Coarse roughness at exit

[AnnieStephenson]

Course roughness at exit should be implemented. This may not have a large effect on overall reflectance but it will impact exit angle significantly, thus affecting goniometer detection results. Below is a start at implementing this exit coarse rougness. It has been commented out in detector.py for quite some time, and I've now removed it.

    # TODO For implementing coarse roughness when the trajectories exit the sample
    nev = z.shape[0]    
    # sample the surface roughness angles theta_a
    if coarse_roughness == 0.:
        theta_a = np.zeros(ntraj)
    else:
        theta_a_full = np.linspace(0.,np.pi/2, 500)
        prob_a = P_theta_a(theta_a_full,coarse_roughness)/sum(P_theta_a(theta_a_full,coarse_roughness))
        
        if np.isnan(prob_a).all(): 
            theta_a = np.zeros(ntraj)
        else: 
            theta_a = np.array([np.random.choice(theta_a_full, ntraj, p = prob_a) for i in range(1)]).flatten()
    
    # In case the surface is rough, then find new coordinates of initial 
    # directions after rotating the surface by an angle theta_a around y axis
    sintheta_a = np.tile(np.sin(theta_a), (nev, 1))
    costheta_a = np.tile(np.cos(theta_a), (nev, 1))
    
    kx_rot = costheta_a * kx - sintheta_a * kz
    ky_rot = ky.copy()
    kz_rot = sintheta_a * kx + costheta_a * kz

    # correct for non-TIR fresnel reflection upon exiting
    reflected = refl_weights * fresnel_pass_frac(kz_rot, refl_indices, n_sample, n_front, n_medium)#<= uncomment
    transmitted = trans_weights * fresnel_pass_frac(kz_rot, trans_indices, n_sample, n_back, n_medium)
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    # For implementing coarse roughness when the trajectories exit the sample
    #trans_detected = detect_correct(kz_rot, transmitted, trans_indices, n_sample, n_medium, detection_angle)
    #refl_detected = detect_correct(kz_rot, reflected, refl_indices, n_sample, n_medium, detection_angle)
#------------------------------------------------------------------------------