Depaitment of Applied Physics, Chalmeis, Gteboig

Maitin Petisme, Paul Eihait, 2014-02-09

Free energy calculations
ln this exeicise you will use the embedded atom method (EAM) potential foi aluminum developed in the
ist task. ln piinciple you can use youi own veision but foi simplyng debugging and comaiison we
iathei have you use the potential le piovided on the homepage. You will peifoim moleculai dynamics
(MD) simulations to test the potential and caiiy out fiee eneigy calculations.
1 Free energy calculation
1.1 ermodynamic integration, -integration
We can couple oui system the one we seek the fiee eneigy of with potential eneigy U
1
to a iefeience
system with potential eneigy U
0
, foi which the fiee eneigy is known. Tis will enable us to nd the fiee
eneigy F of oui system.
We begin by constiucting the potential eneigy of the coupled system
U() = U
0
+ (U
1
U
0
), 0 1, (1)
which inteipolates between the iefeience system and the system of inteiest as iuns fiom 0 to 1. Te
canonical paitition function (NVT ensamble) of the coupled system is
Z

dq
3N
dp
3N
exp [U()/k
B
T] . (2)
Ten we can wiite the deiivative of the fiee eneigy of the coupled system as an ensemble aveiage
(
F

)
NVT
= k
B
T

ln Z

=
k
B
T
Z
Z

dq
3N
dp
3N U

exp [U/k
B
T]

dx dp exp [U/k
B
T]
=

. (3)
We can thus obtain the fiee eneigy dieience between the iefeience system and the system of inteiest by
integiation
F
1
= F
0
+

1
0
d

= F
0
+

1
0
d U
1
U
0

. (4)
By peifoiming e.g., a moleculai dynamics (MD) simulation with the potential eneigy U given by Eq. (1)
we can sample the quantity U
1
U
0
foi dieient values of and then evaluate numeiically the integial
in Eq. (4).
1.2 e Einstein crystal
ln the Einstein ciystal all atoms aie auached to theii equilibiium lauice positions with spiings with a
spiing constant . Te potential eneigy foi such a system with N atoms is
U
ES
({q
i
}) =

2
3N

i=1
(
q
i
q
(0)
i
)
2
. ()
To obtain conveiged iesults with the least eoit it is advisable to keep the integiand in Eq. (4) smooth
and the integial small. Tis can be accomplished by choosing such that it yields a similai mean squaie
displacement as the system of inteiest. Tis can be iealized by employing the ielation
= 2kT/

r
2

. ()
Additional issues can be encounteied in the limit 0, i.e. when sampling U
1
U
0
fioman ensemble
that is dominated by the Einstein ciystal. Fiistly, in this limit the coupling between dieient modes is veiy
small, which can slow down equilibiation and iequiie longei simulation times to conveige U
1
U
0

.
Secondly, one might obseives a steeping of the integiand. Tis eect is due to the lack of inteiatomic
1
iepulsion in the Einstein ciystal. lf this pioblem is encounteied it may be advisable to choose somewhat
stiei spiings than what is obtained fiom Eq. ().
Foi numeiical ieasons, one uses the xed centei of mass constiaint. ln this case the Helmholtz eneigy
of the system of inteiest is given by [1]
F
NkT
=
3
2
ln
k
2
T
2
m

1
NkT

1
0
d U
ief
U
3
2N
ln

2kT

3
2N
ln N +
1
N
ln
N
V
, ()
wheie N is the numbei of atoms, V the system volume, T the tempeiatuie, m the atom mass, Plancks
constant, and k Boltzmanns constant.
2 Melting point calculation
ln the co-existence method, a system is set up so that a solidliquid inteiface is obtained at a tempeiatuie
T. Ten an NPT simulation is peifoimed, and if the system is below the melting point, the ciystalline
phase will giow and the system will solidify. ln the othei case the system will melt. Tis method allow
one to deteimine uppei and lowei bounds on the melting tempeiatuie.
A moie accuiate value can be obtained using NPH simulations (constant enthalpy), see e.g. Mendelev
et al. [2]. lf the aveiage kinetic eneigy and thus the aveiage tempeiatuie in the system deviates stiongly
fiom the actual melting tempeiatuie the system will still eithei melt oi solidify. lf the aveiage kinetic
eneigy, which is deteimined by the initial conditions of the MD simulation, is, howevei, suciently close
to the melting tempeiatuie the system will establish an equilibiium between solid and liquid and the
aveiage tempeiatuie will then yield the melting point.
Figuie 1 A snapshot fiom a co-existence melting point simulation.
2
Task
1. Use ivs to compute the lauice theimal expansion up to 900 K. Compaie with expeiimental
iesults fiom liteiatuie.
2. Use the co-existence method with the NPH ensamble to deteimine the melting point with a proper
error estimate foi youi Al potential.
An example ivs sciipt that you may nd useful is piovided.
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You should visualize the dump les of the atomic cooidinates in oidei to ensuie that solid and
liquid aie indeed in equilibiium. To this end it is stiongly to use the veiy poweiful visualization
and analysis sofwaie ovi1o.
2
3. Deteimine the entiopy of fusion, i.e. the inciease in entiopy upon melting. Use u calculations
using the NPT ensamble foi two bulk systems at the melting point. Also deteimine the volume
change upon melting. Find expeiimental values and compaie.
4. Using the conguiations obtained in the pievious task, calculate the cooidination numbeis foi the
solid and the melt. Te (ist) cooidination numbei n
1
is dened thiough the iadial distiibution
function g(r) as
n
1
= 4

r
1
r
0
r
2
g(r) dr (8)
wheie r
0
is wheie g(r) is ist non-zeio, r
1
is at the ist minimum of g(r), and is the density of
paiticles N/V. To obtain g(r) it is possible to use ovi1o oi the ivs compute command rdf.
3
. Te paitition function and fiee eneigy foi a classical haimonic oscillatoi aie given by
Z = k
B
T/, and F = k
B
T ln(/kT), (9)
iespectively. Deiive these expiessions.
Te coiiesponding quantum expiessions aie
Z = exp(/2k
B
T)/[1 exp(/kT)] and F = kT ln[2 sinh(/2k
B
T)]. (10)
Show that the quantum expiessions ieduce to the classical ones in the appiopiiate limit.
. Use the quasi-haimonic appioximation to compute the Gibbs eneigy foi youi ued potential using
si up to the calculated melting point of youi potential. Use ase.thermochemistry.CrystalThermo.
4
By default, the quantum haimonic oscillatoi expiessions aie used. By pioviding the keywoid
classical=True using the modied thermochemistry.py

one can instead use the classical ex-

piession, which is the ielevant case foi compaiison with the -integiation method.
. Use the -integiation method desciibed in the text to compute the Gibbs eneigy foi tempeiatuies
up to the calculated melting point of youi potential. An example ivs sciipt that you may nd
useful is piovided.

Use a ieasonable numbei of values, on the oidei of 10. How do you choose
youi Einstein ciystal spiing constant`
Te following code snippet may be useful to iead in data fiom the log.lammps le.

1
https://db.tt/WRKrAK8
2
http://www.ovito.org
3
http://lammps.sandia.gov/doc/compute_rdf.html
4
https://wiki.fysik.dtu.dk/ase/ase/thermochemistry.html

Available foi download at https://db.tt/omQYSQbh. To use this module copy the le into youi woiking diiectoiy.
Ten add the line from thermochemistry import CrystalThermo to youi python sciipt and invoke the function as
CrystalThermo(...).

https://db.tt/4HYAcVDg

https://db.tt/I2rwqWY1
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Compaie youi iesults with the civuu
8
expiession[3]
G =

9.1 + 13.093038T 24.319T ln T

1.8842 10
3
T
2
0.84 10

T
3
+ 4092T
1
, 298.1 < T < 00,
112.24 + 223.04844T 38.84429T ln T
+18.31982 10
3
T
2
.422 10

T
3
+ 4092T
1
, 00 < T < 933.43.
(11)
ln the above expiession G is given in J mol
1
. Compaie also with the iesults fiom the pievious task
and comment on youi iesults.
References
[1] J.M. Polson, E. Tiizac, S. Pionk, and D. Fienkel, Finite-size corrections to the free energies of crystalline
solids, J. Chem. Phys. 112, 339, (2000)
[2] M.l. Mendelev et al., Development of NewInteratomic Potentials Appropriate for Crystalline and Liquid
Iron, Phil. Mag. A 83, 39 (2003)
[3] A.T. Dinsdale, SGTE data for pure elements, Calphad 15, 31 (1991)
http://resource.npl.co.uk/mtdata/SGTEelementdata.pdf
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CALculation of PHAse Diagiams, see hup//en.wikipedia.oig/wiki/CALPHAD
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