readme.md

Finite Temperature Properties

Everything we've done so far has in fact been for systems at effectively zero temperature. And even at zero temperature, we haven't taken into account the zero-point motion of the atoms and have treated them as purely classical objects residing at fixed positions.

In actuality, there will be an effect from the zero-point motion of the atoms, and as temperature increases the atoms will vibrate with larger amplitude and this can lead to changes in many properties of a material with temperature. You will learn how the thermodynamic properties of a material can be computed from first principles and be able to predict properties such as the total energy, heat capacity, Helmholtz free energy and Entropy.

Our approach will be to use the type of density functional theory (DFT) and density functional perturbation theory (DFPT) calculations you've already seen, and spend more time analysing the output to produce materials properties. To get the finite temperature properties, we need to get a list of the phonon modes available to the system. The more phonon modes we include in this list, the more accurate the calculation will be, but this comes at the cost of increased computational time. Once the phonon mode list has been obtained, we sum the individual contribution of each phonon mode to get the thermodynamical quantity of interest. This will be done using python.

Example: Total energy for specific temperature in diamond

The total energy due to phonons can be written as

$$E(T) = \sum_{\mathbf{q}\nu}\hbar\omega(\mathbf{q}\nu)\left[\frac{1}{2} + \frac{1}{\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)-1}\right]$$

where the factor $n_{BE}(T) = \frac{1}{\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)-1}$ is recognized as the Bose-Einstein occupation factor.

Notice how the energy requires summing over every single mode $\nu$ and wave-vector $\mathbf{q}$. The amount of wave-vectors that we need to sum over depends on the choice of $\mathbf{q}$-point grid used to run the DFT calculation. For example, in a $10\times10\times10$ grid, you would need to sum over $1000$ vectors. In general terms, finer grids provide better results, but their computation will also take much longer. To do this calculation, we first need to obtain the list of phonon modes

Step 1. Phonon calculations on a fine-grid

We've already done most of the work needed to also calculate phonons on a fine-grid in our previous lab (Lab06/Diamond). This can be done following the q2r.x calculation by choosing some different input options for matdyn.x. Take a look at the input file 05_CD_matdyn-fine.in. The contents are as follows:

 &input
    asr='simple'
    flfrc='CD444.fc'
    flfrq='CD-fine.freq'
    nk1=20,nk2=20,nk3=20
    nosym=.true.
    dos=.true.
 /

This is quite similar to the band plot, but now we're setting nosym to true, choosing a dense q-point grid on which to recalculate our frequencies. Run matdyn.x now with this input file. Please do not forget to copy all the things you did in your previous lab on the same material (Copy the files from (Lab06/Diamond) directory into Lab07/CarbonDiamond. It'll take a bit longer than the band calculation as it is explicitly computing without invoking the symmetry. After it finishes, it will generate the following file: CD-fine.freq. Take a look at the contents of this file. It is organized as such

freq1
freq2
freq3

We will utilize this file to compute several thermodynamic properties using python in the next step.

Step 2. Summing over modes in python

To calculate the total energy due to phonons using python, we will create a simple script that reads in the temperature and a file with the list of frequencies and prints out the energy.

import sys
frequencies = sys.argv[1]
temperature = sys.argv[2]
energy = 0
for frequency in frequencies:

  if abs(frequency) < 1e-5:
    continue

  x = frequency/temperature
  bose = 1.0/(exp(x) - 1)
  energy += x*(0.5 + bose)

print(energy)

Note that this program ignores very small frequencies due to the possibility of dividing by zero.

Thermodynamic properties

Some key quantities are (For reference, see Wikipedia and and the reference therein):

Bose-Einstein distribution

$n_{BE}(T) = \frac{1}{\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)-1}$

Total Energy due to phonons

Total energy due to phonons within harmonic approximation can be written as,

$$E(T) = \sum_{\mathbf{q}\nu}\hbar\omega(\mathbf{q}\nu)\left[\frac{1}{2} + \frac{1}{\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)-1}\right]$$

Constant volume heat capacity

Specific heat at constant volume can be obtained from the total energy calculations:

$$C_{V} = \left(\frac{\partial E}{\partial T} \right ) = \sum_{\mathbf{q}\nu} k_\mathrm{B} \left(\frac{\hbar\omega(\mathbf{q}\nu)}{k_\mathrm{B} T} \right)^2 \frac{\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)}{[\exp(\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)-1]^2}$$

Helmholtz free energy

To compute the Helmholtz free energy, we need the partition function, $Z$.

$$Z = \exp(-\varphi/k_\mathrm{B} T) \prod_{\mathbf{q}\nu} \frac{\exp(-\hbar\omega(\mathbf{q}\nu)/2k_\mathrm{B}T)}{1-\exp(-\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T)}$$

$$H(T) = -k_\mathrm{B} T \ln Z = \varphi + \frac{1}{2} \sum_{\mathbf{q}\nu} \hbar\omega(\mathbf{q}\nu) + k_\mathrm{B} T \sum_{\mathbf{q}\nu} \ln \bigl[1 -\exp(-\hbar\omega(\mathbf{q}\nu)/k_\mathrm{B} T) \bigr]$$

Entropy

Entropy, $S$ can also be computed: $$S = -\frac{\partial H}{\partial T} = \frac{1}{2T} \sum_{\mathbf{q}\nu} \hbar\omega(\mathbf{q}\nu) \coth(\hbar\omega(\mathbf{q}\nu)/2k_\mathrm{B}T)-k_\mathrm{B} \sum_{\mathbf{q}\nu} \ln \left[2\sinh(\hbar\omega(\mathbf{q}\nu)/2k_\mathrm{B}T)\right]$$

Note that the temperature dependence in all these quantities are determined by the Bose-Einstein distribution.

We have implemented these codes using python. For example, you will find a folder Thermodynamics containing a file thermo.py that has all these quantities you need. It reads the phonon bands calculations at a fine-grid and can compute several thermodynamic properties. For the implementation of total energy due to harmonic phonon, look up the function, get_E_T inside the thermo.py file:

 def get_E_T(self):
   """
   Computes total energy at a Temperature
   @output
     E_T, in units of meV
     NOTE: E_T/nkp is returned
   """
   E_T = 0.0
   # For every band n
   for n in range(self.omega_nq.shape[0]):
     # For every band q
     for q in range(self.omega_nq.shape[1]):
       omega = self.omega_nq[n][q]
       E_T = E_T + \
             (omega*\
             (0.5 + self.befactor(omega)))
   return E_T/self.omega_nq.shape[1]

You can compute the total energy at a given temperature by running the compute.py: python compute.py

Try understanding how the calculations are performed and how are they implemented. Note that, all the calculations internaly converts temperature to meV (i.e. $T \to k_{B}T$) and phonon energies to meV (from cm$^{-1}$).

Task

• Run the calculations at a temperature 20 K.
• Compute the temperature dependence of $E, C_{V}, H, S$ for several temperatures, ranging from 10 K to 1000 K in steps of 20 K. What happens to specific heat at low-temperature? You will see a lot more details on your homework. Hint: Write a for loop to do this.
• Plot these data using matplotlib.
• Try increasing the grid-size from $20\times20\times20$ to a larger number and try reducing as well. What happens?

NOTE: An important contribution in the total energy, entropy, etc. are missing in the above calculations: the contribution without the phonons. For example, the total energy of a material at a given temperature is, $$ E(T)= E_{ph}(T) + E_{DFT}$$, where $E_{DFT}$ is the contribution without phonon (sometimes, referred to as lattice energy). Another important point to note is that they are all dependent on the volume of the material. Similarly, the Helmohltz free energy can be written as $H = E_{DFT}+ E_{ph} - TS$. A thermodynamic state is described by two independent parameters, let's take them as $T$ and $V$. The free-energy, $H(T,V)$. So, in principle, one should compute the free-energy for several volumes at any temperature or vice-versa, to represent the thermodynamic state correctly. This leads us to something called, quasi-harmonic approximation. This approximation is a harmonic-phonon-based model used to describe volume-dependent thermal effects, such as the thermal expansion of a material. This approximation assumes that the harmonic approximation holds for every value of the lattice constant, viewed as an adjustable parameter.