Refactoring: Removed references to 'nano' in case of particles, decorators, etc.

App/src/DrawHelper.cpp

@@ -417,7 +417,7 @@ void DrawHelper::DrawMesoCrystal(const MultiLayer *sample)
     const LatticeBasis *lattice_basis = crystal->getLatticeBasis();
     if( !meso ) throw RuntimeErrorException("DrawHelper::DrawMesoCrystal() -> lattice_basis panic");
 
-    const FormFactorFullSphere *ff_sphere = dynamic_cast<const FormFactorFullSphere *>(lattice_basis->getNanoParticle(0)->getFormFactor());
+    const FormFactorFullSphere *ff_sphere = dynamic_cast<const FormFactorFullSphere *>(lattice_basis->getParticle(0)->getFormFactor());
     if( !ff_sphere) throw RuntimeErrorException("DrawHelper::DrawMesoCrystal() -> ff_sphere panic");
 
     double nanoparticle_radius =ff_sphere->getRadius();

App/src/StandardSamples.cpp

@@ -297,10 +297,10 @@ ISample *StandardSamples::IsGISAXS2_CylindersMixture()
 
     // building nano particles
     ParticleBuilder builder;
-    builder.setPrototype(cylinder1,"/NanoParticle/FormFactorCylinder/radius", par1, 0.95);
+    builder.setPrototype(cylinder1,"/Particle/FormFactorCylinder/radius", par1, 0.95);
     builder.plantParticles(particle_decoration);
 
-    builder.setPrototype(cylinder2,"/NanoParticle/FormFactorCylinder/radius", par2, 0.05);
+    builder.setPrototype(cylinder2,"/Particle/FormFactorCylinder/radius", par2, 0.05);
     builder.plantParticles(particle_decoration);
 
     particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());
@@ -377,7 +377,7 @@ ISample *StandardSamples::IsGISAXS3_CylinderBASize()
     StochasticSampledParameter par(StochasticDoubleGaussian(radius, sigma), nbins, nfwhm);
 
     ParticleBuilder builder;
-    builder.setPrototype(nano_particle,"/NanoParticle/FormFactorCylinder/radius", par);
+    builder.setPrototype(nano_particle,"/Particle/FormFactorCylinder/radius", par);
     builder.plantParticles(particle_decoration);
 
     particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());

App/src/TestIsGISAXS10.cpp

@@ -85,10 +85,10 @@ void TestIsGISAXS10::finalise()
 //    substrate_layer.setMaterial(p_substrate_material);
 //    IInterferenceFunction *p_interference_funtion_1 = new InterferenceFunctionNone();
 ////    IInterferenceFunction *p_interference_funtion_2 = new InterferenceFunctionNone();
-//    NanoParticleDecoration particle_decoration;
-//    particle_decoration.addNanoParticle(new NanoParticle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)),
+//    ParticleDecoration particle_decoration;
+//    particle_decoration.addParticle(new Particle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)),
 //                0*Units::nanometer, 0.5);
-//    particle_decoration.addNanoParticle(new NanoParticle(n_particle, new FormFactorPrism3(5*Units::nanometer, 5*Units::nanometer)),
+//    particle_decoration.addParticle(new Particle(n_particle, new FormFactorPrism3(5*Units::nanometer, 5*Units::nanometer)),
 //            0*Units::nanometer, 0.5);
 //    particle_decoration.addInterferenceFunction(p_interference_funtion_1);
 ////    particle_decoration.addInterferenceFunction(p_interference_funtion_2);

Core/Algorithms/inc/DiffuseDWBASimulation.h

@@ -25,7 +25,7 @@ public:
 
     virtual void run();
     size_t getSize() const { return m_np_infos.size(); }
-    void addNanoParticleInfo(DiffuseParticleInfo *p_info);
+    void addParticleInfo(DiffuseParticleInfo *p_info);
     void setRefractiveIndex(complex_t n) { m_refractive_index = n; }
     void setSurfaceDensity(double surface_density) { m_surface_density = surface_density; }
     void rescaleAbundances(double factor);

Core/Algorithms/src/DiffuseDWBASimulation.cpp

@@ -21,7 +21,7 @@ void DiffuseDWBASimulation::run()
     complex_t k_iz = -mp_kz_function->evaluate(-m_alpha_i);
     size_t number_of_nps = m_np_infos.size();
     std::vector<IFormFactor *> form_factors;
-    // collect all nanoparticle formfactors and create dwba formfactors for these
+    // collect all particle formfactors and create dwba formfactors for these
     for (size_t np_index=0; np_index<number_of_nps; ++np_index) {
         ParticleInfo *p_np_info = m_np_infos[np_index];
         Particle *p_np = p_np_info->getParticle()->clone();
@@ -68,7 +68,7 @@ void DiffuseDWBASimulation::run()
     }
 }
 
-void DiffuseDWBASimulation::addNanoParticleInfo(DiffuseParticleInfo *p_info)
+void DiffuseDWBASimulation::addParticleInfo(DiffuseParticleInfo *p_info)
 {
     m_np_infos.push_back(p_info);
 }

Core/Algorithms/src/LayerDecoratorDWBASimulation.cpp

@@ -36,11 +36,11 @@ void LayerDecoratorDWBASimulation::run()
     size_t number_of_particles = p_decoration->getNumberOfParticles();
     std::vector<IFormFactor *> form_factors;
     double total_surface_density = p_decoration->getTotalParticleSurfaceDensity();
-    // collect all nanoparticle formfactors and create dwba formfactors for these
+    // collect all particle formfactors and create dwba formfactors for these
     for (size_t particle_index=0; particle_index<number_of_particles; ++particle_index) {
-//        NanoParticle *p_particle = p_decoration->getNanoParticle(particle_index)->clone();
-//        double depth = p_decoration->getDepthOfNanoParticle(particle_index);
-//        Geometry::Transform3D *transform = p_decoration->getTransformationOfNanoParticle(particle_index);
+//        Particle *p_particle = p_decoration->getParticle(particle_index)->clone();
+//        double depth = p_decoration->getDepthOfParticle(particle_index);
+//        Geometry::Transform3D *transform = p_decoration->getTransformationOfParticle(particle_index);
         Particle *p_particle = p_decoration->getParticleInfo(particle_index)->getParticle()->clone();
         double depth = p_decoration->getParticleInfo(particle_index)->getDepth();
         const Geometry::Transform3D *transform = p_decoration->getParticleInfo(particle_index)->getTransform3D();

Core/Samples/inc/Crystal.h

@@ -10,7 +10,7 @@
 // * mollis quis. Mauris commodo rhoncus porttitor.                   *
 // ********************************************************************
 //! @file   Crystal.h
-//! @brief  Definition of NanoParticleCrystal class
+//! @brief  Definition of Crystal class
 //! @author Scientific Computing Group at FRM II
 //! @date   Jul 12, 2012
 
@@ -20,14 +20,14 @@
 #include "LatticeBasis.h"
 
 //- -------------------------------------------------------------------
-//! @class NanoParticleCrystal
+//! @class Crystal
 //! @brief Definition of a crystal structure with a form factor as a basis
 //- -------------------------------------------------------------------
 class Crystal : public IClusteredParticles
 {
 public:
      //! @brief constructor
-     //! @param nano_particle  the basis which is repeated in the lattice structure
+     //! @param lattice_basis  the basis which is repeated in the lattice structure
      //! @param lattice  the crystal lattice, described by its basis vectors
     Crystal(const LatticeBasis &lattice_basis, const Lattice &lattice);
     ~Crystal();
@@ -43,7 +43,7 @@ public:
             , complex_t ambient_refractive_index) const;
 
     Lattice getLattice() const { return m_lattice; }
-    Particle *createNanoParticle() const { return mp_lattice_basis->clone(); }
+    Particle *createBasis() const { return mp_lattice_basis->clone(); }
 
     const LatticeBasis *getLatticeBasis() const { return mp_lattice_basis; }
 

Core/Samples/inc/CrystalFormFactor.h

@@ -10,7 +10,7 @@
 // * mollis quis. Mauris commodo rhoncus porttitor.                   *
 // ********************************************************************
 //! @file   CrystalFormFactor.h
-//! @brief  Definition of NanoParticleCrystalFormFactor
+//! @brief  Definition of CrystalFormFactor
 //! @author Scientific Computing Group at FRM II
 //! @date   Jul 12, 2012
 

Core/Samples/inc/DiffuseParticleInfo.h

@@ -28,10 +28,10 @@ public:
     //! scale abundance
     void scaleNumberPerMeso(double factor) { m_number_per_meso *= factor; }
 
-    //! set number of nanoparticles per containing mesocrystal
+    //! set number of particles per containing mesocrystal
     void setNumberPerMeso(double n) { m_number_per_meso = n; }
 
-    //! get number of nanoparticles per containing mesocrystal
+    //! get number of particles per containing mesocrystal
     double getNumberPerMeso() const { return m_number_per_meso; }
 protected:
     double m_number_per_meso;

Core/Samples/inc/IClusteredParticles.h

@@ -10,7 +10,7 @@
 // * mollis quis. Mauris commodo rhoncus porttitor.                   *
 // ********************************************************************
 //! @file   IClusteredParticles.h
-//! @brief  Definition of IClusteredNanoParticles interface
+//! @brief  Definition of IClusteredParticles interface
 //! @author Scientific Computing Group at FRM II
 //! @date   Jul 12, 2012
 

Core/Samples/inc/LatticeBasis.h

@@ -39,8 +39,8 @@ public:
     //! return position of element with given index
     kvector_t getPosition(size_t indx) const { return m_positions[check_index(indx)]; }
 
-    //! return nano particle with given index
-    const Particle *getNanoParticle(size_t indx) const { return m_particles[check_index(indx)]; }
+    //! return particle with given index
+    const Particle *getParticle(size_t indx) const { return m_particles[check_index(indx)]; }
 
 private:
     //! check index

Core/Samples/inc/MesoCrystal.h

@@ -21,8 +21,8 @@
 class MesoCrystal : public Particle
 {
 public:
-    MesoCrystal(IClusteredParticles *p_nano_particle_structure, IFormFactor *p_form_factor);
-    MesoCrystal(const IClusteredParticles &nano_particle_structure, IFormFactor &form_factor);
+    MesoCrystal(IClusteredParticles *p_particle_structure, IFormFactor *p_form_factor);
+    MesoCrystal(const IClusteredParticles &particle_structure, IFormFactor &form_factor);
 
     virtual ~MesoCrystal();
     virtual MesoCrystal *clone() const;

Core/Samples/inc/MultiLayer.h

@@ -97,7 +97,7 @@ public:
     //! print class
     friend std::ostream &operator<<(std::ostream &ostr, const MultiLayer &m) { m.print(ostr); return ostr; }
 
-    //! look for the presence of DWBA terms (e.g. included nano particles) and return ISimulation if needed
+    //! look for the presence of DWBA terms (e.g. included particles) and return ISimulation if needed
     virtual MultiLayerDWBASimulation *createDWBASimulation() const;
 
 private:

Core/Samples/inc/ParticleBuilder.h

@@ -10,7 +10,7 @@
 // * mollis quis. Mauris commodo rhoncus porttitor.                   *
 // ********************************************************************
 //! @file   ParticleBuilder.h
-//! @brief  Definition of NanoParticleBuilder class
+//! @brief  Definition of ParticleBuilder class
 //! @author Scientific Computing Group at FRM II
 //! @date   20.08.2012
 

Core/Samples/inc/ParticleDecoration.h

@@ -10,7 +10,7 @@
 // * mollis quis. Mauris commodo rhoncus porttitor.                   *
 // ********************************************************************
 //! @file   ParticleDecoration.h
-//! @brief  Definition of NanoParticleDecoration
+//! @brief  Definition of ParticleDecoration
 //! @author Scientific Computing Group at FRM II
 //! @date   23.05.2012
 
@@ -36,21 +36,21 @@ public:
 	virtual ParticleDecoration *clone() const;
 
 
-    /// add nano particle giving depth and transformation
+    /// add particle giving depth and transformation
     void addParticle(Particle *p_particle, Geometry::Transform3D *transform=0, double depth=0, double abundance=1.0);
     void addParticle(const Particle &p_particle, const Geometry::Transform3D &transform, double depth=0, double abundance=1.0);
 
-    /// add nano particle giving depth
+    /// add particle giving depth
     void addParticle(const Particle &p_particle, double depth=0.0, double abundance=1.0);
     void addParticle(Particle *p_particle, double depth=0.0, double abundance=1.0);
 
-    /// Add nano particle info
+    /// Add particle info
     void addParticleInfo(const ParticleInfo &p_info);
 
 	/// Get number of particles
 	size_t getNumberOfParticles() const { return m_particles.size(); }
 
-    /// get information about nano particle with index
+    /// get information about particle with index
     const ParticleInfo *getParticleInfo(size_t index) const;
 
     /// Get abundance fraction of particle with index
@@ -79,7 +79,7 @@ private:
     ParticleDecoration(const ParticleDecoration &);
     ParticleDecoration &operator=(const ParticleDecoration &);
 
-    //! adding nano particle information with simultaneous registration in parent class
+    //! adding particle information with simultaneous registration in parent class
     void addAndRegisterParticleInfo(ParticleInfo *child)
     {
         m_total_abundance += child->getAbundance();
@@ -95,7 +95,7 @@ private:
     }
 
     std::vector<ParticleInfo *> m_particles;
-    ///< Vector of the types of nano particles
+    ///< Vector of the types of particles
     std::vector<IInterferenceFunction *> m_interference_functions;
     ///< Currently only a scalar interference function (instead of matrix)
     double m_total_abundance;

Core/Samples/inc/ParticleInfo.h

@@ -20,7 +20,7 @@
 
 //- -------------------------------------------------------------------
 //! @class ParticleInfo
-//! @brief holds additional information about particle (used in NanoParticleDecoration)
+//! @brief holds additional information about particle (used in ParticleDecoration)
 //- -------------------------------------------------------------------
 class ParticleInfo : public ICompositeSample
 {

Core/Samples/src/Crystal.cpp

@@ -11,7 +11,7 @@ Crystal::Crystal(const LatticeBasis& lattice_basis,
 : m_lattice(lattice)
 , m_dw_factor(0.0)
 {
-    setName("NanoParticleCrystal");
+    setName("Crystal");
     mp_lattice_basis = lattice_basis.clone();
     registerChild(mp_lattice_basis);
 }

Core/Samples/src/CrystalFormFactor.cpp

@@ -9,7 +9,7 @@ CrystalFormFactor::CrystalFormFactor(
 , m_max_rec_length(0.0)
 {
     m_lattice = p_crystal->getLattice();
-    mp_particle = p_crystal->createNanoParticle();
+    mp_particle = p_crystal->createBasis();
     mp_basis_form_factor = mp_particle->createFormFactor();
     mp_meso_form_factor = meso_crystal_form_factor.clone();
     setAmbientRefractiveIndex(ambient_refractive_index);

Core/Samples/src/LayerDecorator.cpp

@@ -60,7 +60,7 @@ DiffuseDWBASimulation* LayerDecorator::createDiffuseDWBASimulation() const
                          p_info->getAbundance(), *(p_info->getTransform3D()));
         if (p_diffuse_nps) {
             for (size_t j=0; j<p_diffuse_nps->size(); ++j) {
-                p_sim->addNanoParticleInfo((*p_diffuse_nps)[j]);
+                p_sim->addParticleInfo((*p_diffuse_nps)[j]);
                 nps_per_meso += (*p_diffuse_nps)[j]->getNumberPerMeso();
             }
             total_abundance += p_info->getAbundance();

Core/Samples/src/MesoCrystal.cpp

 #include "MesoCrystal.h"
 
-MesoCrystal::MesoCrystal(IClusteredParticles* p_nano_particle_structure,
+MesoCrystal::MesoCrystal(IClusteredParticles* p_particle_structure,
         IFormFactor* p_form_factor)
 : Particle(complex_t(1.0, 0.0))
-, mp_particle_structure(p_nano_particle_structure)
+, mp_particle_structure(p_particle_structure)
 , mp_meso_form_factor(p_form_factor)
 {
     setName("MesoCrystal");
@@ -11,10 +11,10 @@ MesoCrystal::MesoCrystal(IClusteredParticles* p_nano_particle_structure,
     registerChild(mp_meso_form_factor);
 }
 
-MesoCrystal::MesoCrystal(const IClusteredParticles &nano_particle_structure,
+MesoCrystal::MesoCrystal(const IClusteredParticles &particle_structure,
         IFormFactor &form_factor)
 : Particle(complex_t(1.0, 0.0))
-, mp_particle_structure(nano_particle_structure.clone())
+, mp_particle_structure(particle_structure.clone())
 , mp_meso_form_factor(form_factor.clone())
 {
     setName("MesoCrystal");