Update in PythonAPI

Examples/IsGISAXS_examples/ex-1/sim.txt

-Run App with commandline parameter "isgisaxs10"

Examples/IsGISAXS_examples/ex-10/sim.txt

-Run App with commandline parameter "isgisaxs10"

Examples/UsageWithPython/test_mesocrystal2.py

+#
+# first meso crystal test
+#
+import sys, os
+from numpy import linspace, array, zeros
+import pylab
+from matplotlib.colors import LogNorm
+from math import pi as M_PI
+from cmath import sqrt
+
+import matplotlib.pyplot as plt
+
+sys.path.append(os.path.abspath(
+                os.path.join(os.path.split(__file__)[0],
+                '..', '..', 'lib')))
+
+from libScattCore import *
+
+
+
+# ------------------------
+# building mesocrystal
+# ------------------------
+R = 6.1*nanometer
+meso_radius = 300*nanometer
+surface_filling_ratio = 0.25
+surface_density = surface_filling_ratio/M_PI/meso_radius/meso_radius
+lattice = Lattice.createTrigonalLattice(R*2.0, R*2.0*2.3);
+bas_a = lattice.getBasisVectorA()
+bas_b = lattice.getBasisVectorB()
+bas_c = lattice.getBasisVectorC()
+n_particle = complex(1.0-1.55e-5, 1.37e-6)
+avg_n_squared_meso = 0.7886*n_particle*n_particle + 0.2114;
+n_avg = sqrt(surface_filling_ratio*avg_n_squared_meso + 1.0 - surface_filling_ratio)
+n_particle_adapted = sqrt(n_avg*n_avg + n_particle*n_particle - 1.0)
+
+sphere_ff = FormFactorFullSphere(R)
+particle = NanoParticle(n_particle_adapted, sphere_ff )
+
+position_0 = kvector_t(0.0, 0.0, 0.0)
+position_1 = kvector_t(0.0, 0.0, 0.0)
+position_2 = kvector_t(0.0, 0.0, 0.0)
+
+position_1 = 1.0/3.0*(2.0*bas_a + bas_b + bas_c);
+position_2 = 1.0/3.0*(bas_a + 2.0*bas_b + 2.0*bas_c);
+basis = LatticeBasis()
+basis.addParticle(particle, position_0)
+basis.addParticle(particle, position_1)
+basis.addParticle(particle, position_2)
+
+npc = NanoParticleCrystal(basis, lattice)
+cylinder_ff = FormFactorCylinder(0.2*micrometer, meso_radius)
+meso = MesoCrystal(npc, cylinder_ff )
+
+pyramid_ff = FormFactorPyramid(0.2*micrometer, meso_radius, 84*degree)
+meso2 = MesoCrystal(npc, pyramid_ff )
+
+
+
+# ------------------------
+# building multi layer
+# ------------------------
+
+multi_layer = MultiLayer()
+n_air = complex(1.0, 0.0)
+n_substrate = complex(1.0-7.57e-6, 1.73e-7)
+
+matMng = MaterialManager.instance()
+air_material = matMng.addHomogeneousMaterial("Air", n_air )
+average_layer_material = matMng.addHomogeneousMaterial("Averagelayer", n_avg )
+substrate_material = matMng.addHomogeneousMaterial("Substrate", n_substrate )
+
+air_layer = Layer()
+air_layer.setMaterial(air_material)
+
+avg_layer = Layer()
+avg_layer.setMaterial(average_layer_material, 0.2*micrometer)
+
+substrate_layer = Layer()
+substrate_layer.setMaterial(substrate_material)
+
+interference_function = InterferenceFunctionNone()
+particle_decoration = NanoParticleDecoration()
+
+n_phi_rotation_steps = 1
+n_alpha_rotation_steps =1
+phi_step = 2*M_PI/3.0/n_phi_rotation_steps
+alpha_step = 5*degree/n_alpha_rotation_steps
+
+for i in range(0, n_phi_rotation_steps):
+    for j in range(0, n_alpha_rotation_steps):
+        transform1 = RotateZ3D(i*phi_step)
+        transform2 = RotateZ3D(j*alpha_step)
+        particle_decoration.addNanoParticle(meso, transform1*transform2, 0.2*micrometer, 0.5)
+
+particle_decoration.setTotalParticleSurfaceDensity(surface_density)
+particle_decoration.addInterferenceFunction(interference_function)
+
+avg_layer_decorator = LayerDecorator(avg_layer, particle_decoration)
+
+multi_layer.addLayer(air_layer)
+multi_layer.addLayer(avg_layer_decorator)
+multi_layer.addLayer(substrate_layer)
+
+
+# ------------------------
+# build and run experiment
+# ------------------------
+ai=0.4
+experiment = GISASExperiment()
+experiment.setSample(multi_layer)
+experiment.setDetectorParameters(100, 0.3*degree, 0.073, 100 , -0.4*degree, 0.066)
+experiment.setBeamParameters(1.77*angstrom, -ai*degree, 0.0*degree)
+experiment.setBeamIntensity(1e7)
+experiment.runSimulation()
+experiment.normalize()
+
+
+# -------------------------------------
+# getting output data and making plots
+# -------------------------------------
+#ndim = GetOutputDataNdimensions(experiment)
+x = GetOutputDataAxis(experiment, 0)
+y = GetOutputDataAxis(experiment, 1)
+output = GetOutputData(experiment)
+
+x = x*180./3.1415926
+y = y*180./3.1415926
+
+#fg = pylab.figure()
+#Y,X = pylab.meshgrid(y,x)
+#pylab.pcolormesh(X,Y,output,  norm=LogNorm(1, 1e7) )
+#pylab.ylim([0,y.max()])
+#pylab.xlim([0,x.max()])
+#pylab.colorbar()
+#pylab.show()
+
+im=plt.imshow(output, norm=LogNorm(1, 1e7))
+plt.colorbar(im)
+print( "showing" )
+plt.show()
+