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r

[randomize_file_out_normal $file]

Randomizes the calculated pattern Yc using a Normal distribution and writes Yc to the file $file.

[rand_xyz !E]

If continue_after_convergence is defined then rand_xyz is executed at the end of a 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] [tz|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, 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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