Trace:

# Differences

This shows you the differences between two versions of the page.

r [2009/08/06 15:40] clare created |
r [2009/08/27 12:18] (current) clare |
||
---|---|---|---|

Line 1: | Line 1: | ||

====== 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. | ||