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outputting_publication_quality_plots_using_expgui [topas wiki]

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outputting_publication_quality_plots_using_expgui [2020/07/16 10:29] – external edit 127.0.0.1outputting_publication_quality_plots_using_expgui [2025/09/19 15:18] (current) – external edit 127.0.0.1
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 +====== Publication Quality Plots using Liveplot in EXPGUI ======
  
 +
 +Following an update to Liveplot in EXPGUI by Brian Toby, you can now simply produce publication quality plots, with a Yobs, YCalc, Diff, Background, and reflection markers for each phase.  The background output includes all objects in the background.
 +
 +For problems with this, please ask on the forum of this site, rather than contacting Brian Toby.
 +
 +
 +For this to work with TOPAS, output of various parts of information must be combined in one file:
 +
 +
 +  * X, D, Observed, Calculated, Y_error
 +  * H, K, L, M, D, X, Phase_number
 +  * X, D, Background
 +
 +
 +Currently, The background has to be appended to the end of the file as it can not be output at the same time as the calculated pattern.
 +
 +Two macros should be saved to the local.inc file:
 +
 +<code topas>macro OUT_Ycalc_and_Ticks(file)
 +   {
 +    xdd_out file load out_record out_fmt out_eqn
 +       {
 +           " %11.5f  " = X;
 +           " %11.5f  " = 0.5 Lam / Sin(X Pi/360);
 +           " %11.5f  " = Yobs;
 +           " %11.5f  " = Ycalc;
 +           " %11.5f\n" = SigmaYobs;
 +      }
 +
 +      out file append
 +      Out_String("\tHKL reflection markers:\n")
 +
 +      for strs {
 +        phase_out file append load out_record out_fmt out_eqn
 +        {
 +           " %3.0f" = H;
 +           " %3.0f" = K;
 +           " %3.0f" = L;
 +           " %3.0f" = M;
 +           " %11.5f"   = D_spacing;
 +           " %11.5f"   = 2 Rad Th;
 +           " %11.5f\n"   = phase_number;
 +        }
 +      }
 +   } </code>
 +
 +and 
 +
 +<code topas>macro OUT_BKG_Fit_Objs(file)
 +{
 +        iters 0
 +      out "liveplot_output.ascii" append
 +      Out_String("\tBackground fit:\n")
 + 
 +    xdd_out file append load out_record out_fmt out_eqn
 +       {
 +           " %11.5f  " = X;
 +           " %11.5f  " = 0.5 Lam / Sin(X Pi/360);
 +           " %11.5f\n" = Ycalc;
 +      }
 +   }</code>
 +
 +The following structure must be used in the relevant inp file to achieve the desired output:
 +
 +<code topas>
 +/*
 +Normally have the "#define OUT_Ycalc_and_Ticks_" definition activated.
 +To output information (once happy with refinement),
 +          1. Uncomment the "#define OUT_PUT_RUN_" definition
 +          2. Run refinement - this will output X, D, Yobs, Ycalc, and sigYobs, as well as h, k, l, m, D,  X, and phase number.
 +          3. Comment out "#define OUT_Ycalc_and_Ticks_" and uncomment "'#define OUT_BKG_Fit_Objs_" definitions
 +          4. Run refinement - this will do zero iterations and append your calculated background to the previous file.
 +*/
 +
 +'#define OUT_PUT_RUN_                      '' Comment out if no output required '
 +#define OUT_Ycalc_and_Ticks_               '  Normally active'
 +'#define OUT_BKG_Fit_Objs_                 '' Comment previous line, and uncomment here for background '
 +
 +xdd yourdata.xye
 +
 +...
 +...
 +fit_obj
 +...
 +...
 +
 +
 +#ifdef OUT_Ycalc_and_Ticks_                ' This line must be added before the first str section. '
 +
 +str
 +...
 +local !phase_number 1                      ' define for each str section '
 +...
 +
 +str
 +...
 +local !phase_number 2                      ' define for each str section '
 +...
 +
 +/*
 +The following should be placed at the end of all your str parts.
 +There is no need to edit them.
 +*/
 +
 +          #ifdef OUT_PUT_RUN_
 +                    OUT_Ycalc_and_Ticks(liveplot_output.ascii)
 +          #endif
 +          #else
 +          #ifdef OUT_BKG_Fit_Objs_
 +                    #ifdef OUT_PUT_RUN_
 +                    OUT_BKG_Fit_Objs(liveplot_output.ascii)
 +                    #endif
 +          #endif
 +#endif
 +</code>
 +The final output file should look something like this:
 +
 +<code>
 +     5.20000       3.90334    1217.65630    1183.48083      18.30609
 +     5.20400       3.90034    1220.92890    1181.44247      18.23107
 +     5.20800       3.89734    1214.75860    1179.40464      18.27184
 +     ...
 +     ...
 +     ...
 +    29.99200       0.68431     234.54687     245.84482      11.28108
 +    29.99600       0.68422     264.23144     246.44503      11.88096
 +    30.00000       0.68413     245.36497     247.07693      12.07137
 + HKL reflection markers:
 +   0   0   2   2     4.18267     4.85251     1.00000
 +   0   1   1   8     3.51523     5.77458     1.00000
 +   0   1   2   8     2.84214     7.14376     1.00000
 +   ...
 +   ...
 +   ...
 +   3   3   8   8     0.68777    29.83760     1.00000
 +   0   1  12   8     0.68609    29.91244     1.00000
 +   4   4   0   4     0.68481    29.96987     1.00000
 +   1   1   1   8     3.14438     6.45631     2.00000
 +   0   0   2   6     2.72312     7.45643     2.00000
 +   0   2   2  12     1.92553    10.55245     2.00000
 +   ...
 +   ...
 +   ...
 + Background fit:
 +     5.20000       3.90334    1182.94026
 +     5.20400       3.90034    1180.89776
 +     5.20800       3.89734    1178.85567
 +     ...
 +     ...
 +     ...
 +    29.99200       0.68431     236.74789
 +    29.99600       0.68422     236.78480
 +    30.00000       0.68413     236.82286
 +</code>