Merge branch 'master' into lattice

.gitignore

@@ -19,5 +19,8 @@ doc/*.md5
 doc/*.map
 doc/*.css
 doc/*.dot
+doc/*.aux
+doc/*.log
+doc/*.toc
 
 test/*.log

README

@@ -66,15 +66,15 @@ If you want to create dynamic libraries (instead of static libraries)
 you have to pass all the following options to the ./configure script
 
    --disable-static-libs
-   --libext=".so"
-   --make-lib-cmd="gcc -shared -o"
+   --with-lib-ext=".so"
+   --with-make-lib-cmd="gcc -shared -o"
 
 Example:
 
    $ ./configure --with-models=MSSM,NMSSM \
      --disable-static-libs \
-     --libext=".so" \
-     --make-lib-cmd="gcc -shared -o"
+     --with-lib-ext=".so" \
+     --with-make-lib-cmd="gcc -shared -o"
 
 Important remark:
 

configure

@@ -148,7 +148,7 @@ contains() {
 }
 
 contains_not() {
-    # Check if string $1 contains $2
+    # Check if string $1 does not contain $2
     if test $# -lt 2 ; then
         echo "contains: Too few arguments"
         return 1
@@ -521,6 +521,15 @@ check_models() {
                 fi ;;
         esac
     done
+
+    # test model dependencies (snmssm depends on smssm)
+    if contains "${MODELS}" "models/snmssm"; then
+        if contains_not "${MODELS}" "models/smssm"; then
+            message "Error: model snmssm requires model smssm"
+            message "Please also select the smssm"
+            exit 1
+        fi
+    fi
 }
 
 #_____________________________________________________________________
@@ -822,7 +831,7 @@ check_makelib() {
     if test "x$enable_static_libs" = "xno" ; then
         if test "x$makelib_cmd" = "xar" ; then
             message "\n   Error: $makelib_cmd cannot be used to create shared libraries!"
-            message "   Please use --make-lib-cmd=\"gcc -shared -o\" or something similar."
+            message "   Please use --with-make-lib-cmd=\"gcc -shared -o\" or something similar."
             exit 1
         fi
     fi
@@ -897,7 +906,7 @@ enable_defines() {
         if test "x$LIBEXT" = "x.a" ; then
             message "  Warning: library extension $LIBEXT is reserved for static libraries."
             message "    Please consider using .so as library extension, or similar, e.g."
-            message "    --libext=\".so\""
+            message "    --with-lib-ext=\".so\""
         fi
     fi
 
@@ -918,39 +927,39 @@ Usage: ./`basename $0` [options]
 Options:
 
   --help,-h         Print this help message
-  --libext          Library extension (default: $LIBEXT)
-  --make-lib-cmd    Command to make library (default: $MAKELIB)
   --version,-v      Print version information
 
 enable/disable options, prefix with either --enable- or --disable-
 
-  colors            Colored output
-  debug             Debug messages and assertions
-  looptools         Use LoopTools to compute the loop functions
-  silent            Suppress all command line output
+  colors            Colored output (default: $enable_colors)
+  debug             Debug messages and assertions (no default)
+  looptools         Use LoopTools to compute the loop functions (default: $enable_looptools)
+  silent            Suppress all command line output (default: $enable_silent)
   static-libs       Create static libraries (default: $enable_static_libs)
-  verbose           Verbose messages
-
-with options, prefix with --with-, enables corresponding support
-
-  algorithms        Comma separated list of RG solver algorithms
-                    (default: $ALGORITHMS)
-                    possible values: all $available_algorithms
-  boost-libdir      Path to search for BOOST libraries
-  boost-incdir      Path to search for BOOST headers
-  eigen-incdir      Path to search for Eigen headers
-  cxx               C++ compiler (default: $CXX)
-  cxxflags          C++ compiler flags (default: $CXXFLAGS)
-  fc                Fortran compiler (default: $FC)
-  fflags            Fortran compiler flags (default: $FFLAGS)
-  gsl-config        Path to gsl-config (default: $gsl_config)
-  lapack-libdir     Path to search for LAPACK and BLAS libraries
-  looptools-libdir  Path to search for LoopTools libraries
-  looptools-incdir  Path to search for LoopTools headers
-  math-cmd          Mathematic kernel (default: $MATH)
-  models            Comma separated list of models to be build
-                    (default: $MODELS)
-                    possible values: all <model1>,<model2>,...
+  verbose           Verbose messages (default: $enable_verbose)
+
+Package directories, compilation settings and model selection
+
+  --with-algorithms=        Comma separated list of RG solver algorithms
+                            (default: $ALGORITHMS)
+                            possible values: all $available_algorithms
+  --with-boost-libdir=      Path to search for BOOST libraries
+  --with-boost-incdir=      Path to search for BOOST headers
+  --with-cxx=               C++ compiler (default: $CXX)
+  --with-cxxflags=          C++ compiler flags (default: $CXXFLAGS)
+  --with-eigen-incdir=      Path to search for Eigen headers
+  --with-fc=                Fortran compiler (default: $FC)
+  --with-fflags=            Fortran compiler flags (default: $FFLAGS)
+  --with-gsl-config=        Path to gsl-config (default: $gsl_config)
+  --with-lapack-libdir=     Path to search for LAPACK and BLAS libraries
+  --with-lib-ext=           Library extension (default: $LIBEXT)
+  --with-looptools-libdir=  Path to search for LoopTools libraries
+  --with-looptools-incdir=  Path to search for LoopTools headers
+  --with-make-lib-cmd       Command to make library (default: $MAKELIB)
+  --with-math-cmd=          Mathematic kernel (default: $MATH)
+  --with-models=            Comma separated list of models to be build
+                            (default: $MODELS)
+                            possible values: all <model1>,<model2>,...
 EOF
 }
 
@@ -1026,13 +1035,13 @@ if test $# -gt 0 ; then
             --with-fflags=*)         FFLAGS=$optarg ;;
             --with-gsl-config=*)     gsl_config=$optarg ;;
             --with-lapack-libdir=*)  lapack_lib_dir=$optarg ;;
+            --with-lib-ext=*)        LIBEXT=$optarg ;;
             --with-looptools-libdir=*) looptools_lib_dir=$optarg ;;
             --with-looptools-incdir=*) looptools_inc_dir=$optarg ;;
+            --with-make-lib-cmd=*)   MAKELIB=$optarg ;;
             --with-math-cmd=*)       MATH=$optarg ;;
             --with-models=*)         MODELS=$optarg ;;
             --help|-h)               help; exit 0 ;;
-            --libext=*)              LIBEXT=$optarg ;;
-            --make-lib-cmd=*)        MAKELIB=$optarg ;;
             --version|-v)            version; exit 0 ;;
             *)  echo "Invalid option '$1'. Try $0 --help" ; exit 1 ;;
         esac

doc/chapters/output.tex

@@ -0,0 +1,14 @@
+\section{Output}
+\subsection{Files}
+
+Explain the created C++ files and executables, and how to use them.
+
+\subsection{Two-scale algorithm}
+
+Explain the structure of the two-scale algorithm classes and how they
+work and are plugged together.
+
+\subsection{Lattice algorithm}
+
+Explain the structure of the lattice algorithm classes and how they
+work.

doc/chapters/overview.tex

@@ -0,0 +1,21 @@
+\section{Overview}
+
+Explain:
+\begin{itemize}
+\item What is FlexibleSUSY?
+\item Features, design goals
+\end{itemize}
+
+\subsection{Requirements}
+
+\begin{itemize}
+\item Mathematica 7-9
+\item SARAH version 4
+\item a C++11 compatible compiler (g++ 4.7.2 or higher, clang++ 3.1 or
+  higher)
+\item a fortran compiler (gfortran etc.)
+\item Eigen library version 3
+\item Boost library
+\item GNU scientific library
+\item lapack (needed for the Lattice algorithm only)
+\end{itemize}

doc/chapters/quick_start.tex

@@ -0,0 +1,15 @@
+\section{Quick start}
+Create a MSSM spectrum generator
+  \begin{lstlisting}[language=bash]
+$ ./createmodel --models=MSSM
+$ ./configure --with-models=MSSM
+$ make
+  \end{lstlisting}
+Run the spectrum generator using the default parameter point
+  \begin{lstlisting}[language=bash]
+$ ./models/MSSM/run_MSSM.x
+  \end{lstlisting}
+Run the spectrum generator using a SLHA input file
+  \begin{lstlisting}[language=bash]
+$ ./models/MSSM/run_MSSM.x --slha-input-file=templates/MSSM/LesHouches.in.MSSM --slha-output-file=LesHouches.out.MSSM
+  \end{lstlisting}

doc/chapters/usage.tex

@@ -0,0 +1,182 @@
+\section{Usage}
+\subsection{Files and directories}
+
+Explain:
+\begin{itemize}
+\item Soucre code directories and files
+\item Model directories and files
+\end{itemize}
+
+\subsection{Basic commands}
+
+Explain:
+\begin{itemize}
+\item ./createmodel
+\item ./configure
+\item make
+\item Mathematica interface (see models/<model>/start.m)
+\end{itemize}
+
+\subsection{Model files}
+
+Explain how to write a FlexibleSUSY model file (starting from a SARAH
+model file).
+
+A FlexibleSUSY model file is a Mathematica file, where the following
+pieces are defined:
+
+\paragraph{General model information}
+
+\subparagraph{FSModelName}
+Name of the FlexibleSUSY model.
+Example (MSSM):
+\begin{lstlisting}[language=Mathematica]
+FSModelName = "MSSM";
+\end{lstlisting}
+
+\subparagraph{OnlyLowEnergyFlexibleSUSY} If set to True, creates a
+spectrum generator without high-scale constraint, i.e.\ only a
+low-scale and susy-scale constraint will be created (default: False).
+In this case all model parameters, except for gauge and Yukawa
+couplings are input at the susy scale.  This option is similar to
+\texttt{OnlyLowEnergySPheno} in SARAH/SPheno.
+\\
+Example:
+\begin{lstlisting}[language=Mathematica]
+OnlyLowEnergyFlexibleSUSY = False;  (* default *)
+\end{lstlisting}
+
+\paragraph{Input and output parameters}
+
+\subparagraph{MINPAR} This list of two-component lists defines model
+input parameters and their SLHA keys.  These parameters will be read
+from the MINPAR block in the SLHA file.
+\\
+Example (MSSM):
+\begin{lstlisting}[language=Mathematica]
+MINPAR = { {1, m0},
+           {2, m12},
+           {3, TanBeta},
+           {4, Sign[\[Mu]]},
+           {5, Azero}
+         };
+\end{lstlisting}
+
+\subparagraph{EXPAR} This list of two-component lists defines further
+model input parameters and their SLHA keys.  These parameters will be
+read from the EXTPAR block in the SLHA file.
+\\
+Example (E6SSM):
+\begin{lstlisting}[language=Mathematica]
+EXTPAR = { {61, LambdaInput},
+           {62, KappaInput},
+           {63, muPrimeInput},
+           {64, BmuPrimeInput},
+           {65, vSInput}
+         };
+\end{lstlisting}
+
+\subparagraph{DefaultParameterPoint} This list of two-component lists
+defines default values for the model input parameters.
+\\
+Example (MSSM):
+\begin{lstlisting}[language=Mathematica]
+DefaultParameterPoint = {
+    {m0, 125},
+    {m12, 500},
+    {TanBeta, 10},
+    {Sign[\[Mu]], 1},
+    {Azero, 0}
+};
+\end{lstlisting}
+
+\paragraph{Constraints}
+Currently three constraints are supported: low-scale, susy-scale and
+high-scale constraints.  In FlexibleSUSY they are named as
+\texttt{LowScale}, \texttt{SUSYScale} and \texttt{HighScale}.  For
+each constraint there is a scale definition (named after the
+constraint), an initial guess for the scale (concatenation of the
+constraint name and \texttt{FirstGuess}) and a list settings to be
+applied at the constraint (concatenation of the constraint name and
+\texttt{Input}).
+\\
+Example (MSSM):
+\begin{lstlisting}[language=Mathematica]
+(* susy-scale constraint *)
+SUSYScale = Sqrt[M[Su[1]]*M[Su[6]]];        (* scale definition *)
+SUSYScaleFirstGuess = Sqrt[m0^2 + 4 m12^2]; (* first scale guess *)
+SUSYScaleInput = {};                        (* nothing is set here *)
+
+(* high-scale constraint *)
+HighScale = g1 == g2;                       (* scale definition *)
+HighScaleFirstGuess = 1.0 10^14;            (* first scale guess *)
+HighScaleInput = {
+   {T[Ye], Azero*Ye},
+   {T[Yd], Azero*Yd},
+   {T[Yu], Azero*Yu},
+   {mHd2, m0^2},
+   {mHu2, m0^2},
+   {mq2, UNITMATRIX[3] m0^2},
+   {ml2, UNITMATRIX[3] m0^2},
+   {md2, UNITMATRIX[3] m0^2},
+   {mu2, UNITMATRIX[3] m0^2},
+   {me2, UNITMATRIX[3] m0^2},
+   {MassB, m12},
+   {MassWB,m12},
+   {MassG, m12}
+};
+
+LowScale = SM[MZ];                          (* scale definition *)
+LowScaleFirstGuess = SM[MZ];                (* first scale guess *)
+LowScaleInput = {
+   {vd, 2 MZDRbar / Sqrt[GUTNormalization[g1]^2 g1^2 + g2^2] Cos[ArcTan[TanBeta]]},
+   {vu, 2 MZDRbar / Sqrt[GUTNormalization[g1]^2 g1^2 + g2^2] Sin[ArcTan[TanBeta]]}
+};
+\end{lstlisting}
+
+\paragraph{Initial parameter guesses} At the \texttt{LowScale} and
+\texttt{HighScale} it is recommended to make an initial guess for the
+model parameters.  This can be done via
+\begin{lstlisting}[language=Mathematica]
+InitialGuessAtLowScale = {
+   {vd, SM[vev] Cos[ArcTan[TanBeta]]},
+   {vu, SM[vev] Sin[ArcTan[TanBeta]]}
+};
+
+InitialGuessAtHighScale = {
+   {\[Mu]   , 1.0},
+   {B[\[Mu]], 0.0}
+};
+\end{lstlisting}
+
+\begin{sidewaystable}[tb]
+  \centering
+  \begin{tabularx}{\textwidth}{>{\ttfamily}l>{\ttfamily}lX}
+    \toprule
+    variable    & default value & description \\
+    \midrule
+    FSModelName & Model`Name & Name of the FlexibleSUSY model \\
+    OnlyLowEnergyFlexibleSUSY & False & low-energy model \\
+    MINPAR & \{\} & list of input parameters in SLHA MINPAR block \\
+    EXTPAR & \{\} & list of input parameters in SLHA EXTPAR block \\
+    DefaultParameterPoint & \{\} & list of default values for the input parameters \\
+    LowScale & SM[MZ] & Standard Model matching scale (in GeV) \\
+    LowScaleFirstGuess & SM[MZ] & first guess for the Standard Model matching scale (in GeV) \\
+    LowScaleInput & \{\} & settings applied at the low scale \\
+    SUSYScale & 1000 & scale of supersymmetric particle masses (in GeV) \\
+    SUSYScaleFirstGuess & 1000 & first guess for the susy scale (in GeV) \\
+    SUSYScaleInput & \{\} & settings applied at the susy scale \\
+    HighScale & SARAH`hyperchargeCoupling == SARAH`leftCoupling
+      & unification scale (in GeV) \\
+    HighScaleFirstGuess & $10^{14}$ & first guess for the unification scale (in GeV) \\
+    HighScaleInput & \{\} & settings applied at the unification scale \\
+    \bottomrule
+  \end{tabularx}
+  \caption{FlexibleSUSY model file variables}
+  \label{tab:model-file-variables}
+\end{sidewaystable}
+
+\subsection{Makefile modules}
+
+Explain how to write a custom makefile module (module.mk) for a
+FlexibleSUSY model.