Merge branch 'master' of git.jcns.frm2:GISASFW

App/src/TestIsGISAXS10.cpp

@@ -32,8 +32,13 @@ void TestIsGISAXS10::execute()
     experiment.setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree
             , 100, 0.0*Units::degree, 2.0*Units::degree, true);
     experiment.setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
+//    experiment.setBeamIntensity(1e7);
     experiment.runSimulation();
+//    experiment.normalize();
     mp_intensity_output = experiment.getOutputDataClone();
+    double total_count = mp_intensity_output->total();
+    std::cout << "Total count in detector: " << total_count << std::endl;
+    std::cout << "Scattered percentage in detector: " << 100*total_count/experiment.getBeam().getIntensity() << std::endl;
     IsGISAXSTools::drawLogOutputData(*mp_intensity_output, "c1_test_isgisaxs_10", "1D paracrystal islands",
             "CONT4 Z");
     IsGISAXSTools::writeOutputDataToFile(*mp_intensity_output, Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-10/para1dcyl.ima");
@@ -57,6 +62,7 @@ void TestIsGISAXS10::initializeSample()
     NanoParticleDecoration particle_decoration(
                 new NanoParticle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)));
     particle_decoration.addInterferenceFunction(p_interference_funtion);
+//    particle_decoration.setTotalParticleSurfaceDensity(1.0/(20.0*Units::nanometer*20.0*Units::nanometer));
     LayerDecorator air_layer_decorator(air_layer, particle_decoration);
 
     p_multi_layer->addLayer(air_layer_decorator);

App/src/TestMesoCrystal.cpp

@@ -46,12 +46,19 @@ void TestMesoCrystal::execute()
     experiment.setSample(mp_sample);
     experiment.setDetectorParameters(100, 0.3*Units::degree, 0.073
            , 100 , -0.4*Units::degree, 0.066);
+//    experiment.setDetectorParameters(5, 2*Units::degree, 3*Units::degree
+//           , 5 , 1*Units::degree, 2*Units::degree);
 //    experiment.setDetectorResolutionFunction(&testResolutionFunction);
-    experiment.setBeamParameters(1.54*Units::angstrom, -0.4*Units::degree, 0.0*Units::degree);
-    experiment.setBeamIntensity(1e3);
+    experiment.setBeamParameters(1.77*Units::angstrom, -0.4*Units::degree, 0.0*Units::degree);
+    experiment.setBeamIntensity(1e7);
     experiment.runSimulation();
+    double count_before_normalize = experiment.getOutputData()->total();
     experiment.normalize();
     mp_intensity_output = experiment.getOutputDataClone();
+    double total_count = mp_intensity_output->total();
+    std::cout << "Total count in detector: " << total_count << std::endl;
+    std::cout << "Scattered percentage in detector: " << 100*total_count/experiment.getBeam().getIntensity() << std::endl;
+    std::cout << "Total count in detector before normalize: " << count_before_normalize << std::endl;
     IsGISAXSTools::drawLogOutputData(*mp_intensity_output, "c1_test_meso_crystal", "mesocrystal",
             "CONT4 Z");
     IsGISAXSTools::writeOutputDataToFile(*mp_intensity_output, Utils::FileSystem::GetHomePath()+"./Examples/MesoCrystals/mesocrystal.ima");
@@ -105,8 +112,8 @@ void TestMesoCrystal::initializeSample()
 //    IInterferenceFunction *p_interference_funtion = new InterferenceFunction1DParaCrystal(800.0*Units::nanometer,
 //            50*Units::nanometer, 1e7*Units::nanometer);
     NanoParticleDecoration particle_decoration;
-    size_t n_phi_rotation_steps = 11;
-    size_t n_alpha_rotation_steps =3;
+    size_t n_phi_rotation_steps = 1;
+    size_t n_alpha_rotation_steps =1;
     double phi_step = 2*M_PI/3.0/n_phi_rotation_steps;
     double alpha_step = 5*Units::degree/n_alpha_rotation_steps;
     for (size_t i=0; i<n_phi_rotation_steps; ++i) {
@@ -125,4 +132,8 @@ void TestMesoCrystal::initializeSample()
     p_multi_layer->addLayer(avg_layer_decorator);
     p_multi_layer->addLayer(substrate_layer);
     mp_sample = p_multi_layer;
+
+    std::cout << "Average layer index: " << n_avg << std::endl;
+    std::cout << "Adapted particle index: " << n_particle_adapted << std::endl;
+    std::cout << "Substrate layer index: " << n_substrate << std::endl;
 }

Core/Algorithms/inc/DWBAFormFactor.h

@@ -18,7 +18,7 @@
 #include "IDoubleToComplexFunction.h"
 
 
-class DWBAFormFactor: public IFormFactor
+class DWBAFormFactor: public IFormFactorDecorator
 {
 public:
     DWBAFormFactor(IFormFactor* p_form_factor);
@@ -58,7 +58,6 @@ protected:
     void calculateTerms(kvector_t k_i, kvector_t k_f,
             complex_t k_iz, complex_t k_fz) const;
 
-    IFormFactor *mp_form_factor;
     IDoubleToComplexFunction *mp_T;
     IDoubleToComplexFunction *mp_R;
 

Core/Algorithms/inc/FormFactorDecoratorFactor.h

@@ -17,7 +17,7 @@
 #include "IFormFactor.h"
 
 
-class FormFactorDecoratorFactor : public IFormFactor
+class FormFactorDecoratorFactor : public IFormFactorDecorator
 {
 public:
     FormFactorDecoratorFactor(IFormFactor *p_form_factor, complex_t factor);
@@ -30,13 +30,12 @@ public:
 
 protected:
     complex_t m_factor;
-    IFormFactor *mp_form_factor;
 };
 
 inline FormFactorDecoratorFactor::FormFactorDecoratorFactor(
         IFormFactor* p_form_factor, complex_t factor)
-: m_factor(factor)
-, mp_form_factor(p_form_factor)
+: IFormFactorDecorator(p_form_factor)
+, m_factor(factor)
 {
 }
 

Core/Algorithms/inc/FormFactorDecoratorPositionFactor.h

@@ -19,17 +19,13 @@
 
 #include <cmath>
 
-class FormFactorDecoratorPositionFactor : public IFormFactor
+class FormFactorDecoratorPositionFactor : public IFormFactorDecorator
 {
 public:
     FormFactorDecoratorPositionFactor(const IFormFactor &form_factor, kvector_t position);
     virtual ~FormFactorDecoratorPositionFactor();
     virtual FormFactorDecoratorPositionFactor *clone() const;
 
-    virtual void setAmbientRefractiveIndex(complex_t refractive_index) {
-        mp_form_factor->setAmbientRefractiveIndex(refractive_index);
-    }
-
     virtual complex_t evaluate(kvector_t k_i, kvector_t k_f) const;
 
     virtual complex_t evaluateForComplexkz(kvector_t k_i, kvector_t k_f, complex_t k_iz, complex_t k_fz) const;
@@ -39,14 +35,13 @@ public:
     }
 protected:
     kvector_t m_position;
-    IFormFactor *mp_form_factor;
 };
 
 inline FormFactorDecoratorPositionFactor::FormFactorDecoratorPositionFactor(
         const IFormFactor& form_factor, kvector_t position)
-: m_position(position)
+: IFormFactorDecorator(form_factor.clone())
+, m_position(position)
 {
-    mp_form_factor = form_factor.clone();
 }
 
 inline FormFactorDecoratorPositionFactor::~FormFactorDecoratorPositionFactor()

Core/Algorithms/inc/FormFactorDecoratorTransformation.h

@@ -18,7 +18,7 @@
 #include "Transform3D.h"
 
 
-class FormFactorDecoratorTransformation : public IFormFactor
+class FormFactorDecoratorTransformation : public IFormFactorDecorator
 {
 public:
     FormFactorDecoratorTransformation(IFormFactor *p_form_factor, Geometry::Transform3D *transform);
@@ -32,14 +32,13 @@ public:
 protected:
     Geometry::Transform3D *mp_transform;
     Geometry::Transform3D *mp_inverse_transform;
-    IFormFactor *mp_form_factor;
 };
 
 inline FormFactorDecoratorTransformation::FormFactorDecoratorTransformation(
         IFormFactor* p_form_factor, Geometry::Transform3D *transform)
-: mp_transform(transform)
+: IFormFactorDecorator(p_form_factor)
+, mp_transform(transform)
 , mp_inverse_transform(0)
-, mp_form_factor(p_form_factor)
 {
     mp_inverse_transform = new Geometry::Transform3D(mp_transform->inverse());
 }

Core/Algorithms/src/DWBAFormFactor.cpp

 #include "DWBAFormFactor.h"
 
 DWBAFormFactor::DWBAFormFactor(IFormFactor *p_form_factor)
-    : mp_form_factor(p_form_factor)
+    : IFormFactorDecorator(p_form_factor)
     , mp_T(0), mp_R(0)
 {
 }

Core/Samples/inc/IFormFactor.h

@@ -47,6 +47,18 @@ public:
     virtual int getNumberOfStochasticParameters() const { return 0; }
 };
 
+class IFormFactorDecorator : public IFormFactor
+{
+public:
+    IFormFactorDecorator(IFormFactor *p_form_factor) : mp_form_factor(p_form_factor) {}
+    virtual ~IFormFactorDecorator() {}
+    virtual IFormFactorDecorator *clone() const=0;
+
+    virtual void setAmbientRefractiveIndex(complex_t refractive_index) { if (mp_form_factor) mp_form_factor->setAmbientRefractiveIndex(refractive_index); }
+protected:
+    IFormFactor *mp_form_factor;
+};
+
 class IBornFormFactor : public IFormFactor
 {
 public:

Core/Samples/inc/Lattice.h

@@ -31,13 +31,16 @@ public:
     ~Lattice();
 
     //! get basis vector a
-    kvector_t getBasisVectorA() { return m_a1; }
+    kvector_t getBasisVectorA() const { return m_a1; }
 
     //! get basis vector b
-    kvector_t getBasisVectorB() { return m_a2; }
+    kvector_t getBasisVectorB() const { return m_a2; }
 
     //! get basis vector c
-    kvector_t getBasisVectorC() { return m_a3; }
+    kvector_t getBasisVectorC() const { return m_a3; }
+
+    //! get the volume of the unit cell
+    double getVolume() const;
 
     //! get the reciprocal basis vectors
     void getReciprocalLatticeBasis(kvector_t &b1, kvector_t &b2, kvector_t &b3) const;

Core/Samples/inc/NanoParticleCrystalFormFactor.h

@@ -40,6 +40,7 @@ private:
     void calculateLargestReciprocalDistance();
     Lattice m_lattice;
     NanoParticle *mp_nano_particle;
+    IFormFactor *mp_basis_form_factor;
     IFormFactor *mp_meso_form_factor;
     complex_t m_ambient_refractive_index;
     double m_max_rec_length;

Core/Samples/src/Lattice.cpp

@@ -21,6 +21,11 @@ Lattice::~Lattice()
 {
 }
 
+double Lattice::getVolume() const
+{
+    return std::abs(DotProduct(m_a1, CrossProduct(m_a2, m_a3)));
+}
+
 void Lattice::getReciprocalLatticeBasis(kvector_t& b1, kvector_t& b2,
         kvector_t& b3) const
 {

Core/Samples/src/LatticeBasis.cpp

@@ -39,6 +39,7 @@ LatticeBasis* LatticeBasis::clone() const
         p_new->addParticle(*m_particles[index], m_positions[index]);
     }
     p_new->setName(getName());
+    p_new->m_ambient_refractive_index = this->m_ambient_refractive_index;
     return p_new;
 }
 

Core/Samples/src/NanoParticleCrystalFormFactor.cpp

@@ -10,6 +10,7 @@ NanoParticleCrystalFormFactor::NanoParticleCrystalFormFactor(
 {
     m_lattice = p_crystal->getLattice();
     mp_nano_particle = p_crystal->createNanoParticle();
+    mp_basis_form_factor = mp_nano_particle->createFormFactor();
     mp_meso_form_factor = meso_crystal_form_factor.clone();
     setAmbientRefractiveIndex(ambient_refractive_index);
     calculateLargestReciprocalDistance();
@@ -33,6 +34,7 @@ void NanoParticleCrystalFormFactor::setAmbientRefractiveIndex(
         complex_t refractive_index)
 {
     mp_nano_particle->setAmbientRefractiveIndex(refractive_index);
+    mp_basis_form_factor->setAmbientRefractiveIndex(refractive_index);
 }
 
 complex_t NanoParticleCrystalFormFactor::evaluate_for_complex_qz(kvector_t q,
@@ -49,18 +51,18 @@ complex_t NanoParticleCrystalFormFactor::evaluate_for_complex_qz(kvector_t q,
     // perform convolution on these lattice vectors
 //    std::cout << "Number of reciprocal vectors used for convolution: " << rec_vectors.size() << std::endl;
     complex_t result(0.0, 0.0);
-    IFormFactor *p_basis_form_factor = mp_nano_particle->createFormFactor();
     for (std::vector<kvector_t>::const_iterator it = rec_vectors.begin(); it != rec_vectors.end(); ++it) {
         kvector_t q_i = *it;
         kvector_t q_min_q_i = q_real - q_i;
         complex_t q_min_q_i_z = qz - q_i.z();
-        result += p_basis_form_factor->evaluate(q_i, k_zero)
-                *mp_meso_form_factor->evaluateForComplexkz(q_min_q_i, k_zero, q_min_q_i_z, complex_t(0.0, 0.0));
+        complex_t basis_factor = mp_basis_form_factor->evaluate(q_i, k_zero);
+        complex_t meso_factor = mp_meso_form_factor->evaluateForComplexkz(q_min_q_i, k_zero, q_min_q_i_z, complex_t(0.0, 0.0));
+        result += basis_factor*meso_factor;
     }
-    delete p_basis_form_factor;
-    // the transformed delta train gets a factor of (2pi)^3 :
+    // the transformed delta train gets a factor of (2pi)^3/V :
     double pi3 = M_PI*M_PI*M_PI;
-    return 8.0*pi3*result;
+    double volume = m_lattice.getVolume();
+    return 8.0*pi3*result/volume;
 }
 
 void NanoParticleCrystalFormFactor::calculateLargestReciprocalDistance()

Core/Samples/src/WeightedFormFactor.cpp

@@ -38,7 +38,8 @@ complex_t WeightedFormFactor::evaluate(kvector_t k_i, kvector_t k_f) const
 {
     complex_t result(0.0, 0.0);
     for (size_t index=0; index<m_form_factors.size(); ++index) {
-        result += m_weights[index]*m_form_factors[index]->evaluate(k_i, k_f);
+        complex_t ff_evaluate = m_form_factors[index]->evaluate(k_i, k_f);
+        result += m_weights[index]*ff_evaluate;
     }
     return result;
 }

Core/Tools/inc/OutputData.h

@@ -126,6 +126,9 @@ public:
     //! return current value of axis with given name
     template <class U> U getCurrentValueOfAxis(std::string axis_name) const;
 
+    //! get sum of all values in the data structure
+    T total() const;
+
     // ---------
     // modifiers
     // ---------
@@ -311,6 +314,16 @@ template <class U> inline U OutputData<T>::getCurrentValueOfAxis(std::string axi
 }
 
 
+template<class T>
+inline T OutputData<T>::total() const
+{
+    T total = 0;
+    for (size_t i=0; i<m_data_size; ++i) {
+        total += m_data_vector[i];
+    }
+    return total;
+}
+
 // set object into initial state (no dimensions, data)
 template <class T> void OutputData<T>::clear()
 {
@@ -362,5 +375,4 @@ template<class T> inline void OutputData<T>::setRawDataVector(const std::vector<
     m_data_vector = data_vector;
 }
 
-
 #endif // OUTPUTDATA_H