data[:, 0] = pl.radians(data[:, 0])
#pl.ion()
R = 1, 1, 3
thickness = 1000
Energy = 10000
#struct = pyasf.unit_cell("1011117")
struct = pyasf.unit_cell("cif/MgO_52026.cif") #MgO
Sub = reflectivity.Substrate(struct)
v_par = sp.Matrix([1, -1, 0])
v_perp = sp.Matrix([1, 1, 0])
Sub.calc_orientation(v_par, v_perp)
layer1 = reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg = float(
layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle = pl.linspace(0.995, 1.005, 501) * thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
Sub.calc_amplitudes(angle, Energy)
XRl = layer1.XR
XRs = Sub.XR
XT = layer1.XT
crystal.print_values(angle, Energy)
Layers=[]
for i in range(4):
layer=reflectivity.Epitaxial_Layer(pyasf.unit_cell("9008845"), thickness[i])
Layers.append(layer)
Layers[i].structure.subs[Layers[i].structure.a]*=(1+strain[i])
psi=0
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation_from_angle(psi, v_perp)
for i in range(4):
Layers[i].calc_orientation_from_angle(psi, v_perp)
crystal=reflectivity.Sample(Sub, *Layers)
crystal.set_Miller(R)
#crystal.calc_layer_Miller()
crystal.calc_g0_gH(Energy)
#thBragg= float(Sub.calc_Bragg_angle(Energy).subs(Sub.structure.subs).evalf())
thBragg=Sub.thetaBragg
angle=pl.linspace(0.9975, 1.0008,501)*thBragg
#XRl = layer1.calc_reflection_amplitude(angle, Energy)
#XRs = Sub.calc_reflection_amplitude(angle, Energy)
# XT = layer1.calc_transmission_amplitude(angle, Energy)
XR=crystal.calc_reflectivity(angle, Energy)
crystal.print_values(angle, Energy)
#pl.plot(data[:,0], data[:,1])
# pl.plot(angle-thBragg,abs(XT)**2)