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time_of_flight_tof_isis_instrument_standard_files [2016/06/20 13:40]
johnsoevans [Multibank Refinements at ISIS]
time_of_flight_tof_isis_instrument_standard_files [2020/06/19 10:44] (current)
johnsoevans
Line 4: Line 4:
 The files below are input files for fitting standard data sets from isis diffractometers. ​ They can be easily adjusted to fit other samples. ​ Caveat emptor. ​ If you view them in jEdit with folding turned on they are simple 6 or 7 line files! The files below are input files for fitting standard data sets from isis diffractometers. ​ They can be easily adjusted to fit other samples. ​ Caveat emptor. ​ If you view them in jEdit with folding turned on they are simple 6 or 7 line files!
  
-As written any axial divergence from the sample gets "​mopped up" by the instrumental peak shape function. ​ You might decide to separate this out by applying a Simple_Axial_Model convolution due to the sample. 
  
 ===== HRPD ===== ===== HRPD =====
  
 <code topas> <code topas>
-'​-----------------------------------------------------------------  +'​----------------------------------------------------------------- ​  
-'si refiniment with peakshapes fixed at those from ceo2 59832 refinements +'Template to create Input File for HRPD/ISIS multibank tof refinement 
-'May 2014 calibration +'​1. ​Save this file as "​filename.inp" 
-'​-----------------------------------------------------------------  +'2. Update instrumetnal constants in each bank (though values will be close already) 
-r_exp   1.06408232 +'3. Update instrumental peak shape parameters in wifd_pkshape (though values will be close already) 
-r_exp_dash ​ 1.96019465 +'4. Change the CeO2 structure at the end of the file to your structure
-r_wp    ​2.70655155 +
-r_wp_dash ​ 4.98586223 +
-r_p    10.2887672 +
-r_p_dash ​ 27.629927 +
-gof    2.54355465 +
-weighted_Durbin_Watson  ​3.4164746 +
-'-----------------------------------------------------------------  +
-do_errors+
  
-#define HRPD_BS +'​Don'​t worry about the '{{{ and '}}} symbols in the file.  They allow you to use "​Folding/​Collapse Folds" 
-#define HRPD_90 +'This is a convenient way of viewing complex files in jedit - have a play! 
-#define HRPD_30 +'​Developed from HRP64473 CeO2 standard recorded March 2016  
- +'John Evans  
-no_LIMIT_warnings +'​----------------------------------------------------------------- ​  
- +  
-#ifdef HRPD_BS +'{{{ r-factors and control ​information ​ 
-'​---------------------------------------------  +r_exp 0.900894234 
-'hrpd backscattering ​information here  +r_exp_dash 1.52031604  
-'2-theta 168.567 deg +r_wp 4.19280506 
-'​---------------------------------------------  +r_wp_dash 7.07562394  
- +r_p 4.1797566  
-TOF_XYE(hrp59833_b1_tof.dat, 10)  +r_p_dash 10.996074  
-   TOF_LAM(0.001) ​ +gof 4.65404806  
-   scale_pks = D_spacing^4; ​   +weighted_Durbin_Watson ​ 1.29301128 
- x_calculation_step = Yobs_dx_at(Xo); convolution_step 4 +iters 1000000000  
- start_X 13500 +'​do_errors  
- finish_X 125000 +'​continue_after_convergence  
-   ​weighting = If(SigmaYobs < .00011, 1/​SigmaYobs^2); +'}}}  
-' rebin_with_dx_of = 3 0.0001 X; +  
- r_wp  2.98501912 +'{{{ select banks to use here and enter filenames and tof ranges to fit 
- +'use these lines to set stemfilename and information for in gui mode  
- TOF_x_axis_calibration(t0_bs, ​ ​1.94636`_0.51960, difc_bs, ​48270.16922`_0.87403, difa_bs, -4.07045`_0.34362)  +'this stemfilename will allow multitopas_files to run multibank multitemperature runs  
-'peak shape from ceo2_59832_01.inp +#ifdef !GUI_LINES ​  
- wifd_pkshape(two_theta, ​168.567, !aprm, 2.07260, !tauf_2, 284.02163, !tauf_1, 0.30422, !tauf_0, 0.000, !taus_0, 31.69365, !taus_1, 1.13751, !t_eff, 198.21688, !hhh, 12.28803, !hhh_0, 3.24083)   ​ +macro filename {hrp64473} ​   
- +macro information {prm !te prm !time 0  }   
-   bkg @  0.332251605`_0.000839225829 ​ 0.127664108`_0.00159600398 -0.011213406`_0.00146003183 ​-0.0293181373`_0.00141513434 ​-0.0209389353`_0.00132248752 ​-0.0178382845`_0.00129015903  ​0.000795277761`_0.00120065696 ​-0.000495530163`_0.00117741229 ​-0.00402007515`_0.00106715478 ​-0.00706378484`_0.00100865764 ​-0.00318104537`_0.000736948187 ​-0.00515453384`_0.00052887957 +#endif  
- +  
- prm mu_Si_bs ​ 0.05413`_0.00859 '​min ​0.0 +#define USE_HRPD_BS macro filename_bank1 {filename##​_b1_tof.dat}  macro start_end_bank1 {start_X 12000  finish_X 125000}  
-   scale_pks = Exp(-mu_Si_bs*D_spacing); ​          +#define USE_HRPD_90 macro filename_bank2 {filename##​_b2_tof.dat} ​ macro start_end_bank2 {start_X 11500 finish_X 125000}  
- prm !fixb_bs ​0.00000 +#define USE_HRPD_30 macro filename_bank3 {filename##​_b3_tof.dat} ​ macro start_end_bank3 {start_X 13300 finish_X 100000} ​ 
-   scale_pks = (Exp(-2*fixb_bs/​(2 D_spacing)^2));​ +'}}}  
- +  
-str  +'​-----------------------------------------------------------------  ​ 
- r_bragg  ​0.668971754 +  
- scale scal_bs ​ 2.6731775`_0.04243 +'{{{ information specific to bank 1 bs 168.567 deg refinement here  
- tof_sample_peakshape(lor_bs,​ 0.332187466`_0.00427450973,dsp_bs, 35.96212`_0.35011,dspsq_bs, 0.37668`_0.25903) +'You might want to change instrument calibration 
-'​----------------------------------------------------------------- ​ +#ifdef USE_HRPD_BS ​ 
-#endif + TOF_XYE(filename_bank110start_end_bank1 ​ 
- + 'calibration values should come from a Si standard you might want to refine to_bs and difa_bs 
-#ifdef HRPD_90 + TOF_x_axis_calibration(!t0_bs, ​-2.69633!difc_bs, ​48281.70876!difa_bs, -7.11699  
-'---------------------------------------------  + local !bank_two_theta ​168.567 ​ 
-'hrpd combined N + S 90° banks information ​here  + r_wp ​ 4.15346828 ​ 
-'2-theta ​90.2481 deg + bkg @  0.45496336`  0.0152548781 0.0394051043` -0.048312871` -0.00293636592` -0.0165978082-0.0257365654` -0.0126103624` -0.00715708576` -0.00772469188` -0.00759987084` -0.00401261224
-'​---------------------------------------------  + local !mu   0.00000  
- + local ​!fixb 0.00000  
-TOF_XYE(hrp59833_b2_tof.dat, 10)  +   
-   TOF_LAM(0.001)  + str   
-   ​scale_pks = D_spacing^4; ​   + r_bragg  ​7.78536681 ​ 
- x_calculation_step = Yobs_dx_at(Xo);​ convolution_step 4 + scale scal_bs ​ 2.25250609`  
-   ​weighting = If(SigmaYobs < .0001, 1, 1/​SigmaYobs^2);​ + tof_sample_peakshape(!lor_bs, 0.190724033,!dsp_bs, 35.54114,!dspsq_bs, 0.00029)  
-' rebin_with_dx_of = 3 0.0001 X; +#endif  
- r_wp  2.50580453 +'​}}} ​ 
- +  
-   TOF_x_axis_calibration(t0_90, ​ 20.19252`_0.73130, difc_90, ​34811.11035`_0.83689, difa_90, -0.02486`_0.22540)  +'{{{ information ​specific to bank 2 90 deg refinement here  
-'peak shape from ceo2_59832_01.inp +#ifdef USE_HRPD_90 ​ 
- wifd_pkshape(two_theta, ​90.2481, !aprm, 2.07260, !tauf_2, 284.02163, !tauf_1, 0.30422, !tauf_0, 0.000, !taus_0, 31.69365, !taus_1, 1.13751, !t_eff, 198.21688, !hhh, 12.28803, !hhh_0, 3.24083)   ​ + TOF_XYE(filename_bank2, 10) start_end_bank2 ​ 
- + 'all calibration constants could be refined if you trust difc on BS bank 
-   bkg @  0.223277484`_0.000395408778  ​0.0285296995`_0.000770956201 -0.00267454022`_0.000699497265 ​-0.000609289298`_0.000691507478 -0.000481807185`_0.000616939723 ​-0.00192687737`_0.000611544216 -0.00112725434`_0.000533463926 ​-0.00135691268`_0.000535532259 ​ 0.000617273095`_0.000447091267 ​-0.000964892799`_0.000434132414 ​-0.000912077588`_0.000292904938 ​ 0.000798940178`_0.000265176212 +    TOF_x_axis_calibration(!t0_90, ​-8.6875!difc_90, ​34862.4511!difa_90, -10.47717  
- + local !bank_two_theta ​90.2481 ​ 
-   ​start_X 12000 + r_wp ​ 4.17986033 ​ 
-   ​finish_X 125000  +    bkg @  0.359582611-0.041909519 0.0331121168` -0.0373546722 0.0144064496` -0.00382345778 0.00304444576` -0.00265728636` -0.00138170554` -0.00112394508`  0.00116378366` -0.00190092649 
- prm mu_Si_90 ​-0.00691`_0.00221 + local !mu    0.0000  
-   scale_pks = Exp(-mu_Si_90*D_spacing); ​          +    local !fixb  0.0000  
-   prm fixb_90 ​ 0.03683`_0.01719 +   
-   ​scale_pks = (Exp(-2*fixb_90/​(2 D_spacing)^2));​ + str   
- + r_bragg  ​2.93368804 ​ 
-str  + scale scal_90 ​ 1.66478178
- r_bragg  ​0.222352027 + tof_sample_peakshape(!lor_90, 0.0341852952,!dsp_90, ​155.01731,!dspsq_90, ​4.86725)  
- scale scal_90 ​ 1.75332707`_0.01044 +#endif  
- tof_sample_peakshape(lor_90,​ 0.079938561`_0.00166170209,​dsp_90, ​148.59233`_0.33226,​dspsq_90, ​5.47803`_0.17084) +'​}}} ​ 
- +  
-'​----------------------------------------------------------------- ​ +'{{{ information specific to bank 29.9039 deg refinement here  
-#endif +#ifdef USE_HRPD_30 ​ 
- + TOF_XYE(filename_bank3, 10) start_end_bank3 ​ 
-#ifdef HRPD_30 +   ​TOF_x_axis_calibration(!t0_30,-28.63431!difc_30, ​12820.3511!difa_30, ​ 0.09561)  
-'---------------------------------------------  + local !bank_two_theta ​29.9039 ​ 
-'hrpd low angle (30°) ​bank information here  + r_wp  5.87063188 ​ 
-'​2-theta ​29.9039 deg +   bkg @  0.284539356 0.0129274233`  0.0290223565` -0.0152795111`  0.0166152359` -0.0071559248`  0.00994277663` -0.00954234006`  0.0100840968` -0.00527172413`  0.00491156922 0.000459978629
-'​---------------------------------------------  + local !mu    ​0.0000  
- +   local !fixb  0.0000  
-TOF_XYE(hrp59833_b3_tof.dat, 10)  +  
-   ​TOF_LAM(0.001)  + str   
-   ​scale_pks = D_spacing^4; ​   + r_bragg  ​3.59385664 
- x_calculation_step = Yobs_dx_at(Xo);​ convolution_step 4 + scale scal_30 ​ 0.520155313`  
-   ​weighting = If(SigmaYobs < .0001, 1, 1/​SigmaYobs^2);​ + tof_sample_peakshape(!lor_30, ​7.62374695e-19!dsp_30, ​166.04848,!dspsq_30, ​19.50163)  
-'​ rebin_with_dx_of = 3 0.0001 X; +#endif  
- r_wp  5.77012728 +'​}}} ​ 
- +  
-   ​TOF_x_axis_calibration(t0_30,​-58.80287`_49168847.50511, difc_30, ​12816.63753`_42450272.87059, difa_30, ​-5.42280`_7559741.90482+'​----------------------------------------------------------------- ​  
-'peak shape from ceo2_59832_01.inp +  
- wifd_pkshape(two_theta, ​29.9039, !aprm, 2.07260, !tauf_2, 284.02163, !tauf_1, 0.30422, !tauf_0, 0.000, !taus_0, 31.69365, !taus_1, 1.13751, !t_eff, 198.21688, !hhh, 12.28803, !hhh_0, 3.24083)  ​  +'{{{ Overall and structural information here  
- +'First section has information for each bank of refinment (for xdds) 
-   bkg @  0.275404468`_0.00560239442 -0.0308923479`_0.0112235283 ​ 0.0793871247`_0.0104577295 ​-0.0649592869`_0.00992759382 ​ 0.0609366093`_0.0087120793 ​-0.0452147327`_0.00791762519 ​ 0.0435124681`_0.00648279494 ​-0.0270273682`_0.00567214436 ​ 0.0242127755`_0.0041916119 ​-0.0122756108`_0.00359529769 ​ 0.00970750358`_0.0020661031 -0.00204667461`_0.00194120381 +'​Second section contains structural information;​ use parameter names not @ symbols 
- +for xdds {   
- start_X 12000  + weighting = 1 / SigmaYobs^2;​  
- finish_X 100000  + x_calculation_step = Yobs_dx_at(Xo);​ convolution_step 4  
- + TOF_LAM(0.001) ​  
- prm mu_Si_30  ​0.00712`_133511.55639 min 0.0 + scale_pks = D_spacing^4;​  
-   scale_pks = Exp(-mu_Si_30*D_spacing); ​          +   ​scale_pks = Exp(-mu*2 D_spacing Sin(0.00872664626 bank_two_theta)); ​  '​absorption correction local to each bank         
-   prm fixb_30 -7.48882`_4874093.05960 +   ​scale_pks = (Exp(-2*fixb/​(2 D_spacing)^2));​ 'fixb correction local to each bank  
-   ​scale_pks = (Exp(-2*fixb_30/​(2 D_spacing)^2));​ + wifd_pkshape(two_theta,​ =bank_two_theta;,​ !aprm, 1.93637, !tauf_2, 0.15262, !tauf_1, 0.85833, !tauf_0, 1.05944, !taus_0, 29.95983, !taus_1, 1.11856, !t_eff, 189.72881, !hhh, 0.35525, !hhh_0, 0.00100)  ​   
- +   
-str  + for strs 1 to 1 {   
- r_bragg  ​0.979889477 +       ​space_group ​Fm-3m                      
- scale scal_30 ​ 0.407637547`_2.596e+005 +       ​phase_name ​CeO2  
- tof_sample_peakshape(lor_30, ​5.64707181e-015`_0.0257827758,​dsp_30, ​169.45929`_74142685.81580,​dspsq_30, ​6.38789`_23644685.71697) +       ​Cubic( ​lpa_CeO2 ​ 5.412231`)  
- +       ​site Ce1 x  0.00  y 0.00  z 0.00 occ Ce 1 beq   bce   0.18599 
-'​----------------------------------------------------------------- ​ +       site  O1 x  0.25  y 0.25  z 0.25 occ  O 1 beq   ​box ​  ​0.35302`  
-#endif + }  ​
- +
- +
-'​-----------------------------------------------------------------  +
-'​structural information here +
-'----------------------------------------------------------------- ​ +
- +
-for xdds {  +
-for strs 1 to 1 {  +
-      space_group ​Fd3m                    ​ +
-      phase_name ​Si_NBS +
-      Cubic( ​!lpa_Si ​ 5.431195+
-      site Si x  0.00  y 0.00  z 0.00 occ Si 1 beq   bsi  ​0.56521`_0.01350+
  
-}+'}}}  
 +  
 +'​-----------------------------------------------------------------  ​
 </​code>​ </​code>​
  

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