Online Tutorial on

Thermal Analysis
using Phonopy
Tutorial Plan
1 Phonon Basic Theory

2 Phonopy Installation

3 Phonon Bands & DOS

4 Free Energy, Entropy, Heat Capacity

5 Lattice Thermal Conductivity

6 Grüneisen Parameter
Phonon
Basic Theory
(Phonopy Background)
Classical Harmonic Oscillator
Harmonic potential well
1 (
+ = !#
Spring constant, 2
!

# Mass, "

#
Equation of motion: A solution is: with frequency:
' ( #⃗ !
%⃗ = " ( = −!#⃗ # = ./ 012 3=
') "
 we are allowing motion of the masses only
allowing longitudinal motion of the chain,
1D Harmonic Chain
us chapter, if the system is at low enough
a
the potential holding the atoms together
odel ofThe total potential
a solid is a chain energy of the chain:
of masses held to-
!
ng equilibrium +length
262 = 7 a as8#show in (Fig. 9.1.
09: − 8#0
2 κ κ
ntials, and thus the relation
0 to simple har- m m
The force
requently known as a425
on the mass on the
harmonic chain:
chain.
omic potential, we can <+262write the total po- Fig. 9.1 The one-dimensional
%; = − = ! 8#;9: − 8#; + ! 8#;>: − 8#;
monatomic harmonic chain. Each ball
be <# ;
has mass m and each spring has spring
!
The Newton’s
κ equation of motion: constant κ. The lattice constant, or
2
1 − xi ) = (x i+1 − x i − a) spacing between successive masses at
i
2
%; = " 8 #̈ ; = ! 8#;9: + 8#;>: − 28#;
rest, is a.
2
+1 − δx i )
A solution
. to Newton’s equations:
C
8#; = ./ 012>0@AB = ./ 012>0@;D
the chain is then given by
1D Harmonic Chain
Plugging our solution into Newton Eq. of motion we obtain:
−"3(./ 012>0@;D = !./ 012 / >0@ ;9: D + / >0@ ;>: D − 2/ >0@;D
−"3( = ! / >0@D + / 0@D − 2
(
!
3 = 2 − 2 cos HI
"
(
4! ( HI
3 = sin
" 2

We thus obtain the result:

! HI
3=2 sin
" 2
3D Harmonic Crystal
1
The total potential energy: + = 7 7 Φ0O Q, S T0 Q TO S
2
MN 0O
< (+ atomic displacements
Force constant matrix: Φ0O Q, S =
<T0 Q <TO S
1
Hamiltonian: ℋ = V + 7 7 Φ0O QY , SZ T0 QY TO SZ
2
MW ,NX 0O
1 1
Dynamical matrix: [0O \], ^ = 7 Φ0O QY , SZ / 0^` a NX >a MW
"Y "Z S_
MN

• b, c, d , … : Cartesian components • Indices \, ] are used for internal atomic labeling

• Q, S, g , … : Lattice points • ": mass, S_ : number of atoms, a: position vector
Diagonalization problem
Phonon frequencies are obtained as square roots of
Eigenvalues of the dynamical matrix.
[ ^ h ^i = 3 ^i (h ^i
[: dynamical matrix, h: Eigenvector, i: band index

It is convenient for solving Eigenvalue problem using computer:

$ eigvals, eigvecs = numpy.linalg.eigh(dynmat)

Ω ^i / ^i [ ^

After diagonalization:
[ ^ / ^i = Ω ^i / ^i
Frequencies & Eigenvectors
Dynamical Matrix:
[AA 1,1, ^ [Ak 1,1, ^ [Al 1,1, ^ … [Al 1, S, ^
[kA 1,1, ^ [kk 1,1, ^ [kl 1,1, ^ … [kl 1, S, ^
[ ^ = [lA 1,1, ^ [kl 1,1, ^ [ll 1,1, ^ … [ll 1, S, ^
⋮ ⋮ ⋮ ⋱ ⋮
[lA S, 1, ^ [lk S, 1, ^ [ll S, 1, ^ … [ll S, S, ^

Eigenvectors: Frequencies:
": oA 1, ^, i 3( ^, i: 0 0 0 0
": ok 1, ^, i 0 3( ^, i( 0 0 0
/ ^i = ": ol 1, ^, i Ω ^ = 0 0 3( ^, iq 0 0
⋮ 0 0 0 ⋱ 0
"N ol S, ^, i 0 0 0 0 3( ^, iqN
 Quantum Harmonic Oscillator
Quantum Correspondence: If a classical harmonic system has
a normal oscillation mode at frequency 3, the corresponding
Potential energy quantum system will have eigenstates with energy:
Energy

1
t; = ℏ3 4 +
4=3 2
A quantum of vibration is a phonon. Its energy is ℏ3 H .
4=2 Phonon is a BOSON as described by the occupation factor:
1
4=1 4v ]ℏ3 =
/Zℏ1 − 1
4=0 We can use this type of expression to calculate the heat
capacity of our one-dimensional model:
~ ⁄D
r_ 1
Bond length Twxwyz = 7 ℏ3{ 4v ]ℏ3{ +
2
{|>~⁄D
Compression Extension
With ] = 1⁄dv V
We could calculate the heat capacity as Ä = 'T⁄'V.
Ab-initio Thermodynamics
Thermal properties are calculated from frequencies 3 H, i
exp ℏ3 H, i ⁄2dv V
ü Partition function: Å(V) = exp − Tá ⁄dv V à
1 − exp ℏ3 H, i ⁄dv V
@,â

1 1
ü Vibration energy: TÄ V = 7 ℏ3 H, i +
exp ℏ3 H, i ⁄dv V − 1 2
@,â

ü Helmholtz energy: % V = Tá + TÄ V − VãÄ V

TÄ 0å = Ågt
ü Derivatives:
Where:
<T <% Tá = Lattice internal energy Equilibrium DFT
ä = ã= TÄ V = Vibrational internal energy
<V Ä <V
ãÄ V = Vibrational entropy Phonons!
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