Trace: • c

# c

**[ capillary_diameter_mm E]…**

*capillary_u_cm_inv* E

*capillary_parallel_beam***| capillary_divergent_beam**

Calculates an aberration for capillary samples. and convolutes it into phase peaks. *capillary_diameter_mm* corresponds to the capillary diameter in mm and *capillary_u_cm_inv* the linear absorption coefficient of the sample in units of cm^{-1}. The *capillary_diameter_mm* convolution corrects for peak shapes, intensities and 2Th shifts, see example CAPILLARY-SIMULATED.INP.

Use of *capillary_parallel_beam* results in a correction for a parallel primary beam.

Use of *capillary_divergent_beam* results in a correction for a divergent primary beam.

Both *capillary_parallel_beam* and *capillary_divergent_beam* assume that the capillary is fully illuminated by the beam in the equitorial plane.

**[ cell_mass !E] [cell_volume !E] [weight_percent !E]**

**[***spiked_phase_measured_weight_percent***!E] [ corrected_weight_percent !E]**

*cell_mass*, *cell_volume* and *weight_percent* correspond to unit cell mass, volume and weight percent of the phase within the mixture.

*spiked_phase_measured_weight_percent* defines the weight percent of a spiked phase. Used by the xdd dependent keyword *weight_percent_amorphous* to determine amorphous weight percent. Only one phase per xdd is allowed to contain the keyword *spiked_phase_measured_weight_percent*.

*corrected_weight_percent*is the weight percent after considering amorphous content as determined by *weight_percent_amorphous*.

The weight fraction w_{p} for phase “p” is calculated as follows:

_{} | where N_{p} = Number of phases Q_{p} = S_{p}M_{p}V_{p}/B_{p} S_{p} = Rietveld scale factor for phase p. M_{p} = Unit cell mass for phase p. V_{p} = Unit cell volume for phase p. B_{p} = Brindley correction for phase p. |

The Brindley correction is a function of *brindley_spherical_r_cm* and the phase and mixture linear absorption coefficients; the latter two are in turn functions of *phase_MAC* and *mixture_MAC* respectively, or,

B_{p} is function of : (LAC_{phase}-MAC_{mixture}) *brindley_spherical_r_cm*

where

LAC_{phase} = linear absorption coefficient of phase p, packing density of 1.

MAC_{mixture} = linear absorption coefficient of the mixture, packing density of 1.

This makes B_{p} a function of the weight fractions w_{p} of all phases and thus w_{p} as written above cannot be solved analytically. Subsequently w_{p} is solved numerically through the use of iteration.

**[ chi2_convergence_criteria !E]**

Convergence is determined when the change in _{} is less than *chi2_convergence_criteria* for three consecutive cycles and when all defined *stop_when* parameter attributes evaluate to true. Example:

chi2_convergence_criteria = If(Cycle_Iter < 10, .001, .01);

**[ circles_conv E]…**

Defines *e*_{m} in the convolution function:

(1 - ½*e*_{m} / *e*½^{½}) for *e* = 0 to *e*_{m}

that is convoluted into phase peaks. *e*_{m} can be greater than or less than zero. *circles_conv* is used for example by the Simple_Axial_Model macro.

**[ cloud $sites]…**

**[ cloud_population !E]**

**[ cloud_save $file]**

**[ cloud_save_xyzs $file]**

**[ cloud_load_xyzs $file]**

**[ cloud_load_xyzs_omit_rwps !E]**

**[ cloud_formation_omit_rwps !E]**

**[ cloud_try_accept !E]**

**[ cloud_gauss_fwhm !E]**

**[ cloud_extract_and_save_xyzs $file]**

**[ cloud_number_to_extract !E]**

**[ cloud_atomic_separation !E]**

*cloud* allows for the tracking of atoms defined in $sites in three dimensions. It can be useful for determining the average positions of heavy atoms or rigid bodies during refinement cycles. For example, a dummy atom, “site X1” say, can be placed at the center of a benzene ring and then tracked as follows:

continue_after_convergence

…

cloud “X1”

cloud_population 100

cloud_save SOME_FILE.CLD

On termination of refinement the CLD file is saved; it can be viewed using the rigid body editor of the GUI; see examples AE14-12.INP for a cloud example. *cloud_population* is the maximum number of population members. Each population member comprises the fractional coordinates of $sites and an associated Rwp value.

*cloud_save_xyzs* saves a cloud populations to file.

*cloud_load_xyzs* loads and reuses previously saved populations. *cloud_load_xyzs_omit_rwps* can be used to exclude population membes whilst loading; it can be a function of Get(Cloud_Rwp) where Cloud_Rwp is the associated Rwp of a population member.

*cloud_formation_omit_rwps* can be used to limit population membes in the formation of CLD files; it can be a function of Get(Cloud_Rwp).

*cloud_try_accept* accepts population members if it evaluates to non-zero and if the best Rwp since the last acceptance is less than a present population member or if the number of members is less than *cloud_population*. If the number of population members equals *cloud_population* then the population member with the lowest Rwp is discarded. *cloud_try_accept* is evaluated at the end of each refinement cycle; it default value is true. Here’s are some examples:

cloud_try_accept = And(Cycle, Mod(Cycle, 50);

cloud_try_accept = T == 10;

*cloud_gauss_fwhm* is the full width at half maximum of a three dimensional Gaussian that is used to fill the cloud.

*cloud_extract_and_save_xyzs* searches the three dimensional cloud for high densities and extracts xyz positions; these are then saved to $file. *cloud_number_to_extract* defines the number of positions to extract and *cloud_atomic_separation* limits the atomic separation during the extraction. The actual number of positions extracted may be less than *cloud_number_to_extract* depending on the cloud.

** [ conserve_memory]**

Deletes temporary arrays used in intermediate calculations; memory savings of up to 70% can be expected on some problems with subsequent lengthening of execution times by up to 40%. When *approximate_A* is used on dense matrices then *conserve_memory* can reduce memory usage by up to 90%.

**[ continue_after_convergence]**

Refinement is continued after convergence. Before continuing the following actions are performed:

*val_on_continue* equations for independent parameters are evaluated

*randomize_on_errors* process is performed

*rand_xyz* processes are performed

Also, when *val_on_continue* is defined then the corresponding parameter is not randomized according to *randomize_on_errors*.

**[ convolution_step #]**

An integer defining the number of calculated data points per measured data point. It may be useful to increase this number when the measurement step is large. *convolution_step* is set to 1 by default. Only when the measurement step is greater than about 0.03 degrees 2Th or when high precision is required is it necessary to increase *convolution_step*.