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sequential_refinements_-_save_phase_pattern [2020/04/20 13:50]
iangie
sequential_refinements_-_save_phase_pattern [2021/05/13 05:07] (current)
iangie [Extracting the intensity contribution from a certain phase for a batch of dataset]
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 Intensity contribution from individual phase can be saved out from GUI interface "​right-click -> save if displayed..."​. Intensity contribution from individual phase can be saved out from GUI interface "​right-click -> save if displayed..."​.
  
-However, there were multiple questions asked in the forum concerning how to extract phase contribution through Launch Mode .inp file setup, and even do this for in-situ data set.+However, there were multiple questions asked in the forum concerning how to extract phase contribution through Launch Mode .inp file setup, and how to do this even for a batch dataset.
  
-The solution below has been enlightened by the Alan Coelho'​s 2-step refinement & Matthew Rowles'​s Sequential Refinement method.+The solution below has been enlightened by Alan Coelho'​s 2-step refinement ​solution ​& Matthew Rowles'​s Sequential Refinement method.
  
-TOPAS V6 allows a keyword //​num_runs//​ which instructs the programme to run an .inp file multiple times, which means above 2-step solution can be devised in one .inp file with "​num_runs 2" and several #if switches:+TOPAS V6 allows a keyword //​num_runs//​ which instructs the programme to run an .inp file multiple times. This means above 2-step solution can be devised in one .inp file with "​num_runs 2" and several #if switches:
  
 ====== 1. Extracting phase contribution from a single data ====== ​ ====== 1. Extracting phase contribution from a single data ====== ​
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       {       {
        "​ %11.6f ​ " = X + 2 samp_disp Cos(X Deg_on_2)/​Rp Rad;                     /* Correct sample displacement from an internal standard, hkl_Al in this case */               "​ %11.6f ​ " = X + 2 samp_disp Cos(X Deg_on_2)/​Rp Rad;                     /* Correct sample displacement from an internal standard, hkl_Al in this case */       
-       "​ %11.6f\n ​ " = Ycalc;+       "​ %11.6f\n ​ " = Ycalc; ​                                                   /* You can add Ln() in the equation , if you want to plot as the intensity of the 2D plot in logarithm scale. */
        }        }
 #endif #endif
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       xdd_out OUTPUT_NMO_#​out filenum##​.xy load out_record out_fmt out_eqn       xdd_out OUTPUT_NMO_#​out filenum##​.xy load out_record out_fmt out_eqn
       {       {
-       "​ %11.6f ​ " = X + 2 samp_disp Cos(X Deg_on_2)/​Rp Rad;   /* Correct sample displacement of the phase  */        +       "​ %11.6f ​ " = X + 2 samp_disp Cos(X Deg_on_2)/​Rp Rad;   /* Correct sample displacement of the phase, because the in-situ cell pops up */        
-       "​ %11.6f\n ​ " = Ycalc;+       "​ %11.6f\n ​ " = Ycalc; ​                                 /* You can add Ln() in the equation , if you want to plot as the intensity of the 2D plot in logarithm scale. */
        }        }
 #endif #endif
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 </​code> ​     ​ </​code> ​     ​
  
-====== 3. Plot the extracted phase intensity ​in 2D plot using TOPAS V6 ======+====== 3. Plot the extracted phase intensity ​as 2D plot using TOPAS V6 ======
 Note the saved phase intensities .xy files will be in different X step positions. ​ Note the saved phase intensities .xy files will be in different X step positions. ​
  

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