Extracting the intensity contribution from a certain phase for a batch of dataset

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 hoe to do this even for a batch dataset.

The solution below has been enlightened by the 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:

1. Extracting phase contribution from a single data

num_runs 2
 
#if (Run_Number == 1)
iters 0
#endif
 
#if Run_Number == 0;
system_before_save_OUT { copy INP_File##.inp INP_File##.backup }  /* Backup this .inp file in the first run. */
#endif  
 
out_file = Concat(String(INP_File), ".INP");           /* This allow the refinement result to be accepted. */
 
#if Run_Number == 1;
system_after_save_OUT { copy INP_File##.backup INP_File##.inp }    /* Restore this .inp file to its initial status from the backup in the final run */
#endif   
 
xdd "somepattern.raw"
 
#if (Run_Number == 0)
   bkg @ 713.3525387 332.4034599 -218.0099371
   One_on_X(@, 9993.352223)
#else bkg 1                             /* A arbitrary 1 count is added to the phase contribution in case some plotting software does not like 0 intensity.  */
#endif   
 
   LP_Factor( 0)
   Specimen_Displacement(samp_disp, -0.05080112471)
   Radius(300)
   lpsd_th2_angular_range_degrees  2.29
      lpsd_equitorial_divergence_degrees  0.5
      Full_Axial_Model(12, 20, 20, 5, 5)
   CuKa(0.0001)
 
#if (Run_Number == 1)
      xdd_out Output_phase_contribution.xy load out_record out_fmt out_eqn
      {
       " %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;                                                    /* You can add Ln() in the equation , if you want to plot as the intensity of the 2D plot in logarithm scale. */
       }
#endif
 
#if (Run_Number == 0)
 xo_Is                               /* Amorphous Hump */
      xo @ 14.70505682
      peak_type spv
         spv_h1 @ 0.9845624876
         spv_h2 @ 1.396576759
         spv_l1  0.0040801296_LIMIT_MIN_0
         spv_l2  0.9958599408_LIMIT_MAX_1
      I  97.34548273
 
   hkl_Is 
      hkl_m_d_th2 1 1 1 8 2.33311367 38.5568314 I @ 74.14699402
      hkl_m_d_th2 2 0 0 6 2.02053571 44.8203506 I @ 96.76241314
      LVol_FWHM_CS_G_L( 1, 113.2882082, 0.89, 158.3779042,,,@, 177.9527013_LIMIT_MAX_115.908746)
      Stephens_cubic(@, 0.2634600653_LIMIT_MIN_0,@, -2072.424113,@, -5379.345555)
      r_bragg  1.213209076
      phase_MAC 0
      phase_name "hkl_Al"                /*  Internal Standard  */      
      MVW( 0, 65.99173092, 0)
      space_group Fm-3m
      Cubic(!a_000040787 4.049)          /*  Fixed to the lattice parameter from a PDF card. */
 
#endif
 
   hkl_Is 
      hkl_m_d_th2 0 0 2 2 5.54676771 15.9653101 I @ 2.664253279
      hkl_m_d_th2 0 0 4 2 2.77338386 32.2515259 I @ 10.48756371
      ...
      LVol_FWHM_CS_G_L( 1, 173.7971979, 0.89, 242.97,,,, 273_LIMIT_MIN_200 min =200;)
      e0_from_Strain( 0.001701696021,, 0.78,,)
      r_bragg  0.2228689481
      phase_MAC 0
      phase_name "hkl_Na0.53MnO2"        /* This is the phase of interest, which you want its intensity contributions saved out */      
      MVW( 0, 78.20697387, 0)
      space_group P63/mmc
      Hexagonal(a_040201752 2.853135761,c_040201752 11.09353545)
 

It can be seen that, in the first run (Run_Number = 0), the #if switches allow a normal Pawley refinement which refines the sample displacement according to an internal standard (hkl_Al in this case).

In the second run (Run_Number = 1), the #if switches only turn on the phase of interest with “iters 0” and get the intensity saved out.

2. Extracting phase contribution from a batch dataset

To apply this method for a batch of data set (e.g. in-situ data set), which contains, say 100 patterns, an .inp file with “num_run = 2 * 100;” can be set as below:

(The restriction of this setup is, the file names of the dataset must contain an increasing run number: e.g. *_1.raw, *_2.raw, ***_3.raw, ….. A simple windows/DOS batch rename can achieve this. )

num_runs =2*100;                /* This set the Reserved Keywords "Run_Number" goes from 0 to 199 */
 
#if (Mod(Run_Number,2) == 1)    /* Normal Pawley refinement when Run_Number is an even number; Save the phase intensity when Run_Number is an odd number. Refinements goes on like tik-tok tik-tok … */
iters 0
#endif
 
#if Run_Number == 0;
system_before_save_OUT { copy INP_File##.inp INP_File##.backup }
#endif  
 
out_file = Concat(String(INP_File), ".INP");           /* This accepts the refinement result, especially the sample displacement */
 
#if Run_Number == 2*100-1;
system_after_save_OUT { copy INP_File##.backup INP_File##.inp }
#endif   
 
#prm filenum = Round((Run_Number+1)/2);    /* This calculates the run number of the file, __NOTE Round(0.5) evaluates to 0 in TOPAS V5, but evaluates to 1 in TOPAS V6!__ */
 
xdd Somepattern_#out filenum##.raw         /* This allow TOPAS to find the corresponding pattern  */
 
#if (Mod(Run_Number,2) == 0)
   bkg @ 713.3525387 332.4034599 -218.0099371
   One_on_X(@, 9993.352223)
#else bkg 1                             /* A arbitrary 1 count is added to the phase contribution in case some plotting software does not like 0 intensity.  */
#endif   
 
   LP_Factor( 0)
   Specimen_Displacement(samp_disp, -0.05080112471)
   Radius(300)
   lpsd_th2_angular_range_degrees  2.29
      lpsd_equitorial_divergence_degrees  0.5
      Full_Axial_Model(12, 20, 20, 5, 5)
   CuKa(0.0001)
 
#if (Mod(Run_Number,2) == 1)            /* When Run_Number is an odd number, save the phase contribution to a file with the run number of its raw data  */
      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, because the in-situ cell pops up */       
       " %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
 
#if (Mod(Run_Number,2) == 0)
 xo_Is                              /*  Amorphous hump */
      xo @ 14.70505682
      peak_type spv
         spv_h1 @ 0.9845624876
         spv_h2 @ 1.396576759
         spv_l1  0.0040801296_LIMIT_MIN_0
         spv_l2  0.9958599408_LIMIT_MAX_1
      I  97.34548273
 
   hkl_Is 
      hkl_m_d_th2 1 1 1 8 2.33311367 38.5568314 I @ 74.14699402
      hkl_m_d_th2 2 0 0 6 2.02053571 44.8203506 I @ 96.76241314
      LVol_FWHM_CS_G_L( 1, 113.2882082, 0.89, 158.3779042,,,@, 177.9527013_LIMIT_MAX_115.908746)
      Stephens_cubic(@, 0.2634600653_LIMIT_MIN_0,@, -2072.424113,@, -5379.345555)
      r_bragg  1.213209076
      phase_MAC 0
      phase_name "hkl_Al"                   /*  Internal Standard with fixed lattice parameter  */      
      MVW( 0, 65.99173092, 0)
      space_group Fm-3m
      Cubic(!a_000040787 4.049)
 
#endif
 
   hkl_Is 
      hkl_m_d_th2 0 0 2 2 5.54676771 15.9653101 I @ 2.664253279
      hkl_m_d_th2 0 0 4 2 2.77338386 32.2515259 I @ 10.48756371
      ...
      LVol_FWHM_CS_G_L( 1, 173.7971979, 0.89, 242.97,,,, 273_LIMIT_MIN_200 min =200;)
      e0_from_Strain( 0.001701696021,, 0.78,,)
      r_bragg  0.2228689481
      phase_MAC 0
      phase_name "hkl_Na0.53MnO2"    /* The phase of interest, the intensity of which needs be saved out */      
      MVW( 0, 78.20697387, 0)
      space_group P63/mmc
      Hexagonal(a_040201752 2.853135761,c_040201752 11.09353545)
 

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.

Some algorithms require long time to create 2D plot when the data are not in an uniform mesh.

Surprisingly the 2D plot function in TOPAS v6 can create below 2D plot from 100 .xy data of non-uniform data step very quickly, which persuaded me no need to turn to other plotting software:

The example of the plot is like this.


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