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--- sequential_refinements_-_save_phase_pattern [2020/04/20 12:04] – iangie
+++ sequential_refinements_-_save_phase_pattern [2023/05/19 07:47] (current) – iangie
@@ Line 1: / Line 1: @@
+====== 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 how to do this even for a batch dataset.
+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. 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 ======
+<code topas>
+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)
+</code>
+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. )
+<code topas>
+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)
+</code>
+====== 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 [[https://drive.google.com/file/d/1G2ws5Anfzaa2NHtMpf6aRU9AHg1c3JVk/view?usp=sharing | this]].