Getting non smooth spectrum after performing fft on numerically obtained acceleration data I am trying to calculate the spectrum of Bremmstrahlung, which involves calculating the Fourier transformed acceleration. I am solving a non-linear ODE to numerically calculate the acceleration in the time domain. After taking the Fourier transformation using Numpy's fft, the resultant spectrum looks highly non-smooth and "non-physical" .
I cannot paste the entire code so I am posting what I think is relevant snippet. Can someone point out what I am doing wrong? 

Note: My acceleration is a function of two variables (beta, and b, the impact parameter), and I want to plot it for the different b, and in order to factor out the beta term I am just summing over all the values of acceleration for the different beta, for a given impact parameter b.

Also my spectrum is Fourier transformed acceleration square times a constant factor (Larmor's formula)



'''
Fourier Transformation of the acceleration
'''
N = 2**8
sampling_frequency = 10
a_w_normalized = [[] for a in range(len(impact_parameter))]
a_w =[[] for a in range(len(impact_parameter))]
intensity_normalized = [[] for a in range(len(impact_parameter))]
acc_summed_over_velocity = []
intensity_summed_over_velocity =[]

for index,b in enumerate(impact_parameter):
    acc_sum =[0 for x in range(N)]
    intensity_sum = [0 for x in range(N)] 
    for j in range(len(velocity_z_component)):
        #window_kaiser = signal.kaiser(N, 15)
        #window_hann = signal.hann(N,sym=True)
        window =1
        fft_input = acc_normalized[index][j]*window
        ft_acc_normalized = np.abs(np.fft.fft(fft_input,norm=None))

        acc_sum =np.add(ft_acc_normalized,acc_sum )
        intensity_list = [power_spectrum_factor * (a ** 2) for a in ft_acc_normalized]
        intensity_sum = np.add(intensity_list,intensity_sum)
        intensity_normalized[index].append(intensity_list)
        a_w_normalized[index].append(ft_acc_normalized)
    acc_summed_over_velocity.append(acc_sum)
    intensity_summed_over_velocity.append(intensity_sum *acceleration_factor**2)

#intensity_summed_over_velocity=  ma.masked_less_equal(intensity_summed_over_velocity,1e-5)

'''
Plotting acceleration for selected values of impact paramters in time and frequency domain
'''

if plot is True:
    plt.figure(figsize=(12, 8))
    for i in range(len(impact_parameter)):
        plt.plot(t,acc_timedomain_summed_over_velocity[i], label='b={:.3f}'.format(impact_parameter[i]), )
    plt.legend()
    plt.ylabel(r'$ a(\tilde t) $', fontsize=14)
    plt.xlabel(r'$ \tilde t $', fontsize=14)
    ax.spines['left'].set_position('center')
    ax.spines['bottom'].set_position('center')
    ax.spines['top'].set_visible(False)
    ax.spines['right'].set_visible(False)
    ax.spines['left'].set_smart_bounds(True)
    ax.spines['bottom'].set_smart_bounds(True)
    ax.xaxis.set_ticks_position('bottom')
    ax.yaxis.set_ticks_position('left')
    plt.xticks(fontsize=15)
    plt.yticks(fontsize=15)
    if screening is False:
        plt.title('a(t) vs time without screening',fontsize=15)
        plt.savefig('./Plots/acc_without_screening.png')
    else:
        plt.title('a(t) vs time with screening',fontsize=15)
        plt.savefig('./Plots/acc_with_screening.png')

    '''
    Fourier transformed intensity for different impact paramater
    '''

    plt.figure(figsize=(12, 8))
    freq_normalized = np.fft.fftfreq(N)*(2*np.pi*sampling_frequency)
    for index,b in enumerate(plasma.impact_parameter):
        plt.plot(np.abs(freq_normalized), intensity_summed_over_velocity[index], label=r'$ \tilde b={:.2f}$'.format(b), )
    plt.xlabel(r'$ \tilde \omega $', fontsize=14)
    plt.ylabel(r'$ I_{\omega} $', fontsize=16)
    plt.legend(loc="lower left")
    plt.xscale('log')
    plt.yscale('log')
    plt.xticks(fontsize=12)
    plt.yticks(fontsize=12)

    if screening is False:
        plt.title('Single particle spectrum without screening')
        plt.savefig('./Plots/spectrum_no_screening.png')
    else:
        plt.title('Single particle spectrum with screening')
        plt.savefig('./Plots/spectrum_debye_screening.png')

    plt.show()
Most of the time, a non-parametric PSD estimation based on FFT alone (called a Periodogram) will provide a random looking spectrum of the numerical data.

To reduce those random variations, or to get a smoother looking estimate, you can do one of the two things:


Use Periodogram averaging such as Welch's method.
Use a model based parametric PSD estimate instead.  


Note that the first approach will trade-off spectral resolution for reduced variance, whereas the second method will be high resolution but requires a consistent knowledge of the associated physical model of the process.