Manual update

doc/manual/installation.tex

@@ -189,15 +189,15 @@ \subsubsection{Instructions for deal.II}
 \end{verbatim}
 ``Success'', means deal.II was able to use the corresponding vector instructions, and ``Failed'' would mean otherwise. If deal.II is not able to pick an available vector instruction on your high-performance computer, please contact the deal.II developers at \href{https://groups.google.com/d/forum/dealii}{deal.II mailing lists} and/or contact your high-performance computer support for guidance on how to use the correct compiler flags for AVX or AVX-512. 
 
-Ensuring that deal.II picks up AVX-512 is strongly recommended for obtaining maximum performance on the new Intel Xeon Phi (KNL) and Skylake processors, both of which support Intel AVX-512 instructions.
+Ensure that deal.II picks up AVX-512, which is strongly recommended for obtaining maximum performance on the new Intel Xeon Phi (KNL) and Skylake processors, both of which support Intel AVX-512 instructions.
 
 \subsubsection{Important generic instructions for deal.II and its dependencies}
 \begin{itemize}
 \item If using Intel MKL for BLAS-LAPACK library, it is {\bf very important} to use \href{https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor}{Intel MKL Link Line Advisor} to set correctly link with BLAS-LAPACK library as needed in installations of PETSc, ScaLAPACK, and deal.II. To exploit performance benefit from threads, we recommend (strongly recommended for the new Intel Xeon Phi (KNL) and Skylane processors) linking to threaded versions of Intel MKL libraries by using the options ``threading layer'' and  ``OpenMP library'' in \href{https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor}{Intel MKL Link Line Advisor}.
 
 \item Use \verb|-fPIC| compiler flag for compilation of deal.II and its dependencies, to prevent linking errors during \dftfe{} compilation.	
 
-\item \textcolor{red}{\bf CAUTION! It is  very important to ensure that deal.II and its dependencies (p4est, PETSc, SLEPc, and ScaLAPACK), are compiled with the same compilers, BLAS-LAPACK libraries, and MPI libraries to prevent deal.II compilation issues, occurence of run time crashes, and \dftfe{} performance degradation.}  
+\item \textcolor{red}{\bf CAUTION! It is  highly recommended to compile deal.II and its dependencies (p4est, PETSc, SLEPc, and ScaLAPACK),  with the same compilers, same BLAS-LAPACK libraries, and same MPI libraries. This prevents deal.II compilation issues, occurence of run time crashes, and \dftfe{} performance degradation.}  
 \end{itemize}
 
 \subsection{Obtaining and Compiling \dftfe{}}

doc/manual/manual.tex

@@ -121,11 +121,11 @@
 % e.g. height=6.5in
 \begin{center}
 \vspace{1em}
-\includegraphics[height=2.8in]
+\includegraphics[scale=0.35]{N2.png}
 % FILL: image file name
 % e.g. cover_image.png
 %{contour_5x5x5.pdf}
-{SiCTriplet0000.png}
+%{SiCTriplet0000.png}
 \hspace{5em}
 \end{center}
 \end{textblock*}
@@ -195,18 +195,14 @@ \section{Running \dftfe}
 \label{sec:run}
 \input{rundftfe}
 
-
 \section{Future extensions to \dftfe}
 \label{sec:future}
 \input{futurePlans}
 
-
-
 \section{Finding answers to more questions}
 \label{sec:questions-and-answers}
 \input{contacts}
 
-
 \appendix
 
 \section{Run-time input parameters}

doc/manual/rundftfe.tex

@@ -64,7 +64,7 @@ \subsubsection{Example 1}\label{sec:example1}
 
 \item \verb|NATOMS| is the total number of atoms, and \verb|NATOM TYPES| is the total number of atom types.
 
-\item``domainVectors.inp'' (any other file name can be used), given as input to \verb|DOMAIN VECTORS FILE|,  is the external input file which lists the three domain vectors describing the
+\item``domainVectors.inp'' (any other file name can be used), given as input to \verb|DOMAIN VECTORS FILE|,  is the external input file which lists the three domain vectors (in a.u) describing the
 3D parallelepiped computational domain. For the current example we take a cubodial domain with 80 a.u as the edge length. 
 Accordingly, the ``domainVectors.inp'' file is formatted as  
 \begin{verbatim}
@@ -75,8 +75,7 @@ \subsubsection{Example 1}\label{sec:example1}
 wheres each row corresponds to a domain vector.
 It is a requirement that the above vectors must form a right-handed coordinate system i.e. $(v1 \times v2)\cdot v3 >0$.
 
-\item ``coordinates.inp'' (any other file name can be used), given as input to \verb|ATOMIC COORDINATES FILE|, is the name of an external input file present in the same workspace which lists the Cartesian coordinates 
-of the atoms with respect to origin at the center of the domain. For this example, ``coordinates.inp'' is described as 
+\item ``coordinates.inp'' (any other file name can be used), given as input to \verb|ATOMIC COORDINATES FILE|, is the name of an external input file present in the same workspace which lists the Cartesian coordinates of the atoms (in a.u.) with respect to origin at the center of the domain. For this example, ``coordinates.inp'' is described as 
 \begin{verbatim}
 7    5   -1.30000000E+00   0.00000000E+00   0.00000000E+00
 7    5    1.30000000E+00   0.00000000E+00   0.00000000E+00
@@ -208,8 +207,8 @@ \subsubsection{Example 1}\label{sec:example1}
   set ATOMIC COORDINATES FILE      = coordinates.inp 
   set DOMAIN VECTORS FILE = domainVectors.inp
   subsection Optimization
-    set FORCE TOL            = 1e-4
     set ION OPT              = true
+    set FORCE TOL            = 1e-4    
     set ION RELAX FLAGS FILE = relaxationFlags.inp
   end
 end