6_bonds_and_spectra.md

from matplotlib import pyplot
from matplotlib.patches import Circle


import numpy as np

from common import draw_classic_axes, configure_plotting
from scipy.integrate import simps
import plotly.graph_objs as go

configure_plotting()

pi = np.pi

Interatomic interaction and molecular spectra

(based on chapters 6.1, 6.3, 8 of the book)

!!! success "Expected prior knowledge"

Before the start of this lecture, you should be able to:

- Apply a Taylor expansion
- Write down Newton's equations of motion of masses on springs
- Define and diagonalize matrices numerically (for the exercises)

!!! summary "Learning goals"

After this lecture you will be able to:

- Explain the origins of interatomic forces
- Compute vibrational spectra of small molecules in 1D
- Formulate Hamiltonians and equations of motion of bulk materials

Adding repulsion

In the previous lecture, we observed that the diatomic molecule's bonding energy decreases with decreasing interatomic distance. However, the trend is unphysical; the two atoms must start repelling eventually (at least when the nuclei get close, but really already much earlier).

Hence from now on, we consider an interatomic repulsion between atoms that get sufficiently close.

First steps towards phonons

Suppose we have an interatomic potential described by the black curve in the figure below. The atoms are in equilibrium at the botom of the interatomic potential. Let the bottom of the potential be

$U = U_0$

at the interatomic distance

$r = a$

.

Near the minimum, the potential is approximately parabolic. We show this by Taylor expanding the interatomic potential around the minimum:

$$U = U_0 + \frac{\kappa}{2!} (r - a)^2 - \frac{\kappa_3}{3!} (r - a)^3 + …$$

Up to second order, the potential is quadratic and gives rise to a harmonic equations of motion. The higher order term

$\kappa_3$

provides anharmonicity.

Rigidity

We are interested in how materials respond to stretch and compression. To that end, assume we have a material with length

$L$

. If the equilibrium distance between atoms is

$a$

, then there are

$N = L/a$

atoms in the material. Now lets slightly stretch the material to length

$L + \delta L$

. Under such strain, the interatomic distance increases by

$\delta r = \delta L/N$

. We don't stretch too hard and therefore the interatomic distance $\delta r $ is small. For this reason, we approximate the interatomic potential around the minimum to be a quadratic potential (Taylor expansion to second-order). Given the quadratic interatomic potential, the material responds with a returning force:

$$F = - \frac{\mathrm{d} U}{\mathrm{d} r} \Bigr|_{r = a+\delta r} = \kappa a \frac{\delta L}{L}.$$

This result directly leads us to a macroscopic material parameter, its compressibility:

$$\beta \equiv -\frac{1}{L} \frac{\partial L}{\partial F}= \frac{1}{\kappa a}.$$

Furthermore, the compressibility allows us to calculate the speed of sound by using the relation:

$$v = \sqrt{\frac{1}{\rho \beta}},$$

where

$\rho$

is the density of the material. Because

$\rho = m/a$

(in 1D), we finally arrive to the expression for the speed of sound, derived from the atomic properties:

$$v = \sqrt{\frac{\kappa a^2}{m}}.$$

This way we can already see how phonon heat capacity emerges from the microscopic material structure.

Thermal expansion

While the quadratic approximation of the interatomic potential is certainly the most important, the anharmonic term

$\kappa_3(r-a)^3/6$

also has physical significance. Let us examine its role visually by comparing the harmonic and the third order approximations in the plot below. Notice that the second-order approximation is symmetric around the minimum while the third-order term is not.

r = np.linspace(-2, 2.5, 750)

a = 0
b = 0
c = 1
d = -0.2

U_quadratic = a + b * r + c * r**2
U_cubic =     a + b * r + c * r**2 + d * r**3

r_min = -2
r_max = 2.5
U_min = -0.2
U_max = 4

E_t_min = 0.4
E_t_max = 3.5
N_values = 20
l_width = 1.5
N_active = 0

# Create figure
fig = go.Figure()

def U_c(r):
    return a + b * r + c * r**2 + d * r**3


def line(E_t):
    right = min(np.roots([c, b, a-E_t]))
    roots = np.roots([d, c, b, a-E_t])
    roots = np.real(roots[np.isreal(roots)])
    roots.sort()
    left = roots[1]
    return [left, right]

def avg_pos_cubic(E_t):
    Z = simps(np.exp(- U_cubic / E_t), r)
    r_avg = simps(r * np.exp(- U_cubic / E_t), r)
    x = r_avg / Z
    return x


# Add traces, one for each slider step
for E_t in np.linspace(E_t_min, E_t_max, N_values):
    avg = avg_pos_cubic(E_t)
    fig.add_trace(
        go.Scatter(
            visible = False,
            x = r,
            y = U_quadratic,
            mode = 'lines',
            line_color = 'blue',
            name = "Quadratic potential",
        ))
    fig.add_trace(
        go.Scatter(
            visible = False,
            x = r,
            y = U_cubic,
            mode = 'lines',
            line_color = 'red',
            name = "Cubic potential",
        ))
    fig.add_trace(
        go.Scatter(
            visible = False,
            x = line(E_t),
            y = [E_t, E_t],
            mode = 'lines',
            line_color = 'black',
            name =  r'Thermal energy level'
        ))
    fig.add_trace(
        go.Scatter(
            visible = False,
            x = [0, 0],
            y = [0, E_t],
            mode = 'lines',
            line_color = 'blue',
            line_dash = 'dot',
            name =  r'$\langle r \rangle$ for the quadratic potential'
        ))
    fig.add_trace(
        go.Scatter(
            visible = False,
            x = [avg, avg],
            y = [U_c(avg), E_t],
            mode = 'lines',
            line_color = 'red',
            line_dash = 'dot',
            name =  r'$\langle r \rangle$ for the cubic potential'
        ))

# Initial starting image
N_trace = int(len(fig.data)/N_values) # Number of traces added per step
for j in range(N_trace):
    fig.data[N_active*N_trace+j].visible = True

# Creation of the aditional images
steps = []
for i in range(int(len(fig.data)/N_trace)):
    step = dict(
        method = "restyle",
        args = [{"visible": [False] * len(fig.data)}],
        value = str(0.1*(i+1))
    )
    for j in range(N_trace):
        step["args"][0]["visible"][N_trace*i+j] = True  # Toggle i'th trace to "visible"
    steps.append(step)

# Creating the slider
sliders = [dict(
    tickcolor = 'White',
    font_color = 'White',
    currentvalue_font_color = 'Black',
    active = N_active,
    name = r'Thermal Energy',
    font_size = 16,
    currentvalue = {"prefix": r'Thermal Energy k_B T: '},
    pad = {"t": 50},
    steps = steps,
)]

# Updating the images for each step
fig.update_layout(
    sliders = sliders,
    showlegend = True,
    plot_bgcolor = 'rgb(254, 254, 254)',
    width = 700,
    height = 580,
    xaxis = dict(
        range=[r_min, r_max],
        visible = True,
        showticklabels = True,
        showline = True,
        linewidth = l_width,
        linecolor = 'black',
        gridcolor = 'white',
        tickfont = dict(size = 16)),
    yaxis = dict(
        range = [U_min, U_max],
        visible = True,
        showticklabels = True,
        showline = True,
        linewidth = l_width,
        linecolor = 'black',
        gridcolor = 'white',
        tickfont = dict(size = 16)),
    title = {'text': r'Thermal expansion of cubic potential',
        'y':0.9,
        'x':0.45,
        'xanchor': 'center',
        'yanchor': 'top'},
    xaxis_title = r'$r$',
    yaxis_title = r'$U [k_b T]$',
)

# Edit slider labels and adding text next to the horizontal bar indicating T_E
for i in range(N_values):
    fig['layout']['sliders'][0]['steps'][i]['label'] = ' %.1f ' % ((E_t_max-E_t_min)*i/(N_values-1) + E_t_min)

fig

The asymmetry due to nonzero

$\kappa_3$

slows the growth of the potential when the interatomic distance increases. On the other hand, when the interatomic distance decreases, the asymmetry accelerates the growth of the potential. Therefore, stretching the material is more energetically favorable than contracting it. As a result, thermal excitations increase the interatomic distance. This gives us a simple model of thermal expansion.

Van der Waals bond

While we focus on the mechanisms of covalent bonding, let us also review another bond type.

A Van der Waals bond originates from an attraction between the dipole moments of two atoms. Suppose we have two atoms separated by an interatomic distance

$r$

. If one atom has a dipole moment

$\mathbf{p_1}$

, it creates an electric field

$$\mathbf{E} = \frac{\mathbf{p_1}}{4\pi \varepsilon_0 r^3}$$

at the position of the other atom. The other atom then develops a dipole moment

$\mathbf{p_2} = \chi \mathbf{E}$

with

$\chi$

the polarizability of the atom.

The potential energy between between the two dipoles is

\begin{align} U(r) &= \frac{-|\mathbf{p_1}||\mathbf{p_2}|}{4\pi\varepsilon_0 r^3}\ &= \frac{-|\mathbf{p_1}| \chi \mathbf{E}}{4\pi\varepsilon_0 r^3}\ &= \frac{-|\mathbf{p_1}|^2 \chi}{(4\pi\varepsilon_0 r^3)^2}\ &\propto \frac{1}{r^6}. \end{align}

The dipole attraction is much weaker than the covalent bonds but drops slower with increasing distance.

??? question "How does the strength of a covalent bond scale with distance?"

The strength of the bond is determined by the interatomic hopping integral $-t = \langle 1 | H | 2 \rangle$. Since the wavefunction of a bound electron typically decays exponentially, so does the overlap integral.

Although the Van der Waals force is weak, it is the only force when there are no chemically active electrons or when the atoms are too far apart to form covalent bonds. Therefore, there are materials where Van der Waals interactions are the dominant interactions. An example of such a material is graphite. The Van der Waals bonds in graphite hold layers of covalently bonded carbon atoms together:

(image source: Wikipedia)

Looking ahead: multiple atoms

So far we have only considered the interatomic interactions between diatomic systems. However, our aim is to understand electrons and phonons in solids containing

$N\to\infty$

atoms.

Let us see what happens when we consider more than two atoms.

Phonons

In order to understand phonons better, we need to understand how a vibrational motion in a solid arises. To that end, we model an array of atoms that are connected by springs with a spring constant

$\kappa$

. Our plan:

• Consider only a harmonic potential acting between the atoms (
  $\kappa$
  is constant)
• Write down equations of motion
• Compute normal modes

For simplicity we consider 1D motion, and let us start with a chain of 3 atoms:

# Defining constants
y_max = 6
max_m = 3

# Off set for the new masses
deviation_arr = [+2, -2, -3.5]

def plot_spring(x1, x2, y, annotation  = r'$\kappa$'):
    L = (x2-x1)

    width, nturns = 1, 10
    N = 1000
    pad = 200

    # Make the spring, unit scale (0 to 1)
    x_spring = np.linspace(0, L, N) # distance along the spring
    y_spring= np.zeros(N)
    y_spring[pad:-pad] = width * np.sin(2*np.pi * nturns * x_spring[pad:-pad]/L)

    x_plot, y_plot = np.vstack((x_spring, y_spring))

    # And offset it
    x_plot += x1
    y_plot += y
    ax.plot(x_plot, y_plot, c='k')
    ax.annotate(annotation, ((x2+x1)/2,y+2), fontsize = 40)


def plot_mass(x,y, annotation = r'$m$'):
    mass = Circle((x, y), .5, fc='k')
    ax.add_patch(mass)
    ax.annotate(annotation, (x-.5,y+2), fontsize = 30)


def make_plot(u, deviation_arr, max_masses = 3):
    # plotting initial masses
    plot_mass(0,0)
    plot_mass(0+deviation_arr[0],u, annotation = '')

    # Plot initial dotted lines
    pyplot.plot((0,0), (0,u-2.5), 'k--')
    pyplot.plot((deviation_arr[0], deviation_arr[0]), (u, u-2.5), 'k--')
#     pyplot.plot((0, deviation_arr[0]), (u-2.5, u-2.5), 'k--')
    pyplot.arrow(0, u-2.5, deviation_arr[0]-.5, 0, fc="k", ec="k", head_width=.25, head_length=.5)

    # Annotate the deviations
    annot_arr = [r'$u_1$', r'$u_2$', r'$u_3$']
    off_set = -1
    ax.annotate(annot_arr[0], (deviation_arr[0]/2+off_set+.4, u-3+off_set), fontsize = 30)

    # Annotate large arrow containing the interatomic distance
    pyplot.arrow( 0, u/3, 9, 0, fc="k", ec="k", head_width=.5, head_length=1)
    ax.annotate(r'$a$', (5, u/3+off_set), fontsize = 30)

    # Plotting other masses and springs
    for j in range(max_masses-1):
        # Equilibrium plot
        plot_spring(10*j,10*(j+1),0)
        plot_mass(10*(j+1), 0)

        # Plot containing deviations from it's equilibrium
        plot_spring(10*j+deviation_arr[j], 10*(j+1)+deviation_arr[j+1], u, annotation = '')
        plot_mass(10*(j+1)+deviation_arr[j+1], u, annotation = '')

        # Plot dotted lines
        pyplot.plot((10*(j+1), 10*(j+1)), (0,u-2.5), 'k--')
        pyplot.plot((10*(j+1)+deviation_arr[j+1], 10*(j+1)+deviation_arr[j+1]), (u, u-2.5), 'k--')
#         pyplot.plot((10*(j+1), 10*(j+1)+deviation_arr[j+1]), (u-2.5, u-2.5), 'k--')
        pyplot.arrow(10*(j+1), u-2.5, (deviation_arr[j+1]+.5), 0, fc="k", ec="k", head_width=.25, head_length=.5)

        # Annotations
        ax.annotate(annot_arr[j+1], (10*(j+1)+deviation_arr[j+1]/2+off_set+.4, u-3+off_set), fontsize = 30)

# Initializing figure
fig, ax = pyplot.subplots(figsize=(10,7))
pyplot.axis('off')
ax.set_xlim((-1,10*(max_m-1)+1))
ax.set_ylim((-y_max-4.5, y_max-2.5))

# Plottig system
make_plot(-y_max, deviation_arr, max_m);

Let us denote the deviation of atom

$i$

from its equilibrium position by

$u_i$

. Newton's equations of motion for this system are then given by

\begin{align} m \ddot{u}_1 &= - \kappa (u_1 - u_2), \ m \ddot{u}_2 &= - \kappa (u_2 - u_1) - \kappa (u_2 - u_3), \ m \ddot{u}_3 &= - \kappa (u_3 - u_2). \end{align}

We write this system of equations in matrix form

$$m \ddot{\mathbf{u}} = -\kappa \begin{pmatrix} 1 & -1 & 0\\ -1 & 2 & -1\\ 0 & -1 & 1 \end{pmatrix}\mathbf{u}$$

We are interested in phonons, patterns of motion that are periodic and have a fixed frequency

$\omega$

. Hence we guess that the motion of the atoms is

$$\mathbf{u}(t) = \mathbf{u}_0 e^{i\omega t}.$$

We substitute our guess into the equations of motion to yield an eigenvalue problem:

$$\omega^2 \mathbf{u}_0 = \frac{\kappa}{m} \begin{pmatrix} 1 & -1 & 0\\ -1 & 2 & -1\\ 0 & -1 & 1 \end{pmatrix}\mathbf{u}_0.$$

The solutions to the eigenvalue problem are phonon modes.

Electrons

We just looked at how a chain of atoms moves. Let us now look at how the electrons of those atoms behave. To that end, we consider a 3 atom chain without any motion.

In order to understand how electrons behave, we use the LCAO model. The LCAO model generalizes in a very simple way. Let us consider the wavefunction:

$$\vert \psi\rangle = \varphi_1 |1\rangle + \varphi_2 |2\rangle + \varphi_3 |3\rangle.$$

Because the three atoms are identical, the onsite energy is the same on all atoms

$\langle 1|H|1 \rangle = \langle2|H|2 \rangle = \langle3|H|3 \rangle = E_0$

. Furthermore, we assume hopping only between the nearest neighbors and assume that it is real valued:

$\langle1|H|2\rangle = \langle2|H|3\rangle = -t$

. We also assume that the orbitals are orthogonal to eachother. Just as we did in the previous lecture, we use the Schrödinger equation

$H |\psi\rangle = E |\psi\rangle$

to set up a system of equations:

\begin{align} E \varphi_1 &= E_0 \varphi_1 - t \varphi_2\ E \varphi_2 &= E_0 \varphi_2 - t \varphi_1 - t \varphi_3\ E \varphi_3 &= E_0 \varphi_3 -t \varphi_2. \end{align}

Again, we write this in a matrix form:

$$E \begin{pmatrix} \varphi_1 \\ \varphi_2 \\ \varphi_3 \end{pmatrix} = \begin{pmatrix} E_0 & -t & 0 \\ -t & E_0 & -t \\ 0 & -t & E_0 \end{pmatrix} \begin{pmatrix} \varphi_1 \\ \varphi_2 \\ \varphi_3. \end{pmatrix}$$

Numerical test

Diagonalizing large matrices is unwieldy, but let's try and check it numerically to see if we notice a trend. Let us first model 3 atoms on a chain.

The eigenfrequencies of the 3 atoms are: [0.0 1.0 1.732050]

def DOS_finite_phonon_chain(n):
    rhs = 2 * np.eye(n) - np.eye(n, k=1) - np.eye(n, k=-1)
    rhs[0, 0] -= 1
    rhs[-1, -1] -= 1
    pyplot.figure()
    pyplot.hist(np.sqrt(np.abs(np.linalg.eigvalsh(rhs))), bins=30)
    pyplot.xlabel("$\omega$")
    pyplot.ylabel("Number of eigenfrequencies")

DOS_finite_phonon_chain(3)

The eigenenergies of the 3 orbitals are: [-1.41421356 0.0 1.41421356]

def DOS_finite_electron_chain(n):
    rhs = 2 * np.eye(n, k = 0) - np.eye(n, k = 1) - np.eye(n, k = -1)
    pyplot.figure()
    pyplot.hist(np.linalg.eigvalsh(rhs), bins=30)
    pyplot.xlabel("$E$")
    pyplot.ylabel("Number of eigenenergies")

DOS_finite_electron_chain(3)

However, 3 atoms are far too few to model an actual solid. Hence, we need 'many more' atoms.

From 3 atoms to 300

Phonon modes of the many atom chain are shown below.

DOS_finite_phonon_chain(300)

We observe that when

$\omega$

is small, we have a constant DOS. This is in line with what we saw in the Debye model. There the DOS of a 1D system was constant! However, when the frequencies are higher, the DOS is not constant anymore.

A plot of electron energies in the many atom chain is shown below.

DOS_finite_electron_chain(300)

The numerical results once again agree with the models we developed earlier. In the Sommerfeld free electron model, the DOS in 1D is proportional to

$\frac{1}{\sqrt{E}}$

. The above histogram also reflects this proportionality for small energies

$E$

. However, when

$E$

is higher, we observe a significant deviation from the

$\frac{1}{\sqrt{E}}$

behavior.

In both cases, we find that our models agree with the numerical results whenever frequencies/energies are small. When the frequencies/energies are high, we find that there is a significant deviation from the Debye/Sommerfeld models. The nature of this deviation is the subject of the next lecture!

Summary

• The interatomic potential describes the rigidity and the thermal expansion of a material.
• The DOS of phonons used in the Debye model is justified by modeling the atoms as particles on a chain connected by a spring in the small
  $\omega$
  limit.
• The DOS of electrons in the Sommerfeld model is justified by modeling electrons as particles that can hop between atoms in the small
  $E$
  limit.

Exercises

Warm-up question

1. What does the LCAO matrix in the lecture notes look like if we also consider a next nearest-neighbour hopping
   $-\tilde{t}$
   ?
2. What does the LCAO matrix look like if we consider six atoms instead of three? You may assume that each atom has a single orbital, onsite energy
   $E_0$
   and the hopping between neighboring atoms
   $-t$
   .
3. How do you determine which part of the interatomic potential is attractive and which is repulsive? You may assume that the interatomic potential is only a function of the interatomic distance
   $r$
   .

Exercise 1: Linear triatomic molecule

Consider carbon dioxide (C0

$_2$

) which is a linear triatomic molecule shown below

??? info "source"

By Jasek FH. - Own work, [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/3.0 "Creative Commons Attribution-Share Alike 3.0"), [Link](https://commons.wikimedia.org/w/index.php?curid=2875238)

1. How many normal modes does this molecule have assuming motion in only 1D? How many normal modes does it have if the atoms can move in all three dimensions?

2. For simplicity, we only consider 1D motion of the atoms. Write down Newton's equations of motion for the atoms, you may assume that the spring constant is the same for both bonds.

3. Consider a symmetric mode, for which the displacements of the oxygen atoms are equal in magnitude and have an opposite direction. Find the eigenfrequency of this mode.

4. Now consider the antisymmetric mode when both of the oxygen atoms move in phase and have the same displacement. Find the ratio between the displacements of the carbon and oxygen atoms. Make sure that the center of mass of the molecule is at rest.

5. Compute the eigenfrequency of the antisymmetric mode.

   ??? hint

    Compare your answers with [Wikipedia](https://en.wikipedia.org/wiki/Triatomic_molecule).

Exercise 2: Lennard-Jones potential

A simple model approximating the interaction between a pair of noble gas atoms such as Argon is the Lennard-Jones potential, in which the potential energy as a function of interatomic distance is

$$U(r) = 4\epsilon\big[\big(\frac{\sigma}{r}\big)^{12}-\big(\frac{\sigma}{r}\big)^6\big]$$

where

$r$

is the distance between two atoms, \epsilon is the depth of the potential well, and \sigma is the distance at which the inter-particle potential is zero.

1. Sketch U(r) as a function of interatomic distance and mark the regions of repulsive and attractive forces acting between the atoms.

2. Find the distance, r_0 (bond length), at which the potential energy is minimal and find the value of the potential energy at this distance (binding energy of the molecule).

3. Expand U(r) in a Taylor series around r_0 up to second order. By considering a second-order (=harmonic) potential approximation around the minimum (r_0), find an expression for the spring constant, \kappa, in terms of \epsilon and \sigma.

4. Using the spring constant \kappa you found earlier, find the ground state energy of the molecule by comparing the molecule to a quantum harmonic oscillator. What is the energy required to break the molecule apart?

   ??? hint

    Because the diatomic molecule is modeled as a one-body problem (in the center of mass rest frame of the molecule), the mass should be replaced by the [reduced mass](https://en.wikipedia.org/wiki/Reduced_mass).

5. What is the approximate number of phonons that can occupy this mode before the potential becomes anharmonic?

Exercise 3: Numerical simulation

For this exercise, use Python (or any other programming environment you are comfortable with).

1. Define a matrix that relates forces to displacements in a linear 1D chain containing N=5 atoms. Repeat for N=200. You may assume that the masses and spring constants are equivalent throughout the chain.

   ??? hint

    In Python use the function [`numpy.diag`](https://docs.scipy.org/doc/numpy/reference/generated/numpy.diag.html).

2. Using numerical diagonalization (numpy.linalg.eigvalsh), compute the eigenfrequencies of this atomic chain. Plot a histogram of these eigenfrequencies.

3. Make the masses of every even atom different from the masses of every odd atom. Compute the eigenfrequencies of this atomic chain and plot a histogram.

4. Now make the masses of even and odd atoms equivalent again. Furthermore, make the spring constants of every even spring different from the odd spring. Compute the eigenfrequencies of this atomic chain and plot a histogram.