Merge branch 'roughnessbug' into develop

Conflicts:
	GUI/coregui/Models/JobModel.cpp

Core/Algorithms/MultiLayerDWBASimulation.cpp

@@ -82,6 +82,10 @@ void MultiLayerDWBASimulation::run()
     }
 }
 
+// The normalization of the calculated scattering intensities is:
+// For nanoparticles: rho * (scattering cross-section/scattering particle)
+// For roughness: (scattering cross-section of area S)/S
+// This allows them to be added and normalized together to the beam afterwards
 void MultiLayerDWBASimulation::runProtected()
 {
     msglog(MSG::DEBUG2) << "MultiLayerDWBASimulation::runProtected()";

Core/Algorithms/MultiLayerRoughnessDWBASimulation.cpp

@@ -91,9 +91,9 @@ double MultiLayerRoughnessDWBASimulation::evaluate(const SimulationElement& sim_
         for(size_t j=0; j<mp_multi_layer->getNumberOfLayers()-1; j++){
             for(size_t k=0; k<mp_multi_layer->getNumberOfLayers()-1; k++) {
                 if(j==k) continue;
-                crosscorr += rterm[j]*sterm[j]*rterm[k]*
+                crosscorr += rterm[j]*sterm[j]*
                     mp_multi_layer->getCrossCorrSpectralFun(q,j,k)*
-                    std::conj(sterm[k]);
+                    std::conj(rterm[k])*std::conj(sterm[k]);
             }
         }
     }
@@ -114,18 +114,19 @@ complex_t MultiLayerRoughnessDWBASimulation::get_sum4terms(size_t ilayer,
     double wavelength = sim_element.getWavelength();
     double alpha_i = sim_element.getAlphaI();
     double alpha_f = sim_element.getAlphaMean();
-    kvector_t k_i = sim_element.getKI();
-    kvector_t k_f = sim_element.getMeanKF();
-    complex_t qz1 = k_i.z() + k_f.z();
-    complex_t qz2 = k_i.z() - k_f.z();
-    complex_t qz3 = -k_i.z() + k_f.z();
-    complex_t qz4 = -k_i.z() - k_f.z();
 
     const std::unique_ptr<const ILayerRTCoefficients> P_in_coeff(
         mp_specular_info_vector[ilayer + 1]->getInCoefficients(alpha_i, 0.0, wavelength));
     const std::unique_ptr<const ILayerRTCoefficients> P_out_coeff(
         mp_specular_info_vector[ilayer + 1]->getOutCoefficients(alpha_f, 0.0, wavelength));
 
+    complex_t kiz = P_in_coeff->getScalarKz();
+    complex_t kfz = P_out_coeff->getScalarKz();
+    complex_t qz1 = kiz + kfz;
+    complex_t qz2 = kiz - kfz;
+    complex_t qz3 = -qz2;
+    complex_t qz4 = -qz1;
+
     double sigma(0.0);
     if (const LayerRoughness *roughness
         = mp_multi_layer->getLayerBottomInterface(ilayer)->getRoughness()) {

Core/StandardSamples/MesoCrystalBuilder.cpp

@@ -38,7 +38,7 @@ MesoCrystalBuilder::MesoCrystalBuilder()
 , m_sigma_meso_radius(1.3863e+00*Units::nanometer)
 , m_sigma_lattice_length_a(1.1601e+00*Units::nanometer)
 , m_surface_filling_ratio(1.7286e-01)
-, m_roughness(2.8746e+01*Units::nanometer)
+, m_roughness(12e+00*Units::nanometer)
 , m_nphi_rotations(2)
 {
     init_parameters();
@@ -109,7 +109,7 @@ ISample* MesoCrystalBuilder::buildSample() const
                                     n_particle_adapted, &ff_meso) );
             P_meso->setPosition(0.0, 0.0, -m_meso_height);
 //            particle_layout.addParticle(*P_meso, z_rotation);
-            particle_layout.addParticle(*P_meso, 1.0, kvector_t(0,0,0), z_rotation);
+            particle_layout.addParticle(*P_meso, 1.0, kvector_t(0.0, 0.0, 0.0), z_rotation);
         }
     }
 

GUI/coregui/Views/FitWidgets/FitTools.cpp

@@ -175,7 +175,7 @@ void FitTools::onError(const QString &text)
     box.exec();
 }
 
-void FitTools::onUpdatePlots(OutputData<double> *sim, OutputData<double> *chi2)
+void FitTools::onUpdatePlots(OutputData<double> *sim, OutputData<double> *)
 {
     Q_UNUSED(chi2);
     // hack to preserve axis information