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Molecular dynamics simulations of collision-induced

absorption: Implementation in LAMMPS
W Fakhardji and M Gustafsson
Applied Physics, Division of Materials Science, Department of Engineering Science and
Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
E-mail: wissam.fakhardji@ltu.se, magnus.gustafsson@ltu.se

Abstract. We pursue simulations of collision-induced absorption in a mixture of argon and

xenon gas at room temperature by means of classical molecular dynamics. The established
theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with
the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum
are well reproduced with the molecular dynamics simulation in comparison with a laboratory
measurement. The magnitude of the computed absorption, however, is underestimated in a
large part of the spectrum. We suggest some aspects of the simulation that could be improved.

1. Introduction
Collision-induced absorption (CIA) can occur when interacting molecules acquire an electric
dipole moment. The absorption happens even if the individual molecules are spectroscopically
inactive. For example, argon (Ar) or xenon (Xe) atoms do not absorb in the microwave and far
infrared spectral region. In an Ar–Xe gas mixture, however, the absorption due to interacting
Ar–Xe pairs is observable. Note that the (homonuclear) Ar–Ar pairs and the Xe–Xe pairs do
not contribute to the absorption since their symmetry is inconsistent with a dipole moment.
In planetary and cool stellar atmospheres CIA is often a major source of opacity. In the four
gas giants of our solar system, the main atmospheric constituents are hydrogen and helium. CIA
in those gases have been studied much both experimentally and theoretically [1]. Rigourous
quantum mechanical calculations of CIA are possible for those low mass systems and they
are an important complement to the excellent, but difficult and rare, lab measurements. In
atmospheres of smaller planets more massive molecules like N2 , CH4 , and CO2 are the most
abundant. With molecular masses that high quantum mechanical calculations of absorption
coefficients are challenging and, in fact, often not even necessary. Instead methods based on

Figure 1. The molecular dynamics simulation is done for a cubic volume

containing two atomic species. As the particles move around in the box
during the simulation one has to somehow take care of those reaching
the boundary. In MD this is commonly done by using periodic boundary
conditions so that a particle “lost” through one box side instantly reenters
the volume in the same position, but at the opposite wall, with unchanged
momentum.

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classical mechanics may be used, like the bimolecular approach of Ref. [2] or molecular dynamics
(MD) [3]. The latter is a many-body approach and thereby has the advantage that it explores
all phase space so that bound complexes, so-called dimers, can form and dissociate through
three body encounters. All atomic and molecular pairs form dimers and they are generally
abundant in a gas at atmospheric temperature and pressure conditions. In this work we test an
implementation of the MD approach for a gas mixture of argon and xenon.

2. Theory and computational approach

The basic idea of MD is to simulate the motion of the particles in a section of the medium that
is big enough so that macroscopic observables may be obtained, but small enough so that it
is feasible to solve the equations of motion numerically. We are concerned with a gas mixture
of Ar and Xe atoms in a cubic volume, V , as illustrated in Fig. 1. The particles interact with
each other through pair potentials for the combinations Ar–Xe, Ar–Ar, and Xe–Xe, which are
taken from Refs. [5, 6, 7], respectively. The calculations are done as illustrated in Fig. 2. The
absorption coefficient [3]
πω
α(ω, T ) = eh̄ω/2kB T [1 − e−h̄ω/kB T ] C(ω) (1)
3V h̄c0
is computed from the Fourier transform
Z∞
1
C(ω) = cos(ωt) φ(t) dt (2)
π
0

of the dipole autocorrelation function φ(t) = h~

µ(t) · µ
~ (0)i. µ
~ (t) is the time-dependent interaction-
induced dipole moment for an Ar–Xe pair and h...i indicates the canonical ensemble average over
all pairs in the volume V (although the division by number of pairs, ∼ ρAr ρXe , is taken care
of later). The magnitude of µ ~ as a function of pair separation is displayed in Fig. 3. It is the
model dipole that is used in this work and the ab inito data is shown to justify this choice. In
Eq. (1) ω is the angular frequency, 0 is the vacuum permittivity, h̄ is Planck’s constant, kB is
Boltzmann’s constant, and T is temperature.

Figure 2. Schematic diagram showing how the MD simulations of collision-induced absorption

coefficients are done in this work. The MD itself is done with the program LAMMPS [4] while
the post-processing is done using an in-house python program.

2
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IOP Conf. Series: Journal of Physics: Conf. Series 810 (2017) 012031 doi:10.1088/1742-6596/810/1/012031

electric dipole moment [e·bohr]

0.005 0.05

0.004
Ar–Xe ab initio potential
Ar–Xe model dipole 0.04
Figure 3. The Ar–Xe interaction potential
Ar–Xe ab initio dipole
energy [hartree]

0.003 0.03 [5] together with model [8] and ab initio [9]
0.002 0.02 interaction-induced dipole moment, µ(R), versus
0.001 0.01 the interatomic distance, R. The ab initio dipole is
0 0 the MP2 calculation of Ref. [9] and here the values
-0.001
6 8 10 12 14 16
-0.01 are displayed as the negative of those in the original
R [bohr] work due to a difference in sign convention.
-6
3x10
experiment
α/ρArρXe [cm-1 amagat-2]

2.5x10-6
molecular dynamics calc.
Figure 4. The collision-induced absorption coefficient
2x10
-6
at 292 K in a gas mixture of argon and xenon,
1.5x10-6
normalized by the product of densities in units of
1x10-6
amagat. The calculated data from the present molecular
5x10-7
dynamics study is the lower curve. The experimental
0
0 50 100 150 200 250 300 data from Ref. [8] (upper curve) is displayed for
ν [cm-1]
comparison.

We run the molecular dynamics simulations with the temperature held constant by applying
a thermostat. Thermal equilibrium is achieved by allowing a thermalization period of 5 ps before
trajectories are stored for the calculation of the spectrum. There are 105 atoms of each kind
and the size of the box is chosen so that the total number density is 1 amagat, which equals
about 2.7·1019 atoms per cm3 . The densities of Ar and Xe are thus ρAr = ρXe = 0.5 amagat.

3. Results and discussion

Figure 4 shows a comparison between the present results and the laboratory measurement by
Ref. [8]. The oscillatory features with widths on the order of 10 cm−1 are due to dimers that
are dissociated by the radiation. These features are well produced in the calculation. There is
a discrepancy, however, in the magnitude of the absorption, which is underestimated by around
20% by the calculation at the peak absorption. At higher frequencies the difference is larger.
Likely there is room for improvement in the calculation and we will, for example, try with
larger number of particles or time averaged autocorrelation function. We conclude that MD
simulations of CIA with LAMMPS have great potential since the program is well optimized and
documented, and has great flexibility.

Acknowledgments
This work was supported by the Grauduate School of Space Technology at Luleå University of
Technology and the COST Action CM1405 Molecules In Motion (MOLIM).

References
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University Press)
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[3] Hartmann J M, Boulet C and Jacquemart D 2011 J. Chem. Phys. 134 094316
[4] Plimpton S 1995 J. Comp. Phys 117 1 – 19 http://lammps.sandia.gov
[5] Aziz R A and van Dalen A 1983 J. Chem. Phys. 78 2402 – 2412
[6] Aziz R A 1993 J. Chem. Phys. 99 4518 – 4525
[7] Aziz R A and Slaman M 1986 Molec. Phys. 57 825 – 840
[8] Grigoriev I M, Tonkov M V and Frommhold L 1998 Phys. Rev. A 58 4978 – 4980
[9] Haskopoulos A and Maroulis G 2006 J. Math. Chem. 40 233 – 241