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MBartkowiakSTFC committed Feb 17, 2025
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## Background

Quasielastic scattering is a special case of inelastic scattering and leads
to a broad peak around $\omega = 0$. Incoherent
Quasielastic scattering is a special case of inelastic scattering with low
energy transfer and leads to a broad peak around $\omega = 0$. Incoherent
QENS can be used to study diffusion and other similar processes. To understand
how QENS is related to the diffusion of a particle we can start from the
self-part of the van Hove function (see **MDANSE Tutorial 2: the van Hove functions**).
Expand Down Expand Up @@ -77,12 +77,12 @@ S_{\mathrm{inc}}(\vec{q}, t) = \frac{1}{\pi} \frac{\hbar \Gamma(q) }{(\hbar \ome
```
here $S_{\mathrm{inc}}(\vec{q}, t)$ is a Lorentzian function with a
half-width at half maximum of $\hbar \Gamma(q)$ where $\Gamma(q) = D q^2$.
The diffusion constant of can be obtained from a QENS experiment by measuring
The diffusion constant can be obtained from a QENS experiment by measuring
$\hbar \Gamma(q)$ of the QENS peak as a function of $q^2$.

**Question 1**: Some other examples where the Gaussian approximation is
exact include the perfect gas, harmonic oscillator and the Debye lattice. For the
perfect gas (free particles) what is $\langle d^{2}_{j}(t) \rangle$ for this
exact include the ideal gas, harmonic oscillator and the Debye lattice. For the
ideal gas (free particles) what is $\langle d^{2}_{j}(t) \rangle$ for this
system given that the particles velocities are distributed following the
Maxwell-Boltzmann distribution? Finally, what is the van Hove function, the
intermediate scattering function and dynamic structure factor for this system?
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Even though our first DISF and GDISF results looked OK we can see now
that they weren't long enough for $q = 10$. Proper convergence testing
is a must for these scattering related calculations.
is a must for these scattering-related calculations.
Compare the differences for the other values of $q$ and have a look at
how this affected the `s(q,w)` results. We will assume
that the `*_long.mda` results are converged and continue with the rest of the
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## Calculate the diffusion constant of Argon

Using our DISF results lets determine the diffusion constant from it.
Using our DISF results, let's determine the diffusion constant from it.
Obviously, we can determine the diffusion constant from a mean squared
displacement calculation using MDANSE but let's see if we understood the
theory and check if the implementation of DISF calculation in MDANSE looks
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</p>

Load the `mdanse_outputs/meansquareddisplacement_long.mda` results into the
plotter and calculated the diffusion constant from $D = \mathrm{MSD}(t) / 6t$
plotter and calculate the diffusion constant from $D = \mathrm{MSD}(t) / 6t$
with the largest value of $t$ from the calculation. You should find that the
results from the GDISF, DISF and MSD are similar but not exactly the same.
Why not, was this expected?
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From the linear fits the diffusion constant from the GDISF and DISF is
$2.46 \times 10^{-5}$ and $2.08 \times 10^{-5}$ $\mathrm{cm}^2\mathrm{s}^{-1}$ respectively. Calculating the diffusion
$2.46 \times 10^{-5}$ and $2.08 \times 10^{-5}$ $\mathrm{cm}^2\mathrm{s}^{-1}$
respectively. Calculating the diffusion
constant from the MSD using $D = \mathrm{MSD}(t) / 6t$ with $t=60000$ fs
gives a diffusion constant of $1.96 \times 10^{-5}$ $\mathrm{cm}^2\mathrm{s}^{-1}$.

We should expect some differences from all three results,
We should expect some differences from all three results;
it is only at specific limits where they will agree with each other.
This occurs when the MSD is calculated at large $t$ and the
diffusion is calculated from QENS peaks at small $q$. Small $q$ values
are required as this is where the nongaussian effects in the DISF are
small and also where the main contribution to the QENS peak for both GDISF and DISF
are from long wavelength dynamics.

Since our linear fits were made over a range of $q$ our calculations
Since our linear fits were made over a range of $q$, our calculations
for the diffusion constant will be inaccurate due to the effects mentioned
above. Try refitting the data using only the smaller values of $q$ you
above. Try refitting the data using only the smaller values of $q$. You
should see closer agreements with the MSD results.


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