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r [2009/08/06 15:40]
clare created
r [2009/08/27 12:18] (current)
clare
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 ====== r ====== ====== r ======
 +
 +**[//​randomi//​****//​z//​****//​e_file_out_normal//​** **$file]**
 +
 +Randomizes the calculated pattern Y<​sub>​c</​sub>​ using a Normal distribution and writes Y<​sub>​c</​sub>​ 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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