FFT of velocity-auto-correlation to get DOS

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In summary: Best of luck! In summary, the speaker is seeking advice on how to properly Fourier transform a velocity auto-correlation function for phonon density of states calculations from molecular dynamics simulations. They have encountered issues with the behavior at ω → 0 and high frequencies, and have tried two methods (padding the signal and replicating/reflecting the velocity array) without success. The expert suggests looking into windowing functions and checking the simulation parameters for potential improvements, and recommends consulting textbooks, online forums, and research papers for further guidance.
  • #1
tommya
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I'm trying to find out how to "properly" fourier-transform a velocity-auto-correlation function (VAC), for calculation of phonon density of states (DOS), from molecular dynamics simulation.

The problem I'm running into is that my calculated DOS:
a) doesn't fall of to zero as the frequency goes to zero (i.e. as ω → 0)
b) doesn't have a sharp fall-off at some cut-off frequency.

I've tried to read up and found two ways to proceed:
1) Pad the signal, i.e. add suitable number of zeros to the end of the velocity data. This didn't influence a) or b) but only decreased the amplitude of the transformed VAC.
2) DFFT assumes periodic signal. So I to replicated and "reflected" my velocity array in two ways to obtain a periodic signal:
2.1) First doing it "oddly" so that the end-point and the starting point are continuous and have continuous first derivative. --> seem to give nice ω → 0 behavior but influences high frequency in unsatisfactory way.
2.2) Secondly doing it "evenly" so that the end-point and the starting point are continuous but dosen't have continuous first derivative. --> better result for high frequencies but no improvement for ω → 0.

I think the origin to my problem is due to that a VAC have VAC(t→0)=1, VAC(t→∞)=0, and matching these two conditions with the assumption of periodicity in DFFT gives raise to a lot of overtones to try to capture the steplike jump.

Calculating VAC and FFTs thereof is very well established but I haven't been able to find any similar problem description.

Any suggestion for resources to read?
Experience from similar problems?

I'm grateful for all input!
 
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  • #2


Hi there,

Thank you for reaching out and sharing your problem. I am also a scientist working in the field of molecular dynamics simulation and I have encountered similar challenges with Fourier transforming velocity auto-correlation functions for phonon density of states calculations.

Firstly, let me address your two proposed methods for dealing with the issue. Padding the signal with zeros at the end of the velocity data is not an ideal solution as it only decreases the amplitude of the transformed VAC without addressing the underlying problem.

The second method of replicating and reflecting the velocity array to obtain a periodic signal is a more common approach. However, as you have observed, it can lead to undesirable results at high frequencies and does not improve the behavior at ω → 0.

To address your specific concerns, I would suggest looking into windowing functions. These functions are used to reduce the effects of discontinuities in the data, such as the step-like jump in the VAC. Some commonly used windowing functions include Hann, Hamming, and Blackman. By multiplying your velocity data with a suitable windowing function before performing the FFT, you can improve the behavior at ω → 0 and reduce the overtones at high frequencies.

Additionally, I would recommend checking the time-step and length of your simulation. A longer simulation with smaller time-steps can provide more accurate results for the VAC and improve the behavior at ω → 0.

As for resources to read, I would suggest looking into textbooks on molecular dynamics simulation and Fourier analysis. I have also found some helpful discussions and examples on online forums and research papers.

I hope this helps and I wish you all the best in your research. If you have any further questions or would like to discuss this further, please do not hesitate to reach out.
 

1. What is the purpose of performing an FFT on velocity-auto-correlation to obtain DOS?

The Fast Fourier Transform (FFT) is used to convert a time-domain signal, such as velocity-auto-correlation, into its frequency-domain representation. This is useful for obtaining the Density of States (DOS), which is a measure of the number of states per unit of energy that are available to a system. By performing an FFT on the velocity-auto-correlation, we can determine the frequency components that contribute to the DOS.

2. How is the velocity-auto-correlation function related to the DOS?

The velocity-auto-correlation function is the integral of the DOS. This means that by taking the FFT of the velocity-auto-correlation, we are essentially taking the derivative of the DOS. This allows us to obtain the frequency-dependent features of the DOS, such as peaks and bandgaps.

3. What type of systems can be studied using FFT of velocity-auto-correlation to obtain DOS?

The FFT of velocity-auto-correlation can be used to study the DOS of any system that has a time-dependent velocity. This includes a variety of physical and chemical systems, such as molecules, crystals, and fluids.

4. How does the length of the velocity-auto-correlation function affect the accuracy of the FFT and the resulting DOS?

The length of the velocity-auto-correlation function must be long enough to capture the relevant frequency components in order to obtain an accurate DOS. If the function is too short, important features may be missed, leading to an inaccurate DOS. Additionally, a longer function will result in a higher resolution FFT, allowing for more detailed analysis of the DOS.

5. Are there any limitations to using FFT of velocity-auto-correlation to obtain DOS?

One limitation is that the velocity-auto-correlation function must be calculated accurately in order for the FFT to produce a reliable DOS. This can be challenging for complex systems or when dealing with large amounts of data. Additionally, the FFT may not be able to accurately capture very high frequency components, which can affect the accuracy of the resulting DOS.

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