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Initial conditions generation added

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1 parent 923c349 commit 362193eed0c2a1a1bd2fc4e1f81e3edfff4b9cc6 @harre committed Apr 18, 2012
Showing with 261 additions and 29 deletions.
  1. +10 −5 AWESOME_doku.aux
  2. +51 −21 AWESOME_doku.log
  3. +5 −0 AWESOME_doku.out
  4. BIN AWESOME_doku.pdf
  5. +80 −0 AWESOME_doku.tex
  6. +90 −3 AWESOME_doku.tex~
  7. +25 −0 howtogit.txt
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15 AWESOME_doku.aux
@@ -11,10 +11,15 @@
\global \let \hyper@last\relax
\fi
+\@writefile{toc}{\contentsline {section}{\numberline {1}Initial Conditions}{1}{section.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Using Cosmics 1.04 (Standard)}{1}{subsection.1.1}}
\bibdata{AWESOME}
\bibstyle{dcu}
-\@writefile{toc}{\contentsline {section}{\numberline {1}Initial Conditions}{1}{section.1}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}N-body Simulation}{1}{section.2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Halo Finder + Merger Trees}{1}{section.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {4}SAM}{1}{section.4}}
-\@writefile{toc}{\contentsline {section}{\numberline {5}Hydro}{1}{section.5}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Using NGenIC}{3}{subsection.1.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}N-body Simulation}{3}{section.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Halo Finder + Merger Trees}{3}{section.3}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}SAM}{3}{section.4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Galacticus}{3}{subsection.4.1}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {4.1.1}Compilation}{3}{subsubsection.4.1.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Galacticus v0.9.1}{3}{subsection.4.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {5}Hydro}{3}{section.5}}
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5 AWESOME_doku.out
@@ -1,5 +1,10 @@
\BOOKMARK [1][-]{section.1}{Initial Conditions}{}
+\BOOKMARK [2][-]{subsection.1.1}{Using Cosmics 1.04 \(Standard\)}{section.1}
+\BOOKMARK [2][-]{subsection.1.2}{Using NGenIC}{section.1}
\BOOKMARK [1][-]{section.2}{N-body Simulation}{}
\BOOKMARK [1][-]{section.3}{Halo Finder + Merger Trees}{}
\BOOKMARK [1][-]{section.4}{SAM}{}
+\BOOKMARK [2][-]{subsection.4.1}{Galacticus}{section.4}
+\BOOKMARK [3][-]{subsubsection.4.1.1}{Compilation}{subsection.4.1}
+\BOOKMARK [2][-]{subsection.4.2}{Galacticus v0.9.1}{section.4}
\BOOKMARK [1][-]{section.5}{Hydro}{}
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80 AWESOME_doku.tex
@@ -59,12 +59,92 @@
\end{abstract}
\section{Initial Conditions}
+\subsection{Using Cosmics 1.04 (Standard)}
+
+The (constrained) initial conditions generator \texttt{Cosmics 1.04}
+can be downloaded from \texttt{http://web.mit.edu/edbert/cosmics-1.04.tar.gz}.
+The acually used version is to be gotten as git repository
+\texttt{git@github.com:harre/cosmics-initial-conditions.git}.
+
+\begin{description}
+
+\item[Step 1: Make]
+
+For making, one has to specify the system and adapt the corresponding
+Makefile accordingly. In the folder \texttt{Make\_files} one has to adapt
+\texttt{Make.LINUX} to
+\begin{verbatim}
+F77 = ifort
+F77FLAGS = -O2 -parallel -par-report1 -openmp
+FFT_OBJ = fft3r.o
+CC = icc
+CFLAGS = -O2 -parallel -par-report1 -openmp
+\end{verbatim}
+and load the intel compiler \texttt{module load intel/64/12.1}. The intel
+compiler is used since for $512^3$ particle initial conditions there is a
+problem with memory allocation with \texttt{gcc} (can be dealt with flags however).
+When one uses the version from the git repo, changing the
+Makefile should not be necessary anyhow.
+
+\item[Step 2: Linear Extrapolation: \texttt{linger}]
+
+In the folder \texttt{linger\_syn} the program with the same name is to
+be executed. This program generates a file called \texttt{linger.dat} which
+is then used by the actual IC generator \texttt{grafic}.
+
+When one executes the program from github, the message
+\begin{verbatim}
+
+ >>>>> MAKE SURE YOU START THE PROGRAM WITH
+ >>>>> $./linger_syn | tee lingersynIO.out
+
+\end{verbatim}
+motivates the recording of IO in order to ensure reproducability of simulations.
+Ideally one would also indicate some physical parameters in
+the IO file, such as \texttt{lingersynIO\_h70.out}.
+
+\textbf{Note: } There are files already in the repo which can be used, namely
+\texttt{linger\_h100n216.dat} and \texttt{linger\_h70n216.dat} for
+Hubble constants $70.3$ and $100$. They were
+generated using matter transfer functions (choice 0)
+\begin{verbatim}
+ Enter 1 for full Boltzmann equation for CMB (lmax<=10000, linear k)
+ or 0 for matter transfer functions only (lmax=100, log k)
+\end{verbatim}
+and the parameters
+\begin{verbatim}
+ Enter kmin (1/Mpc), kmax (1/Mpc), nk, zend
+\end{verbatim}
+are set to \texttt{1E-5}, \texttt{50}, \texttt{216}, \texttt{0}.
+The last input is then which kind of IC one wants to generate
+\begin{verbatim}
+ Initial conditions cases:
+ 1 for isentropic (adiabatic) fluctuations,
+ 2 for cdm entropy/isocurvature fluctuations, or
+ 3 for baryon entropy/isocurvature fluctuations, or
+ 4 for seed/isocurvature fluctuations
+ Enter 1, 2, 3, or 4 now
+\end{verbatim}
+where we chose \texttt{2}.
+
+\textbf{Note: } If one changes the cosmological parameters for
+\texttt{linger\_syn} one usually hast to delete the files \texttt{linger.dat}
+and \text{lingerg.dat} first.
+
+\end{description}
+
+
+
+\subsection{Using NGenIC}
\section{N-body Simulation}
\section{Halo Finder + Merger Trees}
\section{SAM}
+\subsection{Galacticus}
+\subsubsection{Compilation}
+
\subsection{Galacticus v0.9.1}
View
93 AWESOME_doku.tex~
@@ -13,7 +13,7 @@
\hypersetup
{%
pdftitle={AWESOME documentation},
- pdfauthor={Harald Hoeller},
+ pdfauthor={Harald Hoeller, Markus Haider},
pdfsubject={...},
pdfkeywords={AWEsome Simulations Of Metal Enrichment}
}
@@ -48,23 +48,110 @@
\renewcommand{\labelenumi}{\theenumi}
\title{AWESOME documentation \\
metal enrichment setup 2011ff}
-\author{Harald H\"oller \thanks{Department of Astro- and Particle Physics,
+\author{Harald H\"oller, Markus Haider \thanks{Department of Astro- and Particle Physics,
University of Innsbruck, harald.hoeller@uibk.ac.at}}
\begin{document}
\maketitle
\begin{abstract}
-\textcolor{red}{\bf FOR INTERNAL USE}
+\textcolor{red}{\bf FOR INTERNAL AWESOME USE}
\end{abstract}
\section{Initial Conditions}
+\subsection{Using Cosmics 1.04 (Standard)}
+
+The (constrained) initial conditions generator \texttt{Cosmics 1.04}
+can be downloaded from \texttt{http://web.mit.edu/edbert/cosmics-1.04.tar.gz}.
+The acually used version is to be gotten as git repository
+\texttt{git@github.com:harre/cosmics-initial-conditions.git}.
+
+\begin{description}
+
+\item[Step 1: Make]
+
+For making, one has to specify the system and adapt the corresponding
+Makefile accordingly. In the folder \texttt{Make\_files} one has to adapt
+\texttt{Make.LINUX} to
+\begin{verbatim}
+F77 = ifort
+F77FLAGS = -O2 -parallel -par-report1 -openmp
+FFT_OBJ = fft3r.o
+CC = icc
+CFLAGS = -O2 -parallel -par-report1 -openmp
+\end{verbatim}
+and load the intel compiler \texttt{module load intel/64/12.1}. The intel
+compiler is used since for $512^3$ particle initial conditions there is a
+problem with memory allocation with \texttt{gcc} (can be dealt with flags however).
+When one uses the version from the git repo, changing the
+Makefile should not be necessary anyhow.
+
+\item[Step 2: Linear Extrapolation: \texttt{linger}]
+
+In the folder \texttt{linger\_syn} the program with the same name is to
+be executed. This program generates a file called \texttt{linger.dat} which
+is then used by the actual IC generator \texttt{grafic}.
+
+When one executes the program from github, the message
+\begin{verbatim}
+
+ >>>>> MAKE SURE YOU START THE PROGRAM WITH
+ >>>>> $./linger_syn | tee lingersynIO.out
+
+\end{verbatim}
+motivates the recording of IO in order to ensure the reproducability of simulations.
+Ideally one would also indicate some physical parameters in
+the IO file, such as \texttt{lingersynIO\_h70.out}.
+
+\textbf{Note: } There are files already in the repo which can be used, namely
+\texttt{linger\_h100n216.dat} and \texttt{linger\_h70n216.dat} for
+Hubble constants $70.3$ and $100$. They were
+generated using matter transfer functions (choice 0)
+\begin{verbatim}
+ Enter 1 for full Boltzmann equation for CMB (lmax<=10000, linear k)
+ or 0 for matter transfer functions only (lmax=100, log k)
+\end{verbatim}
+and the parameters
+\begin{verbatim}
+ Enter kmin (1/Mpc), kmax (1/Mpc), nk, zend
+\end{verbatim}
+are set to \texttt{1E-5}, \texttt{50}, \texttt{216}, \texttt{0}.
+The last input is then which kind of IC one wants to generate
+\begin{verbatim}
+ Initial conditions cases:
+ 1 for isentropic (adiabatic) fluctuations,
+ 2 for cdm entropy/isocurvature fluctuations, or
+ 3 for baryon entropy/isocurvature fluctuations, or
+ 4 for seed/isocurvature fluctuations
+ Enter 1, 2, 3, or 4 now
+\end{verbatim}
+where we chose \texttt{2}.
+
+\textbf{Note: } If one changes the cosmological parameters for
+\texttt{linger\_syn} one usually hast to delete the files \texttt{linger.dat}
+and \text{lingerg.dat} first.
+
+\end{description}
+
+
+
+\subsection{Using NGenIC}
\section{N-body Simulation}
\section{Halo Finder + Merger Trees}
\section{SAM}
+\subsection{Galacticus}
+\subsubsection{Compilation}
+
+
+\subsection{Galacticus v0.9.1}
+
+Checkout latest revision:
+\begin{verbatim}
+bzr checkout http://bazaar.launchpad.net/~abenson/galacticus/v0.9.1/
+\end{verbatim}
\section{Hydro}
View
25 howtogit.txt
@@ -0,0 +1,25 @@
+Global setup:
+
+ Set up git
+ git config --global user.name "Your Name"
+ git config --global user.email harald.hoeller@gmx.net
+
+
+Next steps:
+
+ mkdir AWESOME
+ cd AWESOME
+ git init
+ touch README
+ git add README
+ git commit -m 'first commit'
+ git remote add origin git@github.com:harre/AWESOME.git
+ git push -u origin master
+
+
+Existing Git Repo?
+
+ cd existing_git_repo
+ git remote add origin git@github.com:harre/AWESOME.git
+ git push -u origin master
+

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