Computational Materials Science 69 (2013) 428–434

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Computational Materials Science

journal homepage: www.elsevier.com/locate/commatsci

Comparison of Green–Kubo and NEMD heat flux formulations for

thermal conductivity prediction using the Tersoff potential
Masoud H. Khadem ⇑, Aaron P. Wemhoff
Department of Mechanical Engineering, Villanova University, Villanova, PA, United States

a r t i c l e i n f o a b s t r a c t

Article history: The phonon-based thermal conductivity of graphene sheets is estimated using equilibrium and non-equi-
Received 24 August 2012 librium molecular dynamics simulations. Different possible heat flux formulations, as a result of using the
Received in revised form 10 December 2012 three-body Tersoff potential, have been examined to calculate the thermal conductivity by using equilib-
Accepted 12 December 2012
rium molecular dynamics (EMD) with Green–Kubo relations. Non-equilibrium molecular dynamics
Available online 17 January 2013
(NEMD) simulations are also performed to compare the heat flux formulations. We have found that
the selected heat flux formulation has a prominent impact on the calculated thermal conductivity. A heat
Keywords:
flux formulation choice is recommended that best maintains consistency between applied and calculated
Green-Kubo
Tersoff
heat flux values in NEMD simulations.
Molecular dynamics Ó 2012 Elsevier B.V. All rights reserved.
Heat flux formulation
NEMD

1. Introduction
Experimental measurements [1,2] and theoretical calculations
[3–7] have been performed by various researchers to analyze the
unusually high thermal conductivity of graphene. The experimental
measurements range from 600–5000 W/m K and are influenced by
the experimental method and the presence of a substrate [8]. In
addition, the theoretical studies report a wide range of thermal con-
ductivity values for graphene, which is primarily due to differences
in modeling techniques employed by various investigators. The the-
oretical studies commonly employ either atomistic simulations
such as molecular dynamics (MD) [9], Green’s functions [7], BTE-
based approaches [10], or theory based on the original work by
Klemens [11]. For example, Zhixin et al. [4] applied non-equilib-
rium molecular dynamics (NEMD) to predict thermal conductivity
values of 300 W/m K and 500 W/m K at 300 K for graphene in
armchair and zigzag directions, respectively, but Hu et al. [3]
obtained values of 1500 W/m K and 2000 W/m K in armchair
and zigzag directions also using NEMD at 300 K. BTE-based
approaches have also shown a large range of predictions
(1000–5000 W/m K) [12]. Therefore, it is concluded that the choice
of the theoretical approach impacts the predicted values of thermal
conductivity, and that variations within each approach can also
influence the predictions. The selected potential function is known
to influence the predicted thermal conductivity of graphene [13],
⇑ Corresponding author.
E-mail addresses: masoud.khadem@villanova.edu (M.H. Khadem), aaron.
wemhoff@villanova.edu (A.P. Wemhoff).
but the effect of the heat flux calculation method is not yet
understood.
The Tersoff potential is widely used to model the covalent inter-
actions in the structure of graphene by suggesting the following
form:
/ðr ij Þ ¼ fc ðrij Þ½/R ðrij Þ  bij /A ðr ij Þ ð1Þ
R A
where fc ðrij Þ is the cut-off function, / ðr ij Þ and / ðr ij Þ are the repulsive
and attractive parts of the potential, respectively, and bij is the three-
body term. More details and the coefficients for carbon–carbon
interactions can be found in the original papers by Tersoff [14,15].
Recently, Lindsay and Broido [16] proposed new parameters for
graphene that model the phonon dispersion in the center of the
Brillouin zone more precisely, with the result of a modified thermal
conductivity prediction. They showed that the change in Tersoff
parameters results in an increase in predicted thermal conductivity
from 1900 W/m K by the conventional Tersoff to 3500 W/m K with
their optimized version, yet they did not provide many details on
their MD simulation approach. This modified Tersoff potential is
now generally accepted by the MD community over the original
Tersoff when modeling thermal transport in graphene [13]. There-
fore, the optimized Tersoff potential is used in all simulations in this
study.
Equilibrium and non-equilibrium molecular dynamics are two
widely used approaches to predict the thermal conductivity of a
system of atoms in a solid structure [17–19]. Schelling et al. [20]
studied and compared the features of each method. They pointed
out that NEMD might contain nonlinear effects due to the applica-
tion of the required temperature gradient. They also noted that

0927-0256/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.commatsci.2012.12.016
 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434
while both EMD and NEMD approaches exhibit finite size effects,
these effects are much more severe in NEMD due to the presence
of interfaces at the heat source and sink. Furthermore, EMD facili-
tates thermal conductivity prediction in all directions using one
simulation, whereas NEMD requires the use of a thermal gradient
and therefore only enables the calculation of thermal conductivity
in one direction. Therefore, EMD is particularly useful for geome-
tries where periodic boundary conditions can be applied. However,
the basis of EMD is the fluctuation–dissipation theorem, while
NEMD’s basis in Fourier’s Law of conduction makes NEMD to be
analogous to experimental measurements. Furthermore, EMD is
often computationally more expensive and the results are more
sensitive to the simulation parameters [21].
In EMD, the system is set to the desired temperature, and then a
constant energy scheme is used with the well-known Green–Kubo
[22,23] relations to calculate the thermal conductivity tensor. MD
simulations may be applied in different statistical ensembles
[24], namely canonical (NVT), grandcanonical (lPT), and microca-
nonical (NVE). It is worth noting that the derivations of Green [22]
and Kubo [23] have been done in t different ensembles: the former
in microcanonical and the latter in grandcanonical. Lepri et al. [25]
resolved this discrepancy by noting that if the microcanonical
ensemble is used, then the thermal conductivity might diverge
non-trivially unless the velocity of the center of mass of the system
is set to zero or alternatively some terms are subtracted from the
calculated heat flux vectors. However, the canonical ensemble
can also be used with the Green–Kubo formula to predict the ther-
mal conductivity by applying additional thermal forces to all the
atoms [26].
Another issue regarding the EMD is the formulation of heat flux
vectors when the atoms interact under the influence of a three-
body potential. Hardy [27] was the first investigator to derive the
heat flux formulation for a pairwise potential by using localization
functions for mass density, momentum density, and energy den-
sity. He managed to solve the continuity equation for energy con-
servation of the following form:
@E0 ð~
R; tÞ ~ 0 ð~ ~0 ~
þ r~R  ½Q K R; tÞ þ Q V ðR; tÞ ¼ 0
@t
where ~ ~
R is the position vector, is time, E is the system energy, and Q
~ are the kinetic and potential contributions of the total heat
and Q
flux. The superscript ‘‘0’’ designates the case where there is no bulk
motion in the system of particles. In the same study the two above
terms were evaluated to be:
1 X
~ 0 ð~
Q ð~ v Þ~rij
F ij  ~
K R; tÞ ¼
2 i;j
X1 1

~ 0 ð~
Q V R; tÞ ¼ v i j2 þ /ij ~
mi j~ vi
i
2 2
where mi is the mass of particle i, ~F ij is the inter-atomic force
vector between atoms i and, ~ v i is the velocity vector of atom i,
and /ij is the inter-atomic potential. Eqs. (3) and (4) were devel-
oped for a pairwise potential, but extension to a three-body poten-
tial is not straightforward. Different heat flux formulations for
three-body potentials have been proposed recently [18,28–30].
For example, Chen [30] used the same approach employed by
Hardy to derive the heat flux and stress formulations for Stillin-
ger–Weber [31] and Tersoff potentials. However, the results
obtained by other investigators are not identical. So, Guajardo-
Cuellar et al. [32] compared the existing heat flux formulations
for carbon and germanium in the diamond structure by computing
the thermal conductivity using EMD simulations. Their results
show that the values of thermal conductivity for diamond-like
carbon and germanium vary in the range of 920–4500 W/m K
429
and 14–120 W/m K, respectively, depending on the heat flux for-
mulation. However, no similar study has been performed for
graphene. In addition, the question of which formula is the most
accurate for heat flux estimation for graphene using the Tersoff po-
tential is still unanswered. The knowledge of which formulation
provides the most reliable prediction of heat flux is key to thermal
conductivity calculation of graphene using MD simulations. There-
fore, this study examines the various heat flux formulations to
ascertain which appears to provide the most consistent predictions
when compared to a direct method. This will be accomplished by
comparing the applied heat flux using a direct method with the
calculated heat flux using the various correlations.
NEMD simulations provide the means to apply a heat flux by
scaling the velocity of atoms in two regions of the simulation
domain to generate a heat flow of interest. A few studies have com-
pared the applied heat flux and the calculated heat for a system of
atoms interacting with a pairwise potential function [19,33,34].
They all found good agreement between the calculated heat flux
in EMD and NEMD simulations. However, to the best of our knowl-
edge, there has been no attempt to compare the heat flux values in
the presence of the Tersoff potential. The following sections use
EMD and NEMD simulations to compare the calculated thermal
conductivity values and determine how well these formulations
maintain consistency with applied heat fluxes.
2. Heat flux formulations
Combining Eq. (2) with the statistical definition of heat flux vec-
tor, ~
j ¼ ðjx ; jy ; jz Þ, the following equation is obtained [35]:
X
~j ¼ 1 d r i ei
~ ð5Þ
X dt i
where ~ ri is the position of each atom, ei is the energy, ei ¼
P
1
2
v i j2 þ i /ij Þ, of each atom in the system, and X is the system’s
ðmj~
volume. For a simulation that uses a pairwise potential, Eq. (5) takes
the following form:
ð2Þ
!
X 1X ~
~j ¼ 1 v i ei þ
~ v iÞ
r ij ðF ij  ~
~ ð6Þ
X i 2 i;j
In deriving Eq. (6) it was assumed that the potential is equally
divided between two atoms. However, Eq. (6) is invalid for a
many-body potential such as the Tersoff potential, which leads to
numerous proposed heat flux formulations. Guajardo-Cuellar
ð3Þ
et al. [32] have summarized the proposed heat flux formulations
used by various researchers.
Dong et al. [28] considered the equation derived by Hardy [27]
ð4Þ for a pairwise potential (Eq. (6)) to neglect the effect of the third
atom in the triplet interaction. As result they arrived at Eq. (F1)
in Table 1. They have also assumed that the triplet potential is
equally divided between atoms i and j. This assumption has been
also used by Li et. al. [29] except that they also included the effect
of atom k in the derivative of the potential (Eq. (F2)). In addition,
Chen [30] used the localization function stated by Hardy [27],
and after some algebraic steps they derived a theoretical formula-
tion for the heat flux to be used with the Tersoff potential. Later
Guajardo-Cuellar et al. [32] rearranged their equation and wrote
it in the form of Eq. (F4). The same authors also derived Eq. (F3),
which is a result of the term by term differentiation of Eq. (5),
and it contains the position vector of each atom with respect to
the origin rather than the inter-atomic distance of the interacting
atoms. The above mentioned heat flux formulations are summa-
rized in Table 1, and further background and the assumptions
made for each formulation have been discussed in detail [32].
430 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434

Table 1
Possible formulations for the heat flux vector to be used with the Tersoff potential.

Reference Heat flux vector ð~

jÞ
Dong et al. [28] (F1)

X
n X
n X
n  !
~j ¼ 1 v i ei þ
~ r ij v j 
~ ~
@/i
X i¼1 i¼1 j¼1
@r j

Li et. al. [29] (F2)

!
Xn
~j ¼ 1 ~
1
v i ei þ ~rji ðD~F j  ~
v j  D~F i  ~
1
v i Þ  ð~rjk  ~rki ÞðD~F k  ~
v kÞ
X i¼1 2 2

Guajardo-Cuellar et al. [32] (F3)

!!
X
n X
n X
n X
n X
n
~j ¼ 1 v i ei þ
~ r i ð~
~ v iÞ 
Fi  ~
1
~
ri ð~ vi  ~
F ij  ð~ v jÞ þ ~ vi  ~
F ik  ð~ vkÞ
X i¼1 i¼1
2 i¼1 j–i k–i;j

Chen [30,32] (F4)

!!
Xn
1X n X n Xn
~j ¼ 1  ~ v i ei þ rij ð
@U ij
v
~ kÞ þ ~ r ik ð
@U ij
vkÞ
~
X i¼1
2 i¼1 j–i
@~r j k–i;j
@~
rk

It is worthwhile to mention that in all the above heat flux for-
mulations it is assumed that there is no bulk motion in the system
(i.e., the velocity of the center of mass of particles is zero). How-
ever, if there is a bulk velocity in the system then the system center
of mass velocity vector ~ v G must be subtracted from each particle’s
velocity vector to obtain correct results.
3. EMD simulations
3.1. Method
Dynamic properties such as thermal conductivity are calculated
in EMD based on the fluctuation dissipation and linear response
theorem. This method applies the fact that the heat flow in a sys-
tem of particles in the equilibrium state fluctuates around zero.
The heat flux vectors and their correlations are computed through-
out the simulations. The time needed for Heat Auto-Correlation
Functions (HACF) to decay to zero is then used through the
Green–Kubo relation to predict the thermal conductivity. Statisti-
cal thermodynamics coupled with extensive algebra results in
the following equation for thermal conductivity:
Z s
1 steps to mitigate the effects of velocity scaling via the thermostat.
kx ¼ hjx ðtÞ  jx ð0Þidt
XkB T 2 0
conductivity calculation in both directions at once, the simulations
here are performed separately for the two directions so that we can
use rectangular graphene sheets (instead of square), which are
longer in the direction of interest for the thermal conductivity cal-
culation. In these simulations, the graphene sheets are 10 nm long
in the direction in which the thermal conductivity is computed and
2 nm wide. We ensured that a 2 nm width domain is large enough
to resolve the Brillion zone and avoid divergence of the thermal
conductivity prediction. Periodic boundary conditions are imposed
to avoid the boundary effects caused by the long mean free path
(up to 600 nm) [36] in the graphene structure. To reduce statistical
error, each 2  105 time step period is treated as an independent
simulation with new initial velocities. All of the EMD simulations
are performed at 300 K. The temperature is set by equilibrating un-
der a constant temperature (NVT) using a Berendsen thermostat
[37] for 2  105 time steps. The velocity of the center of mass of
the system is set to zero at the beginning of each simulation, which
maintains a zero center of mass velocity during the simulation that
prevents the divergence of the heat flux auto-correlation functions
and erroneous values of thermal conductivity. After the system
reaches the desired temperature (300 K), the thermostat is turned
off and the system relaxes at a constant energy (NVE) for 105 time
ð7Þ

where T is the equilibrium temperature, kB is the Boltzmann con-

stant, and s is the time needed for HACF decay. In order to use
Eq. (7) with EMD simulations, the following discrete form [20] is
used with the simulations:

Dt X M X
1 Nm
kx ¼ 2
jx ðm þ nÞjx ðnÞ ð8Þ
XkB T m¼1 N  m n¼1

where Dt is the simulation time step, N represents the total number

of time steps of the simulation (after equilibrium), and M is the
number of time steps for the correlation of heat flux vectors
(MDt ¼ sÞ. The outer summation in Eq. (8) represents the HACF.

3.2. Simulation details

Eqs. (F1)-(F4) are substituted into Eq. (8) to compute the ther- Fig. 1. Temperature distribution and energy variation for the first 106 time steps of
mal conductivity of graphene sheets in both zigzag and armchair an EMD simulation. The first 2  105 time steps are in the NVT ensemble, where the
directions. Although the Green–Kubo relation enables thermal temperature fluctuations are allowed by the Berendsen thermostat.
 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434
Fig. 1 shows the temperature distribution and energy conservation
for the first 106 time steps in the NVE portion of the simulations.
Simulations continue after equilibrium for an additional 107 time
steps in the microcanonical ensemble to sample the heat flux
vectors. Following Li et al. [29], the statistical error is reduced by
dividing the sampling stage into five individual intervals for ther-
mal conductivity prediction. The averaged thermal conductivity
in five intervals is then calculated upon the completion of the sim-
ulation. Eq. (8) is used to calculate the values of thermal conductiv-
ity upon the completion of the simulations. In our simulations,
t ¼ 0:5 fs, and X is obtained by multiplying the surface area of
the graphene sheets by the graphite interlayer nominal distance
(0.335 nm). The summation limit of HACFs (M) is chosen to be
105 time steps, which corresponds to 50 ps. This choice of M, as
will be shown, is large enough to let the HACFs to decay to zero
for thermal conductivity convergence. However, the value of the
upper limit can be varied for different materials and it increases
with the mean free path of the material. Furthermore, in order to
obtain a good statistical average [20], the total number of time
steps (N) in Eq. (8) must be much larger than M, and is therefore
selected to be 2  106 (1 ns) throughout this study.
3.3. EMD results
The thermal conductivity convergence of a graphene sheet in
the zigzag direction is shown in Fig. 2 by averaging four indepen-
dent thermal conductivity curves and using Eq. (F1) for heat flux
calculations. The figure also shows the corresponding HACF decay
to indicate the thermal conductivity convergence. The figure shows
that although the thermal conductivity might not independently
converge for each simulation, the statistical error can be reduced
by averaging the thermal conductivity. The same behavior has
been observed by Evans et al. [5]. Fig. 2 also enables the computa-
tion of the statistical error in the predictions of thermal conductiv-
ity values.
The average thermal conductivity of graphene sheets along the
zigzag and armchair directions are shown in Fig. 3 using the heat
flux formulations of Eqs. (F1), (F2), and (F4). In general, the figure
shows that while the thermal conductivity is highly influenced
by the selected heat flux formulation, the thermal conductivity
convergence is achieved regardless of the applied formulation. It
is also deduced that thermal conductivity values in the armchair
and zigzag directions are of the same order except for the case
where Eq. (F2) is used to compute the heat flux. Furthermore,
applying Eq. (F2) provides a good agreement with EMD predictions
of thermal conductivity values by Hu et al. [3] and Haskins et al.
[38]. On the other hand, the results obtained by using Eqs. (F1)
and (F4) are also reasonable and in agreement with the obtained
Fig. 2. Thermal conductivity and HACF convergence for a graphene sheet in the
zigzag direction when heat flux is computed by Eq. (F1).
431
Fig. 3. The average thermal conductivity of graphene in zigzag and armchair
directions with three heat flux formulations.
thermal conductivity achieved by Zhixin et al. [4] using NEMD sim-
ulations. Fig. 3 also reports armchair and zigzag thermal conductiv-
ity values much lower than those obtained by Evans et al. (in the
range of 8000–10000 W/m K). We relate this difference to a variety
of factors including the use of a different potential model and heat
flux formulation. It can be concluded that kEq:ðF2Þ > kEq:ðF1Þ > kEq:ðF4Þ
for both zigzag and armchair directions. The same order has been
observed for carbon and germanium in the diamond structure [32].
One interesting result stems from the use of Eq. (F3) for the
computation of the heat flux vectors. It is found that considering
this equation for heat flux calculations will result in the divergence
of thermal conductivity and HACFs for domain sizes larger than
4 nm. This has been shown in Fig. 4 where thermal conductivity
in the armchair direction is plotted for different sizes in the range
of 2–5 nm. In addition, an oscillatory behavior in the thermal con-
ductivity starts to grow at the domain size of 4 nm and it leads to
the divergence of HACFs for graphene sheets larger than 8 nm. We
relate this phenomenon to the fact that Eq. (F3) is the only heat
flux vector formulation that is based solely on the atomic position
~
ri rather than the relative atomic position ~ r ij , and the use of peri-
odic boundary conditions results in nonrealistic atomic position
vectors. This phenomenon has been also pointed out by Donadio
and Galli [39] as ‘‘ill-defined’’ position vectors in periodic systems.
Therefore, the use of Eq. (F3) might not be appropriate for heat flux
calculations with periodic boundary conditions, and it leads to a
divergence in thermal conductivity.
The achieved values of thermal conductivity are tabulated in
Table 2 for both zigzag and armchair directions. We have used
the exponential fits to each curve in order to calculate the
converged values and the associated errors (see Fig. 3). For all
Fig. 4. Thermal conductivity convergence in the armchair direction for different
domain sizes using Eq. (F3).
432 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434

Table 2 path of graphene compared to the simulation domain size. The

Computed thermal conductivities in W/m K of graphene using different heat flux resulting heat flux can then be written as:
formulations.
e
Direction Eq. (F1) Eq. (F2) Eq. (F3) Eq. (F4) jx ¼ ð10Þ
2Adt
Zigzag 830 ± 6% 1600 ± 8% 510 ± 20% (5 nm sheet) 250 ± 8%
Armchair 800 ± 8% 1800 ± 10% 317 ± 15% (5 nm sheet) 300 ± 10% where A is the cross sectional area of the system perpendicular to
the heat flow. The factor of 2 in the denominator of Eq. (10) stems
from the fact that the heat flows from the hot and cold regions in
two directions. The velocities of all the particles in the hot and cold
the formulations, except for the case of Eq. (F3), the corresponding
regions are scaled according to the following equation:
statistical errors are within 10%. It should be noted that the values
in the Table require a quantum correction (QC) to the classical MD v inew ¼ ~
~ v G þ að~
v iold  ~
v GÞ ð11Þ
results for comparison with experimental measurements as per-
formed by some investigators [40,41]. This is due to the high Debye where ~v G is the velocity of center of mass of the associated hot or
temperature of graphene where only at temperatures higher than cold region, and a is calculated from the following equation:
rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
the Debye temperature are all the phonon modes excited. How- e
ever, this study does not impose the QC as the interest here lies a¼ 1 ð12Þ
KE
in the comparison of the existing heat flux formulations, and the P
QC affects the result of each formulation in an equivalent manner. v i j2 , is the kinetic energy of the particles in the
where KE ¼ i 12 mi j~
Furthermore, the effect of a quantum correction was recently hot or cold regions. In our simulations the bulk velocity of the sys-
shown to be insignificant on predictions of the thermal conductiv- tem of particles in hot and cold regions is controlled by applying a
ity of graphene when the system temperature is greater than 280 K Berendsen thermostat, so by setting the velocity of the center of
[42]. mass of the two regions to zero at the beginning of the simulations,
Furthermore, the effect of finite domain size must also be men- Eqs. (11) and (12) reduce to:
tioned. Although large size effects have been reported in NEMD rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
e
simulations, Schelling et al. [20] and Sellan et al. [43] have shown v inew ¼ ~
~ v iold 1 ð13Þ
KE
that these effects are lower in EMD simulations. The EMD domain
size requires that the phonon–phonon scattering processes are The simulation domain is divided into several segments and the
unalte x red by the presence of periodic boundary conditions; this temperature of each segment is recorded at each time step. The
requirement has shown to be low (e.g. 128 atoms for solid simulations are continued until a linear temperature gradient is
argon[17]). The selected 10 nm graphene sheet length used in this achieved.
study contains approximately 2000 atoms, and the comparison of
results for a 10 nm domain length with smaller domain sizes 4.2. Simulation details
shows very low size effects (within the statistical error) on the cal-
culated thermal conductivity. The simulated graphene sheets are 22 nm long and 3 nm wide.
The length of the simulation domain is divided into five regions
4. NEMD simulations for simulations calculating kx in either the zigzag or armchair direc-
tion: a hot region, a cold region, two nonlinear regions, and a middle
In this section we apply NEMD simulations that generate a heat region. Fig. 5 shows the graphene sheet geometry and locations of
flow into the system using a direct approach, and then apply the these regions. Separate simulations have been performed where
formulations of Table 1 to compare the calculated heat flux with zigzag and armchair edges appear along the long edge of the do-
the applied heat flux. main. Hot and cold regions are equally 1 nm wide, which contains
a sufficient number of atoms to calculate the average ensemble
temperature. The portion of the domain between the hot and cold
4.1. Method
regions is divided into 20 segments (each 0.5 nm wide) for statistics
NEMD simulations provide a means to calculate the thermal
conductivity in a way analogous to the experimental measure-
ments either by imposing a thermal gradient into the system of
particles or by introducing a heat flow. Both approaches enable
thermal conductivity prediction using the Fourier’s Law of
conduction:
j
kx ¼  dTx ð9Þ
dx

where x is the direction of heat flow (or thermal gradient).

The method of imposing a thermal gradient by controlling the
temperature of two regions in the system is straightforward to
implement, but it often requires long simulations to obtain a stea-
dy state linear temperature distribution. In this study, the method
proposed by Jund and Jullien [19] is used to apply a specified heat
flux by scaling the atomic velocities in two regions of the simula-
tions in such a way that at each time step a specified amount of
energy, e (set to 10% of KBT, or 2.6 meV at 300 K), is both added
to a hot region and subtracted from a cold region. Periodic bound- Fig. 5. Simulation domain of graphene sheets in the zigzag and armchair directions.
ary conditions are imposed to all boundaries to mitigate the effect The hot, cold, middle, and nonlinear regions are shown. Lengthwise dimensions are
of boundary scattering effects from the high phonon mean free shortened in this figure for clarity.
 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434 433

collection. This 10 nm-wide volume may be separated into two no

5  104 nlinear regions where the influence of the nearby hot/cold
region distorts the statistics, and a middle region where this distor-
tion is not prevalent. The statistics collected in the middle region
5  105 alone are therefore used for heat flux and thermal gradient
calculations. The nonlinearity in the profile is due to phonon scat-
tering at the boundary between the temperature-controlled regions
and the uncontrolled regions. The approximate width of the nonlin-
ear regions is 1–2 nm. The instantaneous temperature of each
segment is calculated using the following equation derived by com-
bining the definition of kinetic energy with the equipartition
theorem:
*  +
1 X 1 2
Ti ¼ v jj
mj j~ ð14Þ
3kB Ni j
2 Fig. 7. The Temperature distributions, average temperature, and the linear fit in the
middle region for the simulation of a graphene sheet in the zigzag direction.

where N i is the number of atoms in segment i. The NEMD simula-

tions start with time steps of an NVT simulation using the Berend-
sen thermostat until the system reaches the desired temperature
(300 K). The hot and cold regions are then initiated to generate a
heat flow using the mentioned method. The simulations continued
for another time steps to allow for a linear temperature distribution
to be established. The temperature and local heat flux (based on the
formulations of Table 1) are recorded for the rest of the simulations
(5  105 time steps). Eq. (14) is used to calculate the thermal con-
ductivity values at the end of each 105 time step interval to reduce
the statistical error by averaging over five obtained thermal conduc-
tivity values.
4.3. NEMD results
The temperature variation of different regions in the simulation
of the graphene sheet in the zigzag direction is shown in Fig. 6.
Although the same amount of energy is added and withdrawn from
the hot and cold regions, the steady state temperature of the mid-
dle region is not the average temperature of hot and cold regions.
The number of atoms in the cold region becomes larger than that of
the hot region due to the lower temperature, which results in a
higher number density and larger pre-adjusted kinetic energy in
the cold region. Therefore a larger velocity scaling parameter (see
Eq. (12)) is associated with the hot region. However, after the
equilibration, the average temperature of the middle region shows
a constant value which demonstrates a steady state in this region.
Fig. 7 shows the average temperature distribution in the middle
region for five consecutive time intervals of the simulation of a
graphene sheet in the zigzag direction. The average temperature
is also plotted to enable the calculation of the temperature
gradient, which equals the slope of the linear fit. By applying the
method to the results obtained from simulations in the armchair
and zigzag directions, the computed temperature gradients are
calculated to be 10.4 K/nm and 6.2 K/nm for zigzag and armchair
directions, respectively. The variation in the average temperature
of the middle region for each time interval is inevitable since the
system is under constant heat flux and not constant temperature.
However, the slope of the independent curves through the middle
of the domain is consistent with that for the averaged curve, show-
ing that the averaging windows are sufficiently large.
As mentioned in the previous sections, adding or removing
energy to create hot and cold regions will generate a heat flow in
the system. The resultant applied heat flux is calculated using Eq.
(10). This heat flux must be the same throughout the simulation
domain. However, a nonlinear temperature gradient caused by
inter-region boundary scattering affects the heat flux in the regions
close to both hot and cold regions. So, only the middle region was
used for heat flux computation.
Eqs. (F1)–(F4) of Table 1 are used to calculate the heat flux in
this region during the steady state portion of the NEMD simula-
tions. The generated heat flux and the averaged applied heat flux
in the middle region are shown in Fig. 8. The variation in the
applied heat flux corresponds to the temperature fluctuations in
the middle region. Fig. 8 also shows that Eq. (F2) gives the closest
estimation of the heat flux with the Tersoff potential when com-
pared to the applied heat flux. However, the heat fluxes obtained
from Eqs. (F1) and (F4) are still of the same order of magnitude
as the applied heat flux.
Fig. 9 shows that plotting the calculated average heat flux using
Eq. (F3) results in a much larger prediction than the applied heat
flux. In addition, the heat flux fluctuations are substantial using this
approach. These results are consistent with the weak convergence

Fig. 6. Temperature distribution in the hot, cold, and middle regions of the
simulation for a graphene sheet in zigzag direction. The dashed line shows a Fig. 8. The applied heat flux and the calculated heat flux and their average values in
constant time-averaged temperature in the middle region. the middle region.
434 M.H. Khadem, A.P. Wemhoff / Computational Materials Science 69 (2013) 428–434
Fig. 9. The computed and averaged heat flux in the middle region using Eq. (F3).
Dash line shows the average heat flux from Eq. (F3).
ability for this heat flux formulation in EMD simulations (see the
explanation of Fig. 4).
The thermal conductivity values calculated based on the ap-
plied heat flux and Eq. (9) are 70 W/m K and 110 W/m K for zigzag
and armchair directions, respectively. These values are much smal-
ler than those achieved by EMD simulations. However, it is worth
noting that (1) the mechanism of heat conduction is different for
the two methods, and (2) boundary scattering associated with
NEMD simulations require domain sizes on the order of the mean
free path, which is larger than the domain used in this study. As a
result the values of thermal conductivity predicted by EMD and
NEMD methods for solids with large mean free path might not
be consistent. For example, while Zhixin Guo et al. [4] and Bi
et al. [44] reported values in the range of 100–500 W/m K using
NEMD method with the original Tersoff potential, Evans et al. [5]
calculated values in the range of 4000–8000 W/m K using EMD
with the same potential model. Therefore, although Sellan et al.
[43] and Schelling et al. [20] have found some agreement between
EMD and NEMD in the simulations of Silicon-based materials, com-
paring the values of thermal conductivity obtained by EMD and
NEMD is not beneficial and often leads to confusion. This is why
we use NEMD simulations only as a means to compare the applied
heat flux using the direct method and the calculated heat flux
using the various heat flux formulations.
5. Conclusions
EMD simulations were used to determine the thermal conduc-
tivity of graphene in both zigzag and armchair directions under
different heat flux formulations for the Tersoff potential. We calcu-
lated thermal conductivity values in the range of 300–2000 W/
m K using the Green–Kubo relation for thermal conductivity pre-
diction. The wide range of obtained values shows that although
the HACFs and thermal conductivity might converge, the choice
of heat flux formulation has a significant impact on the calculated
value. NEMD simulations with a specified heat flux were used to
investigate different heat flux formulations with the Tersoff poten-
tial. Our results showed that Eq. (F2) is recommended for the
future calculations of thermal conductivity using EMD simulations
and the Tersoff potential. We also found that Eqs. (F1) and (F4) do
not exhibit the same level of agreement as Eq. (F2) with the direct
approach but still predict the heat flux in the correct range, while
using Eq. (F3) results in the divergence of HACFs and the thermal
conductivity for graphene domain sizes larger than 5 nm. With
the results of this study, EMD simulations with the Green–Kubo
relation can be applied to a system of particles interacting via
the Tersoff potential to predict the thermal conductivity with high
confidence in accuracy. The same approach used in this study can
also be implemented to investigate the performance of the heat
flux formulations with other many-body potential functions.
Acknowledgment
We acknowledge the support of National Science Foundation
(NSF) through the Grant CBET-0931507.
References
[1] A.A. Balandin, S. Ghosh, B. Wenzhong, I. Calizo, D. Teweldebrhan, M. Feng, L.
Chun Ning, Nano Lett. 8 (2008) 902–907.
[2] S. Ghosh, I. Calizo, D. Teweldebrhan, E.P. Pokatilov, D.L. Nika, A.A. Balandin, W.
Bao, F. Miao, C.N. Lau, Appl. Phys. Lett. 92 (2008) 151911.
[3] J.N. Hu, S. Schiffli, A. Vallabhaneni, X.L. Ruan, Y.P. Chen, Appl. Phys. Lett. 97
(2010) 133107.
[4] G. Zhixin, D. Zhang, G. Xin-Gao, Appl. Phys. Lett. 95 (2009) 163103.
[5] W.J. Evans, L. Hu, P. Keblinski, Appl. Phys. Lett. 96 (2010) 203112.
[6] J.W. Jiang, J.S. Wang, B.W. Li, Phys. Rev. B 79 (2009) 205418.
[7] Z. Huang, T.S. Fisher, J.Y. Murthy, J. Appl. Phys. 108 (2010) 094319.
[8] A.A. Balandin, Nat. Mater. 10 (2011) 569–581.
[9] A.J.H. McGaughey, M. Kaviany, Int. J. Heat Mass Transf. 47 (Copyright 2004,
IEE) (2004) 1783–1798.
[10] D.L. Nika, E.P. Pokatilov, Phys. Rev. B 79 (15) (2009).
[11] P.G. Klemens, D.F. Pedraza, Carbon 32 (4) (1994) 735–741.
[12] Z.W. Tan, J.-S. Wang, C.K. Gan, Nano Lett. 11 (2011) 214–219.
[13] A.P. Wemhoff, Int. J. Transp. Phenomena 13 (2012) 121–141.
[14] J. Tersoff, Phys. Rev. B (Condensed Matter) 37 (1988) 6991–7000.
[15] T. Tersoff, Phys. Rev. Lett. 61 (25) (1988) 2879–2882.
[16] L. Lindsay, D.A. Broido, Phys. Rev. B 82 (2010) 205441.
[17] K.V. Tretiakov, S. Scandolo, J. Chem. Phys. 120 (2004) 3765–3769.
[18] C. Jianwei, C. Tahir, D. Weiqiao, W.A. Goddard, J. Chem. Phys. 113 (2000) 6888–
6900.
[19] P. Jund, R. Jullien, Phys. Rev. B 59 (1999). 13707–13704.
[20] P.K. Schelling, S.R. Phillpot, P. Keblinski, Phys. Rev. B 65 (2002) 144306.
[21] K. Esfarjani, Phys. Rev. B 84 (8) (2011).
[22] M.S. Green, J. Chem. Phys. 20 (1952) 1281–1295.
[23] R. Kubo, J. Phys. Soc. Jpn. 12 (1957) 570–586.
[24] J.M. Haile, Molecular Dynamics Simulation: Elementary Methods, Wiley, New
York, 1997.
[25] S. Lepri, R. Livi, A. Politi, Phys. Rep. 377 (1) (2003) 1–80.
[26] A. Maeda, T. Munakata, Phys. Rev. E 52 (1995) 234–239.
[27] R.J. Hardy, J. Chem. Phys. 76 (1) (1982) 622–628.
[28] D. Jianjun, O.F. Sankey, C.W. Myles, Phys. Rev. Lett. 86 (2001) 2361–2364.
[29] J. Li, L. Porter, S. Yip, J. Nucl. Mater. 255 (1998) 139–152.
[30] Y. Chen, J. Chem. Phys. 124 (2006). 54113–54111.
[31] F.H. Stillinger, T.A. Weber, Phys. Rev. B 31 (8) (1985) 5262–5271.
[32] A. Guajardo-Cuellar, D.B. Go, M. Sen, J.Chem. Phys. 132 (2010) 104111–
104117.
[33] D.G. Cahill, R.O. Pohl, Phys. Rev. B (Condensed Matter) 35 (8) (1987) 4067–
4073.
[34] R.D. Mountain, R.A. MacDonald, Phys. Rev. B (Condensed Matter) 28 (6) (1983)
3022–3025.
[35] D.A. McQuarrie, Statistical Mechanics, University Science Books, 2000.
[36] C. Berger, Z. Song, X. Li, X. Wu, N. Brown, C. Naud, D. Mayou, T. Li, J. Hass, A.N.
Marchenkov, E.H. Conrad, P.N. First, W.A. de Heer, Science 312 (5777) (2006)
1191–1196.
[37] H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, J.R. Haak, J.
Chem. Phys. 81 (8) (1984) 3684–3690.
[38] J. Haskins, A. Kinaci, C. Sevik, H. Sevincli, G. Cuniberti, T. Cagin, ACS Nano 5 (5)
(2011) 3779–3787.
[39] D. Donadio, G. Galli, Nano Lett. 10 (3) (2010) 847–851.
[40] Y.H. Lee, R. Biswas, C.M. Soukoulis, C.Z. Wang, C.T. Chan, K.M. Ho, Phys. Rev. B
43 (8) (1991) 6573–6580.
[41] A. Maiti, G.D. Mahan, S.T. Pantelides, Solid State Commun. 102 (7) (1997) 517–
521.
[42] A. Cao, J. Appl. Phys. 111 (8) (2012).
[43] D.P. Sellan, E.S. Landry, J.E. Turney, A.J.H. McGaughey, C.H. Amon, Phys. Rev. B
(Condensed Matter and Materials Physics) 81 (21) (2010) 214305 (214310
pp.).
[44] B. Kedong, C. Yunfei, C. Minhua, W. Yujuan, Solid State Commun. 150 (29–30)
(2010) 1321–1324.