arXiv:2007.11594v1 [astro-ph.

SR] 22 Jul 2020

c The Authors. Published by the Royal Society under the terms of the
Creative Commons Attribution License http://creativecommons.org/licenses/
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Magnetoacoustic Wave

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Energy Dissipation in the
rsta.royalsocietypublishing.org Atmosphere of Solar Pores
Caitlin A. Gilchrist-Millar1 , David B. Jess1,2 ,
Samuel D. T. Grant1 , Peter H. Keys1 ,
Research
Christian Beck3 , Shahin Jafarzadeh4,5 ,
Article submitted to journal Julia M. Riedl6 , Tom Van Doorsselaere6 ,
Basilio Ruiz Cobo7,8
1 Astrophysics Research Centre, School of
Subject Areas:
Mathematics and Physics, Queen’s University Belfast,
astrophysics, observational Belfast, BT7 1NN, U.K.
2 Department of Physics and Astronomy, California
astronomy, solar system,
spectroscopy, wave motion
State University Northridge, Northridge, CA 91330,
U.S.A.
3 National Solar Observatory (NSO), 3665 Discovery
Keywords: Drive, Boulder, CO 80303, U.S.A.
4 Rosseland Centre for Solar Physics, University of
techniques: polarimetric, Sun:
Oslo, P.O. Box 1029 Blindern, N-0315 Oslo, Norway
atmosphere, Sun: magnetic fields, 5 Institute of Theoretical Astrophysics, University of
Sun: oscillations, Sun: photosphere, Oslo, P.O. Box 1029 Blindern, NO-0315 Oslo, Norway
6 Centre for mathematical Plasma Astrophysics
sunspots
(CmPA), KU Leuven, Celestijnenlaan 200B bus 2400,
3001, Leuven, Belgium
Author for correspondence: 7 Instituto de Astrofísica de Canarias, Vía Láctea s/n,

Caitlin A. Gilchrist-Millar 38205, La Laguna, Tenerife, Spain

8 Departamento de Astrofísica, Universidad de La
e-mail: [email protected]
Laguna, 38206, La Laguna, Tenerife, Spain

The suitability of solar pores as magnetic wave guides has been a key topic of discussion in
recent years. Here we present observational evidence of propagating magnetohydrodynamic
wave activity in a group of five photospheric solar pores. Employing data obtained by the Facility
Infrared Spectropolarimeter at the Dunn Solar Telescope, oscillations with periods on the order of
5 minutes were detected at varying atmospheric heights by examining Si I 10827 Å line bisector
velocities. Spectropolarimetric inversions, coupled with the spatially resolved root mean square
bisector velocities, allowed the wave energy fluxes to be estimated as a function of atmospheric
height for each pore. We find propagating magnetoacoustic sausage mode waves with energy
fluxes on the order of 30 kW/m2 at an atmospheric height of 100 km, dropping to approximately
2 kW/m2 at an atmospheric height of around 500 km. The cross-sectional structuring of the
energy fluxes reveals the presence of both body- and surface-mode sausage waves. Examination
of the energy flux decay with atmospheric height provides an estimate of the damping length,
found to have an average value across all 5 pores of Ld ≈ 268 km, similar to the photospheric
density scale height. We find the damping lengths are longer for body mode waves, suggesting
that surface mode sausage oscillations are able to more readily dissipate their embedded wave
energies. This work verifies the suitability of solar pores to act as efficient conduits when guiding
magnetoacoustic wave energy upwards into the outer solar atmosphere.
1. Introduction 3
The composition of solar pores, which are represented by strong magnetic field concentrations

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in the solar photosphere [1], make them ideal conduits for transporting wave energy from

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the lower solar atmosphere upwards into higher regions [2]. When compared to sunspots,
wave activity in these structures is further enhanced by their small size that makes them more
susceptible to external forces, which promotes more dynamic wave generation [3]. Numerical
simulations have previously predicted that strong downflows (driven by cooling inside the pore
centre) collide with the dense lower layers beneath the photosphere and rebound into upwardly
propagating magnetoacoustic waves that can transport energy flux into the chromosphere [4–6].
Such predictions have since been supported by observational evidence provided by both ground-
and space-based observatories [7,8]. This highlights the importance of studying the photospheric
counterpart of wave phenomena in order to be able to connect it with dynamics occurring in the
outer layers of the solar atmosphere.
Oscillations manifesting in solar pores have been observed many times in the past. Early work,
combining the Transition Region And Coronal Explorer (TRACE) satellite and German Vacuum
Tower Telescope (VTT) observations, revealed oscillations of the photospheric magnetic field
with periods spanning 5 – 8 minutes, and corresponding chromospheric intensity oscillations
with a period of approximately 3 minutes, suggesting the presence of upwardly propagating
magnetoacoustic waves [9]. In the case of magnetohydrodynamic (MHD) sausage mode waves,
a characteristic feature is a periodic fluctuation in the cross-sectional area of the pore. Using an
11-hour time series of white light observations of a large pore, Dorotovic̆ et al. [10,11] revealed
periods in cross-sectional area in the range of 20 – 70 minutes, providing evidence of slow sausage
oscillations, potentially with elusive gravity waves acting as the main driver.
Simultaneous observations of fluctuations in both the intensity and cross-sectional area of
pores was presented by Morton et al. [12], who performed a detailed study of photospheric
sausage modes present in Rapid Oscillations in the Solar Atmosphere (ROSA) 4170 Å continuum
observations of solar pores. In contrast to Dorotovic et al. [10,11], Morton et al. [12] found
much shorter periods in the range of 3 – 5 minutes, indicating that they may be driven by
a global pressure mode (p-mode) oscillation, rather than gravity mode waves. However, no
conclusions were made about the specific wave mode (fast or slow) present, or whether these
were standing or propagating waves. In a later study by Moreels et al. [13], the same dataset
studied by Morton et al. [12] was re-examined, with the waves identified as fast modes due
to the cross-sectional area and intensity variations being in antiphase to each other. On the
contrary, in-phase cross-sectional area and intensity variations indicate the presence of a slow
mode sausage wave. In subsequent work, Dorotovic et al. [14] detected both fast and slow
sausage waves in three separate magnetic waveguides (two sunspots and one pore) in the deep
photosphere, and proposed that the oscillations may be standing harmonics. Evidence of standing
harmonics in a solar pore was also seen by Moreels et al. [15] through the application of MHD
theory. Unfortunately, the simultaneous detection of the chromospheric counterparts to these
photospheric waves was lacking. However, the general ubiquity of sausage mode waves in the
chromosphere was demonstrated by Morton et al. [16], supporting the idea that MHD phenomena
guided by magnetic pores may be able to contribute to upper atmospheric heating.
Combining multiple instruments and wavelength bands, Grant et al. [17] were able to observe
sausage mode oscillations, contained within the confines of a solar pore, propagating upwards
from the lower photosphere to the base of the transition region. The authors utilised wavelet
and Fourier techniques to detect oscillations in both the intensity and cross-sectional area of the
pore, and observed periods in the range of 3 – 7 minutes, remaining consistent with a global
p-mode driver suggested by Morton et al. [12]. The energy flux was calculated [18] to drop
rapidly with height from the solar surface, with the initial energy flux of ∼35 kW m−2 dropping
by three orders of magnitude over an atmospheric height separation of ∼800 km, confirming
that the pore was indeed able to guide wave energy into higher atmospheric layers of the solar
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Figure 1: HMI/SDO continuum image of active region NOAA 12564 (upper left), alongside ..................................................................
the coaligned ROSA 4170 Å continuum image (middle left). Vector magnetogram products from
HMI/SDO, including the total magnetic field strength and inclination angle to the solar normal
are shown in the upper- and middle-right panels, respectively. An enlarged ROSA 4170 Å
continuum image, obtained from within the white dashed lines shown in the middle-left panel, is
displayed in the bottom panel. Here, the position of the FIRS slit is depicted by a dashed yellow
line, with each of the 5 solar pores captured labelled by a number 1–5. The axes employed are all
solar heliocentric coordinates.

atmosphere. Standing slow sausage waves have also been detected in pores by Freij et al. [19],
who characterised the waves as ‘standing’ due to the estimated vertical wavelengths that would
indicate strong reflection at the transition region boundary — i.e., the creation of a chromospheric
resonator that has recently been identified in sunspots [20].
More recently, Keys et al. [21] examined the spatial distributions of wave power contained
within solar pores, and were able to provide further classification of these waves in terms of
surface- or body-mode sausage waves. The authors made use of seven pore data sets, containing
high cadence observations obtained with the ROSA instrument, to demonstrate that surface
modes appear to be more prevalent in pores than body modes, particularly in larger pores. Keys
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Figure 2: AIA/SDO 171 Å (left) and 305 Å (middle) images of active region NOAA 12564,
alongside the coaligned ROSA 4170 Å continuum image (right). The axes employed are all solar
heliocentric coordinates.

et al. [21] suggest that higher magnetic field strengths, and therefore a larger gradient between
the pore and the surrounding quiet Sun in larger pores, may promote surface modes over body
modes.
In this study, we utilise state-of-the-art spectropolarimetric data of a unique solar pore
grouping to further advance our understanding of MHD waves in the lower solar atmosphere.
We employ spectral line bisector methods to obtain height-dependent velocities that allow us to
detect the presence of waves, combined with high precision inversion techniques to track the
evolution of wave energy with geometric height.

2. Observations
The data set presented in this study was acquired between 14:09 – 15:59 UT on 2016 July 12 with
the Facility Infrared Spectropolarimeter (FIRS; [22]), a slit-based spectrograph at the National
Science Foundation’s Dunn Solar Telescope (DST), Sacramento Peak, New Mexico. The telescope
was pointed towards the decaying active region NOAA 12564, positioned at (−425′′ , 98′′ ) in the
solar heliocentric coordinate system, or N10.4E27.5 in the conventional heliographic reference
frame. A set of five solar pores were contained within the field of view, positioned along a unique
straight-line configuration. To cover all pores in a single exposure, the DST’s coude table was
rotated so the FIRS slit passed through the centre of each photospheric pore boundary.
FIRS was employed to obtain high-resolution spectropolarimetric measurements of the
photospheric Si I 10827 Å line, which has an associated Landé factor of geff = 1.5 [23]. The slit
width corresponded to 0 ′′. 225 on the solar surface, while the spatial sampling along the slit was
0 ′′. 15. The spectral sampling was 0.04 Å per pixel. To increase the polarimetric signal to noise,
each time step was the result of the integration of 12 consecutive modulation cycles leading to a
14.6 s cadence. The FIRS data was processed and reduced using the FIRS pipeline provided by the
National Solar Observatory (NSO)1 . In total, 452 scan steps were obtained across the 110 minute
duration of the observing campaign. However, while the seeing conditions remained very good
overall, the final 20 minutes of the sequence suffered from periods of seeing degradation. As a
result, the data was cropped to the first 90 minutes, providing 355 high-quality spectral scans for
subsequent analyses.
Contextual vector magnetograms and continuum images from the Helioseismic and Magnetic
Imager (HMI; [24]), onboard the Solar Dynamics Observatory (SDO; [25]), were obtained to assist
with the co-alignment of our ground-based DST data. The Very Fast Inversion of the Stokes Vector
(VFISV; [26]) algorithm was applied to SDO/HMI vector data to provide vector magnetogram
1
https://nso.edu/telescopes/dunn-solar-telescope/dst-pipelines/
 Doppler Vel city [km/s] 6
-30 -20 -10 0 10 20 30
1.0

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10%
0.9 −0.5
20%
−1.0

]
30%

τ5000
0.8

40% −1.5
Ic

Optical Depth [l g
Intensity I /

0.7
50%
−2.0
60%
0.6

70% −2.5
0.5 80% −3.0
90 %
0.4 −3.5
10826.0 10826.5 10827.0 10827.5 10828.0
Wavelength [Å]

Figure 3: An isolated Si I 10827 Å line profile extracted from a quiescent region of the Sun’s
atmosphere, where the spectral intensity has been normalised by the local continuum intensity,
Ic . Solid red lines indicate line depth percentages, while the dashed blue line traces the bisector
wavelength positions at each line depth percentage, which can be converted into Doppler
velocities using the scale present at the top of the panel. The scale present at the right-hand side
converts the line depth percentages (n.b., not the specific I/Ic values) into corresponding optical
depths following the conversion suggested by González Manrique et al. [32].

information to compare with our subsequent FIRS inversions. Conversion of the heliocentric
coordinates output by the VFISV algorithm into heliographic projections that are parallel (Bx
and By ) and normal (Bz ) to the solar surface was performed using previously documented
techniques [27], allowing the true inclination angles of the magnetic fields, with respect to the
solar normal, to be uncovered (middle-right panel of Figure 1).
Alongside FIRS, the Rapid Oscillations in the Solar Atmosphere (ROSA; [28]) instrument
was employed to capture simultaneous images of the solar atmosphere through a collection of
filters, including the 4170 Å broadband filter used for cross-correlation coalignment with the data
products from HMI/SDO. The co-aligned fields of view are displayed in Figure 1. Additional
images from the Atmospheric Imaging Assembly (AIA; [29]), also onboard the SDO spacecraft,
are displayed in Figure 2 alongside a ROSA 4170 Å continuum image for comparison. The
magnetic connectivity between the photosphere and corona is clearly evident in Figure 2, with
the loop structures seen in the coronal 171 Å channel closely linked to the photospheric pore
features seen in the ROSA 4170 Å continuum image. However, the AIA/SDO 304 Å transition
region filtergram (middle panel of Figure 2) does not contain pronounced pore structures, with
the high contrast synonymous with the photospheric images missing in the transition region. This
may suggest that the pores can no longer be considered magnetically dominated at chromospheric
and transition region heights. As a result, their atmospheres may become plasma dominated and
hence the well defined boundaries of the pores may become volume filling, thus losing contrast.
This is consistent with the magnetic and plasma pressure interplay as a function of atmospheric
height previously discussed in theoretical modelling work [30].
3. Analysis 7

(a) Bisector Velocity Amplitudes

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The Si I 10827 Å line forms over a large range of atmospheric heights in comparison to most
photospheric lines. This allows the line-of-sight (LOS) velocity to be derived at different optical
depths (and hence atmospheric layers) using bisector methods [31]. Through robust spectral
inversions and modelling, recent work has shown that Doppler motions derived at different
percentages of the Si I 10827 Å line depth may be coupled to specific optical depths [32].
Bisectors of the Si I 10827 Å line profile were computed across 10 – 90% of the line depth in
intervals of 10%, with the corresponding wavelength positions, λ, of each bisector noted. Here,
a bisector obtained at ‘90%’ line depth represents the intensities sampled by the FIRS instrument
90% of the way towards the darkest part of the line core (i.e., percentage line depth increases as
one samples closer to the observed line core). Similarly, a single Gaussian fit was applied to the
entire Si I 10827 Å line profile, with the fitted minimum providing the wavelength of the observed
line core (i.e., corresponding to 100% line depth). The measured wavelengths for each component
were then transformed into Doppler velocities. This was performed for all slit positions across the
full 355 scan steps selected for this study. Figure 3 displays an example Si I 10827 Å line profile,
normalised to the continuum intensity, Ic , with the calculated bisectors depicted using a dashed
blue line. Following the work of González Manrique et al. [32], the corresponding optical depths
are added for clarity, alongside a Doppler velocity conversion for the wavelength shifts measured
for each percentage bisector. It can be seen from Figure 3 that the optical depths span the range
−3.29 < log(τ500nm ) < −0.33 between 10 – 90% of the line depth.
In order to better study the observed Doppler motion, two-dimensional space–time plots at
each line depth percentage were created, providing Doppler velocity information as a function of
both the distance along the slit and time. Figure 4 displays one such space–time plot for bisector
velocities calculated at a line depth of 90%, corresponding to an optical depth of log(τ500nm ) ≈
−3.29 [32]. Clear oscillatory motion was detected at all line depths with periods on the order
of 5 minutes, which is consistent with the typical p-mode spectrum that has previously been
demonstrated to be coupled with magnetic structures in the lower solar atmosphere [33,34].
Oscillations with similar velocity amplitudes, ∼ 0.6 km/s, have been shown to be related to the
presence of slow magnetoacoustic waves that propagate through multiple layers of the solar
atmosphere [35]. Importantly, as can be seen in Figure 4, the oscillations demonstrate reduced
velocity amplitudes within the confines of the pore structures, where the root mean square (RMS)
velocities are <100 m/s inside the pores, compared with ∼300–500 m/s in the surrounding quiet
Sun, which are consistent with previous spectroscopic studies [36–41]. To investigate the plasma
parameters associated with the detected wave activity, and subsequently evaluate the energy flux,
it was imperative to undertake spectropolarimetric inversions of the Si I 10827 Å line.

(b) SIR Inversions

To probe the wave activity further, atmospheric plasma parameters were inferred through
the application of the Stokes Inversion based on Response functions (SIR; [42]) code to our
Si I 10827 Å Stokes spectra. SIR performs spectropolarimetric inversions under the assumptions
of local thermodynamic equilibrium (LTE) and vertical hydrostatic equilibrium, and outputs
height-stratified atmospheric parameters that can be related to specific optical depths and/or
geometric heights. The fitting of the Stokes parameters is accomplished by iteratively modifying
an initial model atmosphere until the synthesised profiles match the observed spectra. Differences
between synthetic and observed profiles are minimised using a Marquart non-linear least-
squares algorithm [43]. In order to maximise the signal to noise, the Si I 10827 Å spectral
data were temporally averaged across a set of time steps during optimal seeing conditions
spanning approximately 2 minutes (116.8 s). A time interval of ≈2 minutes was chosen since
this is long enough to generate high signal-to-noise Stokes signals, yet short enough to prevent
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Figure 4: Two-dimensional map revealing the evolution of bisector velocities, calculated at 90%
of the Si I 10827 Å line depth, as a function of both distance across the slit and time. Black dashed
lines represent the visual photospheric boundaries of each pore, labelled 1–5. Clear wave patterns
can be seen throughout by the periodic sign change of the velocity.

solar evolution from contaminating the averaged Stokes profiles. This resulted in a high-quality
[x, λ, S] cube, where x = 355 is the number of pixels along the length of the slit, λ is the
wavelength domain, and S represents the four Stokes vectors. This cube, averaged over ≈
2 minutes during optimal seeing conditions, was then employed in subsequent SIR inversions
to provide plasma parameters representative of the background atmosphere.
All pore pixels along the slit were subsequently inverted using an initial atmosphere based
on the umbral model for a small sunspot [44]. This was considered appropriate since the pore
structures under investigation are smaller and have a lower magnetic field strength than a large-
scale sunspot, and are therefore likely to have higher background temperatures due to their
reduced ability to suppress convective motions. In the surrounding quiescent regions away from
the pore structures, the FAL-C model was used for the initial atmosphere [45]. Stokes Q and
U profiles were not considered in the inversions as the pore magnetic fields are predominantly
vertical in the lower photosphere (see, e.g., the middle-right panel of Figure 1), resulting in the
Stokes Q/U signals being relatively weak and prone to fitting difficulties. Three cycles were
chosen for the SIR inversion code, with increasing numbers of nodes selected per cycle as shown
in Table 1. In the first cycle, relatively few nodes were employed in order to gain a solid foundation
that future cycles of the code could build upon. Additional nodes were subsequently introduced
gradually to allow more freedom for fitting specific line features. For the purpose of investigating
the energy flux of the detected waves (see Section 4 below), accurate plasma parameters linked to
temperature, magnetic field strength, and density are required.
Example fits achieved for Stokes I and V profiles for a pixel inside pore 1 are shown in Figure 5.
To evaluate quantitatively the quality of the fits, a reduced χ2 merit function was calculated
following the standard convention [46],
Nλ
1 X (Isyn − Iobs )2
χ2 = , (3.1)
ν Iobs
n=0

where Isyn is the intensity of the synthesised Stokes profile at a particular wavelength, Iobs is the
intensity of the observed Stokes profile at the same wavelength, Nλ is the number of wavelengths
employed in each inversion, and ν is the degrees of freedom. The average reduced χ2 values
achieved for all inverted pixels were χ2 (I/Ic ) = 0.85 and χ2 (V /Ic ) = 1.96, showing excellent fit
quality across the field of view.
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Table 1: Nodes for each atmospheric parameter, alongside Stokes profile weightings used in each
inversion cycle of the SIR code.

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Nodes
Parameter Cycle 1 Cycle 2 Cycle 3
Temperature 2 3 4
LOS Velocity 1 2 3
Magnetic Field 1 2 3
Inclination 1 2 3
Microturbulence 1 1 1
Weights
Stokes I 1 1 1
Stokes V 1 1 1

SIR computes atmospheric parameters across numerous optical depths, whose corresponding
geometric heights are also derived under the assumption of hydrostatic equilibrium. There is
some natural uncertainty surrounding the conversion between optical depth and geometric
height due to the assumptions that are made, with the reliability of the geometric height scale
being reliant on accurate values for temperature, density, and gas pressure. Note that a top
boundary condition must be specified for the gas pressure, resulting in the ability to shift
the geometric height scale upwards or downwards based on the requirements of hydrostatic
equilibrium. Recent research has shown that the precision of gas pressure and density estimations
may be improved through the application of a magneto-hydrostatic equilibrium [47], but this is
an ongoing area of research and therefore not implemented in the current SIR inversions.
Hence, it must be noted that varying opacities found for different solar structures, and thus
for each pixel along the slit, result in a non-uniform relationship between geometric height and
optical depth. To overcome this, each pixel along the slit had its own independent conversion
between optical depth and geometric height, which was particularly necessary for the conversion
between Si I 10827 Å line depth percentages into optical depths (via the study by González
Manrique et al. [32]), and then subsequently into physical geometric heights. This ensures that
the velocity information derived from the line bisectors can be compared directly with the SIR
inversion outputs, helping to generate two-dimensional plots of temperature, magnetic field
strength, density, and velocity as a function of both distance along the slit and atmospheric height.
Figure 6 displays such two-dimensional plots for the magnetic field strength, temperature,
plasma density, and Si I 10827 Å RMS velocity, where it can be seen that higher magnetic
field strengths and lower temperatures are present in the pores. Importantly, the magnetic
field strengths inferred from the SIR code are consistent with those present in the HMI/SDO
observations (see the upper-right panel of Figure 1), highlighting the suitability of the time-
averaged SIR maps to be used as proxies for the background photospheric solar atmosphere.
For the RMS velocity plot (lower-right panel of Figure 6), RMS velocities are calculated across
the FIRS slit for each of the line depth percentages used in Section 3(a), with the percentage line
depths subsequently converted into optical depths and geometric heights as discussed above.
The results displayed in Figure 6 are consistent with previous photospheric studies of magnetic
phenomena [17,40], but are now displayed as two-dimensional plots to aid visual clarity.

4. Discussion
The energy flux, E, of a propagating slow magnetoacoustic wave can be calculated following,

E = ρ vg hv 2 i , (4.1)
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0.06
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0.04
0.60

0.55 0.02

V/Ic
I/Ic

0.50 0.00

0.45
−0.02

0.40
−0.04

0.35
−0.06
0.30
10826.5 10827.0 10826.5 10827.0
Wavelength [Å] Wavelength [Å]

Figure 5: Sample Si I 10827 Å Stokes I (left) and V (right) spectra for a pixel inside pore 1, each
normalised by the average continuum intensity, Ic . The black lines show the observed Stokes
profiles, while the red dashed lines represent the synthetic profiles generated by SIR.

where ρ is the plasma density, vg is the group velocity of the propagating wave, and hv 2 i is the
mean square velocity [48].
The plasma density has already been obtained through SIR inversions of the spectropolarimetric
Si I 10827 Å data described in Section 3(b), and is displayed in the lower-left panel of Figure 6.
Similarly, the mean square velocities can be found by squaring the RMS velocity signals depicted
in the lower-right panel of Figure 6.
For a slow magnetoacoustic wave, the group velocity can be characterised by the tube speed.
In the thin flux tube approximation [49], the tube speed, cT , is equal to,
cs vA
cT = q , (4.2)
c2s + vA
2

where cs and vA are the local sound and Alfvén speeds, respectively [50,51]. The sound speed is
given by,
r
γkT
cs = , (4.3)
m
where γ = 5/3 is the ratio of specific heats, k is the Boltzmann constant, T is the temperature,
and m = 2.078 × 10−27 kg is the mean photospheric ion mass assuming a composition of 74.9%
hydrogen and 23.8% helium [52]. The Alfvén speed can be calculated via,
B
vA = √ , (4.4)
µ0 ρ
where B is the absolute magnetic field strength, and µ0 is the magnetic permeability.
The plasma parameters required to compute the sound, Alfvén, and tube speeds — notably
the temperatures, densities, and magnetic field strengths — have already been extracted from
the spectropolarimetric SIR inversions and are displayed in Figure 6. Following Equations 4.2 –
4.4, the sound, Alfvén, and tube speeds were computed as a function of both distance along the
FIRS slit and atmospheric height, which are displayed in Figure 7. It can be seen in the upper-left
panel of Figure 7 that the cooler temperatures found inside the pore boundaries result in reduced
sound speeds in these locations. Locations away from the pores have sound speeds on the order
of 9 km/s, which is consistent with previous numerical modelling efforts of granulation [53].
However, the increased magnetic field strengths found within the pores (upper-right panel of
Figure 7) provides increased Alfvén speeds compared to the quiet Sun surroundings, especially
at higher photospheric heights where the density has decreased by multiple orders of magnitude.
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Figure 6: Atmospheric parameters as a function of both distance along the FIRS slit and
atmospheric height, where the magnetic field strength (upper left), temperature (upper right),
and plasma density (lower left) values are computed via SIR inversions of the Si I 10827 Å
spectropolarimetric data. The plasma density is displayed on a logarithmic scale to aid visual
clarity. The RMS velocity amplitudes (lower right) are calculated from bisector velocities over a
range of Si I 10827 Å percentage line depths. Pore boundaries are highlighted by the vertical white
dashed lines, with each pore numbered 1–5 as initially defined in the lower panel of Figure 1.

The Alfvén speeds contained within the pores span the range of approximately 5 km/s . vA .
30 km/s, which is consistent with previous pore modelling studies [17]. Finally, the tube speeds,
which are a product of the sound and Alfvén speeds (see Equation 4.2), show increased speeds
within the pore boundaries across all atmospheric heights, highlighting the ability of magnetic
pores to propagate wave energy flux through the atmosphere with elevated group velocities.
With the tube speeds computed as a function of both distance along the slit and atmospheric
height (lower panel of Figure 7), it is now possible to combine them with the plasma density and
RMS velocity maps shown in the lower-left and lower-right panels of Figure 6, respectively, to
calculate the energy flux following Equation 4.1. The corresponding energy flux map is displayed
in Figure 8. Evidence of wave energy flux is visible both within the pore regions labelled 1–5, in
addition to the more quiescent regions of the Sun outside of the exterior pore boundaries. The
regions outside the pore boundaries are still magnetic in nature, with B 6= 0 G (upper-left panel
of Figure 6), resulting in positive tube speeds (i.e., cT > 0 km/s) everywhere along the FIRS slit
(lower panel of Figure 7). This results in wave energy flux, through the application of Equation 4.1,
being present throughout the entire observed atmosphere. However, the calculated energy fluxes
in these locations may not entirely be related to guided magnetoacoustic wave motion. The larger
RMS velocities in the non-pore regions (see the lower-right panel of Figure 6) may be a result
of other non-oscillatory dynamics, such as convective overshoots [54,55], which may manifest
as artificially heightened energy flux values in Figure 8. The higher energy fluxes calculated in
the quieter solar region to the south-east of the pores (<7 Mm), when compared to the quiet
Sun region to the north-west (>43 Mm), is mostly likely a result of the stronger total magnetic
field strengths found in this location (see the upper-right panel of Figure 1 and the upper-left
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Figure 7: The sound (upper left), Alfvén (upper right), and tube (bottom) speeds displayed as a
function of both distance across the slit and atmospheric height. Pore boundaries are highlighted
by the vertical dashed lines, with each pore numbered 1–5 as initially defined in the lower panel
of Figure 1.

panel of Figure 6). A higher magnetic field strength naturally results in increased Alfvén and tube
speeds for that region. This is confirmed in Figure 7, where increased Alfvén and tube speeds are
preferentially present in the south-east (<7 Mm) region of the field of view. As a result, larger
tube speeds, coupled with similar densities and velocity fluctuations, will manifest as increased
energy fluxes, even if they are not strictly coupled to upwardly propagating magnetoacoustic
wave phenomena. In these locations (e.g., >38 Mm in Figure 8) we see a much more rapid
decrease in energy flux with atmospheric height when compared with the pore regions. This may
be a direct consequence of the more heavily inclined magnetic fields present in these locations,
hence inhibiting the propagation of energy flux (created through wave motion and/or convective
overshoots) into higher regions of the solar atmosphere.
The inclination angles of the magnetic field, which are derived from the HMI/SDO VFISV
vector magnetograms and correspond to a height range of 250 − 300 km [56,57], are displayed
in Figure 8 using a solid green line. Inclination angles, which were calculated from the
heliographic re-projections of the HMI/SDO vector magnetograms, were preferred here due to
these inclinations being relative to the solar normal, unlike the inclination angles output from
SIR inversions which are relative to the line-of-sight of the observer. It can be seen that the
pore structures have magnetic fields approximately normal to the solar surface (consistent with
the HMI/SDO observations shown in the middle-right panel of Figure 1), while locations away
from the pores demonstrate more heavily inclined magnetic fields, with regions > 43 Mm along
the FIRS slit having approximately horizontal magnetic field configurations. This highlights the
efficiency of magnetic pores as wave energy conduits in the lower solar atmosphere.
Another notable feature visible in Figure 8 is the increase in energy flux visible towards the
edges of the pore boundaries for pores 2, 3, and 4. Contrarily, it can be seen in Figure 8 that pore
1 has the dominant energy flux towards its centre, while pore 5 displays more uniform energy
structuring across its entire diameter.
 13

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Figure 8: Energy flux, in units of W/m2 , displayed as a function of both distance across the slit
and atmospheric height. To aid visualisation, the colour scale employed is a logarithmic scale
spanning 103 − 105 W/m2 . Pore boundaries are highlighted by the vertical white dashed lines,
with each pore numbered 1–5 as initially defined in the lower panel of Figure 1. The solid green
line displays the inclination angles of the magnetic field along the slit, with angles of 90◦ and 180◦
highlighting fields that are parallel and perpendicular, respectively, to the solar surface. High
energy fluxes towards the edges of pore structures (i.e., pores 2, 3, and 4) may be the result of
surface mode waves, while more uniform energy structuring (i.e., pores 1 and 5) may be related to
the presence of body mode waves. Energy flux values seen in non-pore regions are likely a result
of convective overshoots and not specifically propagating magnetoacoustic wave phenomena.

Such energy structuring can be attributed to the presence of surface (pores 2, 3, and 4) and
body (pores 1 and 5) mode waves, which have only recently been conclusively observed in
photospheric imaging data [21]. Previous identifications of surface mode waves have come from
theoretical estimations [17,18,58,59]. However, here we clearly show the existence of heightened
wave energy towards the edges of the pore boundaries, which has only been made possible
by the high spectral, spatial, and temporal resolutions of our dataset coupled with modern
spectropolarimetric inversion routines.
A natural question arises as to why pores 1 and 5 demonstrate different wave modes (‘body’
vs ‘surface’) when compared to the more central pores 2 – 4. From inspection of the structuring of
the pores in Figure 1, the more complex physical composition of pores 1 and 5 may help provide
an answer. Pores 1 and 5 are smaller in area than pores 2 – 4, and display weaker magnetic
field strengths at higher atmospheric heights (see the upper-left panel of Figure 6). Reduced field
strengths will result in less inhibition of convection, and the subsequent higher temperatures in
pores 1 and 5 (see the upper-right panel of Figure 6) may contribute to the structuring seen in
the energy flux map shown in Figure 8. For example, the increased temperatures found in pores
1 and 5 result in more elevated sound speeds, which helps negate the effects of reduced Alfvén
speeds on the corresponding tube speeds, where lower Alfvén speeds are caused by the weaker
magnetic field strengths present in these pores (see Figure 7). Hence, the less uniform structuring
of pores 1 and 5 may actually contribute to the more even stratification of wave energy flux visible
in Figure 8.
Indeed, the increased RMS velocity inside pore 1 (see Figure 6), which may be related to
the presence of small-scale convective motions not suppressed by the weaker magnetic fields,
may promote elevated wave energy fluxes towards the centre of these bodies. However, the 14
clear periodicities observed in all pores (see Figure 3) show unequivocal evidence of upwardly
propagating wave motion that could not be replicated simply by the presence of bright structures

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or small-scale granulation within the confines of the pore. This, alongside the very confined
spread of energy fluxes across the diameters of pores 1 and 5 (Figure 9) would suggest the most
likely explanation is that body modes are present in these structures. As a result, we currently do
not have an answer as to why pores 1 and 5 demonstrate different wave modes when compared
to their more central pore counterparts. Future work will need to examine the sub-photospheric
drivers responsible for the observed wave motion, and through intensive numerical modelling
(e.g., [60]), uncover the role of waveguide structuring, composition, and inclination in the visible
wave signatures.
The energy fluxes (including both body and surface modes), visible in Figure 8, demonstrate
the efficiency of magnetic pores as magnetoacoustic wave energy conduits in the lower solar
atmosphere. Indeed, the energy fluxes measured here as a function of atmospheric height also
agree with the findings of Grant et al. [17], who employed imaging observations and a theoretical
framework to estimate the associated energies. Previous work has examined the propagation of
magnetoacoustic waves in coronal fan loops, and estimated the damping lengths of the wave
activity by examining the amplitude decay rates as a function of distance along the waveguide
[61–66]. Specifically, the relation used to uncover the damping length, Ld , is given by [67],

A(h) = A0 e−h/Ld , (4.5)

where A(h) is the amplitude measured at a given height, h, and A0 is the initial amplitude of the
wave. As the energy of the propagating magnetoacoustic waves is proportional to the amplitude
squared, i.e., E(h) ∝ A(h)2 , we can adapt the damping length equation to be compatible with the
energy fluxes displayed in Figure 8, where,

E(h) = E0 e−2h/Ld . (4.6)

For the first time, by employing Equation 4.6, we are able to calculate the photospheric
damping lengths of propagating magnetoacoustic waves in solar pores. Figure 9 displays the
average energy fluxes for each of the 5 pores, alongside a quiescent region away from the pore
structures (averaged over 43 − 50 Mm along the FIRS slit where the magnetic field inclinations
are less vertical; solid green line in Figure 8), as a function of atmospheric height. The average
energy flux for each pore was calculated by taking the mean value at each geometric height
between the vertical dashed lines that outline the respective pore boundaries in Figures 6 – 8.
For each atmospheric height, the energy uncertainties in Figure 9 correspond to the standard
deviations of the averaged energies. It can be seen that pores 1 and 5, which are best characterised
as containing body mode waves, have the smallest energy uncertainties as a result of the relatively
uniform energy structuring spanning their entire cross-section. Importantly, our energy fluxes
also corroborate the work of Keys et al. [21], who suggested that surface mode sausage waves
should carry more energy flux when compared to their body mode counterparts. Lines of best
fit allow the damping lengths to be calculated for each of the structures studied. The quiescent
region, located away from the pores, displays the most rapid damping length with Ld ≈ 210 km.
This may be a consequence of the reduced magnetic field strengths (and hence tube speeds)
and larger inclination angles (see the middle-right panel of Figure 1) being unable to efficiently
guide the magnetoacoustic waves upwards. Pores 1 and 5, which are best characterised as
containing body mode waves, have the longest damping lengths, corresponding to Ld ≈ 276 km
and Ld ≈ 288 km, respectively. On the other hand, pores 2, 3, and 4, which are best characterised
as surface mode waveguides, have slightly smaller damping lengths equating to Ld ≈ 258 km,
Ld ≈ 265 km, and Ld ≈ 256 km, respectively. Recent theoretical work has shown that the degree
of magnetic twist in the waveguide can drastically affect the damping rate of surface sausage
mode waves [68]. Furthermore, the interplay between electric resistivity and resonant absorption
 105 15
Non-pore Pore #1 Pore #2
Energy Flux (W/m2)

Ld = 210 km Ld = 276 km Ld = 258 km

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104

103

105
Pore #3 Pore #4 Pore #5
Energy Flux (W/m2)

Ld = 265 km Ld = 256 km Ld = 288 km

104

103

0 200 400 0 200 400 0 200 400

Geometric Height (km) Geometric Height (km) Geometric Height (km)

Figure 9: Average energy fluxes as a function of geometric height for a non-pore region (upper-
left), in addition to pores 1–5 (upper-middle through to lower-right panels). Uncertainties at
each geometric height correspond to the standard deviations of the energy fluxes included in
the corresponding average. The dotted red lines correspond to exponential lines of best fit, with
the corresponding damping lengths, Ld , indicated in the legend provided at the top-right of each
panel. It can be noted that pores (1 & 5) containing body mode waves exhibit the longest damping
lengths, while pores (2–4) exhibiting surface mode waves demonstrate the shortest damping
lengths.

may also contribute to the differing damping lengths found between the surface- and body-mode
waves [59].
The damping lengths calculated here are much shorter than those deduced for the corona
(approximately 3700 − 4800 km; [67]), which is likely a consequence of the much shorter density
and pressure scale heights found in the lower solar atmosphere [69]. Following the standard
convention [70] for the scale height, H, where,

∆h
H= , (4.7)
∆ log(τ500nm )

the pores in the present study span a geometric height of ∆h = 500 km and an optical depth
of ∆ log(τ500nm ) ≈ 2.96, giving H ≈ 170 km. As a result, the average damping length across all
5 pores, Ld ≈ 268 km, is on the same order of magnitude as the estimated photospheric scale
height. Modelling work has predicted coronal scale heights on the order of 30 – 60 Mm (∼30 000
– 50 000 km; [71–73]), so an initial comparison would suggest that the measured coronal damping
lengths are much shorter than typical coronal scale heights (by at least an order of magnitude).
However, recent theoretical work has calculated the expected coronal damping lengths using
classical Spitzer values for thermal conduction and predicted much longer damping lengths
than observed in coronal loops [67], hence suggesting either a lack of sensitivity in current
coronal observations, or ill-constrained values of thermal conduction in current modelling efforts.
Regardless, this is an area of active research, and our measurements of the damping lengths in
the lower solar atmosphere will be crucial for comparisons to the next generation of numerical
models of MHD wave activity.
5. Concluding Remarks 16

Here we have presented spectropolarimetric Si I 10827 Å data of a collection of five magnetic

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pores acquired by the FIRS instrument at the DST. Our observations show clear evidence of wave
activity occurring in the lower solar atmosphere, with a bisector velocity study of the Si I 10827 Å
line providing velocity oscillations visible across a variety of optical depths with periods on the
order of 5 minutes, consistent with the global p-mode spectrum. Through spectropolarimetric
inversions, we deduce the local plasma densities, temperatures, and magnetic field strengths as a
function of atmospheric height, which allowed us to calculate the corresponding sound, Alfvén,
and tube speeds across our field of view. Parameters derived from the inversions, combined
with root mean square velocities, provides energy flux estimates as a function of height in the
lower solar atmosphere. We find evidence of considerable energy flux trapped within the pore
boundaries, with on the order of 30 kW/m2 at a geometric height of ≈100 km. Examination of the
energy structuring across the diameter of each pore reveals evidence for both propagating surface-
and body-mode sausage waves, something that supports recent imaging observations [21] with
spectropolarimetry.
For the first time, we estimate the damping lengths of the propagating sausage mode waves
trapped within the five pores. We find that the pores demonstrating surface mode characteristics
have an average damping length of Ld ≈ 260 km, while the pores identified as displaying body
mode signatures have a slightly longer average damping length of Ld ≈ 282 km. Both of these
values are on the same order of magnitude as the photospheric scale height, which we estimate
to be H ≈ 170 km. We hypothesise that the surface mode waves may be able to dissipate their
energy more readily, through a combination of magnetic twist, electric resistivity and/or resonant
absorption mechanisms [59,68]. We appreciate that the measured difference in damping lengths
is small and based around a limited number of pores. As a result, we openly encourage the
community to continue this type of study on a larger, more statistically significant basis. It is
hoped that new high-resolution facilities, such as the Daniel K. Inouye Solar Telescope (DKIST;
[74]), with improved polarimetric sensitivity will allow more precise measurements to be made.
For example, the Diffraction Limited Near Infrared Spectropolarimeter (DL-NIRSP) instrument
will enable simultaneous two-dimensional spatial mapping of the Si I 10827 Å line to be obtained
with a spatial resolution as high as 0 ′′. 06 (some five times higher than the data presented in
our current study). The greater spatial resolution will enable the precise energy structuring of
the pores to be deduced with greater clarity, and the two-dimensional fibre-fed nature of the
instrument will allow the entire pore structure to be studied simultaneously. As a result, we
look forward to upcoming DKIST observations to shine light on the propagation of sausage
mode waves in solar pores, and uncover their true role in supplying energy to the outer solar
atmosphere.
Data Accessibility. The data used in this paper are from the observing campaign entitled ‘The Influence of
Magnetism on Solar and Stellar Atmospheric Dynamics’ (NSO-SP proposal T1081; principal investigator: DBJ),
which employed the ground-based Dunn Solar Telescope, USA, during July 2016. The Dunn Solar Telescope
at Sacramento Peak/NM was operated by the National Solar Observatory (NSO). NSO is operated by the
Association of Universities for Research in Astronomy (AURA), Inc., under cooperative agreement with the
National Science Foundation (NSF). Additional supporting observations were obtained from the publicly
available NASAâĂŹs Solar Dynamics Observatory (https://sdo.gsfc.nasa.gov) data archive, which can be
accessed via http://jsoc.stanford.edu/ajax/lookdata.html. The data that support the plots within this paper
and other findings of this study are available from the corresponding author upon reasonable request.

Authors’ Contributions. DBJ carried out the experiments and conceived of and designed the study. CAG-
M performed the data reduction and scientific analysis, with assistance from DBJ, SDTG, PHK, CB, SJ, and
BRC. CAG-M drafted the manuscript, with theoretical input provided by JMR and TVD. All authors read and
approved the manuscript.

Competing Interests. The authors declare that they have no competing interests.
Funding. Funding has come from the following sources:
• Invest NI and Randox Laboratories Ltd. Research & Development Grant (059RDEN-1);
 • European Union’s Horizon 2020 research and innovation programme (grant agreement no. 682462);
17
• Research Council of Norway through its Centres of Excellence scheme (project no. 262622);
• European Union’s Horizon 2020 research and innovation programme (grant agreement No 724326);

rsta.royalsocietypublishing.org Phil. Trans. R. Soc. A 0000000

..................................................................
• Research Council of Norway (project number 262622); and
• The Royal Society (grant Hooke18b/SCTM).

Acknowledgements. CAG-M, DBJ, and SDTG are grateful to Invest NI and Randox Laboratories Ltd. for
the award of a Research & Development Grant (059RDEN-1) that allowed the computational techniques
employed to be developed. SJ acknowledges support from the European Research Council under the
European Union’s Horizon 2020 research and innovation programme (grant agreement no. 682462) and from
the Research Council of Norway through its Centres of Excellence scheme (project no. 262622). JMR and TVD
were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement No 724326). TVD received further support from the C1 grant
TRACEspace of Internal Funds KU Leuven (number C14/19/089). The space-based data employed in this
work is courtesy of NASA/SDO and the AIA, EVE, and HMI science teams. The authors wish to acknowledge
scientific discussions with the Waves in the Lower Solar Atmosphere (WaLSA; www.WaLSA.team) team,
which is supported by the Research Council of Norway (project number 262622), and The Royal Society
through the award of funding to host the Theo Murphy Discussion Meeting “High resolution wave dynamics in
the lower solar atmosphere” (grant Hooke18b/SCTM).

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