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\title{The {\sc Pencil Code} Newsletter}
\author{Issue 2025/2}
%\date{\today,~ $ $Revision: 1.56 $ $}
\date{December 29, 2025,~ $ $Revision: 1.56 $ $}
\begin{document}
\maketitle

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\vspace{5mm}

\noindent
We wish all readers a happy New Year 2026!

\section{PCUM 2025 at CERN}
\label{PCUM2025}

The Pencil Code User Meeting (PCUM) 2025 was a great success combining
both a school on early Universe physics and gravitational waves.
(first week, October 20--24) and the actual user meeting
(second week, October 27--31);
see \url{https://indico.cern.ch/event/1548935/} for the program,
group photos, slides of the talks, and their recordings.
CERN provided a scenic setting for this event; see \Fig{window-view}.
On the technical side, one of the insights from the meeting concerned the
``Merge branch {\textquotesingle}master{\textquotesingle}'' commits;
see \Sec{sec:linear-history} below.

\begin{figure}[h]\begin{center}
\includegraphics[width=\columnwidth]{fig/window-view}
\end{center}\caption[]{
View from the lecture room at CERN toward the mountains to the left of Mont Blanc.
}\label{window-view}\end{figure}

\section{PCUM 2026 in Alicante}
\label{PCUM2026}

The 22nd PCUM will be organized by Clara Dehman at the University of Alicante, Spain; see Figure~\ref{PCUM26}.
A poll to determine the preferred week for the meeting is currently open; interested
participants are kindly invited to cast their vote at the following link:
\scriptsize
\url{https://docs.google.com/forms/d/e/1FAIpQLSddf3fDBfNivf9afTM37StIBoiEpTRwgNWvF1EQqcuzEZOS-A/viewform?usp=header}.
\normalsize
Further details regarding the schedule will be communicated later.
If there are questions, please check with Clara \texttt{<clara.dehman@ua.es>} via email.

\begin{figure*}[t]\begin{center}
\includegraphics[width=\textwidth]{fig/PCUM26}
\end{center}\caption[]{
Poster ad of the 22nd PCUM at the University of Alicante, Spain.
The time is still to be decided.
Photo credit: University of Alicante webpage and GetYourGuide. 
}\label{PCUM26}\end{figure*}

\section{Linear History and Git Usage}
\label{sec:linear-history}

During the last PC user meeting it was unanimously decided by the participants that we like to preserve
the linear commit history in the PC repository's \texttt{Master} branch.
The PC steering committee was tasked to obtain more feedback on how to implement this from the whole community. 
In the following, we reproduce those views.

\subsection{By Philippe Bourdin}
\texttt{<Philippe.Bourdin@oeaw.ac.at>}\\
{\scriptsize received 28 December 2025}\\

Options to prevent \texttt{Merge branch `Master'} commits are: 1) on the server, 2) on the user's local checkouts, or 3) make only suggestions to users.
Possible mechanisms we found on the internet so far would only check the text of the commit message,
which we consider insufficient because users could change that text easily.
GitHub seemingly offers such a prevention mechanism, where we do not know how this is implemented
and if it could be tricked by altering the commit message.

\begin{figure*}[ht]
\begin{center}
\includegraphics[width=0.9 \textwidth]{screenshots/git-hist-1-5.png}
\end{center}
\caption[]{History graph of 15th of October 2025 as shown by GitHub network. From top: a) point of divergence, b+c) linear history of commit 1+2 in the original remote `Master', d) a commit in Matthias' local `Master', and finally e) erroneous merge is pushed and marks Matthias' local history now as the new linear history of the remote `Master'. The green and black lines indicate the linear history of the remote `Master' branch in its original and latest state, respectively. The blue line is from a remote branch that is not relevant here.}\label{git-hist}
\end{figure*}

The root cause of the issue is that someone executed a \texttt{git pull}
without rebasing while there are remote changes and local commits.
This is very often the case in a busy repository like ours.
In principle, an alternative to \texttt{git pull --rebase}
is to use \texttt{git fetch} and \texttt{git rebase origin/master} instead.
There are lengthy discussions on the internet about this\footnote{
\url{https://stackoverflow.com/questions/292357/what-is-the-difference-between-git-pull-and-git-fetch}
},\footnote{
\url{https://longair.net/blog/2009/04/16/git-fetch-and-merge/}}.
We will not go into more detail here.

Looking at Fig.~\ref{git-hist}, another issue here is that \texttt{git blame} would erroneously indicate that Matthias
is now the author of many lines in those files that were originally written by Fred and Axel in our example,
which makes tracing these changes unnecessarily difficult.
The reason is that basically Matthias committed Fred's and Axel's changes again in Matthias' own \texttt{Merge branch `Master'} commit,
of which he is of course the committer but not the original author. This problem scales with the length of the deviating history.

This whole topic has nothing to do with Subversion or the \texttt{subgit} software synchronizing our GIT and SVN repositories
that live fully independently on our server.
Instead, the problem exists purely in GIT alone in the sense that a previously linear history of the \texttt{master} branch
appears to be rewritten and the local \texttt{master} branch relocated to a so-called `anonymous' branch
when the \texttt{Merge branch `master'} happens;
see Fig.~\ref{git-hist}.

This relocation of some commits to an anonymous branch makes it particularly difficult for SVN users to find these commits,
even though they are stored in the \texttt{shelves} branch of SVN that is explicitly created for the anonymous GIT commits -- which can
still be inspected with a checkout of all branches like this:
\begin{verbatim}
svn co https://pencil-code.org/svn/ pc-all
cd pc-all
svn log
\end{verbatim}
My personal opinion is that the behavior of \texttt{git pull} not rebasing by default
is a debatable design feature of GIT -- actually, I would recommend not to use \texttt{git pull} at all.
This is also the opinion of many commentators on the internet discussion in response to the links above.
If we can, we should prevent users from making this mistake by all means possible:
technical means on the server, on the user's local checkout, and with documentation.

\subsection{By Illa R.\ Losada}
\texttt{<illa.rivero.losada@gmail.com>}\\
{\scriptsize received 26 December 2025}\\

During the Pencil Code User Meeting 2025, we discussed at length recurring 
problems related to non-linear Git history on the \texttt{master} branch, in 
particular commits of the form \texttt{Merge branch `master'}.

Such commits are not inherently wrong in Git, nor are they necessarily the 
result of deliberate misuse. In many cases, they are produced automatically by 
Git when running a plain \texttt{git pull}, which by default performs a 
\texttt{fetch} followed by a \texttt{merge}. If this command is executed on a 
branch that has local commits and has diverged from the remote, Git will create 
a merge commit without the user explicitly intending to merge branches.

This behavior can occur in any pure Git environment. However, its consequences 
are significantly amplified in our repository setup, which accepts both Git and 
SVN commits. Git represents history as a directed acyclic graph (DAG), while SVN 
enforces a linear revision history. When a large or unintended Git merge is 
mirrored through the Git--SVN bridge, the resulting linearization can obscure 
ancestry, reintroduce outdated snapshots, and make recovery difficult or 
impossible.

As a concrete example, consider commit \texttt{60cf8c763}. This commit merged a 
branch last updated in 2017 (commit \texttt{316e7d608}) into the then-current 
\texttt{master} (commit \texttt{eff679045}). The merge was performed using a 
simple \texttt{git pull} by a user on the old branch, resulting in a single 
merge commit with the auto-generated message:

\begin{verbatim}
Merge branch 'master' of 
https://github.com/pencil-code/pencil-code
 \end{verbatim} 

Because the local branch had diverged from \texttt{master} for two years, Git 
attempted to reconcile two vastly different trees. This resulted in a merge 
commit affecting 1,415 files, with over 150,000 lines added and 91,000 lines 
removed. While technically valid from Git’s perspective, this commit 
effectively reintroduced or deleted large portions of repository history, 
creating significant disruption and making subsequent merges more error-prone.

This example demonstrates that:
\begin{itemize}
  \item Long-lived branches or edits on a very old check-out, combined with plain \texttt{git pull}, can produce 
    massive, unintended merge commits.
  \item Auto-generated merge messages such as 
    \texttt{Merge branch 'master' ...} are a warning sign of such operations.
  \item Even without \texttt{--force} pushes or rebase, repository history can 
    be disrupted in ways that are difficult to undo.
  \item Hybrid Git+SVN servers exacerbate the risks because Git and SVN handle 
    branching, merges, and history differently, 
    making the consequences of large unintended merges significantly more severe.
\end{itemize}

\begin{figure*}
        \centering
        \includegraphics[width=\textwidth,keepaspectratio]{1_fortran_file_list.png}
 \caption{Code coverage report for the Fortran source files.}
\end{figure*}

In a standard Git environment, each merge commit records its full
ancestry as part of Git's directed acyclic graph (DAG).
Even after a large or unintended merge, both parent histories remain intact and inspectable, making
such events visible and, in most cases, recoverable using standard Git tools
(e.g., inspecting parents, reverting merges, or reconstructing history).
When the same merge is mirrored into an SVN repo, this DAG structure
must be flattened into SVN's strictly linear revision model. As a result, parent
relationships are lost, merge semantics are discarded, and the commit appears in
SVN as a single large linear change. This loss of structural information makes it
difficult to determine the origin of changes, complicates reverts or bisection,
and significantly hampers recovery.

The meeting consensus was that the primary mitigation should be \textbf{clear 
guidance and documentation}, rather than relying solely on technical enforcement 
mechanisms.
Contributors are strongly encouraged to:

\begin{itemize}
  \item use \texttt{git pull --rebase} instead of plain \texttt{git pull},
  \item avoid merge commits on the \texttt{master} branch unless explicitly 
    intended,
  \item use SVN directly if you are not familiar with Git's subtleties described in this newsletter.
\end{itemize}

These recommendations, along with a detailed explanation of the underlying 
problem, are now documented in the 
\href{https://pencil-code.readthedocs.io/en/latest/index.html}{Pencil Code Read 
the Docs} pages:

\begin{itemize}

  \item 
\href{https://pencil-code.readthedocs.io/en/latest/pcdevelopment/howtogit.html#history-rewriting-hazard-git-svn-server}{History Rewriting Hazard (Git + SVN Server)}
  \item 
\href{https://pencil-code.readthedocs.io/en/latest/pcdevelopment/howtogit.html#git-on-an-
svn-backed-server-a-post-mortem}{Git on an SVN-Backed Server: A Post-Mortem}
\end{itemize}

Community feedback is always welcome, especially regarding additional safeguards 
or workflow improvements. 
However, until reliable server-side blocking mechanisms are identified, the
current emphasis is on informed and careful usage.

Users are therefore encouraged to read the documentation carefully and to follow 
the recommended workflows when contributing to the Pencil Code repository.\footnote{
\textit{Note added by Matthias:}
As a technical measure for avoiding \texttt{git pull} to act without rebasing, 
applying \texttt{source sourceme.sh} now sets in \texttt{.git/config} \\
\texttt{
[pull] \\
\phantom{[pull]} rebase = true\\
}
and warns about \texttt{rebase = false} settings in branch-specific entries.
}

\section{Code coverage reports}

\noindent\textit{by G.\ Kishore, Inter-University Centre for Astronomy \& Astrophysics, Pune, India}
%\texttt{<kishore96@gmail.com>}\\
\texttt{<am25r009@smail.iitm.ac.in>}\\
{\scriptsize received 29 December 2025}\\

\input kishore

\section{Python Postproc Meetings}
\label{sec:python-postprocessing}

\noindent\textit{by Illa R.\ Losada}
\texttt{<illa.rivero.losada@gmail.com>}\\
{\scriptsize received 26 December 2025}\\

During the last Pencil Code User Meeting at CERN (see Sec.~\ref{PCUM2025}), 
we decided to resume periodic meetings focused on the development and usage of 
Python as a postprocessing tool for the Pencil Code.

Full information about past meetings, decisions, outcomes, and upcoming sessions 
can now be found on the 
\href{https://pencil-code.readthedocs.io/en/latest/python-meetings/python-index.
html}{Python Postprocessing Meetings} page.

As a follow-up, the first Python postprocessing meeting was held on
\href{https://pencil-code.readthedocs.io/en/latest/python-meetings/python-
pastmeetings.html#nov-26}{Nov 26}. 
During this meeting, the group discussed the meeting format and schedule, 
agreeing to hold Python postprocessing meetings every two months with
rotating organizers. 
Key topics included testing and automated code checks, library installation via 
pip, updating and centralizing tutorials in ReadTheDocs, and improving 
real-time simulation visualization in Jupyter notebooks. 
Several action items were assigned, such as uploading Pencil Code Python as a 
pip package, enhancing documentation, and standardizing data formats.

The next meeting is planned for January (exact date TBD). 
We encourage all members of the Pencil Code community to participate, contribute 
ideas, and share experiences with Python postprocessing.

\section{New ReadTheDocs Additions}
\label{sec:rtd-new}

\noindent\textit{by Illa R.\ Losada}
\texttt{<illa.rivero.losada@gmail.com>}\\
{\scriptsize received 26 December 2025}\\

The {\sc Pencil Code} ReadTheDocs pages have recently been expanded with several 
autogenerated sections directly extracted from the source code, providing 
comprehensive reference material for developers and users alike.

\begin{itemize}
  \item \textbf{Fortran Modules:} Description of all Fortran files with 
filtering options for easy navigation. See the full list at 

\href{https://pencil-code.readthedocs.io/en/latest/code/sourceFortran/index.html
}{Fortran Modules}.

  \item \textbf{Startup and Run-time Parameters:} Detailed list of parameters 
with their placement in configuration files (e.g., \texttt{start.in}, 
\texttt{run.in}, \texttt{print.in}), the associated module, default values, and 
descriptions if available, with filtering options for quick lookup, see: 
  
\href{https://pencil-code.readthedocs.io/en/latest/code/tables/index.html}{
Startup and Run-time Parameters}.

  \item \textbf{Boundary Conditions:} Description of available boundary 
conditions per module, with explanations of their meaning and usage, see 
  
\href{https://pencil-code.readthedocs.io/en/latest/code/tables/boundary.html}{
Boundary Conditions}.

  \item \textbf{Bin Scripts:} List of executable scripts in the \texttt{bin} 
directory, with short descriptions of their functionality, see 

  \href{https://pencil-code.readthedocs.io/en/latest/code/tables/bin.html}{Bin 
Scripts}.
\end{itemize}

Additionally, the \textbf{Scientific Usage of the Pencil Code} document has been 
added, partly autogenerated to catalog publications making use of the code. 
The page includes references to journal articles and conference proceedings, 
classified by year and research topic. 
The primary applications lie in astrophysics, with additional work in 
meteorology and combustion. 
Explore the page here: 
\href{https://pencil-code.readthedocs.io/en/latest/intro/scientific.html}{
Scientific Usage of the Pencil Code}.

For guidance on how to add citations in the documentation, see the separate 
guide at 
\href{https://pencil-code.readthedocs.io/en/latest/dochowto/addcitations.html}{
Adding Citations}.

These additions make it significantly easier for users to explore the code 
structure, runtime options, and scientific impact of Pencil Code.

\begin{figure}[t]\begin{center}
\includegraphics[width=\columnwidth]{fig/dark-matter}
\end{center}\caption[]{
First \textsc{Pencil Code} dark matter trial
during the coding session on the Monday of week~2.
}\label{dark-matter}\end{figure}

\section{PCUM25 developments}

Already during the first coding session, a new dark matter autotest was
constructed based on Wlad's earlier sample called 
\texttt{2d-tests/selfgrav-shearwave-dust-par}.
All that needed to be done was to include a scale factor $a(t)$ on the rhs of
the Poisson equation, expressed in \textit{supercomoving coordinates} as indicated by tildes,
which now reads\footnote{see Martel, H. \& Shapiro, P. R.\ymn{1998}{297}{467}
{485}{A convenient set of comoving cosmological variables and their application}}
\begin{equation}
\widetilde{\nabla}^2\widetilde{\phi}=6a\,\left(\frac{\widetilde{\rho}_\mathrm{tot}}{\rho_0}-1\right).
\end{equation}
The result shown in Figure~\ref{dark-matter} looks impressive
for a first trial.

\section{Relevant job opportunities}

\subsection{PhD at Hamburg Observatory}

We are looking for a PhD student to work on {\sc Pencil Code}
star-in-a-box simulations of intermediate mass stars in the pre-main
sequence phase as a part of the DFG project ``Fossil fields in Ap/Bp
stars: an origin from star formation and protostellar evolution'' in
Hamburg Observatory. The project is an international collaboration
involving Robi Banerjee (Hamburg Observatory), Dominik Schleicher
(Sapienza University, Rome), Petri K\"apyl\"a (Institute for Solar
Physics, Freiburg), and Daniele Galli (INAF Astrophysical Observatory
of Florence). The PhD candidate will work in Hamburg where
Prof.\ Banerjee will act as the formal supervisor, but the project
entails collaboration with and visits to all of the participating
institutes. We ask the senior members of the {\sc Pencil Code}
community to distribute the news to potentially interested students
especially if they already have experience in using the
code. Interested students should contact Petri K\"apyl\"a
({\tt <pkapyla@leibniz-kis.de>}) for more details.

\subsection{COSMOMAG postdoc positions}

Four postdoc positions are available, with deadline 20 January: two at CERN and LPENS, and two at Nordita:
\begin{enumerate}
\item\url{https://inspirehep.net/jobs/3094257}
\item\url{https://inspirehep.net/jobs/3094314}
\end{enumerate}
We would be grateful if you could forward this announcement to potentially interested candidates.
For details regarding the COSMOMAG project, see \url{https://cosmosimfrazza.eu/cosmomag}.

\section{Announcements}

During 12--23 January 2026, there will be the Nordita Winter School 2026, which
is on Cosmological Magnetic Fields: Generation, Observation, and Modeling; see
\url{https://indico.fysik.su.se/event/8554/}.
While the deadline has now passed, there is still the possibility of online
participation via zoom on \url{https://stockholmuniversity.zoom.us/j/62081336983}.
The second week will feature lectures and exercises involving the
\textsc{Pencil Code}.
Teaching material is currently being assembled under the link
\url{https://norlx65.nordita.org/~brandenb/teach/PencilCode/COSMOMAG2026/}.

\section{Papers since Sept 2025}

As usual, we look here at new papers that make use of the {\sc Pencil Code}.
Since the last newsletter of August 2025, six new papers have appeared    
on the arXiv, plus nine others, some of which had been just preprints and now have been published with a journal reference on ADS.
We list both here, altogether 15.
A browsable ADS list of all {\sc Pencil Code} papers can be found on:
\url{https://ui.adsabs.harvard.edu/public-libraries/iGR7N570Sy6AlhDMQRTe_A}.
If something is missing in those entries, you can also include it yourself in:
\url{https://github.com/pencil-code/pencil-code/blob/master/doc/citations/ref.bib},
or otherwise just email brandenb@nordita.org.
A compiled version of this file is available as
\url{https://github.com/pencil-code/website/blob/master/doc/citations.pdf},
where we also list a total of now 136 code comparison papers in the last
section ``Code comparison \& reference''.
Those are not included in our list below, nor among the now total number
of 764 research papers that use the {\sc Pencil Code}.

\nocite{
2025arXiv251026918G,%Ghosh+ "Can galactic magnetic fields diffuse into the voids?"
2025JApA...46...87S,%Singh+ "Combining local and global magnetohydrodynamic simulation frameworks to understand the evolution of coronal mass ejections"
2025arXiv251119508M,%Mtchedlidze "Simulated Rotation Measure Sky from Primordial Magnetic Fields"
2025ApJ...995...39B,%Baehr+ "On the Gravitational Collapse of Small Dust Grains in Self-gravitating Disk Structures"
2025arXiv251209177G,%Gurgenidze+ "Primordial magnetic field from chiral plasma instability with sourcing"
2025arXiv251209725E,%Elias-Lopez "Numerical simulations of astrophysical dynamos and applications to giant planets"
2025arXiv251211973S,%Skalidis+ "Residual energy in weakly compressible turbulence with a mean guide field"
2025arXiv251217770B,%Brandenburg+ "Magnetic field spreading from stellar and galactic dynamos into the exterior"
2025arXiv251217885G,%Gent+ "Asymptotic behaviour of galactic small-scale dynamos at modest magnetic Prandtl number"
2025PhFl...37j5163L,%Lipatnikov+Sabelnikov "A numerical study of velocity-pressure gradient and pressure-dilatation terms in transport equations for subfilter turbulent kinetic energy in premixed flames"
2025arXiv250921141Z,%Zhang+Brandenburg "Resistive Scaling in the Magnetic Helicity-Driven Inverse Cascade"
2025ApJ...993...22B,%Brandenburg "Magnetorotational instability in a solar mean-field dynamo"
2025ApJ...990..223B,%Brandenburg+Ntormousi "Magnetic Field Amplification during a Turbulent Collapse"
2025A&A...701A.185T,%Tschernitz+Bourdin "Kinematic viscosity in solar convection simulations"
2025arXiv250906173Q,%Qazi+ "Mathematical Aspects of Geophysical and Astrophysical Fluid Dynamics: Magnetic buoyancy instability in galaxies"
%
%2024arXiv240115860Z,%Zhou+Jingade "Correlation times of velocity and kinetic helicity fluctuations in nonhelical hydrodynamic turbulence"
%2024arXiv240416096D,%Dey+ "Spinning solar jets explained through the interplay between plasma sheets and vortex columns"
%
% outdated
%2023arXiv231109082K,%Kapyla "Effects of rotation and surface forcing on deep stellar convection zones"
%2023arXiv230705490Z,%Zhu+Shi "Helical and nonhelical (magneto-)Burgers turbulence: I. Compressibility reduction and beyond"
%2023arXiv230300911Y,%Yuvraj "On flame speed enhancement in turbulent premixed hydrogen-air flames during local flame-flame interaction"
%2022arXiv220606566M,%Masada+Sano "Rotational Dependence of Large-scale Dynamo in Strongly-stratified Convection: What Causes It?"
%2022arXiv220509261R,%Roper Pol "Gravitational waves from MHD turbulence at the QCD phase transition as a source for Pulsar Timing Arrays"
%2021arXiv210508287R,%Roper Pol "Gravitational radiation from MHD turbulence in the early universe"
}

\bibliography{ref}
\vspace{5mm}
\hrule
\vspace{2mm}
This {\sc Pencil Code} Newsletter was edited by
Axel Brandenburg {\tt <brandenb@nordita.org>}, Nordita, KTH Royal Institute of Technology and Stockholm University, SE-10691 Stockholm, Sweden;
and Matthias Rheinhardt {\tt <matthias.rheinhardt@aalto.fi>}, Department of Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland.
See \url{http://www.nordita.org/~brandenb/pencil-code/newsletter} or
\url{https://github.com/pencil-code/website/tree/master/NewsLetters}
for the online version as well as back issues.

\end{document}
