Merge pull request #54 from geodynamics/devel

merged with Devel

doc/chap3_input.tex

@@ -10,7 +10,7 @@ \section{Main input file}
 {\it{line\_type}} $arg_1=val_1$, $arg_2=val_2$, ......., $arg_n=val_n$\\
 
 Example:\\
-\texttt{preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenod=8, ngnod=8, \& \\
+\texttt{preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenode=8, ngnode=8, \& \\
 inp\_path=\sq{./input}, part\_path=\sq{./partition}, out\_path=\sq{./output/}}\\
 \\
 OR
@@ -21,8 +21,8 @@ \section{Main input file}
           \hspace*{18pt} ngllx=3,\&\\
           \hspace*{18pt} nglly=3,\&\\
           \hspace*{18pt} ngllz=3,\&\\
-          \hspace*{18pt} nenod=8,\&\\
-          \hspace*{18pt} ngnod=8,\&\\
+          \hspace*{18pt} nenode=8,\&\\
+          \hspace*{18pt} ngnode=8,\&\\
           \hspace*{18pt} inp\_path=\sq{./input},\&\\
           \hspace*{18pt} part\_path=\sq{./partition},\&\\
           \hspace*{18pt} out\_path=\sq{./output/}}\\
@@ -150,7 +150,7 @@ \subsubsection*{Input file for a simple elastic simulation}
 \noindent{\texttt{\#-----------------------------------------------------------------\\
 \#input file elastic.sem\\
 \#pre information\\
-preinfo: ngllx=3, nglly=3, ngllz=3, nenod=8, ngnod=8, \& \\
+preinfo: ngllx=3, nglly=3, ngllz=3, nenode=8, ngnode=8, \& \\
 inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
 \#mesh information \\
 mesh: xfile=\sq{validation1\_coord\_x}, yfile=\sq{validation1\_coord\_y}, \& \\
@@ -173,7 +173,7 @@ \subsubsection*{Serial input file for slope stability}
 \noindent{\texttt{\#-----------------------------------------------------------------\\
 \#input file validation1.sem\\
 \#pre information\\
-preinfo: ngllx=3, nglly=3, ngllz=3, nenod=8, ngnod=8, \& \\
+preinfo: ngllx=3, nglly=3, ngllz=3, nenode=8, ngnode=8, \& \\
 inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
 \#mesh information \\
 mesh: xfile=\sq{validation1\_coord\_x}, yfile=\sq{validation1\_coord\_y}, \& \\
@@ -197,8 +197,8 @@ \subsubsection*{Parallel input file for slope stability}
 \noindent{\texttt{\#-----------------------------------------------------------------\\
 \#input file validation1.psem\\
 \#pre information\\
-preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenod=8, \& \\
-ngnod=8, inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
+preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenode=8, \& \\
+ngnode=8, inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
 \#mesh information \\
 mesh: xfile=\sq{validation1\_coord\_x}, yfile=\sq{validation1\_coord\_y}, \& \\
 zfile=\sq{validation1\_coord\_z}, confile=\sq{validation1\_connectivity}, \& \\
@@ -221,7 +221,7 @@ \subsubsection*{Serial input file for excavation}
 \noindent{\texttt{\#-----------------------------------------------------------------\\
 \#input file excavation\_3d.sem\\
 \#pre information\\
-preinfo: ngllx=3, nglly=3, ngllz=3, nenod=8, ngnod=8, \& \\
+preinfo: ngllx=3, nglly=3, ngllz=3, nenode=8, ngnode=8, \& \\
 inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
 \#mesh information \\
 mesh: xfile=\sq{excavation\_3d\_coord\_x}, yfile=\sq{excavation\_3d\_coord\_y}, \& \\
@@ -230,7 +230,7 @@ \subsubsection*{Serial input file for excavation}
 \#boundary conditions\\
 bc: uxfile=\sq{excavation\_3d\_ssbcux}, uyfile=\sq{excavation\_3d\_ssbcuy}, \& \\
 uzfile=\sq{excavation\_3d\_ssbcuz}\\\\
-\#initial stress
+\#initial stress\\
 stress0: type=0, z0=0, s0=0, k0=0.5, usek0=1\\\\
 \#material list\\
 material: matfile=\sq{excavation\_3d\_material\_list}\\\\
@@ -247,16 +247,16 @@ \subsubsection*{Parallel input file for excavation}
 \noindent{\texttt{\#-----------------------------------------------------------------\\
 \#input file excavation\_3d.psem\\
 \#pre information\\
-preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenod=8, \& \\
-ngnod=8, inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
+preinfo: nproc=8, ngllx=3, nglly=3, ngllz=3, nenode=8, \& \\
+ngnode=8, inp\_path=\sq{./input}, out\_path=\sq{./output/}\\\\
 \#mesh information \\
 mesh: xfile=\sq{excavation\_3d\_coord\_x}, yfile=\sq{excavation\_3d\_coord\_y}, \& \\
 zfile=\sq{excavation\_3d\_coord\_z}, confile=\sq{excavation\_3d\_connectivity}, \& \\
 idfile=\sq{excavation\_3d\_material\_id}, gfile=\sq{excavation\_3d\_ghost}\\\\
 \#boundary conditions\\
 bc: uxfile=\sq{excavation\_3d\_ssbcux}, uyfile=\sq{excavation\_3d\_ssbcuy}, \& \\
 uzfile=\sq{excavation\_3d\_ssbcuz}\\\\
-\#initial stress
+\#initial stress\\
 stress0: type=0, z0=0, s0=0, k0=0.5, usek0=1\\\\
 \#material list\\
 material: matfile=\sq{excavation\_3d\_material\_list}\\\\

doc/chap4_output_and_visualization.tex

@@ -24,7 +24,7 @@ \subsection{CASE file}
 
 \subsection{SOS file}
 
-This is an EnSight Gold server-of-server file for parallel visualization. The \texttt{write\_sos.f90} program provided in the \texttt{/util/} may be used to generate this file. See Chapter~\ref{chap:util}, Section~\ref{sec:sos} for more detail.
+This is an EnSight Gold server-of-server file for parallel visualization. The \texttt{write\_sos.f90} program provided in the \texttt{util/} may be used to generate this file. See Chapter~\ref{chap:util}, Section~\ref{sec:sos} for more detail.
 
 All above EnSight Gold files correspond to the model with spectral-element mesh. Additionally, the CASE file/s and mesh file/s are written for the original model. These file names follow the similar conventions and they have the tag \texttt{\sq{original}} in the file name headers.
 

doc/chap5_utilities.tex

@@ -2,31 +2,31 @@ \chapter{Utilities}
 \label{chap:util}
 \section{Convert EXODUS mesh into SEM files}
 
-The program \texttt{exodus2semgeotech.c} contained in the utilities directory can be used to convert the mesh file in EXODUS II format to input files required by the \pack\ .
+The program \texttt{exodus2semgeotech.c} contained in the \texttt{util/} directory can be used to convert the mesh file in EXODUS II format to input files required by the \pack\ .
 
 \subsubsection*{Compile}
 \texttt{gcc -o exodus2semgeotech exodus2semgeotech.c}
 \subsubsection*{Run}
  \texttt{exodus2semgeotech} {\emph{EXODUS\_mesh\_file}} {\emph{OPTIONS}}\\
- For more details, see \texttt{/util/README\_exodus2semgeotech}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).
+ For more details, see \texttt{util/README\_exodus2semgeotech}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).
 
 \section{Convert GiD mesh into SEM files}
 
-The program \texttt{gid2semgeotech.c} contained in the utilities directory can be used to convert the mesh file in GiD format to input files required by the \pack\ .
+The program \texttt{gid2semgeotech.c} contained in the \texttt{util/} directory can be used to convert the mesh file in GiD format to input files required by the \pack\ .
 
 \subsubsection*{Compile}
 \texttt{gcc -o gid2semgeotech gid2semgeotech.c}
 \subsubsection*{Run}
  \texttt{gid2semgeotech} {\emph{GiD\_mesh\_file}} {\emph{OPTIONS}}\\
- For more details, see \texttt{/util/README\_gid2semgeotech}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).
+ For more details, see \texttt{util/README\_gid2semgeotech}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).
 
 \section{Generate SOS file}
 \label{sec:sos}
 
-The program \texttt{write\_sos.f90} contained in the utilities directory can be used to write EnSight Gold server-of-server file (.sos file, see~\citep{ensight2008}) to visualize the multi-processors data in parallel. This file does not contain the actual data, but only information on the data location and parallel processing.
+The program \texttt{write\_sos.f90} contained in the \texttt{util/} directory can be used to write EnSight Gold server-of-server file (.sos file, see~\citep{ensight2008}) to visualize the multi-processors data in parallel. This file does not contain the actual data, but only information on the data location and parallel processing.
 \subsubsection*{Compile}
 \texttt{gfortran -o write\_sos write\_sos.f90}
 \subsubsection*{Run}
 \texttt{exodus2sem} {\it{input\_file}}\\
 
-For more details, see \texttt{/util/README\_write\_sos}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).
+For more details, see \texttt{util/README\_write\_sos}. It can also be compiled automatically during the build process of main package \pack\ (see Section~\ref{sec:configure}).