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:
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:
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; } } }
and
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; } }
The following structure must be used in the relevant inp file to achieve the desired output:
/* 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
The final output file should look something like this:
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