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Physics_Thesis_Template/content/appendixB.tex
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\chapter{Example for the presentation of programming code \label{chap:appendixCode}}
\chapter{Additional folded lightcurves \label{chap:apB}}
%In this section the code developed for this work is presented. Mention here the general dependencies you used in your development environment.
%\systemDependencies{}
\section{System dependencies \label{sec:SystemDependencies}}
The presented code is written for Python 3.7.
\Table{tab:PyModules} details the used standard and specialized python packages and modules and is structured as follows.
\begin{itemize}
\item The package and module names are listed in the first column. Specialized modules are preceded with the abbreviation of the parent package, whose abbreviated package name is indicated in brackets.
\item The version number of the used library is indicate in the second column.
\item A brief module description is provided in the third column.
%
\end{itemize}
The top panel reports the standard python packages, contained in the standard python distribution. The bottom panel lists specialized packages, which require individual download.
(Modified table based on Table A.1 from Rafael Goldgruber's Bachelor thesis).
\begin{table}[h!]
%{\centering
\vspace{3mm}
\tabcolsep=8pt
\caption{Required Python modules for the presented code.}
\begin{tabular}{p{0.2\textwidth}
p{0.1\textwidth}
p{0.6\textwidth}}
\hline\hline
Package / Module & Version & Modul Description\\
\hline
math & $-$ & Access mathematical functions; \\
os & $-$ & Miscellaneous
operating system interfaces \\
glob & $-$ & Creates iterable lists from folder content \\
matplotlib & 3.3.1 & Core package for scientific computation \& plotting \\
numpy & 1.19.1 & Core package for numerical computing \\
\hline
astropy (ap) & 4.0.1 & Community Python Library for Astronomy \\
\textit{~~ap}.astroquery & 0.4 & Querying astronomical web databases \\
\textit{~~ap}.vizier & 0.4 & Importing online data and catalogues, published along with papers \\
\textit{~~ap}.io.pyfits & & Reading and operating with FITS files \\
mesareader & $-$ & Reading MESA history and profile output files\\
%datetime & $-$ & supplies classes for manipulating dates and times \\
%jdcal & 1.4.1 & functions for converting between Julian dates and calendar dates \\
%PIL & $-$ & Python Imaging Library \\
%unicodedata & $-$ & access to the Unicode CharacterDatabase\\
\hline
\end{tabular}
\label{tab:PyModules}
%\tablefoot{ }
\end{table}
\section{Program to name new Planets \label{cod:HellowWorld}}
Provide a short description of the following script and give a brief description of the key settings or input format. The example below shows how to insert the code of a whole program from its source file.
\lstinputlisting[label=code:sampleCode,
frame=Tb,
caption= HelloPlanet.py: Sophisticated code to name new worlds.,
language=python]{code/helloWorld.py}
\vspace{5mm}
\begin{table}[h!]
\caption{Option menu for helloWorld.py (\Listing{code:sampleCode}), \label{cod:helloWorld}}
%\centering
\hfill\begin{tabular}{p{0.15\textwidth}p{0.15\textwidth}p{0.6\textwidth}}
\hline\hline
Type & Argument & Functionality \\ \hline
InCode & if \hbox{xY==True} & Description of what will happen if this option is used. \\
CmdL & -n & Description of what will happen if this option is used. \\
ReqIn & parameter name & Description of what will happen if this option is used. \\
\hline
\end{tabular}\hfill~
\tablefoot{Usage options:
\textit{InCode} curial options to be set inside the code before excecution of the program,
\textit{CmdL} options set in the command line,
\textit{ReqIn} requested user input during the execution of the program;
}
\label{tab:functionalityTable}
\end{table}
\section{Example for long code listing \label{chap:appendixMesaInlists}}
This section presents styles to present longer code snippets. To save printing space and cost, these are typset in a two-column format.
The combined presentation of \Listing{code:inlist1} and \Listing{code:inlist2} show how two snippets can be shown. \Listing{code:longListing} depicts how long code snippets or full programs can be included as multi-column and multi-page element.
Also for these listings a preamble stating the system requirements is needed.
\begin{landscape}
\begin{multicols}{2}
\begin{lstlisting}[caption=inlist1 \label{code:inlist1}]
&star_job
show_log_description_at_start = .true.
pgstar_flag = .true.
/ ! end of star_job namelist
&controls
extra_terminal_output_file = 'log1'
log_directory = 'LOGS1'
/ ! end of controls namelist
&pgstar
History_Panels1_win_flag = .true.
History_Panels1_win_width = 5
History_Panels1_win_aspect_ratio = 1.0
History_Panels1_title = 'Orbital evolution'
History_Panels1_num_panels = 2
History_Panels1_yaxis_name(1) = 'period_days'
History_Panels1_other_yaxis_name(1) =
'lg_mstar_dot_1'
History_Panels1_yaxis_name(2) = 'Jdot'
History_Panels1_other_yaxis_name(2) =
'binary_separation'
/ ! end of pgstar namelist
\end{lstlisting}
%##########################################################################
\begin{lstlisting}[caption=inlist2 \label{code:inlist2}]
&star_job
show_log_description_at_start = .false.
/ ! end of star_job namelist
&controls
extra_terminal_output_file = 'log2'
log_directory = 'LOGS2'
/ ! end of controls namelist
&pgstar
/ ! end of pgstar namelist
\end{lstlisting}
\end{multicols}
%\tablefoot{}
% \end{table*}
\end{landscape}
\begin{landscape}
\begin{lstlisting}[language=Fortran,
caption = Example for a multi-column and multi-page code listing.
\label{code:longListing},frame=T]
\end{lstlisting}
\begin{lstlisting}[language=Fortran,multicols=2,frame=none]
! inlist to evolve a 15 solar mass star
! For the sake of future readers of this file,
! ONLY include the controls you are actually using.
! DO NOT include all of the other controls that
! simply have their default values.
&star_job
! begin with a pre-main sequence model
create_pre_main_sequence_model = .true.
! save a model at the end of the run
save_model_when_terminate = .false.
save_model_filename = '15M_at_TAMS.mod'
! display on-screen plots
pgstar_flag = .true.
/ !end of star_job namelist
&controls
! starting specifications
initial_mass = 15 ! in Msun units
! options for energy conservation
use_dedt_form_of_energy_eqn = .true.
use_gold_tolerances = .true.
! stop when the star nears ZAMS (Lnuc/L > 0.99)
Lnuc_div_L_zams_limit = 0.99d0
stop_near_zams = .true.
! stop when the center mass fraction
of h1 drops below this limit
xa_central_lower_limit_species(1) = 'h1'
xa_central_lower_limit(1) = 1d-3
/ ! end of controls namelist
&pgstar
! MESA uses PGPLOT for live plotting and
! gives the user a tremendous amount of control
! of the presentation of the information.
! show HR diagram
! this plots the history of L,Teff over many
! timesteps
HR_win_flag = .true.
! set static plot bounds
HR_logT_min = 3.5
HR_logT_max = 4.6
HR_logL_min = 2.0
HR_logL_max = 6.0
! set window size (aspect_ratio = height/width)
HR_win_width = 6
HR_win_aspect_ratio = 1.0
! show temperature/density profile
! this plots the internal structure at single
! timestep
TRho_Profile_win_flag = .true.
! add legend explaining colors
show_TRho_Profile_legend = .true.
! display numerical info about the star
show_TRho_Profile_text_info = .true.
! set window size (aspect_ratio = height/width)
TRho_Profile_win_width = 8
TRho_Profile_win_aspect_ratio = 0.75
/ ! end of pgstar namelist
\end{lstlisting}
\vspace{-\baselineskip}
\noindent\rule{\linewidth}{0.4pt}
\end{landscape}
\section{TYC 4595-107-1 \label{apB:TYC_4595-107-1}}
Physics_Thesis_Template/content/chapter-results.tex
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\subsection{BD-08 995}
BD-08 995, also known by TIC 43472154, is a G type star with a surface temperature of 5231.2 K, which is \textasciitilde87 pc away. It is a very active solar like star, producing over 200 superflares per year (\cite{tess_1st_year_superflares}). It has a rotational period of 2.8 days (\cite{tess_1st_year_superflares}). There are two TESS lightcurves available, sectors 5 and 32.\\
Looking at figure \ref{fig:BD-08_995-Flarecount-10_Bins}, which shows the flare distribution across the normalized phase of the folded lightcurves with 10 bins, it shows a clear peak of flares appearance in the lightcurve minima at phase $1 \pi$. The errorbars of this wide peak only overlap with the first bin of the plot at phase $0 \pi$.
This bin belong to the phase maxima which also shows slight increase in flare activity at phase $0/2 \pi$ compared to the transition regions at around phase $0.5 \pi$ (maxima to minima) and $1.5 \pi$ (minima to maxima). Considering errors for this, the errorbars of the bins at the phase maxima overlap with those of the transition regions.\\
Figure \ref{fig:BD-08_995-Flarecount-30_Bins} shows the same data just with 30 bins instead of 10. Ignoring the errorbars, it shows a similar picture as the previous figure. But due to the low number of total detected flares, and a the relatively large bin count, the errorbars become large compared to the individual bins. Due to this, the errorbars of most bins overlap with each other, with the exceptions of the the first bin at phase $0 \pi$ and the bin at phase \textasciitilde$1.1 \pi$, whichs erorbars only overlap with other higher bins like the ones at phase \textasciitilde$0.9 \pi$ and \textasciitilde$1.4 \pi$.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -199,6 +205,16 @@ This section contains a selection of results for individual stars. The results f
\label{fig:BD-08_995-Flarecount}
\end{figure}
The distribution of normalized flare peaks for BD-08 995 in figure \ref{fig:BD-08_995-flarepeaks_1.2} shows that the highest flare peak appeared at around phase $0.1 \pi$ with a peak of \textasciitilde1.11. Other high flare peaks were detected at phases \textasciitilde$1 \pi$ and \textasciitilde$1.9 \pi$. Furthermore the flares around phase $1 \pi$ seem to have higher average peak.
\begin{figure}[pt!]
\includegraphics[width=.95\textwidth]{plots/sine/BD-08_995/BD-08\space\space\space995-Flarepeaks_maxY-1.2.png}
\caption{Distribution of flare peaks in relation to the normalized phase at which they occured for BD-08 995. Y-Axis shows the flare peak and is limited to the value of the highest peak detected. The x-axis shows the normalized phase.}
\label{fig:BD-08_995-flarepeaks_1.2}
\end{figure}
Looking at the folded TESS lightcurves of sector 5 (\ref{fig:BD-08_995-TESS5_foldedLC}) and 32 (\ref{fig:BD-08_995-TESS32_foldedLC}) one can see the earlier presented distribution of flares and their peaks. In TESS sector 5 there appear comparatively many flares at around phase $-0.2$ (not normalized). The highest detected flare peak which was mentioned prior was detected in the TESS sector 32 lightcurve at phase $-1.2$.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -221,6 +237,10 @@ This section contains a selection of results for individual stars. The results f
\FloatBarrier
\subsection{TYC 1360-957-1}
Not much is published about TYC 1360-957-1. It has been categorized as spectral type K on SIMBAD (\cite{simbad}). It has the TESS Input Catalogue number 247117382, and has been observed by TESS in sectors 44, 45 and 46.\\
Looking at the flare distribution histogram with 10 bins for this star in figure \ref{fig:TYC_1360-957-1-Flarecount-10_Bins} one can see that the highest peaks in order are at phase \textasciitilde$0.7 \pi$, \textasciitilde$0.4 \pi$ and \textasciitilde$1.2 \pi$. The last one being two bins wide. The first two are, including error, above their surrounding bins, while for the third peak, the second peaks errorbar overlaps with those of the smaller bins.
Looking at the histogram with 30 bins of the same dataset (figure \ref{fig:TYC_1360-957-1-Flarecount-30_Bins}), the first 2 peaks mentioned for the histogram with 10 bins are still visible. But compared to the privious figure, the low number of flares result in a rather large error. This causes the errorbars of the two mentioned bin peaks to overlap with the surrounding bins which could be estimated to be the average.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -240,6 +260,17 @@ This section contains a selection of results for individual stars. The results f
\label{fig:TYC_1360-957-1-Flarecount}
\end{figure}
Figure \ref{fig:TYC_1360-957-1-flarepeaks_1.31} presents the overall distribution on the normalized phase detected for TYC 1360-957-1 in this study. The three highest flare peaks detected were at a normalized phase of \textasciitilde$0.8 \pi$, which is very close to the phase minimum at $1 \pi$. Three more higher flare peaks stand out at phase $1.2 \pi$. While they are not as high as the previous three, they have a higher peak than the rest of the detected flares.
\begin{figure}[pt!]
\includegraphics[width=.95\textwidth]{plots/sine/TYC_1360-957-1/TYC 1360-957-1-Flarepeaks_maxY-1.3130771478482715.png}
\caption{Distribution of flare peaks in relation to the normalized phase at which they occured for TYC 1360-957-1. Y-Axis shows the flare peak and is limited to the value of the highest peak detected. The x-axis shows the normalized phase.}
\label{fig:TYC_1360-957-1-flarepeaks_1.31}
\end{figure}
The used folded lightcurves used can be seen in figure \ref{fig:TYC_1360-957-1-TESS_foldedLCs}. This figure is split into the three different TESS sectors. In \subref{fig:TYC_1360-957-1-TESS44_foldedLC} sector 44 is visible. The lowest point of the folded lightcurve is slightly shifted from the center, which represents the lowest point of the sine fit. One can also see that two large flares happened at this point.
No such large flares can be seen in \subref{fig:TYC_1360-957-1-TESS45_foldedLC}, unlike in \subref{fig:TYC_1360-957-1-TESS46_foldedLC} which shows a large flare again.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -269,6 +300,10 @@ This section contains a selection of results for individual stars. The results f
\FloatBarrier
\subsection{TYC 4595-107-1}
TYC 4595-107-1, also known as TIC 394030788, is a G type star with an effective temperature of 5231 K, a radius of 0.9 $R_\odot$ (\cite{tess_2nd_year_superflares}, \cite{superflare_rate_variation_g_type}), mass of 0.89 $M_\odot$ (\cite{superflare_rate_variation_g_type}) and a rotational period of 3.3 days (\cite{tess_2nd_year_superflares}, \cite{superflare_rate_variation_g_type}) and was observed in 20 TESS sectors. The folded lightcurves for TYC 4595-107-1 can be found in appendix \ref{apB:TYC_4595-107-1}.\\
The first histogram, figure \ref{fig:TYC_4595-107-1-Flarecount-10_Bins}, with 10 bins shows the accumulated data for all 20 observed lightcurves. Due to the high number of available lightcurves, and TYC 4595-107-1 being a very active star (\cite{tess_2nd_year_superflares}, \cite{superflare_rate_variation_g_type}), the total flare count is very high. There seems to be a base level of flares per bin of around 30 over the phase, with a large and two bin wide peak at around phase $0.6 to 0.8 \pi$. This increase in flares is high enough to be outside of the error of the base amount of flares. Another peak, even though less certain as its errorbar overlaps with the surrounding bins, appears at the bin at phase $1.9 \pi$. A similar increase in flares can be seen at the bin at $0.2 \pi$.\\
The histogram with 30 bins (figure \ref{fig:TYC_4595-107-1-Flarecount-30_Bins}) shows a similar result. It shows a large increase in flares around phase $0.6 to 1 \pi$, as well at at $1.9 to 0.1 \pi$ and $0.4 \pi$. Only the first mentioned peak managed to be large enough though, to not have overlapping errors with the surrounding lower count bins.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -357,6 +392,13 @@ Figure \ref{fig:V471Tau-flarepeaks_1.053} shows the normalized phase and peak of
\FloatBarrier
\subsection{V* HK Aqr}
HK Aqr is a M dwarf with a mass of 0.57 $M_\odot$, a radius of 0.53 $R_\odot$ and is around 22.3 pc away from our solar system. Its effective temperature is aroun 3800 K (\cite{conch_shell_m_dwarfs}). It was observed in four TESS sectors.
HK Aqr is mentioned here, as it is a star, for which the optimize fold algorithm partially broke. This happened for its lightcurves for the sectors 29 and 42. The algorithm found for both periodograms a second signal for a possible period. This resulted in the folded lightcurves seen in figures \ref{fig:HKAqr-TESS29_foldedLC} and \ref{fig:HKAqr-TESS42_foldedLC}. Figures \ref{fig:HKAqr-Flarecount-10_Bins} and \ref{fig:HKAqr-Flarecount-30_Bins} were created with this dataset.\\
In figure \ref{fig:HKAqr-Flarecount-10_Bins} one can see an increase in flares at around phase $1.3 \pi$. This peak is high enough to be outside the error range of the lower flare count bins between phase $0 to 1 \pi$. Figure \ref{fig:HKAqr-Flarecount-30_Bins} paints a similar picture. Additionally it shows a peak at phase $0 \pi$ though, which is during the phase maximum, as well as one at around phase $1.6 \pi$ which is in the transition from minima to maxima.\\
Figures \ref{fig:HKAqr-Flarecount-10_Bins_Period} and \ref{fig:HKAqr-Flarecount-30_Bins_Period} show the historgrams for the data of the two folded TESS lightcurves of sectors 29 and 42 which were flagged as period folded with 10 and 30 bins respectively. The folded lightcurves can be found in figure \ref{fig:HKAqr-TESS_foldedLCs_Period}.
In figure \ref{fig:HKAqr-Flarecount-10_Bins_Period} the overall flare distribution seems to be relatively high from phase $0.2 \pi$ to $1.4 \pi$, with a peak at phase $1.2 \pi$. The amount of detected flares during the maximum of the lightcurves at phase $1.8$ to $0.2 \pi$ is low compared to that. Even including the errorbars it cannot reach the previous bins. An additional dip of the same flare count can be seen at phase $1.5 \pi$.
The flare count in figure \ref{fig:HKAqr-Flarecount-30_Bins_Period} is very low. Due to this all errorbars overlap. Nontheless there are two bins which stand out at phases \textasciitilde$0.4 \pi$ and \textasciitilde$1.25 \pi$ which would be in the transition from maxima to minima, and shortly after the minima respectively.
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
@@ -391,7 +433,11 @@ Figure \ref{fig:V471Tau-flarepeaks_1.053} shows the normalized phase and peak of
\caption{TESS Sector 29}
\label{fig:HKAqr-TESS29_foldedLC}
\end{subfigure}
\vspace{1em}
\caption{Folded lightcurves for V* HK Aqr. The blue lines shows the sine fits calculated. The red crosses indicate the detected flare peaks.}
\label{fig:HKAqr-TESS_foldedLCs1}
\end{figure}
\begin{figure}[pt!]
\centering
\begin{subfigure}[b]{.95\textwidth}
\centering
\includegraphics[width=\linewidth]{plots/sine/HKAqr/V_star_ HK Aqr_TESS-42-foldedLC-marked_fit_flares.png}
@@ -405,7 +451,7 @@ Figure \ref{fig:V471Tau-flarepeaks_1.053} shows the normalized phase and peak of
\label{fig:HKAqr-TESS69_foldedLC}
\end{subfigure}
\caption{Folded lightcurves for V* HK Aqr. The blue lines shows the sine fits calculated. The red crosses indicate the detected flare peaks.}
\label{fig:HKAqr-TESS_foldedLCs}
\label{fig:HKAqr-TESS_foldedLCs2}
\end{figure}
\begin{figure}[pt!]