Merge pull request #11 from nrc-cnrc/develop

Merging develop branch into master

.gitignore

@@ -7,16 +7,20 @@ mortjob.mortran
 *.log
 HEN_HOUSE/bin/
 HEN_HOUSE/lib/
+HEN_HOUSE/log/
 HEN_HOUSE/egs++/dso/
-HEN_HOUSE/omega/beamnrc/tools/beam_build_linux.f
-HEN_HOUSE/omega/progs/addphsp/addphsp_linux.f
-HEN_HOUSE/omega/progs/beamdp/beamdp_linux.f
-HEN_HOUSE/omega/progs/ctcreate/ctcreate_linux.F
-HEN_HOUSE/omega/progs/readphsp/readphsp_linux.f
-HEN_HOUSE/omega/progs/statdose/statdose_linux.f
-HEN_HOUSE/pegs4/density_corrections/split_del.f
-HEN_HOUSE/pegs4/density_corrections/time_stamp
-HEN_HOUSE/pegs4/pegs4_linux.f
+HEN_HOUSE/mortran3/mortran3_*.f
+HEN_HOUSE/omega/beamnrc/tools/beam_build_*.f
+HEN_HOUSE/omega/progs/addphsp/addphsp_*.f
+HEN_HOUSE/omega/progs/beamdp/beamdp_*.f
+HEN_HOUSE/omega/progs/ctcreate/ctcreate_*.F
+HEN_HOUSE/omega/progs/readphsp/readphsp_*.f
+HEN_HOUSE/omega/progs/statdose/statdose_*.f
+HEN_HOUSE/pegs4/pegs4_*.f
+HEN_HOUSE/pieces/linux/egs_gui_*
+HEN_HOUSE/pieces/linux/egs_inprz_*
+HEN_HOUSE/pieces/linux/egs_view_*
+
 
 ### ignore generated documentation
 doc/*.pdf
@@ -35,10 +39,11 @@ html
 *.so
 
 ### ignore OS generated files
+*~
 ._*
 .DS_Store
 .DS_Store?
 .Spotlight-V100
 .Trashes
 ehthumbs.db
-Thumbs.db
+Thumbs.db

HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex

@@ -500,8 +500,6 @@ \section{Building/compiling/running BEAMnrc}
 the OMEGA/BEAM codes.
 
 \index{.cshrc}
-\index{beamnrc\_cshrc\_additions}
-\index{beamnrc\_bashrc\_additions}
 \index{egsnrc\_cshrc\_additions}
 \index{egsnrc\_bashrc\_additions}
 \index{.bashrc}
@@ -521,16 +519,13 @@ \section{Building/compiling/running BEAMnrc}
 source /full directory path to $HEN_HOUSE/scripts/egsnrc_cshrc_additions
 (or source /full directory path to $HEN_HOUSE/scripts/egsnrc_bashrc_additions
                                                               for .bashrc)
-source /full directory path to $HEN_HOUSE/scripts/beamnrc_cshrc_additions
-(or source /full directory path to $HEN_HOUSE/scripts/beamnrc_bashrc_additions
-                                                              for .bashrc)
 \end{verbatim}
 where {\tt config} is the name of the particular configuration
 (eg {\tt gcc}, {\tt pgf77}) that you have installed BEAMnrc on.  The
 first three statements are required for the
 EGSnrcMP system (see the EGSnrcMP Users Manual\cite{Ka03}), while
-{\tt \$HEN\_HOUSE/scripts/beamnrc\_cshrc\_additions}
-(or {\tt \$HEN\_HOUSE/scripts/beamnrc\_cshrc\_additions}) define aliases
+{\tt \$HEN\_HOUSE/scripts/egsnrc\_cshrc\_additions}
+(or {\tt \$HEN\_HOUSE/scripts/egsnrc\_cshrc\_additions}) define aliases
 for the OMEGA/BEAM system.  Once you have added these statements you
 must source the {\tt .cshrc}
 (or {\tt .bashrc}) file to bring them into effect.

HEN_HOUSE/doc/src/pirs509c-beamdp/pirs509c-beamdp.tex

@@ -329,8 +329,8 @@ \subsection{Compiling and running BEAMDP}
 beamdp_gui
 \end{verbatim}
 Note that you must have sourced the Unix script
-{\tt \$HEN\_HOUSE/scripts/beamnrc\_cshrc\_additions} (or
-{\tt \$HEN\_HOUSE/scripts/beamnrc\_bashrc\_additions}) in your
+{\tt \$HEN\_HOUSE/scripts/egsnrc\_cshrc\_additions} (or
+{\tt \$HEN\_HOUSE/scripts/egsnrc\_bashrc\_additions}) in your
 {\tt .cshrc} (or {\tt .bashrc}) file.  See the BEAMnrc Users Manual\cite{Ro04a}
 for more information about these scripts.  To start the GUI in a Windows
 environment, double click on the GUI icon (or on the name

HEN_HOUSE/doc/src/pirs509e-beamdp-utility/pirs509e-beamdp-utility.tex

@@ -917,8 +917,8 @@ \subsection{Run BEAMDP}
 beamdp_gui
 \end{verbatim}
 from any directory.  You
-must have sourced the file {\tt beamnrc\_cshrc\_additions} (or\\
-{\tt beamnrc\_bashrc\_additions}) in your {\tt .cshrc} (or {\tt .bashrc})
+must have sourced the file {\tt egsnrc\_cshrc\_additions} (or\\
+{\tt egsnrc\_bashrc\_additions}) in your {\tt .cshrc} (or {\tt .bashrc})
 file (See the BEAMnrc User's Manual\cite{Ro04a} for more about this).
 
 To run the GUI in a Windows environment, double click on the GUI icon

HEN_HOUSE/doc/src/pirs623-gui/pirs623-gui.tex

@@ -239,7 +239,7 @@ \section{The BEAMnrc GUI}
 
 To run the BEAMnrc GUI from a Linux/Unix window, type {\tt beamnrc\_gui} at
 the prompt.  Note that you must have sourced the Unix script
-{\tt beamnrc\_cshrc\_additions}\\(or {\tt beamnrc\_bashrc\_additions}) in
+{\tt egsnrc\_cshrc\_additions}\\(or {\tt egsnrc\_bashrc\_additions}) in
 your {\tt .cshrc} (or {\tt .bashrc}) file.  See the BEAMnrc Manual\cite{Ro04a}
 for more information about these scripts.
 
@@ -599,7 +599,7 @@ \section{The DOSXYZnrc GUI}
 
 To run the DOSXYZnrc GUI from a Linux/Unix window, type {\tt dosxyznrc\_gui}
 at the prompt. Note that you must have sourced the Unix script
-{\tt beamnrc\_cshrc\_additions} (or {\tt beamnrc\_bashrc\_additions}) in
+{\tt egsnrc\_cshrc\_additions} (or {\tt egsnrc\_bashrc\_additions}) in
 your {\tt .cshrc} (or {\tt .bashrc}) file.  See the BEAMnrc Manual\cite{Ro04a}
 for more information about these scripts.
 
@@ -801,7 +801,7 @@ \section{The BEAMDP GUI}
 
 In a Linux/Unix window, the GUI is invoked by typing {\tt beamdp\_gui}.
 Note that you must have sourced the Unix script
-{\tt beamnrc\_cshrc\_additions} (or {\tt beamnrc\_bashrc\_additions}) in
+{\tt egsnrc\_cshrc\_additions} (or {\tt egsnrc\_bashrc\_additions}) in
 your {\tt .cshrc} (or {\tt .bashrc}) file.  See the BEAMnrc Manual\cite{Ro04a}
 for more information about these scripts.