main.tex

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%	TITLE SECTION 
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\title{pynucastro: Code Generation and Visualization for Nuclear Reaction Networks} % Poster title

\author{Donald E. Willcox (LBNL), Adam Jacobs (MSU), Xinlong Li (SBU), and Michael Zingale (SBU)}

\institute{Lawrence Berkeley National Laboratory (LBNL), Michigan State University (MSU), Stony Brook University (SBU)} % Institution(s)

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\begin{document}

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\begin{alertblock}{Abstract}

  \textbf{pynucastro} is developed to meet both pedagogical and research needs
  in the field of nuclear astrophysics by providing a Python interface
  to nuclear reaction rate databases (including the JINA Reaclib
  nuclear reaction rate database). It is meant for both 
  \textbf{interactive exploration} of reaction rates (through Jupyter notebooks) and for
  creating \textbf{reaction networks for simulation codes}.

\end{alertblock}

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%	Capabilities
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\begin{block}{Capabilities}

\begin{itemize}
\item Supports Reaclib library snapshots \cite{Reaclib.2010}
\item Supports weak rates \cite{Suzuki.2016} tabulated in $\mathrm{(T, \rho Y_e)}$
\item Visualizes connections between nuclei as a network graph
\item Evaluates rates as a function of temperature
\item Symbolically constructs the ODE right hand side and Jacobian
\item Generates Python or Fortran code implementing the network
\end{itemize}

\end{block}

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%	Reaclib Rates
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\begin{block}{Working with Reaclib}

pynucastro can interpret reaction rates parameterized in the standard
Reaclib formats, storing each rate internally
using the \textbf{Rate} class. \textbf{Rate} interprets the Reaclib
format and knows how to evaluate the rate as a function of
temperature.

\begin{figure}
\includegraphics[width=\linewidth]{figures/library-examples-filtering_cago.png}
%\caption{Temperature dependence of $\isotm{C}{12} + \isotm{He}{4} \rightarrow \isotm{O}{16}$}
\end{figure}

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%	Creating a Network
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\begin{block}{Creating a Network}

The \textbf{Library} class allows pynucastro to work easily with files
containing multiple rates, including Reaclib snapshots. We use
\textbf{Library} to obtain the CNO rates linking our desired nuclei in
just a few lines of Python in the following Jupyter notebook:

\begin{figure}
\includegraphics[width=1.1\linewidth]{figures/library-examples-nuclei.png}
%\caption{Creating a CNO network in a Jupyter notebook}
\end{figure}

Using the \textbf{Composition} and \textbf{Explorer} classes, we also
construct an interactive graph of the network with the value of each
rate indicated by its arrow color with variable density and temperature.

\end{block}

\begin{block}{Python Code Generation}

The \textbf{PythonNetwork} class generates Python code to calculate
each rate as a function of temperature and the ODE right hand
side. pynucastro includes a sample Python integrator using SciPy.

%% \begin{figure}
%% \includegraphics[width=0.8\linewidth]{figures/python-network-code/python-network-code.png}
%% %\caption{Python code evaluating the Reaclib rate for  $\isotm{C}{12} + p \rightarrow \isotm{N}{13}$}
%% \end{figure}

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%	Code Generation
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\begin{block}{StarKiller Microphysics}

The \textbf{StarKillerNetwork} class generates Fortran reaction
network code for astrophysical simulations that use the StarKiller
Microphysics repository \cite{Zingale.astronum.2017}.

\begin{itemize}
    \item Right hand side and Jacobian with SymPy \cite{SymPy.2017}
    \item Couples to a stellar equation of state
    \item Incorporates screening and thermal neutrinos
    \item Supports CUDA Fortran
\end{itemize}

This short Python script builds a \isot{C}{12} burning network with tabulated weak $\mathrm{A=23}$ rates:

\begin{figure}
\includegraphics[width=0.8\linewidth]{figures/starkiller-network/starkiller-urca-network.png}
%\caption{Constructing a StarKiller implementation of an $\mathrm{A=23}$ Urca network with \isot{C}{12} burning.}
\end{figure}

Electron fraction in a Maestro low-Mach hydrodynamics simulation of a
3-D convecting white dwarf core using the $\mathrm{A=23}$ Urca network:

\begin{figure}
\includegraphics[width=\linewidth]{figures/starkiller-network/wd_4lev_Tc5-5e8_rhoc4-5e9_plt06605_slice_x_electron_fraction_asymmetry.png}
%\caption{Electron fraction in a MAESTRO low-Mach hydrodynamics simulation of a convecting white dwarf core using the $\mathrm{A=23}$ Urca network with \isot{C}{12} burning.}
\end{figure}

\end{block}

\begin{block}{Ongoing Development}

\begin{itemize}
    \item Implementing nuclear partition functions
    \item Expanding support for weak rate tabulations
\end{itemize}

%\begin{itemize}
%    \item \small{\rmfamily{Implementing nuclear partition functions}}
%    \item \small{\rmfamily{Expanding support for various weak rate tabulations}}
%    \item \small{\rmfamily{\textit{Tell us what features you would like ...}}}
%\end{itemize}

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% %	IMPORTANT RESULT
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%	Getting pynucastro
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\begin{block}{Getting pynucastro}

\begin{itemize}
\item pynucastro is freely available under the \textbf{BSD 3-Clause open source} license.
\item For the companion \textbf{software paper}, see \cite{pynucastro.joss.2018}.
\item Visit us on GitHub to \textbf{download} pynucastro or report \textbf{issues} and \textbf{request features}:
\end{itemize}

\url{https://github.com/pynucastro/pynucastro}

\begin{itemize}
\item For pynucastro \textbf{documentation} and examples, visit the pynucastro website:
\end{itemize}

\url{https://pynucastro.github.io/pynucastro}

\end{block}

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%	ACKNOWLEDGEMENTS
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\begin{block}{Acknowledgements}

\small{\rmfamily{This work was supported by DOE/Office of Nuclear
    Physics grant DE-FG02-87ER40317. This research used resources of
    the Oak Ridge Leadership Computing Facility, which is a DOE Office
    of Science User Facility supported under Contract
    DE-AC05-00OR22725.}}

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%	REFERENCES
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\begin{block}{References}

%\nocite{*} % Insert publications even if they are not cited in the poster
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\bibliography{paper}\vspace{0.75in}}

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%% %	CONTACT INFORMATION
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%% \item Web: \href{https://dwillcox.github.io}{https://dwillcox.github.io}
%% \item Email: \href{mailto:donald.willcox@stonybrook.edu}{donald.willcox@stonybrook.edu}
%% \item Phone: +1 (631) 632-8236
%% \end{itemize}

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