Updated manual

doc/manual/installation.tex

@@ -3,7 +3,7 @@ \subsection{Obtaining \dftfe{}}
 \begin{verbatim}
  git clone https://[email protected]/dftfedevelopers/dftfe.git
 \end{verbatim}
-For internal group testing, use the internalGroupTesting
+For internal group testing, use the \verb|internalGroupTesting| branch.
 \begin{verbatim}
  git checkout internalGroupTesting
 \end{verbatim}
@@ -12,6 +12,7 @@ \subsection{Compiling required external libraries}
 Not required for internal group testing if trying to run \dftfe{} on flux.
 
 \subsection{Compiling \dftfe{}}
+Following are the steps to compile DFT-FE (only for flux)
 \begin{enumerate}
 \item \begin{verbatim}
 cd dftfe
@@ -31,11 +32,22 @@ \subsection{Compiling \dftfe{}}
 ./setup.sh
 \end{verbatim} 
 \end{enumerate}
-If \dftfe{} compiled successfully, the following executables will be created in the \verb|build| directory:
+, which by default compiles in the release mode (the fast version). If \dftfe{} compiled successfully, the following executables will be created in the \verb|build| directory:
 \begin{verbatim}
 /build/release/real/main
 /build/release/complex/main
+\end{verbatim}
+One could also set
+\begin{verbatim}
+optimizedFlag=1
+\end{verbatim}
+inside \verb|setup.sh|, and run
+\begin{verbatim}
+./setup.sh
+\end{verbatim}
+, which will create debug mode executables (useful for debugging purposes but much slower than the release mode executable) in the folders
+\begin{verbatim}
 /build/debug/real/main
 /build/debug/complex/main
 \end{verbatim}
-Among the above executables, the ones in the \verb|build/release/| folder are the fast version, which are meant for production runs. For debugging crashes and bugs, use the executables in the \verb|build/debug/| folder. 
+

doc/manual/parameters.tex

@@ -665,7 +665,7 @@ \subsection{Parameters in section \tt Geometry/Optimization}
 \index[prmindexfull]{Geometry!Optimization!FORCE TOL}
 
 
-{\it Default:} 5e-5
+{\it Default:} 1e-4
 
 
 {\it Description:} [Standard] Sets the tolerance of the maximum force (in a.u.) on an ion when forces are considered to be relaxed.
@@ -745,7 +745,7 @@ \subsection{Parameters in section \tt Geometry/Optimization}
 \index[prmindexfull]{Geometry!Optimization!STRESS TOL}
 
 
-{\it Default:} 5e-7
+{\it Default:} 1e-6
 
 
 {\it Description:} [Standard] Sets the tolerance of the cell stress (in a.u.) when cell stress is considered to be relaxed.

doc/manual/rundftfe.tex

@@ -1 +1,9 @@
-The \verb|real/main| executable uses only real data-structures, which are sufficient for fully non-periodic problems, and periodic and semi-periodic problems with only one Brillouin zone sampling point at the origin. The \verb|complex/main| executable uses complex data-structrues which are required for periodic and semi-periodic problems with multiple Brillouin zone sampling points.
+After compiling \dftfe{} as described above, we have now the \verb|real/main| executable, which uses real data-structures for the Kohn-Sham DFT eigen solve. This is sufficient for fully non-periodic problems, and periodic and semi-periodic problems with only one Brillouin zone sampling point at the origin. The other executable is \verb|complex/main|, which uses complex data-structrues for the Kohn-Sham DFT eigen solve. This is required for periodic and semi-periodic problems with multiple Brillouin zone sampling points. These executables are to be used as follows:
+\begin{verbatim}
+ ./main parameterFile.prm
+\end{verbatim}
+or, for a parallel program:
+\begin{verbatim}
+ mpirun -n N ./main parameterFile.prm
+\end{verbatim}
+to run with N processors. In the above, an input file with \verb|.prm| extension is used. This file contains user-defined parameters as described in Section~\ref{sec:parameters}. For the structure of the input \verb|.prm| file, please follow the examples in the \verb|/dftfe/demo/| folder.