _atom_type_description | + | |
- | 'Mg' 'Mg' | + | |
- | 'Si' 'Si' | + | |
- | 'O' 'O' | + | |
- | + | ||
- | loop_ | + | |
- | _atom_site_label | + | |
- | _atom_site_occupancy | + | |
- | _atom_site_fract_x | + | |
- | _atom_site_fract_y | + | |
- | _atom_site_fract_z | + | |
- | _atom_site_B_iso_or_equiv | + | |
- | _atom_site_type_symbol | + | |
- | Mg1 1.0 0.000000 0.000000 0.000000 1.000000 Mg | + | |
- | Mg2 1.0 0.276500 0.250000 0.990900 1.000000 Mg | + | |
- | Si 1.0 0.094800 0.250000 0.427800 1.000000 Si | + | |
- | O1 1.0 0.092500 0.250000 0.767000 1.000000 O | + | |
- | O2 1.0 0.448100 0.250000 0.215400 1.000000 O | + | |
- | O3 1.0 0.164000 0.033500 0.281000 1.000000 O | + | |
- | </code> | + |