# Differences

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 r [2009/08/06 15:40]clare created r [2009/08/27 12:18] (current)clare 2009/08/27 12:18 clare 2009/08/06 15:40 clare created 2009/08/27 12:18 clare 2009/08/06 15:40 clare created Line 1: Line 1: ====== r ====== ====== r ====== + + **[//​randomi//​****//​z//​****//​e_file_out_normal//​** **\$file]** + + Randomizes the calculated pattern Y<​sub>​c​ using a Normal distribution and writes Y<​sub>​c​ to the file \$file. + + **[//​rand_xyz//​ !E]** + + If //​[[#​k016|continue_after_convergence]]//​ is defined then //​rand_xyz//​ is executed at the end of a [[#​k144|refinement cycle]]. It adds to the site fractional coordinate a vector **u**,the direction of which is random and the magnitude in Å is: + + %%|%%**u**%%|%% = T //​rand_xyz//​ + + where T is the current //​temperature//​. Thus to add a shift to an atom between 0 and 1 Å the following could be used: + + temperature 1 + + site  . . .  occ 1 C beq 1  rand_xyz = Rand(0,1); + + Note that only fractional coordinates (//x//, //y//, //z//) that are independent parameters are randomized. + + **[//​r_bragg//​ #]** + + Reports on the R-Bragg value. R-Bragg is independent of hkl's and thus can be calculated for all phase types that contain phase peaks. + + **[//​rebin_with_dx//​_of !E]** + + //​rebin_with_dx//​_of rebins the observed data, see example CLAY.INP. It can be a function of the reserved parameter X as demonstrated in tof_bank2_1.inp. If //​rebin_with_dx//​_of evaluates to a constant then the observed data is re-binned to equal x-axis steps. For observed data that is of unequal x-axis steps then re-binning provides a means of converting to equal x-axis steps. + + **[//​rigid//​]...** + + **[//​point_for_site//​ \$site [//​ux//​%%|%%//​ua//​ E] [//​uy//​%%|%%//​ub//​ E] [//​uz//​%%|%%//​uc//​ E] ]...** + + **[//​in_cartesian//​] [//​in_FC//​]** + + **[//​z_matrix//​ \$atom_1 [\$atom_2 E] [\$atom_3 E] [\$atom_4 E] ] …** + + **[//​rotate//​ E [//​qx//​%%|%%//​qa//​ E] [//​qy//​%%|%%//​qb//​ E] [//​qz//​%%|%%//​qc//​ E] ]...** + + **[//​operate_on_points//​ \$sites]** + + **[//​in_cartesian//​] [//​in_FC//​]** + + **[//​translate//​ [//​tx//​%%|%%//​ta//​ E] [//​ty//​%%|%%//​tb//​ E] [t//​z//​%%|%%//​tc//​ E] ]...** + + **[//​operate_on_points//​ \$sites]** + + **[//​rand_xyz//​ #​displacement]** + + **[//​in_cartesian//​] [//​in_FC//​]** + + **[//​start_values_from_site//​ \$unique_site_name]** + + //rigid// defines a rigid body and associated translation and rotation operations. These operations are capable of creating and manipulating rigid bodies with hinges (torsion angles). + + //​point_for_site//​  defines a point in space with Cartesian coordinates given by the parameters //ux, uy uz//. Fractional equivalents can be defined using //ua//, //ub// and //uc//. \$site is the //site// that the //​point_for_site//​ represents. + + //​z_matrix//​ defines a point in space with coordinates given in Z-matrix format as follows:: + + * E can be an equation, constant or a parameter name with a value. + * \$atom_1 specifies the site that the new Z-matrix point represents. + * The E after \$atom_2 specifies the distance in Å between \$atom_2 and \$atom_1. \$atom_2 must exist if \$atom_1 is preceded by at least one point. + * The E \$atom_3 specifies the angle in degrees between \$atom_3-\$atom_2- \$atom_1. \$atom_3 must exist if \$atom_1 is preceded by at least two points. + * The E \$atom_4 specifies the dihedral angle in degrees between the plane formed by \$atom_3-\$atom_2-\$atom_1 and the plane formed by \$atom_4-\$atom_3-\$atom_2. This angle is drawn using the right hand rule with the thumb pointing in the direction \$atom_3 to \$atom_2. \$atom_4 must exist if \$atom_1 is preceded by at least three sites of the rigid body. + * If \$atom_1 is the first point of the rigid body then it is placed at Cartesian (0, 0, 0). If \$atom_1 is the second point of the rigid body then it is placed on the positive z-axis at Cartesian (0, 0, E) where E corresponds to the E in [\$atom_2 E]. If \$atom_1 is the third point of the rigid body then it is placed in the x-y plane. + + //rotate// rotates //​point_for_site//​’s an amount as defined by the //rotate// E equation around the vector defined by the Cartesian vector //qx//, //qy//, //qz//. The vector can be defined in fractional coordinates using //qa//, //qb// and //qc// instead. + + //​translate//​ performs a translation of //​point_for_site//​’s an amount in Cartesian equal to //tx//, //ty//, //tz//. The amount can be defined in fractional coordinates using //ta//, //tb// and //tc// instead. + + If //​in_cartesian//​ or //in_FC// is defined then the coordinates are interpreted as Cartesian or fractional atomic coordinates,​ respectively. + + //rotate// and //​translate//​ operates on any previously defined //​point_for_site//​’s;​ alternatively,​ //​point_for_site//​’s operated on can be identified using the //​operate_on_points//​ keyword//​.//​ The //​operate_on_points//​ keyword must refer to previously defined //​point_for_site//​’s (see section 7.6 for a description of how to identify sites). + + When //​continue_after_convergence//​ is defined, //​[[#​k128|rand_xyz]]//​ processes are initiated after convergence. It introduces a random displacement to the translate fractional coordinates (//tx//, //ty//, //tz//) that are independent parameters. The size of the random displacement is given by the current //​temperature//​ multiplied by #​displacement where #​displacement is in Å. + + //​start_values_from_site//​ initializes the values //ta//, //tb//, //tc// with corresponding values taken from the site \$unique_site_name. + + See section 7.10 for a description of rigid bodies. + + **[//Rp// #] [//Rs// #]** + + Defines the primary and secondary radius of the diffractometer in mm. The default is 217.5 mm. + + **[//r_p// #] [//​r_p_dash//​ #] [//r_wp// #] [//​r_wp_dash//​ #] [//r_exp// #] [//​r_exp_dash//​ #] [//gof// #]** + + **[//​weighted_Durbin_Watson//​ #]** + + //xdd// dependent or global refinement indicators. Keywords ending in “_dash” correspond to background subtracted values, see section 5.6.

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