Added general SPH theory file and EoS description

.gitignore

@@ -84,6 +84,8 @@ theory/SPH/Kernels/kernels.pdf
 theory/SPH/Kernels/kernel_derivatives.pdf
 theory/SPH/Kernels/kernel_definitions.pdf
 theory/SPH/Flavours/sph_flavours.pdf
+theory/SPH/EoS/eos.pdf
+theory/SPH/*.pdf
 theory/paper_pasc/pasc_paper.pdf
 
 m4/libtool.m4

theory/SPH/EoS/eos.tex

+aa
+

theory/SPH/EoS/eos_standalone.tex

+\documentclass[fleqn, usenatbib, useAMS,a4paper]{mnras}
+\usepackage{graphicx}
+\usepackage{amsmath,paralist,xcolor,xspace,amssymb}
+\usepackage{times}
+
+\newcommand{\swift}{{\sc Swift}\xspace}
+
+%opening
+\title{Equation of state in SWIFT}
+\author{Matthieu Schaller}
+
+\begin{document}
+
+\maketitle
+
+\input{eos}
+
+\bibliographystyle{mnras}
+\bibliography{./bibliography.bib}
+
+
+\end{document}

theory/SPH/EoS/run.sh

+#!/bin/bash
+python kernels.py
+pdflatex -jobname=eos eos_standalone.tex
+bibtex eos.aux
+pdflatex -jobname=eos eos_standalone.tex
+pdflatex -jobname=eos eos_standalone.tex

theory/SPH/bibliography.bib

+@ARTICLE{Price2012,
+   author = {{Price}, D.~J.},
+    title = "{Smoothed particle hydrodynamics and magnetohydrodynamics}",
+  journal = {Journal of Computational Physics},
+archivePrefix = "arXiv",
+   eprint = {1012.1885},
+ primaryClass = "astro-ph.IM",
+     year = 2012,
+    month = feb,
+   volume = 231,
+    pages = {759-794},
+      doi = {10.1016/j.jcp.2010.12.011},
+   adsurl = {http://adsabs.harvard.edu/abs/2012JCoPh.231..759P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Springel2005,
+   author = {{Springel}, V.},
+    title = "{The cosmological simulation code GADGET-2}",
+  journal = {\mnras},
+   eprint = {astro-ph/0505010},
+ keywords = {methods: numerical, galaxies: interactions, dark matter},
+     year = 2005,
+    month = dec,
+   volume = 364,
+    pages = {1105-1134},
+      doi = {10.1111/j.1365-2966.2005.09655.x},
+   adsurl = {http://adsabs.harvard.edu/abs/2005MNRAS.364.1105S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+@ARTICLE{Hopkins2013,
+   author = {{Hopkins}, P.~F.},
+    title = "{A general class of Lagrangian smoothed particle hydrodynamics methods and implications for fluid mixing problems}",
+  journal = {\mnras},
+archivePrefix = "arXiv",
+   eprint = {1206.5006},
+ primaryClass = "astro-ph.IM",
+ keywords = {hydrodynamics, instabilities, turbulence, methods: numerical, cosmology: theory},
+     year = 2013,
+    month = feb,
+   volume = 428,
+    pages = {2840-2856},
+      doi = {10.1093/mnras/sts210},
+   adsurl = {http://adsabs.harvard.edu/abs/2013MNRAS.428.2840H},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Springel2002,
+   author = {{Springel}, V. and {Hernquist}, L.},
+    title = "{Cosmological smoothed particle hydrodynamics simulations: the entropy equation}",
+  journal = {\mnras},
+   eprint = {astro-ph/0111016},
+ keywords = {methods: numerical, galaxies: evolution, galaxies: starburst, methods: numerical, galaxies: evolution, galaxies: starburst},
+     year = 2002,
+    month = jul,
+   volume = 333,
+    pages = {649-664},
+      doi = {10.1046/j.1365-8711.2002.05445.x},
+   adsurl = {http://adsabs.harvard.edu/abs/2002MNRAS.333..649S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Balsara1995,
+   author = {{Balsara}, D.~S.},
+    title = "{von Neumann stability analysis of smooth particle hydrodynamics--suggestions for optimal algorithms}",
+  journal = {Journal of Computational Physics},
+     year = 1995,
+   volume = 121,
+    pages = {357-372},
+      doi = {10.1016/S0021-9991(95)90221-X},
+   adsurl = {http://adsabs.harvard.edu/abs/1995JCoPh.121..357B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Schaller2015,
+   author = {{Schaller}, M. and {Dalla Vecchia}, C. and {Schaye}, J. and 
+	{Bower}, R.~G. and {Theuns}, T. and {Crain}, R.~A. and {Furlong}, M. and 
+	{McCarthy}, I.~G.},
+    title = "{The EAGLE simulations of galaxy formation: the importance of the hydrodynamics scheme}",
+  journal = {\mnras},
+archivePrefix = "arXiv",
+   eprint = {1509.05056},
+ keywords = {methods: numerical, galaxies: clusters: intracluster medium, galaxies: formation, cosmology: theory},
+     year = 2015,
+    month = dec,
+   volume = 454,
+    pages = {2277-2291},
+      doi = {10.1093/mnras/stv2169},
+   adsurl = {http://adsabs.harvard.edu/abs/2015MNRAS.454.2277S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+@ARTICLE{Dehnen2012,
+   author = {{Dehnen}, W. and {Aly}, H.},
+    title = "{Improving convergence in smoothed particle hydrodynamics simulations without pairing instability}",
+  journal = {\mnras},
+archivePrefix = "arXiv",
+   eprint = {1204.2471},
+ primaryClass = "astro-ph.IM",
+ keywords = {hydrodynamics, methods: numerical },
+     year = 2012,
+    month = sep,
+   volume = 425,
+    pages = {1068-1082},
+      doi = {10.1111/j.1365-2966.2012.21439.x},
+   adsurl = {http://adsabs.harvard.edu/abs/2012MNRAS.425.1068D},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

theory/SPH/run.sh

+#!/bin/bash
+cd Kernels
+python kernels.py
+cp kernels.pdf ..
+cp kernel_derivatives.pdf ..
+cd ..
+pdflatex swift_sph.tex
+bibtex swift_sph.aux 
+pdflatex swift_sph.tex
+pdflatex swift_sph.tex

theory/SPH/swift_sph.tex

+\documentclass[fleqn, usenatbib, useAMS]{mnras}
+\usepackage{graphicx}
+\usepackage{amsmath,paralist,xcolor,xspace,amssymb}
+\usepackage{times}
+\usepackage[super]{nth}
+
+\newcommand{\swift}{{\sc swift}\xspace}
+\newcommand{\gadget}{{\sc gadget}\xspace}
+\newcommand{\dd}[2]{\frac{\partial #1}{\partial #2}}
+\renewcommand{\vec}[1]{{\mathbf{#1}}}
+\newcommand{\Wij}{\overline{\nabla_xW_{ij}}}
+\newcommand{\tbd}{\textcolor{red}{TO BE DONE}}
+
+\newcommand{\MinimalSPH}{\textsc{minimal-sph}\xspace}
+\newcommand{\GadgetSPH}{\textsc{gadget-sph}\xspace}
+\newcommand{\PESPH}{\textsc{pe-sph}\xspace}
+%\setlength{\mathindent}{0pt}
+
+%opening
+\title{SPH implementation in \swift}
+\author{Matthieu Schaller}
+
+\begin{document}
+
+\maketitle
+\section{Kernel functions}
+\input{Kernels/kernel_definitions}
+
+\section{Equation of state}
+\input{EoS/eos}
+
+\section{SPH flavours}
+\input{Flavours/sph_flavours}
+
+\bibliographystyle{mnras}
+\bibliography{./bibliography}
+
+\end{document}