User examples modified to correspond to changes in IParticle

Core/Samples/src/MaterialManager.cpp

@@ -68,7 +68,7 @@ const IMaterial *MaterialManager::this_getHomogeneousMaterial(
             HomogeneousMaterial *non_const_mat =
                 const_cast<HomogeneousMaterial *>(old);
             non_const_mat->setRefractiveIndex(refractive_index);
-            msglog(MSG::WARNING) << "MaterialManager::addHomogeneousMaterial()" <<
+            msglog(MSG::ERROR) << "MaterialManager::addHomogeneousMaterial()" <<
                 "-> Redefining refractive index for material '" << name << "'";
         }
         return mat;

Examples/python/ex001_CylindersAndPrisms/CylindersAndPrisms.py

@@ -18,17 +18,19 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     prism_ff = FormFactorPrism3(5*nanometer, 5*nanometer)
-    prism = Particle(n_particle, prism_ff)
+    prism = Particle(mParticle, prism_ff)
     particle_decoration = ParticleDecoration()
     particle_decoration.addParticle(cylinder, 0.0, 0.5)
     particle_decoration.addParticle(prism, 0.0, 0.5)
     interference = InterferenceFunctionNone()
     particle_decoration.addInterferenceFunction(interference)
+    
     # air layer with particles and substrate form multi layer
     air_layer = Layer(mAmbience)
     air_layer.setDecoration(particle_decoration)

Examples/python/ex002_CylindersWithSizeDistribution/CylindersWithSizeDistribution.py

@@ -16,16 +16,17 @@ from utils.show2d import PlotNumpyArray
 def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)
     radius1 = 5.0*nanometer
     radius2 = 10.0*nanometer
     height1 = radius1
     height2 = radius2
     cylinder_ff1 = FormFactorCylinder(height1, radius1)
-    cylinder1 = Particle(n_particle, cylinder_ff1)
+    cylinder1 = Particle(mParticle, cylinder_ff1)
     cylinder_ff2 = FormFactorCylinder(height2, radius2)
-    cylinder2 = Particle(n_particle, cylinder_ff2)  
+    cylinder2 = Particle(mParticle, cylinder_ff2)  
     nbins = 150
     sigma1 = radius1*0.2
     sigma2 = radius2*0.02

Examples/python/ex003_CylinderFormfactor/CylinderFormfactorInBA.py

@@ -19,10 +19,11 @@ def RunSimulation():
      # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     particle_decoration = ParticleDecoration()
     particle_decoration.addParticle(cylinder, 0.0, 1.0)
     interference = InterferenceFunctionNone()

Examples/python/ex003_CylinderFormfactor/CylinderFormfactorInBASize.py

@@ -19,16 +19,16 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
 
     multi_layer = MultiLayer()
 
-    n_particle = complex(1.0-6e-4, 2e-8)
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
     particle_decoration = ParticleDecoration()
     # preparing prototype of nano particle
     radius = 5*nanometer
     sigma = 0.2*radius
-    nano_particle = Particle(n_particle, cylinder_ff)
+    nano_particle = Particle(mParticle, cylinder_ff)
     # radius of nanoparticles will be sampled with gaussian probability
     nbins = 100
     nfwhm = 2

Examples/python/ex003_CylinderFormfactor/CylinderFormfactorInDWBA.py

@@ -20,10 +20,12 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )    
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
     n_particle = complex(1.0-6e-4, 2e-8)    
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     particle_decoration = ParticleDecoration()
     particle_decoration.addParticle(cylinder, 0.0, 1.0)
     interference = InterferenceFunctionNone()

Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_1DDL.py

@@ -18,10 +18,11 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)   
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     interference = InterferenceFunction1DParaCrystal(20.0*nanometer,7*nanometer, 1e3*nanometer)
     particle_decoration = ParticleDecoration()
     particle_decoration.addParticle(cylinder, 0.0, 1.0)

Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_2DDL.py

@@ -18,11 +18,12 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)
 
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
 
     interference = InterferenceFunction2DParaCrystal.createHexagonal(20.0*nanometer, 0.0,20.0*micrometer, 20.0*micrometer)
     pdf = FTDistribution2DCauchy(1.0*nanometer, 1.0*nanometer)

Examples/python/ex006_LatticeWithDisorder/LatticeWithDisorder1.py

@@ -19,6 +19,8 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
     lattice_params = Lattice2DIFParameters()
     lattice_params.m_length_1 = 10.0*nanometer
@@ -36,7 +38,7 @@ def RunSimulation():
 
     n_particle = complex(1.0-6e-4, 2e-8)
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff.clone())
+    cylinder = Particle(mParticle, cylinder_ff.clone())
     position = kvector_t(0.0, 0.0, 0.0)
     particle_decoration = ParticleDecoration()
     particle_info =  PositionParticleInfo(cylinder, position, 1.0)

Examples/python/ex006_LatticeWithDisorder/LatticeWithDisorder2.py

@@ -19,6 +19,8 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+
     # collection of particles
     lattice_params = Lattice2DIFParameters()
     lattice_params.m_length_1 = 10.0*nanometer
@@ -33,12 +35,11 @@ def RunSimulation():
     pdf = FTDistribution2DCauchy(300.0*nanometer/2.0/M_PI, 100.0*nanometer/2.0/M_PI)
     interference.setProbabilityDistribution(pdf)
 
-    n_particle = complex(1.0-6e-4, 2e-8)
     particle_decoration = ParticleDecoration()
     position = kvector_t(0.0, 0.0, 0.0)
     # particle 1
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     position = kvector_t(0.0, 0.0, 0.0)
     particle_info = PositionParticleInfo(cylinder, position, 1.0)
     particle_decoration.addParticleInfo(particle_info)

Examples/python/ex006_LatticeWithDisorder/LatticeWithDisorder3.py

@@ -19,6 +19,8 @@ def RunSimulation():
 # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+
     # collection of particles
     lattice_params = Lattice2DIFParameters()
     lattice_params.m_length_1 = 10.0*nanometer
@@ -34,9 +36,8 @@ def RunSimulation():
     pdf.setGamma(30.0*degree)
     interference.setProbabilityDistribution(pdf)
     
-    n_particle = complex(1.0-6e-4, 2e-8)
     cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
-    cylinder = Particle(n_particle, cylinder_ff)
+    cylinder = Particle(mParticle, cylinder_ff)
     position = kvector_t(0.0, 0.0, 0.0)
     particle_decoration = ParticleDecoration()
     particle_info =  PositionParticleInfo(cylinder, position, 1.0)

Examples/python/ex006_LatticeWithDisorder/LatticeWithDisorder4.py

@@ -51,9 +51,10 @@ def RunSimulation():
 
 # IsGISAXS6 functional test sample builder for varying xi angle
 def buildSample(xi_value):
-    n_particle = complex(1.0-6e-4, 2e-8)
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     air_layer = Layer(mAmbience)
     substrate_layer = Layer(mSubstrate)
     
@@ -74,7 +75,7 @@ def buildSample(xi_value):
     # particle
     ff_cyl = FormFactorCylinder(5.0*nanometer, 5.0*nanometer)
     position = kvector_t(0.0, 0.0, 0.0)
-    cylinder = Particle(n_particle, ff_cyl.clone())
+    cylinder = Particle(mParticle, ff_cyl.clone())
     particle_info = PositionParticleInfo( cylinder, position, 1.0)
     particle_decoration.addParticleInfo(particle_info)
     particle_decoration.addInterferenceFunction(p_interference_function)

Examples/python/ex009_RotatedPyramids/Pyramids.py

@@ -18,10 +18,11 @@ def RunSimulation():
     # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)
     pyramid_ff = FormFactorPyramid(5*nanometer, 5*nanometer, deg2rad(54.73 ) )
-    pyramid = Particle(n_particle, pyramid_ff)
+    pyramid = Particle(mParticle, pyramid_ff)
     interference = InterferenceFunctionNone()
     particle_decoration = ParticleDecoration()
     particle_decoration.addParticle(pyramid, 0.0, 1.0)

Examples/python/ex009_RotatedPyramids/RotatedPyramids.py

@@ -17,10 +17,11 @@ def RunSimulation():
    # defining materials
     mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
     mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 6e-6, 2e-8 )
+    mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+    
     # collection of particles
-    n_particle = complex(1.0-6e-4, 2e-8)   
     pyramid_ff = FormFactorPyramid(5*nanometer, 5*nanometer, deg2rad(54.73 ) )
-    pyramid = Particle(n_particle, pyramid_ff)
+    pyramid = Particle(mParticle, pyramid_ff)
     interference = InterferenceFunctionNone()
     angle_around_z = 45.*degree
     #rotatez3d = RotateZ3D(angle_around_z)

Tests/UnitTests/TestCore/ParticleTest.h

@@ -73,8 +73,6 @@ TEST_F(ParticleTest, ParticleConstructors)
 
     delete p3;
     delete p4;
-
-
 }
 
 

dev-tools/python-bindings/MakePyCore.py

@@ -210,6 +210,8 @@ def ManualClassTunings(mb):
     # including back methods which have been excluded by our pointer policy
     for fun in cl.member_functions():
         if fun.name == "setMaterial":fun.include()
+    for fun in cl.member_functions():
+        print "XXX", fun
     cl.constructors().include() # including back constructors with pointers
     #
     cl = mb.class_("Simulation")