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manual_part_2 [2009/08/26 15:02]
127.0.0.1 external edit
manual_part_2 [2009/08/26 15:05]
clare
Line 1: Line 1:
 +
 +====== 8             Keywords ======
 +
 +===== 8.1        Data structures =====
 +
 +The following describes keyword dependencies. Trailing ‘…’ implies that more than one node of that type can be inserted under its parent. Items enclosed in square brackets are optional. Items beginning with a capital T corresponds to keyword groups analogous to complex types in XML.
 +
 +Ttop
 +
 +[[#​hy6|Tcomm_1]]
 +
 +[[#​hy7|Tcomm_2]]
 +
 +[[#​hy13|Ttop_xdd]]
 +
 +[[#​hy1|Tglobal]]
 +
 +[[#​hy3|Txdd]]
 +
 +[[#​hy2|Txdd_scr]]
 +
 +[[#​i13|Tindexing]]
 +
 +[[#​cf1|Tcharge_flipping]]
 +
 + 
 +
 +Ttop_xdd
 +
 +[[#​k017|[]]//​[[#​k017|convolution_step]]//​[[#​k017| #]]]
 +
 +[[#​k071|[]]//​[[#​k071|r_p]]//​[[#​k071| #] []]//​[[#​k071|r_wp]]//​[[#​k071| #] []]//​[[#​k071|r_exp]]//​[[#​k071| #] []]//​[[#​k071|gof]]//​[[#​k071| #] []]//​[[#​k071|r_p_dash]]//​[[#​k071| #] []]//​[[#​k071|r_wp_dash]]//​[[#​k071| #] []]//​[[#​k071|r_exp_dash]]//​[[#​k071| #]]]
 +
 +[[#​k070|[]]//​[[#​k070|Rp]]//​[[#​k070| !E] []]//​[[#​k070|Rs]]//​[[#​k070| !E]]]
 +
 +[[#​k071|[]]//​[[#​k071|weighted_Durbin_Watson]]//​[[#​k071| #]]]
 +
 +[[#​k094|[]]//​[[#​k094|x_calculation_step]]//​[[#​k094| !E]]]
 +
 + 
 +
 +Tglobal
 +
 +[[#​k003|[]]//​[[#​k003|A_matrix]]//​[[#​k003|][]]//​[[#​k003|C_matrix]]//​[[#​k003|][]]//​[[#​k003|A_matrix_normalized]]//​[[#​k003|][]]//​[[#​k003|C_matrix_normalized]]//​[[#​k003|]]]
 +
 +[[#​k158|[]]//​[[#​k158|approximate_A]]//​[[#​k158|]]]
 +
 +[//​A_matrix_memory_allowed_in_Mbytes//​ #]
 +
 +[//​A_matrix_elements_tollerance//​ #]
 +
 +[//​A_matrix_report_on//​]
 +
 +[[#​k160|[]]//​[[#​k160|bootstrap_errors]]//​[[#​k160| !E]]]
 +
 +[//​fraction_of_yobs_to_resample//​ !E]
 +
 +[determine_values_from_samples]
 +
 +[//​resample_from_current_ycalc//​]
 +
 +[[#​k013|[]]//​[[#​k013|chi2_convergence_criteria]]//​[[#​k013| !E]]]
 +
 +[[#​k015|[]]//​[[#​k015|conserve_memory]]//​[[#​k015|]]]
 +
 +[[#​k016|[]]//​[[#​k016|continue_after_convergence]]//​[[#​k016|]]]
 +
 +[[#​k020|[]]//​[[#​k020|do_errors]]//​[[#​k020|]]]
 +
 +[[#​k023|[]]//​[[#​k023|file_name_for_best_solutions]]//​[[#​k023| $file]]]
 +
 +[[#​k031|[]]//​[[#​k031|iters]]//​[[#​k031| #]]]
 +
 +[[#​k034|[line_min] [use_extrapolation] [no_normal_equations] [use_LU]]]
 +
 +[[#​k139|[]]//​[[#​k139|marquardt_constant]]//​[[#​k139| !E]…]]
 +
 +[[#​k156|[]]//​[[#​k156|no_LIMIT_warnings]]//​[[#​k156|]]]
 +
 +[[#​k044|[]]//​[[#​k044|only_penalties]]//​[[#​k044|]]]
 +
 +[[#​k165|[]]//​[[#​k165|out_A_matrix]]//​[[#​k165| $file]]]
 +
 +[//​A_matrix_prm_filter//​ $filter]
 +
 +[[#​k046|[]]//​[[#​k046|out_rwp]]//​[[#​k046| $file]]][[#​k046| ]]
 +
 +[[#​k159|[]]//​[[#​k159|out_prm_vals_per_iteration]]//​[[#​k159| $file]... | []]//​[[#​k159|out_prm_vals_on_convergence]]//​[[#​k159| $file]...]]
 +
 +[//​out_prm_vals_filter//​ $filter]
 +
 +[[#​k053|[]]//​[[#​k053|penalties_weighting_K1]]//​[[#​k053| !E]]]
 +
 +[[#​k054|[]]//​[[#​k054|percent_zeros_before_sparse_A]]//​[[#​k054| #]]]
 +
 +[[#​k062|[]]//​[[#​k062|process_times]]//​[[#​k062|]]]
 +
 +[[#​k064|[]]//​[[#​k064|quick_refine]]//​[[#​k064| !E []]//​[[#​k064|quick_refine_remove]]//​[[#​k064| !E]]]]
 +
 +[[#​k065|[]]//​[[#​k065|randomise_file_out_normal]]//​[[#​k065| $file]]]
 +
 +[[#​k133|[]]//​[[#​k133|randomize_on_errors]]//​[[#​k133|]]]
 +
 +[[#​k074|[]]//​[[#​k074|seed]]//​[[#​k074|]]]
 +
 +[[#​k086|[]]//​[[#​k086|temperature]]//​[[#​k086| !E]...]]
 +
 +[[#​k132|[]]//​[[#​k132|do_processes]]//​[[#​k132|]]]
 +
 +[[#​k129|[]]//​[[#​k129|move_to_the_next_temperature_regardless_of_the_change_in_rwp]]//​[[#​k129|]]]
 +
 +[[#​k130|[]]//​[[#​k130|save_values_as_best_after_randomization]]//​[[#​k130|]]]
 +
 +[[#​k131|[]]//​[[#​k131|use_best_values]]//​[[#​k131|]]]
 +
 +[[#​k090|[]]//​[[#​k090|use_tube_dispersion_coefficients]]//​[[#​k090|]]][[#​k090| ]]
 +
 +[[#​k091|[]]//​[[#​k091|verbose]]//​[[#​k091| #​]]][[#​k091| ]]
 +
 + 
 +
 +Txdd
 +
 +[[#​k095|[]]//​[[#​k095|xdd]]//​[[#​k095| $file [{$data}] []]//​[[#​k095|range]]//​[[#​k095| #] []]//​[[#​k095|xye_format]]//​[[#​k095|] []]//​[[#​k095|gsas_format]]//​[[#​k095|] []]//​[[#​k095|fullprof_format]]//​[[#​k095|] ]...]][[#​k095| ]]
 +
 +[[#​hy13|Ttop_xdd]]
 +
 +[[#​hy5|Txdd_comm_1]]
 +
 +[[#​hy6|Tcomm_1]]
 +
 +[[#​hy7|Tcomm_2]]
 +
 +[[#​hy19|Tmin_max_r]]
 +
 +[[#​k038|[]]//​[[#​k038|mixture_MAC]]//​[[#​k038| !E]]]
 +
 +[[#​k037|[]]//​[[#​k037|mixture_density_g_on_cm3]]//​[[#​k037| !E]]]
 +
 +[[#​k093|[]]//​[[#​k093|weight_percent_amorphous]]//​[[#​k093| !E]]]
 +
 +[[#​k099|[]]//​[[#​k099|xo_Is]]//​[[#​k099|]...]]
 +
 +[[#​k099|[]]//​[[#​k099|xo]]//​[[#​k099| E]][[#​k099| ]][[#​k099| ]]//​[[#​k099|I]]//​[[#​k099| E]...]]
 +
 +[[#​hy24|Tcomm_1_2_phase_1_2]]
 +
 +[[#​k019|[]]//​[[#​k019|d_Is]]//​[[#​k019|]...]]
 +
 +[[#​k019|[]]//​[[#​k019|d]]//​[[#​k019| E]][[#​k019| ]][[#​k019| ]]//​[[#​k019|I]]//​[[#​k019| E]...]]
 +
 +[[#​hy24|Tcomm_1_2_phase_1_2]]
 +
 +[[#​hy11|Tlebail]]
 +
 +[[#​k029|[]]//​[[#​k029|hkl_Is]]//​[[#​k029|]...]]
 +
 +[[#​k029|[]]//​[[#​k029|lp_search]]//​[[#​k029| !E]]]
 +
 +[[#​k150|[]]//​[[#​k150|I_parameter_names_have_hkl]]//​[[#​k150| $start_of_parameter_name]]]
 +
 +[[#​k029|[]]//​[[#​k029|hkl_m_d_th2]]//​[[#​k029| # # # # # #​]][[#​k029| ]][[#​k029| E ]]//​[[#​k029|I]]//​[[#​k029| E]...]]
 +
 +[[#​hy22|Tspace_group]]
 +
 +[[#​hy24|Tcomm_1_2_phase_1_2]]
 +
 +[[#​hy12|Thkl_lat]]
 +
 +[[#​hy11|Tlebail]]
 +
 +[[#​k083|[]]//​[[#​k083|str]]//​[[#​k083|]...]]
 +
 +[[#​hy9|Tstr_details]]
 +
 +[[#​hy12|Thkl_lat]]
 +
 +[[#​hy24|Tcomm_1_2_phase_1_2]]
 +
 +[[#​hy19|Tmin_max_r]]
 +
 +[[#​hy14|Trigid]]
 +
 +[[#​hy22|Tspace_group]]
 +
 +[[#​k030|[]]//​[[#​k030|hkl_Is_from_hkl4]]//​[[#​k030|]]]
 +
 +[[#​hy24|Tcomm_1_2_phase_1_2]]
 +
 +[[#​hy12|Thkl_lat]]
 +
 +[[#​hy22|Tspace_group]]
 +
 +[[#​hy4|Tscr_1]]
 +
 + 
 +
 +Tcomm_1_2_phase_1_2
 +
 +[[#​hy6|Tcomm_1]]
 +
 +[[#​hy7|Tcomm_2]]
 +
 +[[#​hy8|Tphase_1]]
 +
 +[[#​hy10|Tphase_2]]
 +
 + 
 +
 +Txdd_scr
 +
 +[[#​k097|[]]//​[[#​k097|xdd_scr]]//​[[#​k097| $file] …]]
 +
 +[[#​hy5|Txdd_comm_1]]
 +
 +[[#​hy7|Tcomm_2]]
 +
 +[[#​hy13|Ttop_xdd]]
 +
 +[[#​hy19|Tmin_max_r]]
 +
 +[[#​k108|[]]//​[[#​k108|dont_merge_equivalent_reflections]]//​[[#​k108|]]]
 +
 +[[#​k109|[]]//​[[#​k109|dont_merge_Friedel_pairs]]//​[[#​k109|]]]
 +
 +[[#​k110|[]]//​[[#​k110|ignore_differences_in_Friedel_pairs]]//​[[#​k110|]]]
 +
 +[[#​k083|[]]//​[[#​k083|str]]//​[[#​k083|]...]]
 +
 +[[#​hy9|Tstr_details]]
 +
 +[[#​hy8|Tphase_1]]
 +
 +[[#​hy7|Tcomm_2]]
 +
 +[[#​hy12|Thkl_lat]]
 +
 +[[#​hy19|Tmin_max_r]]
 +
 +[[#​hy14|Trigid]]
 +
 +[[#​hy22|Tspace_group]]
 +
 +[[#​hy4|Tscr_1]]
 +
 + 
 +
 +Tscr_1
 +
 +[[#​k167|[]]//​[[#​k167|Flack]]//​[[#​k167| E]]]
 +
 +[[#​k105|[]]//​[[#​k105|i_on_error_ratio_tolerance]]//​[[#​k105| ]][[#​k105|#​]]]
 +
 +[[#​k106|[]]//​[[#​k106|num_highest_I_values_to_keep]]//​[[#​k106| #]]]
 +
 + 
 +
 +Txdd_comm_1
 +
 +[[#​k008|[]]//​[[#​k008|bkg]]//​[[#​k008| [@] # # #...]]]
 +
 +**Error! Hyperlink reference not valid.**
 +
 +[//​crystalline_area//​  #]
 +
 +[//​amorphous_area//​  #]
 +
 +[[#​k141|[]]//​[[#​k141|d_spacing_to_energy_in_eV_for_f1_f11]]//​[[#​k141| !E]]]
 +
 +[[#​k021|[]]//​[[#​k021|exclude]]//​[[#​k021| #ex1 #ex2]...]]
 +
 +[[#​k136|[]]//​[[#​k136|extra_X_left]]//​[[#​k136| !E] []]//​[[#​k136|extra_X_right]]//​[[#​k136| !E]]]
 +
 +[[#​k025|[]]//​[[#​k025|fit_obj]]//​[[#​k025| E []]//​[[#​k025|min_X]]//​[[#​k025| !E] []]//​[[#​k025|max_X]]//​[[#​k025| !E] ]...]]
 +
 +[[#​k039|[]]//​[[#​k039|neutron_data]]//​[[#​k039|]]]
 +
 +[[#​k065|[]]//​[[#​k065|randomize_file_out_normal]]//​[[#​k065| $file]]]
 +
 +[[#​k068|[]]//​[[#​k068|rebin_with_dx]]//​[[#​k068|_of !E]]]
 +
 +[[#​k078|[s]]//​[[#​k078|mooth #​]]//​[[#​k078|]]]
 +
 +[[#​k082|[]]//​[[#​k082|start_X]]//​[[#​k082| !E] []]//​[[#​k082|finish_X]]//​[[#​k082| !E]]]
 +
 +[[#​k092|[]]//​[[#​k092|weighting]]//​[[#​k092| !E []]//​[[#​k092|recal_weighting_on_iter]]//​[[#​k092|]]]]
 +
 +[[#​k096|[]]//​[[#​k096|xdd_out]]//​[[#​k096| $file ]][[#​k096|[]]//​[[#​k096|append]]//​[[#​k096|]]][[#​k096| ]...]]
 +
 +[[#​hy21|T]][[#​hy21|out_record]]
 +
 +[[#​k140|[]]//​[[#​k140|yobs_eqn]]//​[[#​k140| !N E]]]
 +
 +[[#​k137|[]]//​[[#​k137|yobs_out]]//​[[#​k137| $file] []]//​[[#​k137|ycalc_out]]//​[[#​k137| $file] []]//​[[#​k137|diff_out]]//​[[#​k137| $file]]]
 +
 +[[#​k100|[]]//​[[#​k100|yobs_to_xo_posn_yobs]]//​[[#​k100| ]][[#​k100|!E]]]
 +
 + 
 +
 +Tcomm_1
 +
 +[[#​k007|[]]//​[[#​k007|axial_conv]]//​[[#​k007|]]]//​[[#​k007|...]]//​[[#​k007| ]]
 +
 +//​[[#​k114|filament_length]]//​[[#​k114| ]][[#k114|E ]]//​[[#​k114|sample_length]]//​[[#​k114| E ]]//​[[#​k114|receiving_slit_length]]//​[[#​k114| E]]
 +
 +[[#​k117|[]]//​[[#​k117|primary_soller_angle]]//​[[#​k117| E]]]
 +
 +[[#​k118|[]]//​[[#​k118|secondary_soller_angle]]//​[[#​k118| E]]]
 +
 +[[#​k120|[]]//​[[#​k120|axial_n_beta]]//​[[#​k120| !E]]]
 +
 +[[#​k151|[]]//​[[#​k151|capillary_diameter_mm]]//​[[#​k151| E]...]]
 +
 +//​capillary_u_cm_inv//​ E
 +
 +//​capillary_parallel_beam//​ %%|%% //​capillary_divergent_beam//​
 +
 +[[#​k152|[]]//​[[#​k152|lpsd_th2_angular_range_degrees]]//​[[#​k152| E]...]]
 +
 +//​lpsd_equitorial_divergence_degrees//​ E
 +
 +//​lpsd_equitorial_sample_length_mm//​ E
 +
 +[[#​k014|[]]//​[[#​k014|circles_conv]]//​[[#​k014| E]...]]
 +
 +[[#​k022|[]]//​[[#​k022|exp_conv_const]]//​[[#​k022| E]][[#​k022| ]][[#​k022| []]//​[[#​k022|exp_limit]]//​[[#​k022| E] ]...]]
 +
 +[[#​k026|[]]//​[[#​k026|gauss_fwhm]]//​[[#​k026| E]...]]
 +
 +[[#​k047|[]]//​[[#​k047|h1]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|h2]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|m1]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|m2]]//​[[#​k047| E]]]
 +
 +[[#​k028|[]]//​[[#​k028|hat]]//​[[#​k028| E []]//​[[#​k028|num_hats]]//​[[#​k028| #] ]...]]
 +
 +[[#​k035|[]]//​[[#​k035|lor_fwhm]]//​[[#​k035| E]...]]
 +
 +[[#​k043|[]]//​[[#​k043|one_on_x_conv]]//​[[#​k043| E]...]]
 +
 +[[#​k057|[]]//​[[#​k057|pk_xo]]//​[[#​k057| E]]]
 +
 +[[#​k143|[]]//​[[#​k143|push_peak]]//​[[#​k143|]]]//​[[#​k143|…]]//​[[#​k143|[]]//​[[#​k143|bring_2nd_peak_to_top]]//​[[#​k143|]…[]]//​[[#​k143|add_pop_1st_2nd_peak]]//​[[#​k143|]…[]]//​[[#​k143|scale_top_peak]]//​[[#​k143| E]…]]
 +
 +[[#​k047|[]]//​[[#​k047|pv_lor]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|pv_fwhm]]//​[[#​k047| E]]]
 +
 +[[#​k047|[]]//​[[#​k047|spv_h1]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|spv_h2]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|spv_l1]]//​[[#​k047| E]][[#​k047| ]][[#​k047| ]]//​[[#​k047|spv_l2]]//​[[#​k047| E]]]
 +
 +[[#​k081|[]]//​[[#​k081|stacked_hats_conv]]//​[[#​k081| []]//​[[#​k081|whole_hat E]]//​[[#​k081| []]//​[[#​k081|hat_height E]]//​[[#​k081|]]]]//​[[#​k081|...]]//​[[#​k081|[]]//​[[#​k081|half_hat E]]//​[[#​k081| []]//​[[#​k081|hat_height E]]//​[[#​k081|]]...]]]//​[[#​k081|...]]//​
 +
 +[[#​k087|[]]//​[[#​k087|th2_offset]]//​[[#​k087| E]...]]
 +
 +[[#​k089|[]]//​[[#​k089|user_defined_convolution]]//​[[#​k089| E ]]//​[[#​k089|min]]//​[[#​k089| E ]]//​[[#​k089|max]]//​[[#​k089| E]...]]
 +
 + 
 +
 +Tcomm_2
 +
 +[[#​k032|[]]//​[[#​k032|lam]]//​[[#​k032| []]//​[[#​k032|ymin_on_ymax]]//​[[#​k032| #] []]//​[[#​k032|no_th_dependence]]//​[[#​k032|] [Lam !E] [calculate_Lam]]]]
 +
 +[[#​k032|[]]//​[[#​k032|la]]//​[[#​k032| E]][[#​k032| ]][[#​k032| ]]//​[[#​k032|lo]]//​[[#​k032| E]][[#​k032| ]][[#​k032| []]//​[[#​k032|lh]]//​[[#​k032| E] | []]//​[[#​k032|lg]]//​[[#​k032| E]]...]]
 +
 +[[#​k073|[]]//​[[#​k073|scale_pks]]//​[[#​k073| E]...]]
 +
 +[[#​k148|[]]//​[[#​k148|prm|local]]//​[[#​k148| E []]//​[[#​k148|min]]//​[[#​k148| !E] []]//​[[#​k148|max]]//​[[#​k148| !E] []]//​[[#​k148|del]]//​[[#​k148| !E] []]//​[[#​k148|update]]//​[[#​k148| !E] []]//​[[#​k148|stop_when]]//​[[#​k148| !E] []]//​[[#​k148|val_on_continue]]//​[[#​k148| !E]]...]]
 +
 +[[#​k052|[]]//​[[#​k052|penalty]]//​[[#​k052| !E]...]][[#​k052| ]]
 +
 +[[#​k045|[o]]//​[[#​k045|ut]]//​[[#​k045| $file []]//​[[#​k045|append]]//​[[#​k045|] ]...]]
 +
 +[[#​hy21|T]][[#​hy21|out_record]]
 +
 + 
 +
 +Tphase_1
 +
 +[[#​k134|[]]//​[[#​k134|atom_out]]//​[[#​k134| $file []]//​[[#​k134|append]]//​[[#​k134|]]…]]
 +
 +[[#​hy21|T]][[#​hy21|out_record]]
 +
 +[[#​k104|[]]//​[[#​k104|auto_scale]]//​[[#​k104| !E]]]
 +
 +[[#​k012|[]]//​[[#​k012|cell_mass]]//​[[#​k012| !E] []]//​[[#​k012|cell_volume]]//​[[#​k012| !E] []]//​[[#​k012|weight_percent]]//​[[#​k012| !E]]]
 +
 +[[#​k012|[]]//​[[#​k012|spiked_phase_measured_weight_percent]]//​[[#​k012| ]][[#​k012|!E]][[#​k012|] []]//​[[#​k012|corrected_weight_percent]]//​[[#​k012| !E]]]
 +
 +[[#​k055|[]]//​[[#​k055|phase_MAC]]//​[[#​k055| !E]]]
 +
 +[[#​k135|[]]//​[[#​k135|phase_name]]//​[[#​k135| $phase_name]]]
 +
 +[[#​k056|[]]//​[[#​k056|phase_out]]//​[[#​k056| $file ]][[#​k056|[]]//​[[#​k056|append]]//​[[#​k056|]]][[#​k056| ]...]]
 +
 +[[#​k011|[]]//​[[#​k011|brindley_spherical_r_cm]]//​[[#​k011| !E]]]
 +
 +[[#​k067|[]]//​[[#​k067|r_bragg]]//​[[#​k067| #]]]
 +
 +[[#​k072|[]]//​[[#​k072|sc]]//​[[#​k072|a]]//​[[#​k072|le]]//​[[#​k072| ]][[#​k072|E]]]
 +
 + 
 +
 +Tphase_2
 +
 +**Error! Hyperlink reference not valid.**
 +
 +[[#​k051|[]]//​[[#​k051|peak_buffer_step]]//​[[#​k051| ]][[#​k051| E []]//​[[#​k051|report_on]]//​[[#​k051|] ]]]
 +
 +[[#​k047|[]]//​[[#​k047|peak_type]]//​[[#​k047| $type]]]
 +
 +[[#​k041|[]]//​[[#​k041|numerical_area]]//​[[#​k041| E]]]
 +
 + 
 +
 +Tlebail
 +
 +[[#​k033|[]]//​[[#​k033|lebail]]//​[[#​k033| #]]]
 +
 + 
 +
 +Tstr_details
 +
 +[[#​k004|[]]//​[[#​k004|append_cartesian]]//​[[#​k004|] []]//​[[#​k004|append_fractional]][[#​k004| ]]//​[[#​k004| []]//​[[#​k004|in_str_format]]//​[[#​k004|] ]]]
 +
 +[[#​k005|[]]//​[[#​k005|append_bond_lengths]]//​[[#​k005| ]][[#​k005| []]//​[[#​k005|consider_lattice_parameters]]//​[[#​k005|] ]]]
 +
 +[[#​k006|[]]//​[[#​k006|atomic_interaction]]//​[[#​k006| N E] | []]//​[[#​k006|ai_anti_bump]]//​[[#​k006| N]...]][[#​k006| ]]
 +
 +//​ai_sites_1//​ $sites_1 //​ai_sites_2//​ $sites_2
 +
 +[//​ai_no_self_interation//​]
 +
 +[//​ai_closest_N//​ !E]
 +
 +[//​ai_radius//​  !E]
 +
 +[//​ai_exclude_eq_0//​]
 +
 +[//​ai_only_eq_0//​]
 +
 +[[#​k009|[]]//​[[#​k009|box_interaction]]//​[[#​k009| []]//​[[#​k009|from_N]]//​[[#​k009| #] []]//​[[#​k009|to_N]]//​[[#​k009| #] []]//​[[#​k009|no_self_interaction]]//​[[#​k009|]]][[#​k009| ]][[#​k009| $site_1 $site_2 N E]...]]
 +
 +[[#​k010|[]]//​[[#​k010|break_if_been_there]]//​[[#​k010| ]][[#​k010| $sites !E []]//​[[#​k010|been_there_buffer]]//​[[#​k010| #​buffer_size] []]//​[[#​k010|been_there_clear_buffer]]//​[[#​k010| !E]]]]
 +
 +[[#​k161|[]]//​[[#​k161|cloud]]//​[[#​k161| $sites]...]]
 +
 +[//​cloud_population//​ !E]
 +
 +[//​cloud_save//​ $file]
 +
 +[//​cloud_load_xyzs//​ $file]
 +
 +[//​cloud_load_xyzs_omit_rwps//​ !E]
 +
 +[//​cloud_save_xyzs//​ $file]
 +
 +[//​cloud_formation_omit_rwps//​ !E]
 +
 +[//​cloud_extract_and_save_xyzs//​ $file]
 +
 +[//​cloud_number_to_extract//​ !E]
 +
 +[//​cloud_atomic_separation//​ !E]
 +
 +[//​cloud_try_accept//​ !E]
 +
 +[//​cloud_gauss_fwhm//​ !E]
 +
 +[[#​k162|[]]//​[[#​k162|hkl_plane]]//​[[#​k162| $hkl]…]]
 +
 +[[#​k027|[]]//​[[#​k027|grs_interaction]]//​[[#​k027| []]//​[[#​k027|from_N]]//​[[#​k027| #] []]//​[[#​k027|to_N]]//​[[#​k027| #] []]//​[[#​k027|no_self_interaction]]//​[[#​k027|] $site_1 $site_2 ]]//​[[#​k027|qi]]//​[[#​k027| # ]]//​[[#​k027|qj]]//​[[#​k027| # N E]...]]
 +
 +[[#​k040|[]]//​[[#​k040|normalize_FCs]]//​[[#​k040|]]]
 +
 +[[#​k042|[]]//​[[#​k042|occ_merge]]//​[[#​k042| $sites []]//​[[#​k042|occ_merge_radius]]//​[[#​k042| !E]]…]]
 +
 +[[#​k075|[]]//​[[#​k075|site]]//​[[#​k075| $site]...]]
 +
 +[//x// E] [//y// E] [//z// E]
 +
 +[num_posns #] [rand_xyz !E] [inter !E]
 +
 +[//occ// $atom E  //beq// E]...
 +
 +[[#​k002|[]]//​[[#​k002|adps]]//​[[#​k002|] []]//​[[#​k002|u11]]//​[[#​k002| E] []]//​[[#​k002|u22]]//​[[#​k002| E] []]//​[[#​k002|u33]]//​[[#​k002| E] []]//​[[#​k002|u12]]//​[[#​k002| E] []]//​[[#​k002|u13]]//​[[#​k002| E] []]//​[[#​k002|u23]]//​[[#​k002| E]]]
 +
 +[[#​hy19|Tmin_r_max_r]]
 +
 +[[#​k076|[]]//​[[#​k076|sites_distance]]//​[[#​k076| N] | []]//​[[#​k076|sites_angle]]//​[[#​k076| N] | []]//​[[#​k076|sites_flatten]]//​[[#​k076| N []]//​[[#​k076|sites_flatten_tol]]//​[[#​k076| !E]]...]]
 +
 +[[#​k076|[]]//​[[#​k076|site_to_restrain]]//​[[#​k076| $site [ #ep [ #n1 #n2 #n3 ] ] ]...]]
 +
 +[[#​k154|[]]//​[[#​k154|sites_geometry]]//​[[#​k154| N]...]]
 +
 +[//​site_to_restrain//​ $site [ #ep [ #n1 #n2 #n3 ] ] ]...
 +
 +[[#​k077|[]]//​[[#​k077|siv_s1_s2]]//​[[#​k077| # #]]]
 +
 +[[#​k146|[]]//​[[#​k146|swap_sites]]//​[[#​k146| $sites_1 $sites_2]…]]
 +
 +[[#​k166|[]]//​[[#​k166|fourier_map]]//​[[#​k166| !E] ]]
 +
 +[//​fourier_map_formula//​ !E]
 +
 +[//​extend_calculated_sphere_to//​ !E]
 +
 +[//​min_grid_spacing//​ !E]
 +
 +[//​correct_for_atomic_scattering_factors//​ !E]
 +
 +[//​f_atom_type//​ $type [//​f_atom_quantity//​ !E]]…
 +
 +[[#​k147|[]]//​[[#​k147|try_site_patterns]]//​[[#​k147| $sites []]//​[[#​k147|num_patterns_at_a_time]]//​[[#​k147| #] ]...]]
 +
 +[[#​k149|[]]//​[[#​k149|view_structure]]//​[[#​k149|]]]
 +
 + 
 +
 +Thkl_lat
 +
 +[[#​k000|[]]//​[[#​k000|a]]//​[[#​k000| E] []]//​[[#​k000|b]]//​[[#​k000| E] []]//​[[#​k000|c]]//​[[#​k000| E] []]//​[[#​k000|al]]//​[[#​k000| E] []]//​[[#​k000|be]]//​[[#​k000| E] []]//​[[#​k000|ga]]//​[[#​k000| E]]]
 +
 +[[#​k061|[]]//​[[#​k061|phase_penalties]]//​[[#​k061| $sites N []]//​[[#​k061|hkl_Re_Im]]//​[[#​k061| #h #k #l #Re #​Im]...]…]]
 +
 +[//​accumulate_phases_and_save_to_file//​ $file]
 +
 +[//​accumulate_phases_when//​ !E]
 +
 +[[#​k080|[]]//​[[#​k080|spherical_harmonics_hkl]]//​[[#​k080| $name]...]]
 +
 +[[#​k111|[]]//​[[#​k111|sh_Cij_prm]]//​[[#​k111| $Yij E]...]]
 +
 +[[#​k112|[]]//​[[#​k112|sh_order]]//​[[#​k112| #]]]
 +
 +[[#​k113|[]]//​[[#​k113|sh_alpha]]//​[[#​k113| !E]]]
 +
 +[[#​k084|[]]//​[[#​k084|str_hkl_angle]]//​[[#​k084| N h k l]...]]
 +
 +[[#​k153|[]]//​[[#​k153|omit_hkls]]//​[[#​k153| !E]]]
 +
 + 
 +
 +Trigid
 +
 +[[#​k069|[]]//​[[#​k069|rigid]]//​[[#​k069|]...]][[#​k069| ]]
 +
 +[[#​k121|[]]//​[[#​k121|point_for_site]]//​[[#​k121| $site []]//​[[#​k121|ux|ua]]//​[[#​k121| E] []]//​[[#​k121|uy|ub]]//​[[#​k121| E] []]//​[[#​k121|uz|uc]]//​[[#​k121| E] ]...]][[#​k121| ]]
 +
 +[[#​k125|[]]//​[[#​k125|in_cartesian]]//​[[#​k125|] []]//​[[#​k125|in_FC]]//​[[#​k125|]]]
 +
 +[[#​k122|[]]//​[[#​k122|z_matrix]]//​[[#​k122| $atom_1 [$atom_2 E] [$atom_3 E] [$atom_4 E] ] …]]
 +
 +[[#​k123|[]]//​[[#​k123|rotate]]//​[[#​k123| E []]//​[[#​k123|qx]]//​[[#​k123||]]//​[[#​k123|qa]]//​[[#​k123| E] []]//​[[#​k123|qy]]//​[[#​k123||]]//​[[#​k123|qb]]//​[[#​k123| E] []]//​[[#​k123|qz]]//​[[#​k123||]]//​[[#​k123|qc]]//​[[#​k123| E] ]...]][[#​k123| ]]
 +
 +[[#​k126|[]]//​[[#​k126|operate_on_points]]//​[[#​k126| $sites]]]
 +
 +[[#​k125|[]]//​[[#​k125|in_cartesian]]//​[[#​k125|] []]//​[[#​k125|in_FC]]//​[[#​k125|]]]
 +
 +[[#​k124|[]]//​[[#​k124|translate]]//​[[#​k124| []]//​[[#​k124|tx]]//​[[#​k124||]]//​[[#​k124|ta]]//​[[#​k124| E] []]//​[[#​k124|ty]]//​[[#​k124||]]//​[[#​k124|tb]]//​[[#​k124| E] []]//​[[#​k124|tz]]//​[[#​k124||]]//​[[#​k124|tc]]//​[[#​k124| E] ]...]][[#​k124| ]]
 +
 +[[#​k126|[]]//​[[#​k126|operate_on_points]]//​[[#​k126| $sites]]]
 +
 +[[#​k128|[]]//​[[#​k128|rand_xyz]]//​[[#​k128| !E]]]
 +
 +[[#​k125|[]]//​[[#​k125|in_cartesian]]//​[[#​k125|] []]//​[[#​k125|in_FC]]//​[[#​k125|]]]
 +
 +[[#​k127|[]]//​[[#​k127|start_values_from_site]]//​[[#​k127| $unique_site_name]]]
 +
 + 
 +
 +Tout_record
 +
 +[[#​k045|[]]//​[[#​k045|out_record]]//​[[#​k045|]]]…
 +
 +[out_eqn !E]
 +
 +[//​out_fmt//​ $c_fmt_string]
 +
 +[//​out_fm//​t//​_err//​$c_fmt_string]...
 +
 + 
 +
 +Tmin_r_max_r
 +
 +[[#​k036|[]]//​[[#​k036|min_r]]//​[[#​k036| #] []]//​[[#​k036|max_r]]//​[[#​k036| #]]]
 +
 + 
 +
 +Tspace_group
 +
 +[[#​sg|[]]//​[[#​sg|space_group]]//​[[#​sg| ]][[#​sg|$symbol]]]
 +
 + 
 +
 +Miscellanous
 +
 +[[#​k001|[]]//​[[#​k001|aberration_range_change_allowed]]//​[[#​k001| !E]]]
 +
 +[[#​k018|[]]//​[[#​k018|default_I_attributes]]//​[[#​k018| !E]]]
 +
 +//​[[#​k101|load]]//​[[#​k101| ]]
 +
 +//​[[#​k102|move_to]]//​
 +
 +//​[[#​k103|for]]//​
 +
 +===== 8.2        Alphabetical listing of keywords =====
 +
 +**[//a// E] [//b// E] [//c// E] [//al// E] [//be// E] [//ga// E]**
 +
 +Lattice parameters in Angstroms and lattice angles in degrees.
 +
 +**[//​adps//​] [//u11// E] [//u22// E] [//u33// E] [//u12// E] [//u13// E] [//u23// E]**
 +
 +//adps// when used generates the //unn// atomic displacement parameters with considerations made for special positions. On termination of refinement the //adps// keyword is replaced with the //unn// parameters; see example AE1-ADPS.INP. Instead of using the //adps// keyword the //unn// parameters can be manually entered.
 +
 +The //unn// matrix can be kept positive definite with the site dependent macro ADPs_Keep_PD;​ this can stabilize refinement.  The ADPs_Keep_PD macro can be used after the //unn// parameters are created.
 +
 +**[//​amorphous_phase//​]**
 +
 +Signals that the associated phase is amorphous when calculating //​degree_of_crystallinity//​.
 +
 +** [//​A_matrix//​][//​C_matrix//​][//​A_matrix_normalized//​][//​C_matrix_normalized//​]**
 +
 +Generates the un-normalized and normalized A and correlation matrices. If //​do_errors//​ is defined then //​C_matrix_normalized//​ is automatically generated and appeneded to the OUT file.
 +
 +**[//​append_cartesian//​] [//​append_fractional//​ [//​in_str_format//​] ]**
 +
 +Appends site fractional coordinates in Cartesian or fractional coordinates respectively to the *.OUT file at the end of a refinement. For the case of //​append_fractional//,​ the //​in_str_format//​ keyword formats the output in INP format.
 +
 +**[//​append_bond_lengths//​ [//​consider_lattice_parameters//​] ]**
 +
 +Appends bond lengths to the end of the *.OUT file at the end of refinement. A number corresponding to equivalent positions is appended to site names.
 +
 +//​consider_lattice_parameters//​ includes the effects of lattice parameter errors in the calculation of bond length and bond angle errors.
 +
 +An example of bond lengths output is as follows:
 +
 +Y1:0    O1:0    2.23143
 +
 +        O2:0    2.23143    88.083
 +
 +        O3:0    2.28045    109.799    99.928
 +
 +The first line gives the distance between the sites Y1 and O2. The first number in the second line gives the distance between sites Y1 and O2. The third number of 88.083 gives the angle between the vectors Y1 to O1 and Y1 to O2. The first number on the third line contains the distance between sites Y1 and O3. The second number in the third line contains the angle between the vectors Y1 to O3 and Y1 to O2. The third number in line three contains the angle between the vectors Y1 to O3 and Y1 to O1. Thus bond lengths correspond to the first number in each line and bond angles start from the second number. The numbers after the site name and after the ‘:’ character corresponds to the site equivalent position as found in the *.SG space group files found in the SG directory
 +
 +**[//​approximate_A//​]**
 +
 +**[//​A_matrix_memory_allowed_in_Mbytes//​ !E]**
 +
 +**[//​A_matrix_elements_tollerance//​ !E]**
 +
 +**[//​A_matrix_report_on//​]**
 +
 +See section 5.2 for a description of //​approximate_A//​.
 +
 +//​A_matrix_memory_allowed_in_Mbytes//​ limits the memory used by the **A** matrix to a maximum of //​A_matrix_memory_allowed_in_Mbytes//​. If the matrix requires less than //​A_matrix_memory_allowed_in_Mbytes//​ then the full matrix is used otherwise the matrix is treated as a sparse matrix.
 +
 +//​A_matrix_elements_tollerance//​ removes elements in the **A** matrix with values less than //​A_matrix_elements_tollerance.//​ The comparison is made againts normalized elements of **A** such that the diagonals have a values of 1.  The **A** matrix is made sparse when //​A_matrix_elements_tollerance//​ is defined. Typical values of //​A_matrix_memory_allowed_in_Mbytes//​ range from 0.0001 to 0.01.
 +
 +//​A_matrix_memory_allowed_in_Mbytes//​ and //​A_matrix_elements_tollerance//​ can be used simultanuously.
 +
 +//​A_matrix_report_on//​ displays the percentage of non-zero elements in the **A** matrix.
 +
 +** [//​atomic_interaction//​ N E] |  [//​ai_anti_bump//​ N]...**
 +
 +**//​ai_sites_1//​** **$sites_1 //​ai_sites_2//​ $sites_2**
 +
 +**[//​ai_no_self_interation//​]**
 +
 +**[//​ai_closest_N//​ !E]**
 +
 +**[//​ai_radius//​  !E]**
 +
 +**[//​ai_exclude_eq_0//​]**
 +
 +**[//​ai_only_eq_0//​]**
 +
 +Defines an atomic interaction with the name N between [[#​k142|sites identified]] by $site_1 and $site_2. For //​atomic_interaction//​ E is the site interaction equation that can be a function of R and Ri. R returns the distance in Å between two atoms; these distances are updated when dependent fractional atomic coordinates are modified. The name of the //​atomic_interaction//​ N can be used in equations and in particular penalty equations.
 +
 +For //​ai_anti_bump//​ an anti-bump interaction equations is internally generated. For anti-bumping only the //​ai_anti_bump//​ is faster than using //​atomic_interaction//​. The macro AI_Anti_Bump uses//​ai_anti_bump//​.
 +
 +//​no_self_interaction//​ prevents any interactions between equivalent positions of a site. This is useful when a general position is used to describe a special position.
 +
 +//​ai_closest_N//:​ interactions between $sites_1 and $sites_2 are sorted by distance and only the first //​ai_closest_N//​ number of interactions are considered.
 +
 +//​ai_radius//:​ only the interactions between $sites_1 and $sites_2 that are within the distance //​ai_radius//​ are considered.
 +
 +When //​ai_radius//​ and //​ai_closest_N//​ are both defined then interactions from both sets of corresponding interaction are considered.
 +
 +//​ai_exclude_eq_0//:​ only interactions that is not the first equivalent positions in $sites_2 are considered. For example, in the following:
 +
 +atomic_interaction...
 +
 +ai_exclude_eq_0
 +
 +ai_sites_1 Pb
 +
 +ai_sites_1 “O1 O2”
 +
 +the following interactions are considered:
 +
 +Pb:0 and O1:​n      (n ¹ 0)
 +
 +Pb:0 and O2:​n      (n ¹ 0)
 +
 +where the number after the ‘:’ character corresponds to the equivalent positions of the sites.
 +
 +//​ai_only_eq_0//:​only interactions between equivalent positions 0 are considered.
 +
 +**__Functions__**
 +
 +The //​atomic_interaction//​’ equation can be a function of the following functions:
 +
 +AI_R(#ri): Returns the distance between the current site and the atom defined with Ri = #ri.
 +
 +AI_R_CM: A function of no arguments that returns the geometric center of the current atom and the atoms defined in $sites_2.
 +
 +AI_Flatten(#​toll):​ A function that returns the sum of distances of the current atom and those defined in $sites_2 to an approximate plane of best fit. The plane of best fit is constructed such that the sum of the perpendicular distances to the current atom plus those defined in $sites_2 are a minimum
 +
 +AI_Cos_Angle(#​ri1,​ #ri2): Returns the Cos of the angle between the atom define as Ri=#ri1, the current atom and the atom defined as Ri=#ri2.
 +
 +AI_Angle(#​ri1,​ #ri2) : Similar to AI_Cos_Angle except that the value returned is the angle in degrees.
 +
 +Examples BENZENE_AI1.INP,​ BENZENE_AI2.INP and BENZENE_AI3.INP demonstrates the use of the //​atomic_interation//​ functions.
 +
 +//​atomic_interaction//​’s can be used to apply geometric restraints. For example, an anti-bump interaction between symmetry related molecules can be formulated as follows:
 +
 +atomic_interaction ai1 =
 +
 +IF R < 3 THEN
 +
 +(R-3)^2
 +
 +ELSE
 +
 +0
 +
 +ENDIF
 +
 +;
 +
 +ai_exclude_eq_0
 +
 +ai_sites_1 C*
 +
 +ai_sites_1 C*
 +
 +ai_radius 3
 +
 +penalty = If(Cycle_Iter < 10, ai1, 0);
 +
 +This example demonstrates anti-bumping between molecules for the first ten iterations of a [[#​k144|refinement cycle]].
 +
 +**[//​atom_out//​ $file [append] ]...**
 +
 +Used for writing //site// dependent details to file. See the keyword //out// for a description of //​[[#​k045|out_record]]//​. The Out_CIF_STR uses //​atom_out//​
 +
 +**[//​axial_conv//​]...  **
 +
 +**//​filament_length//​** **E //​sample_length//​ E //​receiving_slit_length//​ E**
 +
 +**[//​primary_soller_angle//​ E]**
 +
 +**[//​secondary_soller_angle//​ E]**
 +
 +**[//​axial_n_beta//​ !E]**
 +
 +Defines the full axial divergence model using the method of Cheary & Coelho (1998b).
 +
 +//​filament_length,​ sample_length//​ and //​receiving_slit_length//​ define the length of the tube filament, sample and receiving slit in the axial plane in mm.
 +
 +//​primary_soller_angle//:​ primary Soller slit angle in degrees.
 +
 +//​secondary_soller_angle//:​  secondary Soller slit angle in degrees.
 +
 +//​axial_n_beta//:​ Define the number of rays emanating from a point X-ray source in the axial plane. Larger values for //​axial_n_beta//​ increases both accuracy and calculation time.
 +
 +The macro Full_Axial_Model simplifies the use of //​axial_conv//​.
 +
 +**[//bkg// [@] # # #...]**
 +
 +Defines a Chebyshev polynomial where the number of coefficients are equal to the number of numeric values appearing after the //bkg// keyword.
 +
 +**[//​bootstrap_errors//​ !Ecycles]**
 +
 +**[//​fraction_of_yobs_to_resample//​ !E]**
 +
 +**[//​determine_values_from_samples//​]**
 +
 +**[//​resample_from_current_ycalc//​]**
 +
 +//​bootstrap_errors//​ uses the bootstrap method of error determination (Efron & Tibshirani 1986, DiCiccio & Efron 1996, Chernick 1999). Bootstrapping comprises a series of refinements each with a fraction Yobs data modified to obtain a new bootstrap sample. The standard deviations of the refined values then become the bootstrap errors. !Ecycles corresponds to the number of refinement cycles to perform, it defaults to 200. The resulting bootstrap errors are written to the *.OUT file.
 +
 +//​fraction_of_yobs_to_resample//​ corresponds to the fraction of the observed data that is to be replaced each refinement cycle, it defaults to 0.37. Replacement data is by default obtained randomly from the calculated pattern obtained at the end of the first refinement cycle. If //​resample_from_current_ycalc//​ is defined then replacement data are obtained from the currently completed refinement cycle. The updated Yobs data is additionally modified such that the change in Rwp is unchanged in regards to the current Ycalc.
 +
 +Parameter values used at the start of each refinement cycle are obtained from the end of the first refinement cycle. //​val_on_continue//​ can additionlly be used to change parameter values at the start of a cycle.
 +
 +If //​determine_values_from_samples//​ is defined then parameter values at the end of bootstrapping are updated with values determined from the bootstrapping refinement cycles.
 +
 +Parameter values obtained at the end of each bootstrap refinement cycle is written to disk in binary format. These values are then read and processed at the end of the bootstrap process without actually storing all of the values in memory. Thus the bootstrap process has a small memory footprint.
 +
 +**[//​box_interaction//​ [//from_N// #] [//to_N// #] [//​no_self_interaction//​] $site_1 $site_2 N E]...**
 +
 +Defines a site interaction with the name N between [[#​k142|sites identified]] by $site_1 and $site_2. E represents the site interaction equation which can be a function of R and Ri. R returns the distance in Å between two atoms; these distances are updated when dependent fractional atomic coordinates are modified. The name of the //​box_interaction//​ N can be used in equations and in particular penalty equations.
 +
 +When either //from_N// or //to_N// are defined, the interactions between $site_1 and $site_2 are sorted by distance and only the interactions between the //from_N// and //to_N// are considered.
 +
 +//​no_self_interaction//​ prevents any interactions between equivalent positions of the same site. This is useful when a general position is used to describe a special position.
 +
 +For example, the following could be used to iterate from the nearest atom to the third atom from a site called Si1:
 +
 +str
 +
 +site Si1...
 +
 +site O1...
 +
 +site O2...
 +
 +site O3...
 +
 +box_interaction Si1 O* to_N 2 !si1o = (R-2)^2;
 +
 +penalty = !si1o;
 +
 +In this example the nearest three oxygen atoms are soft constrained to a distance of 2 Angstroms by the use of the penalty function. Counting starts at zero and thus //to_N// is set to 2 to iterate up to the third nearest atom.
 +
 +The wild card character ‘*’ used in “O*” means that sites with names starting with ‘O’ are considered. In addition to using the wild card character, the site names can be explicitly written within double quotation marks, for example:
 +
 +box_interaction Si1 “O1 O2 O3” to_N 3 etc...
 +
 +Interactions between Si1 and the three oxygen atoms O1, O2, O3 may not all be included, for example, if Si1 had as its nearest neighbours the following:
 +
 +Si1 ↔ O1,1 at a distance of 1.0 Angstroms
 +
 +Si1 ↔ O2,3 at a distance of 1.1 Angstroms
 +
 +Si1 ↔ O2,1 at a distance of 1.2 Angstroms
 +
 +Si1 ↔ O1,2 at a distance of 1.3 Angstroms
 +
 +then two equivalent positions of site O1 and two equivalent positions of O2 are included in the interaction equation; thus no interaction between Si1-O3 is considered. To ensure that each of the three oxygens had Si1 included in an interaction equation then the following could be used:
 +
 +box_interaction “O1 O2 O3” Si1 to_N 0 etc…
 +
 +Thus the order of $site_1 and $site_2 is important when either from_N or to_N is defined.
 +
 +The reserved parameters Ri and Break can also be used in interaction equations when either from_N or to_N is defined. Ri returns the index of the current interaction being operated on with the first interaction starting at Ri=0.
 +
 +//​box_interaction//​ is used for example in the Anti_Bump macro.
 +
 +**[//​break_if_been_there//​  $sites !E [//​been_there_buffer//​ #​buffer_size]** **[//​been_there_clear_buffer//​ !E]]**
 +
 +Breaks the current [[#​k144|refinement cycle]] if the [[#​k142|sites identified]] in $sites are less than !E away to a previous configuration. //​been_there_buffer//​ determines the number of previous site configurations to keep. If //​been_there_clear_buffer//​ is defined and it evaluates to non-zero then the "been there buffer"​ is cleared.
 +
 +Example ALVO4-GRS.INP demonstrates the use of //​break_if_been_there//​. When the current atomic configuration is similar to a previous configuration then that particular refinement cycle is terminated and the temperature is advanced to the next temperature. 
 +
 +//​break_if_been_there//​ is typically not used with //​[[#​k133|randomize_on_errors]]//​ as the latter includes its own version of remembering parameter values and breaking a cycle early.
 +
 +**[//​brindley_spherical_r_cm//​ !E]**
 +
 +Used for applying the Brindley correction for spherical particles. The macro Apply_Brindley_Spherical_R_PD(R,​ PD) is defined as:
 +
 +macro Apply_Brindley_Spherical_R_PD(R,​ PD)
 +
 +{
 +
 +brindley_spherical_r_cm = (R) (PD);
 +
 +}
 +
 +R is the radius of the particle in cm and PD is the packing density, a number that is not updated and not refined. Here’s an example:
 +
 +xdd...
 +
 +str
 +
 +Apply_Brindley_Spherical_R_PD(R,​ PD)
 +
 +MVW(0,0,0)
 +
 +str
 +
 +Apply_Brindley_Spherical_R_PD(R,​ PD)
 +
 +MVW(0,0,0)
 +
 +Note, that PD is incorporated by way of an equation definition for //​brindley_spherical_r_cm//​. Also, //​phase_MAC//​ or MVW need not be defined as they are created as needed; their definition however is necessary in order to obtain their respective values. The Brindley correction is not applied to phases without the //​brindley_spherical_r_cm//​ defined.
 +
 +The Brindley correction can be applied to all phases including //xo_Is//. In the case of phases that do not have lattice parameters or sites then the User would need to enter values for //​cell_volume//,​ //​cell_mass//​ and //​phase_MAC//​ in order for the Brindley correction to work and for the weight percents to be obtained. This allows for the incorporation of non-structural phases in quantitative analysis. For example, the following works as the necessary information have been included.
 +
 +xo_Is
 +
 +Apply_Brindley_Spherical_R_PD(.002,​ .6)
 +
 +MVW(654, 230, 0)
 +
 +phase_MAC 200
 +
 +**[//​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>​{{Technical_Reference%20V4-1_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>​{{Technical_Reference%20V4-1_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//​.
 +
 +**[//​default_I_attributes//​ E]**
 +
 +Changes the attributes of the //I// parameter, for example,
 +
 +xo_Is
 +
 +   default_I_attributes 0 min 0.001 val_on_continue 1
 +
 +Useful when randomising lattice parameters during Le Bail refinements with //​continue_after_convergence//​.
 +
 +**[//​degree_of_crystallinity//​ #]**
 +
 +**[//​crystalline_area//​  #]**
 +
 +**[//​amorphous_area//​  #]**
 +
 +//​degree_of_crystallinity//​ reports on the degree of crystallinity which is calculated as follows:
 +
 +degree_of_crystallinity = 100
 +
 +Get(crystalline_area)%%/​(%%Get(crystalline_area)+Get(amorphous_area));​
 +
 +//​crystalline_area//​ and //​amorphous_area//​ corresponds to the sum of the numerical areas under the crystallines phases and amorphous phases respectively. Phases that have //​amorphous_phase//​ defined are treated as amorphous phases in the calculation.
 +
 +**[//​d_Is//​]... **
 +
 +**[//d// E  //I// E]...**
 +
 +Defines a phase type that uses d-spacing values for generating peak positions. //d// corresponds to the peak position in d-space in Å and //I// is the intensity parameter before applying any //​scale_pks//​ equations.
 +
 +**[//​do_errors//​]**
 +
 +Errors for refined parameters (ESD'​s) and a correlation matrix are calculated at the end of refinement. The correlation matrix if defined using //​C_matrix_normalized//​ is updated, if not defined then //​C_matrix_normalized//​ is automatically defined and appeneded to the OUT file.
 +
 +**[//​d_spacing_to_energy_in_eV_for_f1_f11//​ !E]**
 +
 +Can be a function of the reserved parameter D_spacing. Changes f<​sup>'</​sup>​ and f<​sup>"</​sup>​ (see section 7.1) to correspond to energies as given by //​d_spacing_to_energy_in_eV_for_f1_f11//​. Used for refining on energy dispersive data, for example,
 +
 +' E(eV) = 10^5 / (8.065541 Lambda(A))
 +
 +prm !detector_angle_in_radians = 7.77 Deg_on_2;
 +
 +prm wavelength = 2 D_spacing Sin(detector_angle_in_radians);​
 +
 +prm energy_in_eV = 10^5 /  (8.065541 wavelength);​
 +
 +pk_xo = 10^-3 energy_in_eV + zero;
 +
 +d_spacing_to_energy_in_eV_for_f1_f11 = energy_in_eV;​
 +
 +See example ED_SI_STR.INP.
 +
 +**[//​exclude//​ #ex1 #ex2]...**
 +
 +Excludes an x-axis region between #ex1 and #ex2. The macro "​Exclude"​ simplifies the use of //​exclude//​. Example CEO2.INP demonstrates the use of excluded regions.
 +
 +**[//​exp_conv_const//​ E  [//​exp_limit//​ E] ]...**
 +
 +Defines //​e//<​sub>​m</​sub>​ in the convolution function:
 +
 +Exp(Ln(0.001) //e / e//<​sub>​m</​sub>​ )    for //e// = 0 to //​exp_limit //​
 +
 +that is convoluted into phase peaks. //​exp_conv_const//​ is used by the Absorption and Absorption_With_Sample_Thickness_mm macros. If //​exp_limit//​ is not defined then it defaults to //​e//<​sub>​m</​sub>​. //​e//<​sub>​m</​sub>​ can be greater than or less than zero.
 +
 +**[//​extra_X_left//​ !E]  [//​extra_X_right//​ !E]**
 +
 +Determines the extra range to which hkls are generated. For TOF data //​extra_X_left//​ is typically used. For x-ray data then //​extra_X_right//​ is typically used. Both default to 0.5.
 +
 +**[//​file_name_for_best_solutions//​ $file]**
 +
 +Appends INP file details to $file during refinement with independent parameter values updated. The operation is performed every time a particular convergence gives the best Rwp. For example, suppose that at convergence the following was obtained:
 +
 +Rwp:
 +
 +30   All prms appended to file in INP format
 +
 +20   All prms appended to file in INP format
 +
 +35
 +
 +40
 +
 +15   All prms appended to file in INP format
 +
 +18
 +
 +10   All prms appended to file in INP format
 +
 +15
 +
 +**[//​fit_obj//​ E [//min_X// !E] [//max_X// !E] ]...**
 +
 +//​fit_obj//'​s allows the insertion of User defined functions, see example PVS.INP. //​fit_obj//​’s can be a function of X.
 +
 +//min_X// and //max_X// define the x-axis range of the fit_obj; if //min_X// is omitted then the fit_obj is calculated from the start of the x-axis; similarly if //max_X// is omitted then the fit_obj is calculated to the end of the x-axis.
 +
 +**[//​fourier_map//​ !E]**
 +
 +**[//​fourier_map_formula//​ !E]**
 +
 +**[//​extend_calculated_sphere_to//​ !E]**
 +
 +**[[#​cf_e8|[]]//​[[#​cf_e8|min_grid_spacing]]//​[[#​cf_e8| !E]]]**
 +
 +**[[#​cf_e45|[]]//​[[#​cf_e45|correct_for_atomic_scattering_factors]]//​[[#​cf_e45| !E]]]**
 +
 +**[[#​cf_e4|[]]//​[[#​cf_e4|f_atom_type]]//​[[#​cf_e4| $type ]]//​[[#​cf_e4|f_atom_quantity]]//​[[#​cf_e4| !E]…]]**
 +
 +If //​fourier_map//​ is non-zero then a Fourier map is calculated on refinement termination and shown in the OpenGL window; maps can be calculated for x-ray or neutron single crystal or powder data, see test examples FOURIER-MAP-AE14.INP and FOURIER-MAP-CIME.INP. The type of map is determined by //​fourier_map_formula//​ which can be a function of the reserved parameter names Fcalc, Fobs and D_spacing; here are some examples:
 +
 +fourier_map_formula = Fobs; ‘ The default
 +
 +fourier_map_formula = 2 Fobs - Fcalc;
 +
 +Fobs corresponds to the obserbed structure moduli; in the powder data case Fobs is calculated from the Rietveld decomposition formula. Phases are determined from Fcalc.
 +
 +Reflections that are missing from within the Ewald sphere are included with Fobs set to Fcalc. If //​extend_calculated_sphere_to//​ is defined then the Ewald sphere is extended.
 +
 +//​scale_pks//​ definitions are removed from Fobs. In the event that //​scale_pks//​ evaluates to zero for a particular reflection then Fobs is set to Fcalc; the number of Fobs reflections set to Fcalc is reported on.
 +
 +**[//​gauss_fwhm//​ E]...**
 +
 +Defines the FWHM of a Gaussian function to be convoluted into phase peaks. //​gauss_fwhm//​ is used for example by the CS_G and Strain_G macros.
 +
 +**[//​hkl_plane//​ $hkl] ...**
 +
 +Used by the OpenGL viewer to display hkl planes, see the CeO2.STR file in the “Rigid” directory. Here are some examples:
 +
 +str…
 +
 +hkl_plane 1 1 1
 +
 +hkl_plane “2 -2 0”
 +
 +** [//​grs_interaction//​ [//from_N// #] [//to_N// #] [//​no_self_interaction//​] $site_1 $site_2 qi # qj # N E]...**
 +
 +Defines a GRS interaction with a name of N between [[#​k142|sites identified]] by $site_1 and $site_2. E represents the GRS interaction equation that can be a function of R, which returns the distance in Angstroms between two atoms; these distances are updated when dependent fractional atomic coordinates are modified. The name of the //​grs_interaction//​ N can be used in equations and in particular penalty equations.
 +
 +When either //from_N// or //to_N// are defined, the interactions between $site_1 and $site_2 are sorted by distance and only the interactions between the //from_N// and //to_N// are considered.
 +
 +//​no_self_interaction//​ prevents any interactions between equivalent positions of the same site. This is useful when a general position is used to describe a special position.
 +
 +//qi// and //qj// corresponds to the valence charges used to calculate the Coulomb sum for the sites $site_1 and $site_2 respectively.
 +
 +//​grs_interaction//​ is typically used for applying electrostatic restraints in inorganic materials. The GRS_Interaction macro simplifies the use of //​grs_interaction//​.
 +
 +**[//hat// E [//​num_hats//​ #] ]...**
 +
 +Defines the X-axis size of an impulse function that is convoluted into phase peaks. //​num_hats//​ corresponds to the number of hats to be convoluted. //​num_hats//​ is set to 1 by default. //hat// is used for example by the Slit_Width and Specimen_Tilt macros.
 +
 +**[//​hkl_Is//​]...**
 +
 +**[//​lp_search//​ !E]**
 +
 +**[//​I_parameter_names_have_hkl//​ $start_of_parameter_name]**
 +
 +**[//​hkl_m_d_th2//​ # # # # # # I E]...**
 +
 +Defines a phase type that uses hkls for generating peak positions.
 +
 +//​lp_search//​ uses a new indexing algorithm that is independent of d-spacing extraction; lp-search-pbso4.inp demonstrates its use. lp_search minimizes on a new figure of merit function that gives a measure of correctness for a particular set of lattice parameters. More specifically the figure of merit function assigns parts of the diffraction pattern to peaks and then sums the absolute values of the products of the diffraction intensities multiplied by the distance to the peaks:
 +
 +<​sub>​{{Technical_Reference%20V4-1_files:​image158.gif?​213x39}}</​sub>​where the summation in ‘j’ is over the calculated Bragg positions 2//​q<​sub>​0</​sub>//​ and the summation in ‘i’ is  over part of the diffraction pattern such that (2//​q//<​sub>​</​sub><​sub>​0,​ j-1</​sub>​ + 2//​q//<​sub>​</​sub>​ <​sub>​0,​ j</​sub>​.)/​2 < 2//​q//<​sub>​i</​sub>​  <  (2//​q//<​sub>​</​sub>​ <​sub>​0,​ j+1</​sub>​ + 2//​q//<​sub>​</​sub><​sub>​0,​ j</​sub>​.)/​2. The method avoids difficulties associated with extracting d-spacings from complex patterns comprising heavily overlapped lines; the primary difficulty being that of ascertaining the number of lines present.
 +
 +//​I_parameter_names_have_hkl//​ gives generated Intensity parameters a name starting with $start_of_parameter_name and ending with the corresponding hkl.
 +
 +//​hkl_m_d_th2//:​ The numbers after the keyword //​hkl_m_d_th2//​ define h k l m d and 2q values, where
 +
 +h, k, l          : Miller indices
 +
 +m               :​ multiplicity.
 +
 +//d// and th2     : d and 2q values (not used by).
 +
 +//I//                 :​ Peak intensity parameter before applying any //​scale_pks//​.
 +
 +If no //​hkl_m_d_th2//​ keywords are defined then the hkls are generated using the space group; the generated //​hkl_m_d_th2//​ details are appended at the end of the //​space_group//​ keyword on refinement termination. Intensity parameters are given an initial starting value of 1. If the Le Bail keyword is not defined then the intensity parameters are given the unique code of @ .
 +
 +For example, the following input segment:
 +
 +xdd quartz.xdd
 +
 +...
 +
 +hkl_Is         
 +
 +   Hexagonal(4.91459,​ 5.40603)
 +
 +   space_group P_31_2_1
 +
 +will generate the following OUT file:
 +
 +xdd quartz.xdd
 +
 +...
 +
 +hkl_Is
 +
 +Hexagonal(4.91459,​ 5.40603)
 +
 +space_group P_31_2_1
 +
 +load hkl_m_d_th2 I
 +
 +{
 +
 +1   0   0   6    4.25635   20.85324 @ 3147.83321
 +
 +1   0   1   6    3.34470   26.62997 @ 8559.23955
 +
 +1   0  -1   6    3.34470   26.62997 @ 8559.23955
 +
 +...
 +
 +}
 +
 +The Create_hklm_d_Th2_Ip_file macro creates an hkl file listing from structures in the same format as the "load hkl_m_d_th2 I" as shown above. Even though the structure would have no sites, the //​weight_percent//​ keyword can still be used; it will use whatever value is defined by //​cell_mass//​ in order to calculate //​weight_percent//​.
 +
 +**[//​hkl_Is_from_hkl4//​]**
 +
 +**[****//​i_on_error_ratio_tolerance//​** **#]**
 +
 +**[//​num_highest_I_values_to_keep//​ #num]**
 +
 +//​hkl_Is_from_hkl4//​ is used for generating a powder pattern from single crystal data in ShelX HKL4 format, see example HKL4_TO_PP.INP.
 +
 +**[//​iters//​ #]**
 +
 +The maximum number of refinement iterations, //iters// is set to 500000 by default
 +
 +**[//lam// [//​ymin_on_ymax//​ #] [//​no_th_dependence//​] [Lam !E] [calculate_Lam]]**
 +
 +**[//la// E  //lo// E  [//lh// E] | [//lg// E]]...**
 +
 +Defines an emission profile where each "​[//​la//​ E  //lo// E  [//lh// E] | [//lg// E] ]" determines an emission profile line, where
 +
 +//la//:   Area under the emission profile line
 +
 +//lo//:   Wavelength in [Å] of the emission profile line
 +
 +//lh//:   HW in mÅ of a Lorentzian convoluted into the emission profile line.
 +
 +//lg//:   HW in mÅ of a Gaussian convoluted into the emission profile line.
 +
 +//​ymin_on_ymax//​ determines the x-axis extent to which an emission profile line is calculated. It is set to 0.001 by default.
 +
 +//​no_th_dependence//​ defines an emission profile that is 2q independent. Allows the use of non-X-ray data or fitting to negative 2q values.
 +
 +//Lam// defines the value to be used for the reserved parameter Lam. When //Lam// is not defined then the reserved parameter Lam is defined as the wavelength of the emission profile line with the largest //la// values. Note that //Lam// is used to determine the Bragg angle.
 +
 +//​calculate_Lam//​ calculates //Lam// such that it corresponds to the wavelength at the peak of the emission profile. //Lam// needs to be set to an approximate value corresponding to the peak of the emission profile.
 +
 +See section 6 for a description of emission profiles.
 +
 +**[//​lebail//​ #]**
 +
 +A 1 for the //lebail// keyword flags the use of the Le Bail method for peak intensity extraction.
 +
 +**[//​line_min//​] [//​use_extrapolation//​] [//​no_normal_equations//​] [//​use_LU//​]**
 +
 +//​no_normal_equations//​ prevents the use of normal equations in the minimization routine; it is useful when the effects of line minimization only is sought or when there are a large number of parameters being refined. Refer to section 5 for a description of the minimization routines .
 +
 +**[//​lor_fwhm//​ E]...**
 +
 +Defines the FWHM of a Lorentzian function that is convoluted into phase peaks. //​lor_fwhm//​ is used for example by the CS_L and Strain_L macros.
 +
 +**[//​lpsd_th2_angular_range_degrees//​ E]...**
 +
 +**//​lpsd_equitorial_divergence_degrees//​** **E**
 +
 +**//​lpsd_equitorial_sample_length_mm//​** **E**
 +
 +Calculates an aberration for a Linear Position Sensitive Detector and convolutes it into phase peaks. //​lpsd_th2_angular_range_degrees//​ corresponds to the angular range of the LPSD in 2Th degrees. //​lpsd_equitorial_divergence_degrees the equitorial divergence in degrees of the primary beam// and//​lpsd_equitorial_sample_length_mm//​ is the lengths of the sample in the equitorial plane.
 +
 +The //​lpsd_th2_angular_range_degrees//​ convolution corrests for peak shapes, intensities and 2Th shifts; see example LPSD-SIMULATED.INP.
 +
 +**[//​marquardt_constant//​ !E]…**
 +
 +Allows for changing the Marquardt constants, the Simulated_Annealing_1 macro changes the Marquardt constants as follows:
 +
 +load marquardt_constant { 0 1 }
 +
 +**[//​min_r//​ #] [//max_r// #]**
 +
 +Defines the minimum and maximum radii for calculating bond lengths. //min_r// and //max_r// are by default set to 0 and 3.2 Å respectively.
 +
 +**[//​mixture_density_g_on_cm3//​ !E]**
 +
 +Calculates the density of the mixture assuming a packing density of 1, see also //​[[#​k038|mixture_MAC]]////​.//​
 +
 +**[//​mixture_MAC//​ !E]**
 +
 +Calculates the mass absorption coefficient in cm<​sup>​2</​sup>/​g for a mixture as follows:
 +
 +<​sub>​{{Technical_Reference%20V4-1_files:​image160.gif?​160x45}}</​sub>​where //​w//<​sub>​i</​sub>​ and (//​m/////​r//​)<​sub>​i</​sub>​ is the weight percent and //​phase_MAC//​ of phase i respectively. Errors are reported for //​phase_MAC//​ and //​mixture_MAC//​.
 +
 +The following example provides phase and mixture mass absorption coefficients.
 +
 +xdd...
 +
 +mixture_MAC 0
 +
 +str...
 +
 +phase_MAC 0
 +
 +The macros Mixture_LAC_1_on_cm,​ Phase_LAC_1_on_cm and Phase_Density_g_on_cm3 calculates the mixture and phase linear absorption coefficients (for a packing density of 1) and phase density, for example:
 +
 +xdd...
 +
 +Mixture_LAC_1_on_cm(0)
 +
 +str...
 +
 +Phase_Density_g_on_cm3(0)
 +
 +Phase_LAC_1_on_cm(0)
 +
 +Errors for these quantities are also calculated. Mass absorption coefficients obtained from NIST at [[http://​physics.nist.gov/​PhysRefData/​XrayMassCoef|http://​physics.nist.gov/​]][[http://​physics.nist.gov/​PhysRefData/​XrayMassCoef|P]][[http://​physics.nist.gov/​PhysRefData/​XrayMassCoef|hysRefData/​XrayMassCoef]] are used to calculate //​mixture_MAC//​ and //​phase_MAC//​.
 +
 +**[//​neutron_data//​]**
 +
 +Signals the use of neutron atomic scattering lengths.Scattering lengths for isotopes can be used by placing the isotope name after “//​occ//​” as in:
 +
 +occ 6Li 1
 +
 +occ 36Ar 1
 +
 +The scattering lengths data, contained in the file NEUTSCAT.CPP,​ is from
 +
 +www.ccp14.ac.uk/​ccp/​web-mirrors/​neutrons/​n-scatter/​n-lengths/​LIST~1.HTM
 +
 +Constant wavelength neutron diffraction requires a Lorentz correction using the Lorentz_Factor  macro (defined in TOPAS.INC); it is defined as follows:
 +
 +scale_pks = 1 / (Sin(Th)^2 Cos(Th));
 +
 +**[//​no_LIMIT_warnings//​]**
 +
 +Surpresses [[#​k157|LIMIT_MIN]] and LIMIT_MAX warning messages.
 +
 +**[//​normalize_FCs//​]**
 +
 +If defined then site fractional coordinates are normalized. Normalization of a particular fractional coordinate does not occur if it has //​min/////​max//​ limits, is part of a //rigid// body or part of a site constraint of any kind.
 +
 +**[//​numerical_area//​ E]**
 +
 +Returns the numerically calculated area under the phase.
 +
 +**[//​occ_merge//​ $sites [//​occ_merge_radius//​ !E]]...**
 +
 +//​occ_merge//​ rewrites the site occupancy of the sites defined in $sites in terms of their fractional atomic coordinates (Favre-Nicolin and R. Cerny 2002). This is useful during structure solution for merging ocathedra or other types of defined rigid bodies. It is also useful for identifying special positions as seen in the example PBSO4-DECOMPOSE.INP.
 +
 +In the present implementation $sites are thought of as spheres with a radius //​occ_merge_radius.//​ When two atoms approach within a distance less than the sum of their respective //​occ_merge_radius//​’s then the spheres intersect. The occupancies of the sites, occ_xyz,  thus become:
 +
 +occ_xyz = 1 / (1 + Intersection fractional volumes)
 +
 +In this way any number of sites can be merged.
 +
 +Sites appearing in $sites cannot have their occupancies refined. On termination of refinement the //occ// parameter values are updated with their corresponding occ_xyz.
 +
 +**[//​omit_hkls//​ !E]**
 +
 +Allows for the filtering of hkls using the reserved parameter names of H, K, L and D_spacing. More than one omit_hkls can be defined, for example:
 +
 +omit_hkls = If(And(H==0,​ K==0), 1, 0);
 +
 +omit_hkls = And(H==0, K==1);
 +
 +omit_hkls = D_spacing < 1;
 +
 +**[//​one_on_x_conv//​ E]...**
 +
 +Defines //​e//<​sub>​m</​sub>​  in the convolution function:
 +
 +(4 ½//​e//<​sub>​m</​sub>​ //e//½) <​sup>​-</​sup><​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. //​one_on_x_conv//​ is used for example by the Divergence macro.
 +
 +**[//​only_penalties//​]**
 +
 +Instructs the minimization procedure to minimize on penalty functions only. The //​only_penalties//​ switch is assumed when there are only penalties to minimize, i.e. when there are no observed data. Note, parameters that are not functions of penalties are not refined.
 +
 +**[//​out_A_matrix//​ $file]**
 +
 +**[//​A_matrix_prm_filter//​ $filter]**
 +
 +//​out_A_matrix//​ outputs the least squares **A** matrix to the file $file; used in the Out_for_cf macro. Output can be limited by using //​A_matrix_prm_filter//,​ here’s an example for outputting A matrix elements corresponding to parameters with names starting with ‘q’:
 +
 +out_A_matrix file.a
 +
 +A_matrix_prm_filter q*
 +
 +**[//out// $file [//​append//​] ]...**
 +
 +**[//​out_record//​]**
 +
 +**[//​out_eqn//​ !E]**
 +
 +**[//​out_fmt//​ $c_fmt_string]**
 +
 +**[//​out_fmt_err//​ $c_fmt_string]...**
 +
 +Used for writing parameter details to a file. The details are appended to $file when //append// is defined. //out_eqn// defines the equation or parameter to be written to $file using the //​out_fmt//​. $c_fmt_string describes a format string in c syntax containing a single format specified for a double precision number. //​out_fmt_err//​ defines the $c_fmt_string used for formatting the error of //eqn.//
 +
 +Both //out_fmt// and //​out_fmt_err//​ requires an //out_eqn// definition. //out_fmt// can be used without //out_eqn// for writing strings. The order of //out_fmt// and //​out_fmt_err//​ determines which is written to file first; thus if //​out_fmt_err//​ is defined first then it will be operated on first.
 +
 +The following example illustrates the use of //out// using the Out macros.
 +
 +xdd...
 +
 +out "​sample output.txt"​ append
 +
 +str...
 +
 +CS_L(cs_l, 1000)
 +
 +Out_String("​\tCrystallite Size Results:​\n"​)
 +
 +Out_String("​\t=========================\n"​)
 +
 +Out(cs_l, "​\tCrystallite Size (nm):​\t%11.5f",​
 +
 +          "​\tError in Crystallite Size:​\t%11.5f\n"​)
 +
 +//out// provides a means of defining individual refinement result files, see example OUT-1.INP.
 +
 +**[//​out_rwp//​ $file]**
 +
 +Outputs a list of R<​sub>​wp</​sub>​ values encountered during refinement to the file $file.
 +
 +**[//​out_prm_vals_per_iteration//​ $file]... | [//​out_prm_vals_on_convergence//​ $file]...**
 +
 +**[//​out_prm_vals_filter//​ $filter]**
 +
 +Outputs refined parameter values per iteration or on convergence into the file $file. In the absence of //​out_prm_vals_filter//​ then all parameters are outputted otherwise only parameters with names defined in //​out_prm_vals_filter//​ are considered where $fliter can contain the wild card charatcter ’*’ and the negation character ’!’, for example:
 +
 +out_prm_vals_per_iteration PRM_VALES.TXT
 +
 +out_prm_vals_filter "* !u*"
 +
 +More than one //​out_prm_vals_per_iteration/////​out_prm_vals_on_convergence//​ can be defined outputting different parameters into different files depending on the corresponding //​out_prm_vals_filter//​.
 +
 +**[//​peak_typ//​****//​e//​** **$type]**
 +
 +Sets the peak type for a phase. The following //​peak_type//​’s are available:
 +
 +| **Peak type** | **$type** | **Parameters** |
 +| Fundamental Parameters | fp |   |
 +| Pseudo-Voigt   | pv | [//pv_lor E  pv_fwhm E//] //pv_lor// is the Lorentzian fraction of the peak profile(s). //pv_fwhm// is the FWHM of the peak profile(s). |
 +| Split-PearsonVII   | spvii | [//h1// E  //h2// E  //m1// E  //m2// E] The sum of //h1// and //h2// gives the FWHM of the composite peak. //m1, m//2 are the PearsonVII exponents of the left and right composite peak, respectively. |
 +| Split-PseudoVoigt   | spv | [//spv_h1// E  //spv_h2// E  //spv_l1// E  //spv_l2// E] The sum of //spv_h1// and //spv_h2// gives the full width at half maximum of the composite peak. //spv_l1, spv_l2//: the Lorentzian fractions of the left and right composite peak, respectively. |
 +
 +**[//​peak_buffer_step//​ E [//​report_on//​]]**
 +
 +As the shapes of phase peaks do not change significantly over a short 2q range, a new peak shape is calculated only if the position of the last peak shape calculated is more than the distance defined by //​peak_buffer_step//​. Various stretching and interpolation procedures are used in order to calculate in-between peaks. See also section 6.4.
 +
 +The reserved parameter names of H, K, L, M or parameter names associated with the keywords //​sh_Cij_prm//​ and //​hkl_angle//​ when used in the peak convolution equations result in irregular peak shapes over short 2q ranges and thus a separate peak shape is calculated for each peak.
 +
 +When defined //​report_on//​ causes the display of the number of peaks in the peaks buffer.
 +
 +//​peak_buffer_step//​ is set to 500*//​Peak_Calculation_Step//​ by default.
 +
 +**[//​penalty//​ !E]...**
 +
 +Defines a penalty function that can be a function of other parameters. Penalties are useful for stabilizing refinements as in for example their use in bond-length restraints.
 +
 +Example HOCK.INP uses penalties to minimize on the Hock and Schittkowski problem number 65 function.
 +
 +prm x1 1 min -4.5 max 4.5  val_on_continue = Rand(-4.5, 4.5); del .01
 +
 +prm x2 1 min -4.5 max 4.5  val_on_continue = Rand(-4.5, 4.5); del .01
 +
 +prm x3 1 min -5.0 max 5.0  val_on_continue = Rand(-5.0, 5.0); del .01
 +
 + 
 +
 +' Hock and Schittkowski problem number 65 function
 +
 +penalty = (x1-x2)^2 + (1/9) (x1 + x2 - 10)^2 + (x3 - 5)^2; : 0
 +
 + 
 +
 +prm contraint_1 = x1^2 + x2^2 + x3^2;
 +
 +penalty = If(contraint_1 < 48, 0, (contraint_1-48)^2);​ : 0
 +
 +The next example applies a User defined penalty function to lattice and crystallite size parameters, which are expected to be 5.41011 Å and 200 nm respectively:​
 +
 +str...
 +
 +Cubic(lp_ceo2 5.41011)
 +
 +penalty = (lp_ceo2-5.41011)^2;​
 +
 +CS_L(cs_l, 200)
 +
 +penalty =(cs_l-200)^2;​
 +
 +Minimizing on penalty functions in the presence of observed data is possible with the use of the //​only_penalties//​ keyword.
 +
 +**[//​penalties_weighting_K1//​ !E]**
 +
 +Defines the weighting K<​sub>​1</​sub>​ given to penalty functions as defined in Eq. (5‑2). //​penalties_weighting_K1//​ is set to 1 by default.
 +
 +**[//​percent_zeros_before_sparse_A//​ #]**
 +
 +Defines the percentage of the A matrix than can be zero before sparse matrix methods are invoked. The default value is 60%.
 +
 +**[//​phase_MAC//​ !E]**
 +
 +Calculates the mass absorption coefficient in cm<​sup>​2</​sup>/​g for the current phase. See description for //​[[#​k038|mixture_MAC]]//​.
 +
 +**[//​phase_out//​ $file [//​append//​] ]...**
 +
 +Used for writing phase dependent details to file. See the keyword //out// for a description of //​[[#​k045|out_record]]//​. The Create_hklm_d_Th2_Ip_file uses //​phase_out//​.
 +
 +**[//​pk_xo//​ E]**
 +
 +Provides a mechanism for transforming peak position to an x-axis position. For example, the peak position for neutron time-of-flight data is typically calculated in time-of-flight space, tof, or:
 +
 +tof = t0 + t1 d<​sub>​hkl</​sub>​ + t2 d<​sub>​hkl</​sub><​sup>​2</​sup>​
 +
 +where t0 and t1 and t2 are diffractometer constants. //pk_xo// can be used to refine TOF data as shown in examples TOF_Balzar_sh1.inp and TOF_Balzar_br1.inp.
 +
 +**[//​phase_name//​ $phase_name]**
 +
 +The name given to a phase; used for reporting purposes.
 +
 +**[//​phase_penalties//​** **$sites N]...****[//​hkl_Re_Im//​ #h #k #l #Re #Im]...**
 +
 +**[//​accumulate_phases_and_save_to_file//​ $file]**
 +
 +**[//​accumulate_phases_when//​ !E]**
 +
 +//​phase_penalties//​ for a single hkl is defined as follows:
 +
 +<​sub>​{{Technical_Reference%20V4-1_files:​image162.gif?​444x50}}</​sub>​where <​sub>​{{Technical_Reference%20V4-1_files:​image164.gif?​21x29}}</​sub>​= assigned phase, <​sub>​{{Technical_Reference%20V4-1_files:​image166.gif?​20x25}}</​sub>​= calculated phase, I<​sub>​c</​sub>​ = calculated intensity and //d// is the reflection d-spacing.  The name N returns the sum of the //​phase_penalties//​ and it can be used in equations and in particular //penalty// equations. <​sub>​{{Technical_Reference%20V4-1_files:​image166.gif?​20x25}}</​sub>​ is calculated from sites identified in [[#​k142|$sites]].
 +
 +#h, #k, #l are user defined hkls; they are used for formulating the phase penalties. #Re and #Im are the real and imaginary parts of <​sub>​{{Technical_Reference%20V4-1_files:​image164.gif?​21x29}}</​sub>​. An example use of phase penalties (see examples AE14-12.INP and AE5-AUTO.inp) is as follows:
 +
 +penalty = pp1;
 +
 +phase_penalties * pp1
 +
 +load hkl_Re_Im
 +
 +{
 +
 +0   1   2   1  0
 +
 +1   0  -2   1  0
 +
 +1  -2  -1   1  0
 +
 +}
 +
 +hkls chosen for phase penalties should comprise those that are of high intensity, large d-spacing and isolated from other peaks to avoid peak overlap. Origin defining hkls are typically chosen.
 +
 +//​accumulate_phases_and_save_to_file//​ saves the average phases collected to $file//.// Phases are collected when //​accumulate_phases_when//​ evaluates to true; //​accumulate_phases_when//​ defaults to true. Here’s an example use:
 +
 +temperature 1
 +
 +temperature 1
 +
 +temperature 1
 +
 +temperature 1
 +
 +temperature 10
 +
 +...move_to_the_next_temperature_regardless_of_the_change_in_rwp
 +
 +accumulate_phases_and_save_to_file SOME_FILE.TXT
 +
 +accumulate_phases_when = T == 10;
 +
 +Here phases with the best Rwp since the last accumulation are accumulated when the current temperature is 10.
 +
 +** [//​process_times//​]**
 +
 +Displays process times on termination of refinement.
 +
 +**[//​quick_refine//​ !E [//​quick_refine_remove//​ !E]]**
 +
 +//​quick_refine//​ removes parameters that influence <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​ in a small manner during a [[#​k144|refinement cycle]]. Use of //​quick_refine//​ speeds up simulated annealing, see for example the macro Auto_T which is used in example AE1-AUTO.INP. All refined parameters are reinstated for refinement at the start of subsequent cycles. Large //​quick_refine//​ values aggressively removes parameters and convergence to low <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​ maybe hindered. A value of 0.1 works well.
 +
 +//​quick_refine//​ has the following consequences:​
 +
 +  * If parameters are not reinstated using //​quick_refine_remove//​ then<​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​ does not get to its lowest possible value for a particular refinement cycle. 
 +  * The degree of parameter randomization increases with increasing values of //​quick_refine//​. Thus randomization should be reduced as //​quick_refine//​ increases. Alternatively //​randomize_on_errros//​ can be used which automatically determines the amount a parameter is randomized.
 +
 +//​quick_refine_remove//​removes a parameter from refinement if it evaluates to non-zero or reinstates a parameter if it evaluates to zero. It can be a function of the reserved parameters QR_Removed or QR_Num_Times_Consecutively_Small and additionally global reserved parameter names such as Cycle_Iter, Cycle and T. If //​quick_refine_remove//​ is not defined then the removal scheme of section 5.6 is used and parameters are not reinstated until the next refinement cycle.
 +
 +In most refinements the following will produce close to the lowest <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​ and in a shorter time period (see for example PAWLEY1.INP). ​
 +
 +quick_refine .1
 +
 +   quick_refine_remove =
 +
 +      IF QR_Removed THEN
 +
 +         0 ' reinstate the parameter
 +
 +      ELSE
 +
 +         IF QR_Num_Times_Consecutively_Small > 2 THEN
 +
 +            1 ' remove the parameter
 +
 +         ELSE
 +
 +            0 ' dont remove the parameter
 +
 +         ENDIF
 +
 +      ENDIF;
 +
 +**[//​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.
 +
 +**[//​scale//​ E]**
 +
 +The Rietveld scale factor, can be applied to all phase types     .
 +
 +**[//​scale_pks//​ E]...**
 +
 +Used for applying intensity corrections to phase peaks. The following example defines a Lorentz-Polarisation correction:
 +
 +scale_pks = (1+Cos(c Deg)^2 Cos(2 Th)^2)%%/​(%%Sin(Th)^2 Cos(Th));
 +
 +//​scale_pks//​ is used for example in the LP_Factor, Preferred_Orientation and Absorption_With_Sample_Thickness_mm_Intensity macros.
 +
 +**[//​seed//​]**
 +
 +Initialises the random number generator with a seed based on the computer clock.
 +
 +**[//site// $site [//x// E] [//y// E] [//z// E] ]...**
 +
 +**[//occ// $atom E [//beq// E]]...**
 +
 +**[//​num_posns//​ #] [****//​[[#​k128|rand_xyz]]//​** **!E] [//inter// !E #]**
 +
 +Defines a site where $site is a User defined string used to identify the site.
 +
 +//x//, //y//, and //z// defines the fractional atomic coordinates,​ see also section 7.7.
 +
 +//occ// and //beq// defines the site occupancy factor and the equivalent isotropic temperature factor beq. $atom corresponds to a valid atom symbol or isotope the data of which is contained in the file ATMSCAT.CPP for x-ray data and NEUTSCAT.CPP for //​[[#​k039|neutron_data]]//​.
 +
 +//​num_posns//​ corresponds to the number of unique equivalent position generated from the space group; //​num_posns//​ is updated on termination of refinement.
 +
 +//inter// corresponds to the sum of all GRS interactions which are a function of the //site//. The value of //inter// can represent the site electrostatic potential depending on the type of GRS interactions defined.
 +
 +Definition of a site fully occupied by aluminium:
 +
 +site Al1  x 0       y 0       z 0.3521  occ Al+3 1    beq 0.3
 +
 +Definition of a site occupied by two cations:
 +
 +site Fe2  x 0.9283  y 0.25    z 0.9533  occ Fe+3 0.5  beq 0.25
 +
 +                                        occ Al+3 0.5  beq 0.25
 +
 +**[//​sites_distance//​ N] | [//​sites_angle//​ N] | [//​sites_flatten//​ N [//​sites_flatten_tol//​ !E]]...**
 +
 +**[//​site_to_restrain//​ $site [ #ep [ #n1 #n2 #n3 ] ] ]...**
 +
 +When used in equations the name N of //​sites_distance//​ and //​sites_angle//​ returns the distance in Å between two sites and angle in degrees between three sites respectively. The sites are defined by //​site_to_restrain//​.In particular N can be used in penalty equations to restrain bond lengths.
 +
 +N of //​sites_flatten//​ returns a restraint term that decreases as the sites become coplanar; it is defined as follows:
 +
 +<​sub>​{{Technical_Reference%20V4-1_files:​image169.gif?​529x47}}</​sub>​ 
 +
 +where tol corresponds to //​sites_flatten_tol//,​ n corresponds to the number of sites defined with the //​site_to_restrain//​ keyword, b are Cartesian unit length vectors between the sites and the geometric centre of the sites.
 +
 +#eq, #n1, #n2 and #n3 correspond to the site equivalent position and fractional offsets to add to the sites. This is useful if the structure is already known and constraints are required, for example, in the bond length output (see //​append_bond_lengths//​):​
 +
 +Zr1:0  O1:20  0  0 -1  2.08772
 +
 +       O1:7   0 -1  0  2.08772  89.658
 +
 +       O1:10  0  0 -1  2.08772  90.342   90.342
 +
 +       O1:15 -1  0  0  2.08772  180.000  89.658   89.658
 +
 +       O1:18 -1  0  0  2.08772  90.342   89.658   180.000 90.342    
 +
 + 
 +
 +P1:0   O1:4   0  0  0  1.52473
 +
 +       O1:8   0  0  0  1.52473  112.923
 +
 +       O1:0   0  0  0  1.52473  112.923  112.923
 +
 +       O2:0   0  0  0  1.59001  105.749  105.749  105.749
 +
 +Example constraints using macros could look like the following:
 +
 +Angle_Restrain(O1 P1 O1 8, 112, 112.92311, 0, 0.001)
 +
 +Angle_Restrain(O1 18 -1 0 0 Zr1 O1 10 0 0 -1, 89, 89.65750, 0, 0.001)
 +
 +Distance_Restrain(Zr1 O1 20 0 0 -1, 2.08, 2.08772, 0, 1)
 +
 +BENZENE.INP demonstrates the use of the restraint macros Distance_Restrain,​ Angle_Restrain and Flatten. OpenGL viewing is recommended. Note, for more than 6 sites then //​sites_flatten//​ becomes computationally expensive.
 +
 +**[//​sites_geometry//​ $Name]...**
 +
 +**[//​site_to_restrain//​ $site [ #ep [ #n1 #n2 #n3 ] ] ]...**
 +
 +//​sites_geometry//​ defines a grouping of up to  four sites; $Name is the name given to ths grouping. The sites that are part of the group is defined using //​site_to_restrain//,​ for example:
 +
 +sites_geometry some_name
 +
 +load site_to_restrain { C1 C2 C3 C4 }
 +
 +Three functions, Sites_Geometry_Distance($Name),​ Sites_Geometry_Angle($Name) and Sites_Geometry_Dihedral_Angle($Name) can be used in equations to obtain the distance between sites C1 and C2, the angle between C1-C2-C3 and the dihedral angle formed between the planes C1-C2-C3 and C2-C3-C4. The convention used are the same as for z-matrices, see  example SITES_GEOMETRY_1.INP:​
 +
 +If $Name contains only two sites then only Sites_Geometry_Distance($Name) can be used. Three sites defined additionally allows the use of Sites_Geometry_Angle($Name) and four sites defined additionally allows the use of Sites_Geometry_Dihedral_Angle($Name).
 +
 +Examples SITES_GEOMETRY_1.INP and SITES_GEOMETRY_2.INP demonstartes the use of //​sites_geometry//​.
 +
 +**[//​siv_s1_s2//​ # #]**
 +
 +Defines the S<​sub>​1</​sub>​ and S<​sub>​2</​sub>​ integration limits for the spherical interaction volume of the GRS series.
 +
 +**[//​smooth//​ #​num_pts_left_right]**
 +
 +Performs a Savitzky-Golay smoothing on the observed data. The smoothing encompasses (2 * #​num_pts_left_right + 1) points.
 +
 +**[//​spherical_harmonics_hkl//​ $name]...**
 +
 +**[//​sh_Cij_prm//​ $Yij E]...**
 +
 +**[//​sh_alpha//​ !E]**
 +
 +**[//​sh_order//​ #]**
 +
 +Defines a hkl dependent symmetrized spherical harmonics series (see section 7.9.2). $name defines the name given to the series and when used in equations it returns the value of the spherical harmonics series.
 +
 +//​sh_Cij_prm//​ is the spherical harmonics coefficients,​ which can be defined by the User, or, alternatively if there are no coefficients defined then the //​sh_Cij_prm//​ parameters are generated. Only the coefficients allowed by the selection rules of the point group are generated (Järvinen, 1993). At the end of refinement the generated //​sh_Cij_prm//​ parameters are appended to //​sh_order//​. This allows for control over the //​sh_Cij_prm//​ parameters in subsequent refinements. $Yij corresponds to valid symmetrized harmonics that has survived symmetrization. It is internally generated when there are no //​sh_Cij_prm//​ parameters defined by the User.
 +
 +//​sh_alpha//​ corresponds to the angle in degrees between the polar axis and the scattering vector; //​sh_alpha//​ defaults to zero degrees which is required for symmetric reflection as is the case for Bragg-Brentano geometry.
 +
 +//​sh_order//​ corresponds to the order of the spherical harmonic series which are even numbers ranging from 2 to 8 for non-cubic and from 2 to 10 for cubic systems.
 +
 +The PO_Spherical_Harmonics macro simplifies the use of //​spherical_harmonics_hkl//​. CLAY.INP demonstrates the use of //​spherical_harmonics_hkl//​ for describing anisotropic peak shapes.
 +
 +**[//​stacked_hats_conv//​ [//​whole_hat//​ E [//​hat_height//​ E]]...[//​half_hat//​ E [//​hat_height//​ E]...]...**
 +
 +Defines hat sizes for generating an aberration function comprising a summation of hat functions. //​whole_hat//​ defines a hat with an X axis extent of ±//​whole_hat///​2. //​half_hat//​ defines a hat with an X-axis range of //​half_hat//​ to zero if //​half_hat//<​0;​ or zero to //​half_hat//​ if //​half_hat//>​ 0. //​hat_height//​ defines the height of the hat; it defaults to 1. //​stacked_hats//​ is used for example to describe tube tails using the Tube_Tails macro.
 +
 +**[//​start_X//​ !E] [//​finish_X//​ !E]**
 +
 +Defines the start and finish X region to fit to.
 +
 +**[//​str//​]...**
 +
 +Defines a new structure node.
 +
 +**[//​str_hkl_angle//​ N h k l]...**
 +
 +Defines a parameter name and a vector normal to the plane defined by h, k and l. When the parameter name is used in an equation, it returns angles (in radians) between itself and the normal to the planes defined by hkls; see the Preferred_Orientation and PO_Two_Directions  macros. An example in two directions is as follows:
 +
 +**[****//​swap_sites//​** **$sites_1 $sites_2]…**
 +
 +//​swap_sites//​ attempts to find a lower <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​ by swapping [[#​k142|sites defined]] in $sites_1 with those defined in $sites_2. The swapping continues until all swaps are performed. Outline of the algorithm:
 +
 +While //​swap_site//​ processes still to be processed {
 +
 +k = 0
 +
 +Do
 +
 +Randomize the cation configuration according to //​swap_sites//​.
 +
 +Find the local minimum of <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​
 +
 +k = k + 1
 +
 +If <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k+1) > <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k) then reset site positions
 +
 +While <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k+1) > <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k) or all swap possibility exhausted
 +
 +}
 +
 +Starting from a particular cation configuration,​ a single swap of two different cation species does not exhaust all possible cation configurations. For example, three sites A, B and C have the six possible configurations of ABC, ACB, BAC, CAB, BCA, CBA. Swapping any two from the starting configuration of ABC results in the possible configurations of BAC, CBA, ACB with CAB and BCA absent. The absent configurations can be obtained by a double swap where, for example, the swapping of A and C yields CBA and then the swapping of A and B yields CAB. Thus all possible configurations can be visited if in between swapping steps are realized by the simulated annealing process.
 +
 +Swapping the Zr sites with and Ca sites in the example above can be performed as follows:
 +
 +swap_sites Ca Zr
 +
 +If the sites were named Ca1, Ca2, Ca3, Zr1, Zr2, Zr3 then the following could be used:
 +
 +swap_sites Ca* Zr*
 +
 +**[//​temperature//​ !E]...**
 +
 +**[****//​move_to_the_next_temperature_regardless_of_the_change_in_rwp//​****]**
 +
 +**[****//​save_values_as_best_after_randomization//​****]**
 +
 +**[****//​use_best_values//​****]**
 +
 +**[****//​do_processes//​****]**
 +
 +A temperature regime has no affect unless the reserved parameter name T is used in //​[[#​x000|val_on_continue]]//​ attributes, or, if the following temperature dependent keywords are used:
 +
 +[[#​k128|rand_xyz]]
 +
 +[[#​k133|randomize_on_errors]]
 +
 +//​randomize_on_errors//​automatically determines parameter displacements without the need for //​[[#​k128|rand_xyz]]//​or //​val_on_continue//​. It performs well on a wide range of problems.
 +
 +The reserved parameter T returns the current temperature and it can be used in equations and in particular the //​[[#​x000|val_on_continue]]//​ attribute. The first //​temperature//​ defined becomes the starting temperature;​ subsequent //​temperature//​(s) become the current temperature.
 +
 +If <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​ increases relative to a previous cycle then the temperature is advanced to the next //​temperature//​. If <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​ decreases relative to previous temperatures of lesser values then the current temperature is rewound to a previous temperature such that its previous is of a greater value.
 +
 +//​move_to_the_next_temperature_regardless_of_the_change_in_rwp//​ forces the refinement to move to the next temperature regardless of the change in Rwp from the previous temperature.
 +
 +//​save_values_as_best_after_randomization//​ saves the current set of parameters and gives them the status of “best solution”. Note, this does not change the global “best solution” which is saved at the end of refinement.
 +
 +//​use_best_values//​ replaces the current set of parameters with those marked as “best solution”.
 +
 +//​do_processes//​ executes any //​swap_sites//​ or //​try_site_patterns//​ processes.
 +
 +The temperature regime as defined in the macro Auto_T is sufficient for most problems.
 +
 +A typical temperature regime starts with a high value and then a series of annealing temperatures,​ for example:
 +
 +temperature 2
 +
 +move_to_the_next_temperature_regardless_of_the_change_in_rwp
 +
 +temperature 1
 +
 +temperature 1
 +
 +temperature 1
 +
 +If the current temperature is the last one defined (the fourth one), and <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​ decreased relative to the second and third //​temperature//​s,​ then the current temperature is set to the second temperature.
 +
 +The current temperature can be used in all equations using the reserved parameter T, for example:
 +
 +x @ 0.123 val_on_continue = Val + T Rand(-.1, .1)
 +
 +The following temperature regime will allow parameters to randomly walk for the first temperature. At the second temperature the parameters are reset to those that gave the "best solution"​.
 +
 +temperature 1
 +
 +temperature 1   use_best_values
 +
 +temperature 1
 +
 +temperature 1   use_best_values
 +
 +temperature 1
 +
 +temperature 10
 +
 +   save_values_as_best_after_randomization
 +
 +   move_to_the_next_temperature_regardless_of_the_change_in_rwp
 +
 +Note, that when a "best solution"​ is encountered the temperature is rewound to a position where the temperature decreased. For example, if the R<​sub>​WP</​sub>​ dropped at lines 2 to 5 then the next temperature will be set to "​line 1"​.
 +
 +The following will continuously use the "best solution"​ before randomisation. This particular temperature regime has a tendency to remain in a false minimum.
 +
 +temperature 1 use_best_values
 +
 +**[//​th2_offset//​ E]...**
 +
 +Used for applying 2q corrections to phase peaks. The following example applies a sample displacement correction:
 +
 +th2_offset = -2 Rad (c) Cos(Th) / Rs;
 +
 +//​th2_offset//​ is used for example in the Zero_Error and Specimen_Displacement macros.
 +
 +**[//​try_site_patterns//​ $sites [//​num_patterns_at_a_time//​ #] ]...**
 +
 +//​try_site_patterns//​ performs an exhaustive search of all possible cation configurations where the cations in question is [[#​k142|identified]] by $sites. //​num_patterns_at_a_time//​ defines the number of patterns to process at any one time. Outline of the algorithm:
 +
 +While //​try_site_patterns//​ processes still to be processed {
 +
 +k = 0
 +
 +Do
 +
 +Change the cation configuration according to //​try_site_patterns//​
 +
 +Find the local minimum of <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​
 +
 +If <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k+1) > <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k) then reset site positions
 +
 +k = k + 1
 +
 +While <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k+1) > <​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>​(k) or //k// < //​num_patterns_at_a_time//​
 +
 +}
 +
 +The number of possible cation configurations determines the approximate magnitude of a structure determination problem. A structure consisting of N<​sub>​A</​sub>​ cation sites of species A and N<​sub>​B</​sub>​ cation sites of species B has, for a particular set of cation positions, a number of possible configurations N<​sub>​AB</​sub>​ calculated as follows:
 +
 +N<​sub>​AB</​sub>​ = <​sup>​(NA+NB)</​sup>​C<​sub>​NB</​sub>​ / N<​sub>​B</​sub>​!
 +
 +where the notation <​sup>​u</​sup>​C<​sub>​v</​sub>​=(u-0)(u-1)(u-2)…(u-(v-1)) has been used. Thus for N<​sub>​A</​sub>​=3 and N<​sub>​B</​sub>​=4 we have N<​sub>​AB</​sub>​=(7 6 5 4)%%/(%%4 3 2 1)=N<​sub>​BA</​sub>​=(7 6 5)%%/(%%3 2 1)=35. The number of configurations N<​sub>​ABD</​sub>​ for and additional set of cation sites of species D becomes:
 +
 +N<​sub>​ABD</​sub>​ = N<​sub>​AB</​sub>​ (<​sup>​(NA+NB+NDD)</​sup>​C<​sub>​ND</​sub>​ / N<​sub>​D</​sub>​! )
 +
 +An additional two D sites, or, N<​sub>​A</​sub>​=3,​ N<​sub>​B</​sub>​=4 and N<​sub>​D</​sub>​=2 gives and N<​sub>​ABD</​sub>​=1260. Thus the number of configurations quickly becomes prohibitive for an exhaustive search.
 +
 +Here is an example of using //​try_site_patterns//​ on three Ca sites and two Zr sites:
 +
 +str...
 +
 +site Ca...
 +
 +site Ca...
 +
 +site Ca...
 +
 +site Zr...
 +
 +site Zr...
 +
 +//​try_site_patterns//​ "Ca Zr" //​num_patterns_at_a_time//​ 3
 +
 +N<​sub>​CaZr</​sub>​=10 and thus //​try_site_patterns//​ will cycle through the 10 patterns searching for a reduction in <​sub>​{{Technical_Reference%20V4-1_files:​image002.gif?​20x23}}</​sub>​.
 +
 +**[//​user_defined_convolution//​ E //min// E //max// E]...**
 +
 +User defined convolutions are convoluted into phase peaks and can be a function of X. The //​min/////​max//​ equations are mandatory, they define the x-axis extents of the //​user_defined_convolution//​ where min <= 0 and max >= 0. For example, a sinc function can be convoluted into phase peaks (example AU111.INP) as follows:
 +
 +str
 +
 +   prm k 10 min 0.001 max 100
 +
 +   user_defined_convolution =
 +
 +      If(Abs(X) < 10^(-10), 1, (Sin(k X) %%/(%%k X))^2);
 +
 +      min -3 max 3
 +
 +**[//​use_tube_dispersion_coefficients//​]**
 +
 +Forces the use of Laboratory tube anomalous dispersion coefficients instead of the more accurate data from http://​www‑cxro.lbl.gov/​optical_constants/​asf.html.
 +
 +**[//​verbose//​ #]...**
 +
 +A value of 1 (the default) instructs the kernel to output in a verbose manner.
 +
 +A value of 0 reduces kernel output such that text output is only initiated at the end of a [[#​k144|refinement cycle]].
 +
 +A value of -1 reduces kernel output such that text output is initiated every second and only Rwp values at the end of a refinement cycle is kept.
 +
 +The Simulated_Annealing_1 macro has //verbose// set to -1; this ensures that long simulated annealing runs do not exhaust memory due to saving Rwp values and text output buffers.
 +
 +**[//​view_structure//​]**
 +
 +Informs a driver GUI to display the structure.
 +
 +**[//​weighting//​ !E  [//​recal_weighting_on_iter//​]]**
 +
 +Used for calculating the //xdd// dependent weighting function  in<​sub>​{{Technical_Reference%20V4-1_files:​image016.gif?​20x23}}</​sub>,​ see equation Eq. (5‑2). Can be a function of the reserved parameter names X, Yobs, Ycalc and  SigmaYobs. The default is as follows:
 +
 +weighting = 1 / Max(Yobs, 1);
 +
 +In cases where //​weighting//​ is a function of [[#​_Reserved_parameter_names|Ycalc]] then //​recal_weighting_on_iter//​ can be used to recalculate the weighting at the start of refinement iterations. Otherwise the weighting is recalculated at the start of each [[#​k144|refinement cycle]].
 +
 +Note that some goodness of fit indicators such as //r_wp// are a function of //​weighting//,​ see Table 5‑2.
 +
 +**[//​weight_percent_amorphous//​ !E]**
 +
 +Determines the amorphous content in a sample. The phase dependent keyword of //​spiked_phase_measured_weight_percent//​ needs to be defined in order for //​weight_percent_amorphous//​ to be calculated.
 +
 +**[//​x_calculation_step//​ !E]**
 +
 +Calculation step used in the generation of phase peaks and //​fit_obj//​’s. Peak_Calculation_Step is the actual step size used, it is defined is as follows:
 +
 +For and x-axis with equal steps and //​x_calculation_step//​ not defined then
 +
 +Peak_Calculation_Step =  “Observed data step size” / //​convolution_step//​
 +
 +otherwise
 +
 +Peak_Calculation_Step =  //​x_calculation_step//​ / //​convolution_step//​
 +
 +//​x_calculation_step c//an be a function of Xo and Th. In some situations it may be computationally efficient to write //​x_calculation_step//​ in terms of the function Yobs_dx_at and the reserved parameter Xo. It is also mandatory to define //​x_calculation_step//​ for data with unequal x-axis steps %%(*%%.xy or *.xye data files). Example uses of //​x_calculation_step//​ is as follows:
 +
 +x_calculation_step .01
 +
 +x_calculation_step = .02 (1 + Tan(Th));
 +
 +x_calculation_step = Yobs_dx_at(Xo);​
 +
 +**[//xdd// $file %%[{%% $data }] [//range// #] [//​xye_format//​] [//​gsas_format//​] [//​fullprof_format//​] ]...**
 +
 +Defines the start of //xdd// dependent keywords and the file containing the observed data.
 +
 +{$data} allow for insertion of ASCII data directly into the INP file.
 +
 +//range// applies to Bruker AXS *.RAW data files; in multi-range files it defines the range to be refined with the first range starting at 1. //range// is set to 1 by default.
 +
 +xye_format (see section 10 as well) signals the loading of columns of x, y and error values; additional columns are ignored. gsas_format and fullprof_format signals the loading of GSAS and FullProf file formats.
 +
 +The following instruction will refine on the first range in the data file pbso4.raw:
 +
 +xdd pbso4.raw
 +
 +To following will refine on the third range:
 +
 +xdd pbso4.raw range 3
 +
 +To read data directly from an INP file, the following can be used:
 +
 +xdd {
 +
 +1 1 10  ' start, step and finish (equidistant data)
 +
 +1 2 3 4 5 6 7 8 9 10
 +
 +}
 +
 +// //
 +
 +xdd {
 +
 +_xy ' switch indicating x-y format
 +
 +0.1 1   0.2 2   ...
 +
 +}
 +
 +**[//​xdd_out//​ $file [//​append//​] ]...**
 +
 +Used for writing //xdd// dependent details to file. The //​[[#​k045|out_eqn]]//​ can contain the reserved parameter names of X, Yobs, Ycalc and SigmaYobs. See the keyword //out// for a description of //​out_record//​. The Out_Yobs_Ycalc_and_Difference macro is a good example of using //​xdd_out//​.
 +
 +**[//​xdd_scr//​  $file] …**
 +
 +**[//​dont_merge_equivalent_reflections//​]**
 +
 +**[//​dont_merge_Friedel_pairs//​]**
 +
 +**[//​ignore_differences_in_Friedel_pairs//​]  **
 +
 +**[//​str//​]…**
 +
 +**[//​auto_scale//​ !E] **
 +
 +**[//​i_on_error_ratio_tolerance//​ #]**
 +
 +**[//​num_highest_I_values_to_keep//​ #num]**
 +
 +//​xdd_scr//​defines single crystal data from the file $file. The file can have extensions of *.HKL for ShelX HKL4 format or *.SCR for SCR format. All //xdd// and //str// keywords that are not dependent on powder data can be used by //xdd_scr// and //​hkl_Is_from_hkl4//​. Single crystal data is internally stored in 2q versus F<​sub>​o</​sub><​sup>​2</​sup>​ format. This means that a //lam// definition is necessary and the keywords //​start_X//,​ //​finish_X//​ and //exclude// can be used with //​xdd_scr.//​
 +
 +//​dont_merge_equivalent_reflections//​ unmerges equivalent reflections,​ see also section 7.3.3.
 +
 +//​dont_merge_Friedel_pairs//​ prevents the merging of Friedel pairs.
 +
 +//​ignore_differences_in_Friedel_pairs//​ forces the use of Eq. (7‑12) for calculating F<​sup>​2</​sup>​.
 +
 +//​auto_scale//​ rewrites  the //scale// parameter in terms of F<​sup>​2</​sup>​. This eliminates the need for the //scale// parameter. The value determined for //​auto_scale//​ is updated at the end of refinement.
 +
 +//​i_on_error_ratio_tolerance//​ filters out hkl’s that does not meet the condition:
 +
 +%%|%%F<​sub>​o</​sub>​%%|%%  >   i_on_error_ratio_tolerance |Sigma(F<​sub>​o</​sub>​)|
 +
 +//​num_highest_I_values_to_keep r//emoves all hkl’s except for //#//num hkl’s with the highest F<​sub>​o</​sub>​ values.
 +
 +An example input segment for single crystal data refinement is as follows:
 +
 +xdd_scr ylidm.hkl
 +
 +MoKa2(0.001)
 +
 +finish_X 35
 +
 +weighting = 1 / (Sin(X Deg / 2) Max(1, Yobs));
 +
 +STR(P212121)
 +
 +   a  5.9636
 +
 +   b  9.0390
 +
 +   c 18.3955
 +
 +   scale @ 1.6039731906
 +
 +   i_on_error_ratio_tolerance 4
 +
 +   site S1  x @ 0.8090  y @ 0.1805  z @ 0.7402  occ S 1  beq 2
 +
 +   site O1  x @ 0.0901  y @ 0.8151  z @ 0.2234  occ O 1  beq 2
 +
 +   ...
 +
 +The SCR format is white space delimited and consists of entries of h, k, l, m, d, 2q, F<​sub>​o</​sub><​sup>​2</​sup>​ which is the format outputted by the Create_hklm_d_Th2_Ip_file macro.
 +
 +**[//​xo_Is//​]...**
 +
 +**[//xo// E  //I// E]...**
 +
 +Defines a phase type that uses x-axis space for generating peak positions, see example XOIS.INP. //xo// corresponds to the peak position and //I// is the intensity parameter before applying any //​scale_pks//​ equations.
 +
 +**[//​yobs_eqn//​ !N E]**
 +
 +The keyword //​yobs_eqn//​ is used in place of the //xdd// keyword. It describes the observed data as an equation. This is very useful for approximating functions, see examples in section **Error! Reference source not found.**. The name given to the equation !N is used for identifying the equation in the GUI.
 +
 +**[//​yobs_out//​ $file] [//​ycalc_out//​ $file] [//​diff_out//​ $file]**
 +
 +Outputs the observed, calculated and difference patterns respectively in a format as specified in the extension of $file. Extensions *.xy, *.scr, *.xdd are supported. Further formats are accommodated using any number of macros including Out_Yobs_Ycalc_and_Difference,​ Out_X_Yobs etc…
 +
 +**[****//​yobs_to_xo_posn_yobs//​** **!E]**
 +
 +At the start of refinement //​yobs_to_xo_posn_yobs//​ decomposes an X-ray diffraction pattern into a new pattern comprising at most one data point per hkl. Fitting to the decomposed pattern in a normal Rietveld refinement manner is then possible due to the ability to refine data of unequal x-axis step sizes. This normal Rietveld manner of fitting is important in structure solution from simulated annealing as the back ground can still be refined and the problem of peak overlap avoided. These new data points are not extracted intensities and thus the problem  of peak overlap, as occurs in intensity extraction, is avoided. The much smaller number of data points in the new diffraction pattern can greatly improve speed in structure solution; in other words the calculation time in synthesizing the diffraction pattern becomes close to that of when dealing with single crystal data.
 +
 +If the distance between two hkls is less than the value of //​yobs_to_xo_posn_yobs//​ then the proposed data point at one of these hkls is discarded. Thus the final decomposed pattern may in fact have less data points than hkls. A reasonable value for //​yobs_to_xo_posn_yobs//​ is  Peak_Calculation_Step,​ or,
 +
 +yobs_to_xo_posn_yobs = Peak_Calculation_Step;​
 +
 +//​yobs_to_xo_posn_yobs//​ can be a function of the reserved parameter X with X being the value of the x-axis at the hkl//.//
 +
 +It is important to determine and then fix all peak shape, zero error and lattice parameters before using yobs_to_xo_posn_yobs. Also, if the original diffraction pattern is noisy then it may be best to smooth it using the //smooth// keyword or re-binned using //​rebin_with_dx_of//​. Alternatively,​ a calculated pattern could be used as input into the yobs_to_xo_posn_yobs
 +
 +Note that structure solution can be speed up by preventing graphical output or by increasing the Graphics Response Time in the GUI.
 +
 +See examples CIME-DECOMPOSE.INP and PBSO4-DECOMPOSE.INP.
 +
 +===== 8.3        Keywords to simplify User input =====
 +
 +==== 8.3.1              The "load { }" keyword and attribute equations ====
 +
 +The "//​load//​ { }" keyword can be used to simplify User input. It allows the loading of keywords of the same type by typing the keywords once, for example, the //exclude// keyword in the following input segment:
 +
 +xdd...
 +
 +exclude 20 22
 +
 +exclude 32 35
 +
 +exclude 45 47
 +
 +can be rewritten using "//​load//​ { }" as follows:
 +
 +xdd...
 +
 +load exclude { 20 22 32 35 45 47 }
 +
 +This input can be further simplified using the Exclude macro:
 +
 +Exclude { 20 22 32 35 45 47 }
 +
 +In some cases attribute equations are loaded by the parameter itself. For example, in the following:
 +
 +prm t 0.01  val_on_continue = Rand(-Pi, Pi); min 0.4 max 0.5
 +
 +the //prm// will actually load the attribute. But, in the following:
 +
 +load prm val_on_continue min max { t 0.01 = Rand(-Pi, Pi); 0.4 0.5 }
 +
 +the //load// keyword will load the attributes.
 +
 +The following is valid:
 +
 +load sh_Cij_prm
 +
 +{
 +
 +   y00 !sh_c00 1
 +
 +   y20  sh_c20 0.26202642  min 0 max 1
 +
 +   y40  sh_c40 0.06823548
 +
 +   ...
 +
 +}
 +
 +In this case the //load// keyword does not contain //min/max// and the parameter will load its attributes. The //load// keyword however can contain attributes, for example:
 +
 +load sh_Cij_prm min max
 +
 +{
 +
 +   y00 !sh_c00 1           0 1
 +
 +   y20  sh_c20 0.26202642  0 1
 +
 +   y40  sh_c40 0.06823548  0 1
 +
 +   ...
 +
 +}
 +
 +In this case the attributes must be entered for all //load// entries.
 +
 +==== 8.3.2              The "​move_to $keyword"​ keyword ====
 +
 +The //move_to// keyword provides a means of entering parameter attributes without having to first load the parameter name and value, see for example the Keep_Atom_Within_Box macro. The site dependent ADPs_Keep_PD macro defines //min/max// limits; here's part of that macro:
 +
 +move_to u12
 +
 +min = -Sqrt(Get(u11) Get(u22));
 +
 +max =  Sqrt(Get(u11) Get(u22));
 +
 +The $keyword of //move_to// can be any keyword and not just a parameter keyword.
 +
 +==== 8.3.3              The "for xdds { }" and "for strs { }" constructs ====
 +
 +The “//for// //xdds// { }” and "//​for//​ //strs// { }" constructs simplify the construction of input files when there are multiple diffraction patterns with similar structures, see example QUARTZ2_FPA.INP. For example, two diffraction patterns with the same structures can be composed as follows:
 +
 + 
 +
 +| xdd ... | ‘ first //xdd// |
 +|       bkg ...  \\       th2_offset ...     \\       ... | ‘ //xdd// dependent, __not common__ to the //​xdd//'​s |
 +|    str... | ‘ first //str// |
 +|       scale ...  \\       ... | ‘ //str// dependent, __not common__ to the //​str//'​s |
 +| xdd ... | ‘ second //xdd// |
 +|    bkg ... \\    th2_offset ...\\    ... | ‘ //xdd// dependent, __not common__ to the //​xdd//'​s |
 +|    str... | ‘ second //str// |
 +|       scale ...  \\       ... | ‘ //str// dependent, __not common__ to the //​str//'​s |
 +| for xdds { |   |
 +|    Slit_Width(.2)\\    CuKa2\\    ... | ‘ //xdd// dependent, __common__ to the //​xdd//'​s |
 +|    for strs { | ‘ //str// dependent, __common__ to the //​xdd//'​s |
 +|       ... |   |
 +|    } |   |
 +|    for strs 1 to 1 { |   |
 +|       space_group p1\\       site ... | ‘ //str// dependent, __specific__ to the __first__ //str// |
 +|    } |   |
 +| } |   |
 +
 +For obvious reasons, parameters should not be given the @ name within //for// constructs. The effect this would have is to give unique parameter names to the parameters iterated over; the output file would contain the parameter value corresponding to the last “//for xdds//” or “//for strs//” iteration.
 +
 ====== 9             Macros and Include Files ====== ====== 9             Macros and Include Files ======
  
Line 833: Line 3174:
 | ***.XY** |   | 2q and intensity data values | | ***.XY** |   | 2q and intensity data values |
 | ***.XYE** |   | 2q, intensity and intensity error values. | | ***.XYE** |   | 2q, intensity and intensity error values. |
- 

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