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McXtrace Single_crystal: absorption from mu/rho times mass density #2938

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willend merged 2 commits into from
Oct 30, 2026
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McXtrace Single_crystal: absorption from mu/rho times mass density #2938

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74cc36d
McXtrace Single_crystal: absorption from mu/rho times mass density
willend Oct 30, 2026
7bbee98
McXtrace SSRL: update %Example and %Scan references for density-based…
willend Oct 30, 2026
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10 changes: 5 additions & 5 deletions mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_not_white_src/SSRL_bl_11_2_not_white_src.instr
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Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,12 @@
* A jupyter notebook will soon be available regrouping everything.
* You may scan like so for example:
* %Scan: mxrun SSRL_bl_11_2_not_white_src.instr -N31 Etohit=6900,7500 -n1e6 Detector: EnergyMonitor_first_I={
* 4.15283e+11,4.17392e+11,4.14761e+11,4.23379e+11,3.93893e+11,4.24456e+11,4.29582e+11,4.28066e+11,
* 3.79748e+11,3.61699e+11,4.34572e+11,4.42236e+11,4.41343e+11,4.49551e+11,4.23516e+11,3.22482e+11,
* 4.51675e+11,4.52176e+11,4.55269e+11,4.57613e+11,4.60047e+11,4.62858e+11,4.63228e+11,4.65942e+11,
* 3.43853e+11,4.48835e+11,4.73898e+11,4.73046e+11,4.74146e+11,4.79029e+11,4.89455e+11 }
* 1.95875e+11,1.96364e+11,1.96145e+11,2.00332e+11,1.91626e+11,2.01053e+11,2.04481e+11,2.0406e+11,
* 1.97086e+11,1.92699e+11,2.0782e+11,2.112e+11,2.11742e+11,2.1643e+11,2.11361e+11,1.73107e+11,
* 2.18527e+11,2.17407e+11,2.19354e+11,2.20923e+11,2.22335e+11,2.24776e+11,2.25364e+11,2.284e+11,
* 1.82832e+11,2.29721e+11,2.32073e+11,2.31561e+11,2.33712e+11,2.36214e+11,2.41345e+11 }
*
* Example: Etohit=6900 Detector: EnergyMonitor_first_I=4.17271e+11
* Example: Etohit=6900 Detector: EnergyMonitor_first_I=1.94915e+11
*
* %Parameters
* Etohit: [eV.] Energy used to calculate the bragg angle the monochromator is put at. This is the energy we select.
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10 changes: 5 additions & 5 deletions mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@
* A jupyter notebook will soon be available regrouping everything.
* You may scan like so for example:
* %Scan: mxrun SSRL_bl_11_2_white_src.instr -N31 Etohit=6900,7500 detuning_percentage=40 -n1e7 Detector: EnergyMonitor_first_I={
* 3.53209e+09,3.14111e+09,2.29489e+09,2.09782e+09,2.60157e+09,5.02242e+09,6.82888e+09,5.70155e+09,
* 3.63909e+09,3.66976e+09,4.55549e+09,6.4332e+09,6.3975e+09,5.51199e+09,5.81204e+09,5.14268e+09,
* 5.31883e+09,4.70285e+09,4.76321e+09,4.07989e+09,4.65539e+09,4.37134e+09,4.14511e+09,2.04488e+09,
* 4.0761e+09,3.5035e+09,4.15753e+09,3.83112e+09,3.74015e+09,3.70074e+09,3.86447e+09 }
* 7.76648e+08,7.00468e+08,5.4798e+08,4.99356e+08,5.83372e+08,1.43056e+09,1.8697e+09,1.67391e+09,
* 1.1819e+09,1.17907e+09,1.41455e+09,1.77964e+09,1.74873e+09,1.62426e+09,1.66217e+09,1.47739e+09,
* 1.51503e+09,1.37426e+09,1.42738e+09,1.25464e+09,1.37414e+09,1.36235e+09,1.30217e+09,6.18817e+08,
* 1.18021e+09,1.08398e+09,1.20147e+09,1.14165e+09,1.16105e+09,1.14638e+09,1.14533e+09 }
*
* %Example: Etohit=6900 Detector: EnergyMonitor_first_I=1.65837e+10
* %Example: Etohit=6900 Detector: EnergyMonitor_first_I=3.74674e+09
*
* %Parameters
* Etohit: [eV.] Energy used to calculate the bragg angle the monochromator is put at. This is the energy we select.
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15 changes: 12 additions & 3 deletions mcxtrace-comps/samples/Single_crystal.comp
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Expand Up @@ -1203,6 +1203,7 @@ SHARE
struct sx_abs_data {
int muc; // column where mu is to be found
double atomic_weight;
double density; // mass density [g/cm^3]
double delta_prefactor;
t_Table table;
};
Expand All @@ -1219,6 +1220,7 @@ SHARE
exit (-1);
}
abs->muc = (abs->table.columns == 3 ? 1 : 5);
abs->density = 0;

parsing = Table_ParseHeader (abs->table.header, "Z", "A[r]", "rho", NULL);
if (parsing) {
Expand All @@ -1228,7 +1230,11 @@ SHARE
info.mat_weight = strtod (parsing[1], NULL); // aka A[r] in g/mol
if (parsing[2] && !info.rho)
info.rho = strtod (parsing[2], NULL);
if (parsing[2])
abs->density = strtod (parsing[2], NULL); // nominal density of the absorption material
}
if (info.mat_density > 0)
abs->density = info.mat_density; // crystal density from the reflections file wins

if (info.rho && info.mat_weight)
abs->delta_prefactor = NA * (info.rho * 1e-24) / info.mat_weight * 2.0 * M_PI * RE;
Expand Down Expand Up @@ -1540,12 +1546,15 @@ TRACE
event_counter = 0;

V0 = hkl_info.V0;
/* absorption: sigma [cm^2] = atomic_weight [g/mol] / NA [1/mol] * mu [cm^2/g],
then * 1e26 -> [fm^2] and / V0 [Angs^3] -> [1/m]. Independent of the barns flag. */
/* absorption: linear attenuation = mu [cm^2/g] * density [g/cm^3] = [1/cm], * 100 -> [1/m].
Without a density, fall back to one atom of atomic_weight per unit cell V0. */
abs_xlen = 0;
if (abs_info.muc) {
double mu = Table_Value (abs_info.table, ki * K2E, abs_info.muc);
abs_xlen = abs_info.atomic_weight / NA * mu * 1e26 / V0;
if (abs_info.density > 0)
abs_xlen = mu * abs_info.density * 100;
else
abs_xlen = abs_info.atomic_weight / NA * mu * 1e26 / V0; // ponytail: per-atom weight over full cell, too weak for multi-atom cells; give a density
}

/*look into Compton scattering*/
Expand Down
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