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fileformat:cif [2018/11/13 09:43]
estelle 		fileformat:cif [2019/02/18 10:11] (current)
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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>​+
fileformat/cif.1542102210.txt.gz · Last modified: 2019/02/18 10:11 (external edit)

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