Differences

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--- r [2009/08/27 11:18] – clare
+++ r [2022/11/03 15:08] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+====== 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.