MesoCrystal C++ functional test

App/src/TestMesoCrystal2.cpp

@@ -140,7 +140,7 @@ void TestMesoCrystal2::draw_results()
     hist_simu->GetYaxis()->SetTitleOffset(1.35);
     hist_simu->DrawCopy("CONT4 Z");
 
-//    OutputDataIOFactory::writeOutputData(*m_simulation->getOutputData(), "meso_simul.txt");
+    OutputDataIOFactory::writeOutputData(*m_simulation->getOutputData(), "meso_simul.txt");
 //    OutputDataIOFactory::writeOutputData(*m_real_data, "meso_real.txt");
 //    OutputData<double> *tmp_real = OutputDataIOFactory::getOutputData("meso_real.txt");
 //    OutputData<double> *tmp_simul = OutputDataIOFactory::getOutputData("meso_simul.txt");

Tests/FunctionalTests/TestCore/IsGISAXS01/IsGISAXS01.cpp

@@ -109,7 +109,8 @@ int FunctionalTests::IsGISAXS01::analyseResults()
 
     std::cout << m_name << " " << m_description << " " <<
         (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS02/IsGISAXS02.cpp

@@ -110,7 +110,8 @@ int FunctionalTests::IsGISAXS02::analyseResults()
     delete reference;
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+
+    return (status_ok ? 0 : 1);
 }
 
 #ifdef STANDALONE

Tests/FunctionalTests/TestCore/IsGISAXS03/IsGISAXS03.cpp

@@ -157,7 +157,7 @@ int FunctionalTests::IsGISAXS03::analyseResults()
     }
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS04/IsGISAXS04.cpp

@@ -123,7 +123,8 @@ int FunctionalTests::IsGISAXS04::analyseResults()
     }
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
+
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS06/IsGISAXS06.cpp

@@ -317,7 +317,7 @@ int FunctionalTests::IsGISAXS06::analyseResults()
     }
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS07/IsGISAXS07.cpp

@@ -138,8 +138,7 @@ int FunctionalTests::IsGISAXS07::analyseResults()
     if( diff > threshold || std::isnan(diff)) status_ok=false;
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
-
+    return (status_ok ? 0 : 1);
 }
 
 #ifdef STANDALONE

Tests/FunctionalTests/TestCore/IsGISAXS08/IsGISAXS08.cpp

@@ -127,8 +127,7 @@ int FunctionalTests::IsGISAXS08::analyseResults()
     }
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
-
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS09/IsGISAXS09.cpp

@@ -129,7 +129,7 @@ int FunctionalTests::IsGISAXS09::analyseResults()
     }
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS10/IsGISAXS10.cpp

@@ -76,7 +76,7 @@ int FunctionalTests::IsGISAXS10::analyseResults()
     delete reference;
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS11/IsGISAXS11.cpp

@@ -79,7 +79,7 @@ int FunctionalTests::IsGISAXS11::analyseResults()
     delete reference;
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/IsGISAXS15/IsGISAXS15.cpp

@@ -88,7 +88,7 @@ int FunctionalTests::IsGISAXS15::analyseResults()
     if( diff > threshold || std::isnan(diff)) status_ok=false;
 
     std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
-    return (int)status_ok;
+    return (status_ok ? 0 : 1);
 }
 
 

Tests/FunctionalTests/TestCore/MesoCrystal1/MesoCrystal1.cpp

+#include "MesoCrystal1.h"
+#include "SampleBuilder.h"
+
+#include "Simulation.h"
+#include "ResolutionFunction2DSimple.h"
+#include "OutputDataIOFactory.h"
+#include "Utils.h"
+#include "Units.h"
+#include "Types.h"
+
+using namespace FunctionalTests;
+
+
+
+MesoCrystal1::MesoCrystal1()
+    : m_test_name("MesoCrystal1")
+    , m_test_description("Meso crystal simulation")
+{ }
+
+
+MesoCrystal1::~MesoCrystal1()
+{ }
+
+
+int MesoCrystal1::MesoCrystal1::run()
+{
+    // setting up sample and simulation
+    SampleBuilder *sample_builder = new SampleBuilder();
+    Simulation *simulation = createSimulation();
+    simulation->setSampleBuilder( sample_builder );
+
+    // loading reference data
+    std::string filename = Utils::FileSystem::GetHomePath() +
+        "/Tests/FunctionalTests/TestCore/MesoCrystal1/mesocrystal1_reference.txt.gz";
+    OutputData<double > *reference_data = OutputDataIOFactory::getOutputData(filename);
+
+    // setting detector axis as in reference data
+    simulation->setDetectorParameters(*reference_data);
+
+    //running simulation
+    simulation->runSimulation();
+    simulation->normalize();
+    OutputData<double > *result = simulation->getOutputDataClone();
+
+    // analysing results
+    double diff = getDifference(result, reference_data);
+    const double threshold(1e-10);
+    bool status_ok(true);
+    if( diff > threshold || std::isnan(diff) ) status_ok=false;
+
+    delete sample_builder;
+    delete simulation;
+    delete result;
+    delete reference_data;
+
+    std::cout << m_test_name << " " << m_test_description << " " <<
+        (status_ok ? "[OK]" : "[FAILED]") << std::endl;
+
+    return (status_ok ? 0 : 1);
+}
+
+
+double MesoCrystal1::getDifference(OutputData<double> *result, const OutputData<double> *reference)
+{
+    double diff(0);
+    // Calculating average relative difference.
+    *result -= *reference;
+    *result /= *reference;
+    for(OutputData<double>::const_iterator it =
+            result->begin(); it!=result->end(); ++it) {
+        diff+= std::fabs(*it);
+    }
+    diff /= result->getAllocatedSize();
+    return diff;
+}
+
+
+// create simulation
+Simulation *MesoCrystal1::createSimulation()
+{
+    Simulation *simulation = new Simulation();
+    simulation = new Simulation();
+    simulation->setBeamParameters(1.77*Units::angstrom, -0.4*Units::degree, 0.0*Units::degree);
+    simulation->setBeamIntensity(5.0090e+12);
+    simulation->setDetectorResolutionFunction(new ResolutionFunction2DSimple(0.0002, 0.0002));
+    return simulation;
+}
+
+
+
+
+#ifdef STANDALONE
+int main()
+{
+    //Utils::EnableFloatingPointExceptions();
+    FunctionalTests::MesoCrystal1 test;
+    return test.run();
+}
+#endif
+

Tests/FunctionalTests/TestCore/MesoCrystal1/MesoCrystal1.h

+#ifndef _TESTMESOCRYSTAL1_H
+#define _TESTMESOCRYSTAL1_H
+
+#include "ISampleBuilder.h"
+#include "OutputData.h"
+#include <string>
+#include <vector>
+
+class ISample;
+class Simulation;
+#include "OutputData.h"
+
+
+namespace FunctionalTests {
+
+//! functional test: mesocrystal simulation
+
+class MesoCrystal1
+{
+public:
+    MesoCrystal1();
+    ~MesoCrystal1();
+
+    //! run fitting
+    int run();
+
+private:
+
+    Simulation *createSimulation();
+    double getDifference(OutputData<double> *result, const OutputData<double> *reference);
+
+    std::string m_test_name;
+    std::string m_test_description;
+};
+
+}
+
+
+#endif

Tests/FunctionalTests/TestCore/MesoCrystal1/MesoCrystal1.pro

+TEMPLATE = app
+CONFIG  += console
+CONFIG  -= qt app_bundle
+QT      -= core gui
+
+include($$PWD/../../../../shared.pri)
+DEFINES += STANDALONE
+LIBS += $$PWD/../../../../lib/libBornAgainCore.so
+
+SOURCES += MesoCrystal1.cpp SampleBuilder.cpp
+HEADERS += MesoCrystal1.h SampleBuilder.h
+
+

Tests/FunctionalTests/TestCore/MesoCrystal1/SampleBuilder.cpp

+#include "SampleBuilder.h"
+#include "FormFactorCylinder.h"
+#include "FormFactorDecoratorDebyeWaller.h"
+#include "MultiLayer.h"
+#include "InterferenceFunctions.h"
+#include "Crystal.h"
+#include "MesoCrystal.h"
+#include "ParticleDecoration.h"
+#include "LayerDecorator.h"
+#include "Units.h"
+#include "MaterialManager.h"
+#include "FormFactorSphereGaussianRadius.h"
+
+using namespace FunctionalTests;
+
+
+SampleBuilder::SampleBuilder()
+    : m_lattice_length_a(6.2091e+00*Units::nanometer)
+    , m_lattice_length_c(6.5677e+00*Units::nanometer)
+    , m_nanoparticle_radius(4.6976e+00*Units::nanometer)
+    , m_sigma_nanoparticle_radius(3.6720e-01*Units::nanometer)
+    , m_meso_height(1.1221e+02*Units::nanometer)
+    , m_meso_radius(9.4567e+02*Units::nanometer)
+    , m_sigma_meso_height(1.3310e+00*Units::nanometer)
+    , 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)
+{
+    init_parameters();
+}
+
+
+// create mesocrystal
+ISample* SampleBuilder::buildSample() const
+{
+    double surface_density = m_surface_filling_ratio/M_PI/m_meso_radius/m_meso_radius;
+    complex_t n_particle(1.0-2.84e-5, 4.7e-7); // data from http://henke.lbl.gov/optical_constants/getdb2.html
+    complex_t avg_n_squared_meso = 0.7886*n_particle*n_particle + 0.2114;
+    complex_t n_avg = std::sqrt(m_surface_filling_ratio*avg_n_squared_meso + 1.0 - m_surface_filling_ratio);
+    complex_t n_particle_adapted = std::sqrt(n_avg*n_avg + n_particle*n_particle - 1.0);
+    FormFactorCylinder ff_cyl(m_meso_height, m_meso_radius);
+    FormFactorDecoratorDebyeWaller ff_meso(ff_cyl.clone(), m_sigma_meso_height*m_sigma_meso_height/2.0, m_sigma_meso_radius*m_sigma_meso_radius/2.0);
+
+    // Create multilayer
+    MultiLayer *p_multi_layer = new MultiLayer();
+    complex_t n_air(1.0, 0.0);
+    complex_t n_substrate(1.0-7.57e-6, 1.73e-7);
+
+    const IMaterial *p_air_material = MaterialManager::getHomogeneousMaterial("Air", n_air);
+    const IMaterial *p_average_layer_material = MaterialManager::getHomogeneousMaterial("Averagelayer", n_avg);
+    const IMaterial *p_substrate_material = MaterialManager::getHomogeneousMaterial("Substrate", n_substrate);
+    Layer air_layer;
+    air_layer.setMaterial(p_air_material);
+    Layer avg_layer;
+    avg_layer.setMaterial(p_average_layer_material);
+    avg_layer.setThickness(m_meso_height);
+    Layer substrate_layer;
+    substrate_layer.setMaterial(p_substrate_material);
+    IInterferenceFunction *p_interference_funtion = new InterferenceFunctionNone();
+    ParticleDecoration particle_decoration;
+    size_t n_max_phi_rotation_steps = 180;
+    size_t n_alpha_rotation_steps = 1;
+
+    double alpha_step = 5.0*Units::degree/n_alpha_rotation_steps;
+    double alpha_start = - (n_alpha_rotation_steps/2.0)*alpha_step;
+
+    double phi_step = 2*M_PI/3.0/n_max_phi_rotation_steps;
+    double phi_start = 0.0;
+    for (size_t i=0; i<n_max_phi_rotation_steps; ++i) {
+        for (size_t j=0; j<n_alpha_rotation_steps; ++j) {
+            Geometry::RotateZ3D transform1(phi_start + (double)i*phi_step);
+            Geometry::RotateY3D transform2(alpha_start + j*alpha_step);
+            Geometry::Transform3D *p_total_transform = new Geometry::Transform3D(transform1);
+            particle_decoration.addParticle(createMesoCrystal(m_lattice_length_a, m_lattice_length_c,
+                    n_particle_adapted,& ff_meso), p_total_transform, m_meso_height);
+        }
+    }
+
+    particle_decoration.setTotalParticleSurfaceDensity(surface_density);
+    particle_decoration.addInterferenceFunction(p_interference_funtion);
+    LayerDecorator avg_layer_decorator(avg_layer, particle_decoration);
+
+    LayerRoughness roughness(m_roughness, 0.3, 500.0*Units::nanometer);
+
+    p_multi_layer->addLayer(air_layer);
+    p_multi_layer->addLayer(avg_layer_decorator);
+    p_multi_layer->addLayerWithTopRoughness(substrate_layer, roughness);
+
+    return p_multi_layer;
+}
+
+
+void SampleBuilder::init_parameters()
+{
+    clearParameterPool();
+    registerParameter("meso_radius",& m_meso_radius);
+    registerParameter("surface_filling_ratio",& m_surface_filling_ratio);
+    registerParameter("meso_height",& m_meso_height);
+    registerParameter("sigma_meso_height",& m_sigma_meso_height);
+    registerParameter("sigma_meso_radius",& m_sigma_meso_radius);
+    registerParameter("lattice_length_a",& m_lattice_length_a);
+    registerParameter("lattice_length_c",& m_lattice_length_c);
+    registerParameter("nanoparticle_radius",& m_nanoparticle_radius);
+    registerParameter("sigma_nanoparticle_radius",& m_sigma_nanoparticle_radius);
+    registerParameter("sigma_lattice_length_a",& m_sigma_lattice_length_a);
+    registerParameter("roughness",& m_roughness);
+}
+
+
+MesoCrystal* SampleBuilder::createMesoCrystal(double stacking_radius_a, double stacking_radius_c, complex_t n_particle,
+        const IFormFactor* p_meso_form_factor) const
+{
+    const Lattice *p_lat = createLattice(stacking_radius_a, stacking_radius_c);
+    kvector_t bas_a = p_lat->getBasisVectorA();
+    kvector_t bas_b = p_lat->getBasisVectorB();
+    kvector_t bas_c = p_lat->getBasisVectorC();
+    Particle particle(n_particle, new FormFactorSphereGaussianRadius(m_nanoparticle_radius, m_sigma_nanoparticle_radius));
+    kvector_t position_0 = kvector_t(0.0, 0.0, 0.0);
+    kvector_t position_1 = 1.0/3.0*(2.0*bas_a + bas_b + bas_c);
+    kvector_t position_2 = 1.0/3.0*(bas_a + 2.0*bas_b + 2.0*bas_c);
+    std::vector<kvector_t> pos_vector;
+    pos_vector.push_back(position_0);
+    pos_vector.push_back(position_1);
+    pos_vector.push_back(position_2);
+    LatticeBasis basis(particle, pos_vector);
+
+    Crystal npc(basis, *p_lat);
+    delete p_lat;
+    double dw_factor = m_sigma_lattice_length_a*m_sigma_lattice_length_a/6.0;
+    npc.setDWFactor(dw_factor);
+    return new MesoCrystal(npc.clone(), p_meso_form_factor->clone());
+}
+
+const Lattice *SampleBuilder::createLattice(double stacking_radius_a, double stacking_radius_c) const
+{
+    Lattice *p_result = new Lattice(Lattice::createTrigonalLattice(stacking_radius_a*2.0, stacking_radius_c*2.0*2.3));
+    p_result->setSelectionRule(SimpleSelectionRule(-1, 1, 1, 3));
+    return p_result;
+}

Tests/FunctionalTests/TestCore/MesoCrystal1/SampleBuilder.h

+#ifndef MESOSAMPLEBUILDER_H
+#define MESOSAMPLEBUILDER_H
+
+#include "ISampleBuilder.h"
+#include "Types.h"
+class MesoCrystal;
+class Lattice;
+class IFormFactor;
+
+namespace FunctionalTests {
+
+//! Builds sample using set of input parameters.
+//! Mesocrystal of cylindrical shape composed by sperical nanoparticles
+//! at FCC lattice points
+class SampleBuilder : public ISampleBuilder
+{
+public:
+    SampleBuilder();
+
+    virtual ~SampleBuilder(){}
+    virtual ISample *buildSample() const;
+
+protected:
+    virtual void init_parameters();
+private:
+    MesoCrystal *createMesoCrystal(double stacking_radius_a, double stacking_radius_c, complex_t n_particle, const IFormFactor *p_meso_form_factor) const;
+    const Lattice *createLattice(double stacking_radius_a, double stacking_radius_c) const;
+    double m_lattice_length_a;
+    double m_lattice_length_c;
+    double m_nanoparticle_radius;
+    double m_sigma_nanoparticle_radius;
+    double m_meso_height;
+    double m_meso_radius;
+    double m_sigma_meso_height;
+    double m_sigma_meso_radius;
+    double m_sigma_lattice_length_a;
+    double m_surface_filling_ratio;
+    double m_roughness;
+};
+
+}
+
+
+
+#endif // SAMPLEBUILDER_H

Tests/FunctionalTests/TestCore/README

@@ -10,14 +10,15 @@ To run tests
 python TestCore.py
 
 List of tests
-IsGISAXS01 - Mixture of cylinders and prisms without interference (IsGISAXS example #1)
-IsGISAXS02 - Mixture cylinder particles with different size distribution (IsGISAXS example #2)
-IsGISAXS03 - Cylinder formfactor in BA and DWBA (IsGISAXS example #3)
-IsGISAXS04 - 1D and 2D paracrystal (IsGISAXS example #4)
-IsGISAXS06 - 2D lattice with different disorder (IsGISAXS example #6)
-IsGISAXS07 - Mixture of different particles defined in morphology file (IsGISAXS example #7)
-IsGISAXS08 - 2DDL paracrystal (IsGISAXS example #8)
-IsGISAXS09 - Pyramids on top of substrate - Rotated pyramids on top of substrate (IsGISAXS example #9)
-IsGISAXS10 - Cylinders with interference on top of substrate (IsGISAXS example #10)
-IsGISAXS11 - Core shell nanoparticles (IsGISAXS example #11)
-IsGISAXS15 - Size spacing correlation approximation (IsGISAXS example #15)
+IsGISAXS01   - Mixture of cylinders and prisms without interference (IsGISAXS example #1)
+IsGISAXS02   - Mixture cylinder particles with different size distribution (IsGISAXS example #2)
+IsGISAXS03   - Cylinder formfactor in BA and DWBA (IsGISAXS example #3)
+IsGISAXS04   - 1D and 2D paracrystal (IsGISAXS example #4)
+IsGISAXS06   - 2D lattice with different disorder (IsGISAXS example #6)
+IsGISAXS07   - Mixture of different particles defined in morphology file (IsGISAXS example #7)
+IsGISAXS08   - 2DDL paracrystal (IsGISAXS example #8)
+IsGISAXS09   - Pyramids on top of substrate - Rotated pyramids on top of substrate (IsGISAXS example #9)
+IsGISAXS10   - Cylinders with interference on top of substrate (IsGISAXS example #10)
+IsGISAXS11   - Core shell nanoparticles (IsGISAXS example #11)
+IsGISAXS15   - Size spacing correlation approximation (IsGISAXS example #15)
+MesoCrystal1 - Meso crystal simulation

Tests/FunctionalTests/TestCore/TestCore.pro

@@ -12,6 +12,7 @@ SUBDIRS += \
     IsGISAXS09 \
     IsGISAXS10 \
     IsGISAXS11 \
-    IsGISAXS15
+    IsGISAXS15 \
+    MesoCrystal1
 
 CONFIG += ordered