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--- c [2009/08/06 14:37] – clare
+++ c [2025/09/19 15:18] (current) – external edit 127.0.0.1
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+====== 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<sup>-1</sup>. 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<sub>p</sub> for phase "p" is calculated as follows:
+| <sub>{{techref_files:image156.gif?76x70}}</sub>   | where   N<sub>p</sub> = Number of phases Q<sub>p</sub> = S<sub>p</sub>M<sub>p</sub>V<sub>p</sub>/B<sub>p</sub> S<sub>p</sub> = Rietveld scale factor for phase p. M<sub>p</sub> = Unit cell mass for phase p. V<sub>p</sub> = Unit cell volume for phase p. B<sub>p</sub> = 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<sub>p</sub> is function of :  (LAC<sub>phase</sub>-MAC<sub>mixture</sub>) //brindley_spherical_r_cm//
+where
+LAC<sub>phase</sub>       = linear absorption coefficient of phase p, packing density of 1.
+MAC<sub>mixture</sub>     = linear absorption coefficient of the mixture, packing density of 1.
+This makes B<sub>p</sub> a function of the weight fractions w<sub>p</sub> of all phases and thus w<sub>p</sub> as written above cannot be solved analytically. Subsequently w<sub>p</sub> is solved numerically through the use of iteration.
+**[//chi2_convergence_criteria// !E]**
+Convergence is determined when the change in <sub>{{techref_files:image002.gif?20x23}}</sub> 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//<sub>m</sub>  in the convolution function:
+(1 - ½//e//<sub>m</sub> / //e//½<sup>½</sup>)          for //e// = 0 to //e//<sub>m</sub>
+that is convoluted into phase peaks. //e//<sub>m</sub> 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:
+//[[#x000|val_on_continue]]// equations for independent parameters are evaluated
+//[[#k133|randomize_on_errors]]// process is performed
+//[[#k128|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//.