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Added profile sims from CIF file, uses CCTBX, linux only for now
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| #====================================================================== | ||
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| # CRYSTAL DATA | ||
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| #---------------------------------------------------------------------- | ||
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| data_VESTA_phase_1 | ||
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| _pd_phase_name 'New structure' | ||
| _cell_length_a 4.07820 | ||
| _cell_length_b 4.07820 | ||
| _cell_length_c 4.07820 | ||
| _cell_angle_alpha 90 | ||
| _cell_angle_beta 90 | ||
| _cell_angle_gamma 90 | ||
| _symmetry_space_group_name_H-M 'F m -3 m' | ||
| _symmetry_Int_Tables_number 225 | ||
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| loop_ | ||
| _symmetry_equiv_pos_as_xyz | ||
| 'x, y, z' | ||
| '-x, -y, -z' | ||
| '-x, -y, z' | ||
| 'x, y, -z' | ||
| '-x, y, -z' | ||
| 'x, -y, z' | ||
| 'x, -y, -z' | ||
| '-x, y, z' | ||
| 'z, x, y' | ||
| '-z, -x, -y' | ||
| 'z, -x, -y' | ||
| '-z, x, y' | ||
| '-z, -x, y' | ||
| 'z, x, -y' | ||
| '-z, x, -y' | ||
| 'z, -x, y' | ||
| 'y, z, x' | ||
| '-y, -z, -x' | ||
| '-y, z, -x' | ||
| 'y, -z, x' | ||
| 'y, -z, -x' | ||
| '-y, z, x' | ||
| '-y, -z, x' | ||
| 'y, z, -x' | ||
| 'y, x, -z' | ||
| '-y, -x, z' | ||
| '-y, -x, -z' | ||
| 'y, x, z' | ||
| 'y, -x, z' | ||
| '-y, x, -z' | ||
| '-y, x, z' | ||
| 'y, -x, -z' | ||
| 'x, z, -y' | ||
| '-x, -z, y' | ||
| '-x, z, y' | ||
| 'x, -z, -y' | ||
| '-x, -z, -y' | ||
| 'x, z, y' | ||
| 'x, -z, y' | ||
| '-x, z, -y' | ||
| 'z, y, -x' | ||
| '-z, -y, x' | ||
| 'z, -y, x' | ||
| '-z, y, -x' | ||
| '-z, y, x' | ||
| 'z, -y, -x' | ||
| '-z, -y, -x' | ||
| 'z, y, x' | ||
| 'x, y+1/2, z+1/2' | ||
| '-x, -y+1/2, -z+1/2' | ||
| '-x, -y+1/2, z+1/2' | ||
| 'x, y+1/2, -z+1/2' | ||
| '-x, y+1/2, -z+1/2' | ||
| 'x, -y+1/2, z+1/2' | ||
| 'x, -y+1/2, -z+1/2' | ||
| '-x, y+1/2, z+1/2' | ||
| 'z, x+1/2, y+1/2' | ||
| '-z, -x+1/2, -y+1/2' | ||
| 'z, -x+1/2, -y+1/2' | ||
| '-z, x+1/2, y+1/2' | ||
| '-z, -x+1/2, y+1/2' | ||
| 'z, x+1/2, -y+1/2' | ||
| '-z, x+1/2, -y+1/2' | ||
| 'z, -x+1/2, y+1/2' | ||
| 'y, z+1/2, x+1/2' | ||
| '-y, -z+1/2, -x+1/2' | ||
| '-y, z+1/2, -x+1/2' | ||
| 'y, -z+1/2, x+1/2' | ||
| 'y, -z+1/2, -x+1/2' | ||
| '-y, z+1/2, x+1/2' | ||
| '-y, -z+1/2, x+1/2' | ||
| 'y, z+1/2, -x+1/2' | ||
| 'y, x+1/2, -z+1/2' | ||
| '-y, -x+1/2, z+1/2' | ||
| '-y, -x+1/2, -z+1/2' | ||
| 'y, x+1/2, z+1/2' | ||
| 'y, -x+1/2, z+1/2' | ||
| '-y, x+1/2, -z+1/2' | ||
| '-y, x+1/2, z+1/2' | ||
| 'y, -x+1/2, -z+1/2' | ||
| 'x, z+1/2, -y+1/2' | ||
| '-x, -z+1/2, y+1/2' | ||
| '-x, z+1/2, y+1/2' | ||
| 'x, -z+1/2, -y+1/2' | ||
| '-x, -z+1/2, -y+1/2' | ||
| 'x, z+1/2, y+1/2' | ||
| 'x, -z+1/2, y+1/2' | ||
| '-x, z+1/2, -y+1/2' | ||
| 'z, y+1/2, -x+1/2' | ||
| '-z, -y+1/2, x+1/2' | ||
| 'z, -y+1/2, x+1/2' | ||
| '-z, y+1/2, -x+1/2' | ||
| '-z, y+1/2, x+1/2' | ||
| 'z, -y+1/2, -x+1/2' | ||
| '-z, -y+1/2, -x+1/2' | ||
| 'z, y+1/2, x+1/2' | ||
| 'x+1/2, y, z+1/2' | ||
| '-x+1/2, -y, -z+1/2' | ||
| '-x+1/2, -y, z+1/2' | ||
| 'x+1/2, y, -z+1/2' | ||
| '-x+1/2, y, -z+1/2' | ||
| 'x+1/2, -y, z+1/2' | ||
| 'x+1/2, -y, -z+1/2' | ||
| '-x+1/2, y, z+1/2' | ||
| 'z+1/2, x, y+1/2' | ||
| '-z+1/2, -x, -y+1/2' | ||
| 'z+1/2, -x, -y+1/2' | ||
| '-z+1/2, x, y+1/2' | ||
| '-z+1/2, -x, y+1/2' | ||
| 'z+1/2, x, -y+1/2' | ||
| '-z+1/2, x, -y+1/2' | ||
| 'z+1/2, -x, y+1/2' | ||
| 'y+1/2, z, x+1/2' | ||
| '-y+1/2, -z, -x+1/2' | ||
| '-y+1/2, z, -x+1/2' | ||
| 'y+1/2, -z, x+1/2' | ||
| 'y+1/2, -z, -x+1/2' | ||
| '-y+1/2, z, x+1/2' | ||
| '-y+1/2, -z, x+1/2' | ||
| 'y+1/2, z, -x+1/2' | ||
| 'y+1/2, x, -z+1/2' | ||
| '-y+1/2, -x, z+1/2' | ||
| '-y+1/2, -x, -z+1/2' | ||
| 'y+1/2, x, z+1/2' | ||
| 'y+1/2, -x, z+1/2' | ||
| '-y+1/2, x, -z+1/2' | ||
| '-y+1/2, x, z+1/2' | ||
| 'y+1/2, -x, -z+1/2' | ||
| 'x+1/2, z, -y+1/2' | ||
| '-x+1/2, -z, y+1/2' | ||
| '-x+1/2, z, y+1/2' | ||
| 'x+1/2, -z, -y+1/2' | ||
| '-x+1/2, -z, -y+1/2' | ||
| 'x+1/2, z, y+1/2' | ||
| 'x+1/2, -z, y+1/2' | ||
| '-x+1/2, z, -y+1/2' | ||
| 'z+1/2, y, -x+1/2' | ||
| '-z+1/2, -y, x+1/2' | ||
| 'z+1/2, -y, x+1/2' | ||
| '-z+1/2, y, -x+1/2' | ||
| '-z+1/2, y, x+1/2' | ||
| 'z+1/2, -y, -x+1/2' | ||
| '-z+1/2, -y, -x+1/2' | ||
| 'z+1/2, y, x+1/2' | ||
| 'x+1/2, y+1/2, z' | ||
| '-x+1/2, -y+1/2, -z' | ||
| '-x+1/2, -y+1/2, z' | ||
| 'x+1/2, y+1/2, -z' | ||
| '-x+1/2, y+1/2, -z' | ||
| 'x+1/2, -y+1/2, z' | ||
| 'x+1/2, -y+1/2, -z' | ||
| '-x+1/2, y+1/2, z' | ||
| 'z+1/2, x+1/2, y' | ||
| '-z+1/2, -x+1/2, -y' | ||
| 'z+1/2, -x+1/2, -y' | ||
| '-z+1/2, x+1/2, y' | ||
| '-z+1/2, -x+1/2, y' | ||
| 'z+1/2, x+1/2, -y' | ||
| '-z+1/2, x+1/2, -y' | ||
| 'z+1/2, -x+1/2, y' | ||
| 'y+1/2, z+1/2, x' | ||
| '-y+1/2, -z+1/2, -x' | ||
| '-y+1/2, z+1/2, -x' | ||
| 'y+1/2, -z+1/2, x' | ||
| 'y+1/2, -z+1/2, -x' | ||
| '-y+1/2, z+1/2, x' | ||
| '-y+1/2, -z+1/2, x' | ||
| 'y+1/2, z+1/2, -x' | ||
| 'y+1/2, x+1/2, -z' | ||
| '-y+1/2, -x+1/2, z' | ||
| '-y+1/2, -x+1/2, -z' | ||
| 'y+1/2, x+1/2, z' | ||
| 'y+1/2, -x+1/2, z' | ||
| '-y+1/2, x+1/2, -z' | ||
| '-y+1/2, x+1/2, z' | ||
| 'y+1/2, -x+1/2, -z' | ||
| 'x+1/2, z+1/2, -y' | ||
| '-x+1/2, -z+1/2, y' | ||
| '-x+1/2, z+1/2, y' | ||
| 'x+1/2, -z+1/2, -y' | ||
| '-x+1/2, -z+1/2, -y' | ||
| 'x+1/2, z+1/2, y' | ||
| 'x+1/2, -z+1/2, y' | ||
| '-x+1/2, z+1/2, -y' | ||
| 'z+1/2, y+1/2, -x' | ||
| '-z+1/2, -y+1/2, x' | ||
| 'z+1/2, -y+1/2, x' | ||
| '-z+1/2, y+1/2, -x' | ||
| '-z+1/2, y+1/2, x' | ||
| 'z+1/2, -y+1/2, -x' | ||
| '-z+1/2, -y+1/2, -x' | ||
| 'z+1/2, y+1/2, x' | ||
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| loop_ | ||
| _atom_site_label | ||
| _atom_site_occupancy | ||
| _atom_site_fract_x | ||
| _atom_site_fract_y | ||
| _atom_site_fract_z | ||
| _atom_site_adp_type | ||
| _atom_site_B_iso_or_equiv | ||
| _atom_site_type_symbol | ||
| Au 1.0 0.000000 0.000000 0.000000 Biso 1.000000 Au |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,28 @@ | ||
| def run(): | ||
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| import iotbx.cif | ||
| import sys | ||
| # print sys.argv | ||
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| cif_structure_list = iotbx.cif.reader(sys.argv[1]).build_crystal_structures() | ||
| cif_structure = cif_structure_list.values()[0] | ||
| cif_structure.scattering_type_registry(table="it1992") | ||
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| # Now calculate some structure factors | ||
| f_calc = cif_structure.structure_factors(d_min=float(sys.argv[2])).f_calc() | ||
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| f_calc_sq = f_calc.as_intensity_array() | ||
| if sys.argv[3] == 'sf': | ||
| #print f_calc_sq | ||
| f_calc_sq.show_array() | ||
| if sys.argv[3] == 'ds': | ||
| f_calc_sq.d_spacings().show_array() | ||
| if sys.argv[3] == 'mt': | ||
| #f_calc_sq.show_summary() | ||
| f_calc_sq.multiplicities().show_array() | ||
| # miller = cif_structure.build_miller_set(anomalous_flag=False, d_min = float(sys.argv[2]), d_max=None) | ||
| # print miller.all_selection().show_array() | ||
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| if __name__ == "__main__": | ||
| run() |
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