Implementing my own absorption macro

jespersimonsen

Hello TOPAS users,

I have been trying to implement this function for the transmission coefficient for a flat plate sample in my refinement:

I have written the macro in a PrivateUserMacro.inc file which I am including in my input file. When I try and run the input file with my I get: "Uninitialized_Variable in equation: d". I have also tried adding my macro to Topas.inc, but I still getting the same error.

What am I doing wrong here to implement the macro? Is there any guide somewhere on how to write macros in TOPAS that I am missing?

Thank you for your help in advance,
Jesper

Here is the macro I wrote (practically a copy of Absorption_With_Sample_Thickness_mm_Shape_Intensity with a new equation):

macro AbsorptionTest(u, uv, d, dv)
{
#m_argu u
#m_argu d
#m_ifarg u ""
#m_unique_not_refine u
#m_endif
scale_pks = (1 - ((2 Cos(2 Th) (Exp(-CeV(u, uv) CeV(d, dv)) - Exp(-CeV(u, uv) CeV(d, dv) / Cos(2 Th)))) / (1 - Cos(2 Th))));
}

and my input file:

'-------------------------------------------------------------------------------
'Jesper Simonsen 01/2025
'Single frame refinement of NIST SRM 660c (LaB6) a = 4.156826 +/- 0.00008 Å
'Setup for DanMAX 2025
'-------------------------------------------------------------------------------
#include O:\Nat_Uorg\MCH\StudentFolders\JesperSimonsen\TOPAS\inps\PrivateUserMacros.inc

r_wp 8.32412739 r_exp 17.4962779 r_p 6.0467918
r_wp_dash 11.0881092 r_p_dash 9.83301832 r_exp_dash 23.3058231
weighted_Durbin_Watson 1.31575213 gof 0.475765614

iters 1000
continue_after_convergence
do_errors

macro data_directory {O:\Nat_Uorg\MCH\DATA_beamtimes\2024_06_MAXIV_DanMAX\calibrants\xy}
macro file_stem {NIST_SRM660c_T492um_Om0_1640}
macro suffix {.xy}

macro file_dets(data_directory, file_stem, suffix) {data_directory##file_stem##suffix}
macro file {file_dets(data_directory, file_stem, suffix)}

macro ResultsName {##file_stem##_Results.txt}

xdd file
x_calculation_step = Yobs_dx_at(Xo);
start_X 4.5
finish_X 23.5

'Background Chebyshev
prm bkg0 14.3535687_0.073959209 prm bkg1 -8.381307910.125189758
prm bkg2 4.86044004_0.115148926 prm bkg3 -2.795833810.0930832915
prm bkg4 1.27888351`_0.0884453891
prm !bkg5 0
prm !bkg6 0
prm !bkg7 0
prm !bkg8 0
prm !bkg9 0
prm !bkg10 0
prm !bkg11 0

bkg =bkg0; =bkg1; =bkg2; =bkg3; =bkg4; =bkg5; =bkg6; =bkg7; =bkg8; =bkg9; =bkg10; =bkg11;
 
prm !wavlen  0.3542449 'Calculated based on wavelength, from PONI: 0.35424490084445085 Å
lam ymin_on_ymax 0.0001 la 1 lo =wavlen; lh 0.0001
Rs 423.28 'Sample to detector distance, from PONI: 0.42327769500162377 m

LP_Factor_Synchrotron_Simple ' Uses the Lorentz_Factor macro, 1 / (Sin(Th)^2 Cos(Th)))

AbsorptionTest(!u, 20, !d, 0.0492)
Zero_Error(zero, 9.80015643e-06`_9.48525348e-05)

str 
	phase_name "LaB6"
	space_group 221
	Cubic(!lpa  4.156826)																	  '4.156826
	
	site La   x 0.000   y 0.000   z 0.000   occ La 1   beq bLa  0.52122`_0.02172
	site B    x 0.198   y 0.500   z 0.500   occ B  1   beq bB  0.07688`_0.13702
 
	scale scale  9.79058328e-06`_5.049e-08
	r_bragg  2.0933997
	
	TCHZ_Peak_Type(
						!pku, 0,
						 pkv, 0.0103738026`_0.000448607496,
						 pkw,-0.00408608128`_4.95131523e-05,
						!pkz, 0,
						!pky, 0,
						!pkx, 0
						)
	Phase_Density_g_on_cm3( 4.71093703)

rowlesmr

You haven't actually declared the u and d prms in that macro. One way to help diagnose issues is to look at the topas.log file after you press the refine button. THat will show you how the input file was parsed and the macros replaced with the low-level keywords.

If you bung in a If_Prm_Eqn_Rpt(u, uv, ) into the macro body, your issue goes away. How that interacts with your #m_unique_not_refine is left as an exercise for the interested reader.

macro AbsorptionTest(u, uv, d, dv)
{
	#m_argu u
	#m_argu d
	#m_ifarg u ""
	#m_unique_not_refine u
	#m_endif
	
	If_Prm_Eqn_Rpt(u, uv, )
	If_Prm_Eqn_Rpt(d, dv, )

	scale_pks = (1 - ((2 Cos(2 Th) (Exp(-CeV(u, uv) CeV(d, dv)) - Exp(-CeV(u, uv) CeV(d, dv) / Cos(2 Th)))) / (1 - Cos(2 Th))));
}

rowlesmr

and the reason yours fails, but Absorption_With_Sample_Thickness_mm_Shape_Intensity works is that Absorption_With_Sample_Thickness_mm_Shape_Intensity calls Absorption_With_Sample_Thickness_mm_Shape, which calls AB which calls If_Prm_Eqn_Rpt

Is there any guide somewhere on how to write macros in TOPAS that I am missing?

The best guide is to read tech ref and topas.inc. Then write/use macros and look at the output in topas.log to see how the macros get turned into the low-level code which is actually interpretted.