'-------------------------------------------------------------- 'Input File for Isodisplace Distortion Mode Rietveld Refinement 'Use isodisplace to produce _distortion.str files 'These are automatically read into topas via jedit menus 'Modes 1-3 will produce matrices to convert high to low symmetry structures 'Mode 4 will produce mode amplitudes from two cif files 'Refine on distortion mode amplitudes instead of fractional coordinates 'Values of an are summed rms displacements of atom in superstructure 'http://stokes.byu.edu/isodisplace.html 'http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2007nov/ 'Branton J. Campbell, Harold T. Stokes, David E. Tanner, Dorian M. Hatch, J. Appl. Cryst., 2006, 39, 607-614 'Use save/set current button then run with F6 in topas '-------------------------------------------------------------- r_wp 9.354 r_exp 5.027 r_p 7.302 r_wp_dash 13.939 r_p_dash 12.758 r_exp_dash 7.491 weighted_Durbin_Watson 0.661 gof 1.861 '-------------------------------------------------------------- 'General information about refinement here 'Remove comments as required '-------------------------------------------------------------- iters 100000 chi2_convergence_criteria 0.001 'randomize_on_errors continue_after_convergence 'do_errors '-------------------------------------------------------------- 'Information on datafile etc here 'Check that default weighting is appropriate for your data '-------------------------------------------------------------- xdd d8_03901_030c.xy finish_X 90 x_calculation_step = Yobs_dx_at(Xo); convolution_step 4 bkg @ 216.217852` -237.420221` 124.70033` -64.1641246` 29.489219` -6.57693318` 'd8 Lynx Eye Cu Ka1/a2 2 line emission LP_Factor(!th2_monochromator, 0) CuKa2(0.0001) Specimen_Displacement(height, 0.17477`) 'Topas .str file generated by ISODISPLACE str space_group P121/n1 a @ 7.29747` val_on_continue = Rand(7.3,7.8); b @ 7.53272` val_on_continue = Rand(7.3,7.8); c @ 7.68712` val_on_continue = Rand(7.3,7.8); al 90.00000 val_on_continue = Rand(88,92); be @ 90.83262` val_on_continue = Rand(88,92); ga 90.00000 val_on_continue = Rand(88,92); 'mode definitions prm !a1 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[W:a]T1u(a) prm a2 0.68342` min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[W:a]T1u(b) prm !a3 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M3-(a,0,b)[W:a]T1u(a) prm a4 -0.73720` min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M3-(a,0,b)[W:a]T1u(b) prm !a5 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[W:a]T1u(a) prm !a6 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[W:a]T1u(b) prm a7 1.12459` min -4.00 max 4.00 'Pm-3m[1/2,1/2,1/2]R4+(a,0,b)[O:d]Eu(a) prm a8 1.12053` min -4.00 max 4.00 'Pm-3m[1/2,1/2,1/2]R4+(a,0,b)[O:d]Eu(b) prm !a9 0.00000 min -4.00 max 4.00 'Pm-3m[1/2,1/2,1/2]R5+(a,0,b)[O:d]Eu(a) prm !a10 0.00000 min -4.00 max 4.00 'Pm-3m[1/2,1/2,1/2]R5+(a,0,b)[O:d]Eu(b) prm !a11 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5+(0,0,0,0,a,b)[O:d]Eu(a) prm !a12 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5+(0,0,0,0,a,b)[O:d]Eu(b) prm !a13 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[O:d]A2u(a) prm !a14 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[O:d]A2u(b) prm !a15 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[O:d]Eu(a) prm !a16 0.00000 min -2.83 max 2.83 'Pm-3m[0,1/2,0]X5-(a,a,b,-b,0,0)[O:d]Eu(b) prm !a17 0.00000 min -4.00 max 4.00 'Pm-3m[1/2,1/2,0]M1+(0,a,0)[O:d]A2u(a) prm !a18 0.00000 min -4.00 max 4.00 'Pm-3m[1/2,1/2,0]M2+(0,a,0)[O:d]A2u(a) prm a19 0.92598` min -4.00 max 4.00 'Pm-3m[1/2,1/2,0]M3+(0,a,0)[O:d]Eu(a) prm !a20 0.00000 min -4.00 max 4.00 'Pm-3m[1/2,1/2,0]M4+(0,a,0)[O:d]Eu(a) prm !a21 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M3-(a,0,b)[O:d]A2u(a) prm !a22 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M3-(a,0,b)[O:d]A2u(b) prm !a23 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[O:d]Eu(a) prm !a24 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[O:d]Eu(b) prm !b1 0.00000 min -2.83 max 2.83 'Pm-3m[0,0,0]GM1+(a)[W:a]order(a) prm !b2 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M1+(0,a,0)[W:a]order(a) prm !b3 0.00000 min -4.90 max 4.90 'Pm-3m[0,0,0]GM1+(a)[O:d]order(a) prm !b4 0.00000 min -3.46 max 3.46 'Pm-3m[0,0,0]GM3+(a,b)[O:d]order(a) prm !b5 0.00000 min -4.00 max 4.00 'Pm-3m[0,0,0]GM3+(a,b)[O:d]order(b) prm !b6 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M1+(0,a,0)[O:d]order(a) prm !b7 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[O:d]order(a) prm !b8 0.00000 min -2.83 max 2.83 'Pm-3m[1/2,1/2,0]M5-(a,-a,b,b,0,0)[O:d]order(b) 'mode-amplitude to delta-coord/occ transformation prm W_1_dx = - 0.04419*a3 - 0.04419*a5;: -0.00000 prm W_1_dy = - 0.04419*a1 + 0.04419*a2;: 0.03020` prm W_1_dz = + 0.04419*a4 + 0.04419*a6;: -0.03258` prm W_2_dx = + 0.04419*a3 - 0.04419*a5;: 0.00000 prm W_2_dy = + 0.04419*a1 + 0.04419*a2;: 0.03020` prm W_2_dz = + 0.04419*a4 - 0.04419*a6;: -0.03258` prm O_1_dx = + 0.03125*a8 - 0.03125*a10 + 0.03125*a11 - 0.03125*a12;: 0.03502` prm O_1_dy = - 0.04419*a13 + 0.04419*a14;: 0.00000 prm O_1_dz = + 0.03125*a7 + 0.03125*a9 + 0.03125*a11 + 0.03125*a12;: 0.03514` prm O_2_dx = - 0.03125*a8 + 0.03125*a10 + 0.03125*a11 - 0.03125*a12;: -0.03502` prm O_2_dy = + 0.04419*a13 + 0.04419*a14;: 0.00000 prm O_2_dz = - 0.03125*a7 - 0.03125*a9 + 0.03125*a11 + 0.03125*a12;: -0.03514` prm O_3_dx = - 0.03125*a17 + 0.03125*a18 - 0.04419*a21;: 0.00000 prm O_3_dy = - 0.03125*a8 - 0.03125*a10 - 0.04419*a15;: -0.03502` prm O_3_dz = - 0.03125*a19 + 0.03125*a20 - 0.04419*a24;: -0.02894` prm O_4_dx = - 0.03125*a17 + 0.03125*a18 + 0.04419*a21;: 0.00000 prm O_4_dy = + 0.03125*a8 + 0.03125*a10 - 0.04419*a15;: 0.03502` prm O_4_dz = - 0.03125*a19 + 0.03125*a20 + 0.04419*a24;: -0.02894` prm O_5_dx = - 0.03125*a19 - 0.03125*a20 + 0.04419*a23;: -0.02894` prm O_5_dy = + 0.03125*a7 - 0.03125*a9 + 0.04419*a16;: 0.03514` prm O_5_dz = + 0.03125*a17 + 0.03125*a18 + 0.04419*a22;: 0.00000 prm O_6_dx = + 0.03125*a19 + 0.03125*a20 + 0.04419*a23;: 0.02894` prm O_6_dy = - 0.03125*a7 + 0.03125*a9 + 0.04419*a16;: -0.03514` prm O_6_dz = - 0.03125*a17 - 0.03125*a18 + 0.04419*a22;: 0.00000 prm W_1_do = + 0.35355*b1 + 0.35355*b2;: 0.00000 prm W_2_do = + 0.35355*b1 - 0.35355*b2;: 0.00000 prm O_1_do = + 0.20412*b3 + 0.14434*b4 + 0.25000*b5 + 0.35355*b6;: 0.00000 prm O_2_do = + 0.20412*b3 + 0.14434*b4 + 0.25000*b5 - 0.35355*b6;: 0.00000 prm O_3_do = + 0.20412*b3 - 0.28868*b4 + 0.35355*b7;: 0.00000 prm O_4_do = + 0.20412*b3 - 0.28868*b4 - 0.35355*b7;: 0.00000 prm O_5_do = + 0.20412*b3 + 0.14434*b4 - 0.25000*b5 + 0.35355*b8;: 0.00000 prm O_6_do = + 0.20412*b3 + 0.14434*b4 - 0.25000*b5 - 0.35355*b8;: 0.00000 'distorted coordinates prm W_1_x = 1/4 + W_1_dx;: 0.25000 prm W_1_y = 0 + W_1_dy;: 0.03020` prm W_1_z = 3/4 + W_1_dz;: 0.71742` prm W_2_x = 1/4 + W_2_dx;: 0.25000 prm W_2_y = 0 + W_2_dy;: 0.03020` prm W_2_z = 1/4 + W_2_dz;: 0.21742` prm O_1_x = 1/4 + O_1_dx;: 0.28502` prm O_1_y = 3/4 + O_1_dy;: 0.75000 prm O_1_z = 3/4 + O_1_dz;: 0.78514` prm O_2_x = 1/4 + O_2_dx;: 0.21498` prm O_2_y = 3/4 + O_2_dy;: 0.75000 prm O_2_z = 1/4 + O_2_dz;: 0.21486` prm O_3_x = 0 + O_3_dx;: 0.00000 prm O_3_y = 0 + O_3_dy;: -0.03502` prm O_3_z = 3/4 + O_3_dz;: 0.72106` prm O_4_x = 0 + O_4_dx;: 0.00000 prm O_4_y = 1/2 + O_4_dy;: 0.53502` prm O_4_z = 3/4 + O_4_dz;: 0.72106` prm O_5_x = 1/4 + O_5_dx;: 0.22106` prm O_5_y = 0 + O_5_dy;: 0.03514` prm O_5_z = 0 + O_5_dz;: 0.00000 prm O_6_x = 1/4 + O_6_dx;: 0.27894` prm O_6_y = 0 + O_6_dy;: -0.03514` prm O_6_z = 1/2 + O_6_dz;: 0.50000 prm W_1_occ = 1 + W_1_do;: 1.00000 prm W_2_occ = 1 + W_2_do;: 1.00000 prm O_1_occ = 1 + O_1_do;: 1.00000 prm O_2_occ = 1 + O_2_do;: 1.00000 prm O_3_occ = 1 + O_3_do;: 1.00000 prm O_4_occ = 1 + O_4_do;: 1.00000 prm O_5_occ = 1 + O_5_do;: 1.00000 prm O_6_occ = 1 + O_6_do;: 1.00000 'mode-dependent atoms site W_1 x = W_1_x; y = W_1_y; z = W_1_z; occ W = W_1_occ; beq bvalue -1.5559` site W_2 x = W_2_x; y = W_2_y; z = W_2_z; occ W = W_2_occ; beq bvalue -1.5559` site O_1 x = O_1_x; y = O_1_y; z = O_1_z; occ O = O_1_occ; beq bvalue -1.5559` site O_2 x = O_2_x; y = O_2_y; z = O_2_z; occ O = O_2_occ; beq bvalue -1.5559` site O_3 x = O_3_x; y = O_3_y; z = O_3_z; occ O = O_3_occ; beq bvalue -1.5559` site O_4 x = O_4_x; y = O_4_y; z = O_4_z; occ O = O_4_occ; beq bvalue -1.5559` site O_5 x = O_5_x; y = O_5_y; z = O_5_z; occ O = O_5_occ; beq bvalue -1.5559` site O_6 x = O_6_x; y = O_6_y; z = O_6_z; occ O = O_6_occ; beq bvalue -1.5559` scale @ 5.64572948e-005` r_bragg 3.87875769 TCHZ_Peak_Type(pku, 0.29879`,pkv, -0.20207`,pkw, 0.02693`,!pkz, 0.0000,pky, 0.21779`,!pkx, 0.0000) Simple_Axial_Model(axial, 8.32206`) Phase_Density_g_on_cm3( 7.28958`)