nrc-cnrc · ftessier · Feb 9, 2023 · Feb 9, 2023 · Feb 9, 2023 · Feb 9, 2023
@@ -2501,7 +2501,7 @@ \subsection{Build a new BEAMnrc accelerator}
 Create a new text file, that will provide the dynamic motion of the jaws. There are examples for all of the syncronized CMs in \,\Verb|$HEN_HOUSE/omega/beamnrc/CMs/sample_sequences/|. Copy the text at the end of this section and save the file as \,\Verb|example.sequence|\, in \\
 \,\Verb|$EGS_HOME/BEAM_syncjaws|\,. Now go back to the settings of the SYNCJAWS CM, click the \,\Verb|Browse|\, button and select the file (make sure the mode is set to \,\Verb|Dynamic|\,). Click \,\Verb|Preview|\, to view the first position of the jaws, before motion begins.
 
-The format of the sequence file is described in section 15.3.8 of the BEAMnrc Users Manual (\href{https://nrc-cnrc.github.io/EGSnrc/doc/pirs509a-beamnrc.pdf}{PIRS509a}). Using this file, it is possible to model motion like jaw tracking, based on the the \textit{index} parameter (i.e. fractional MU or cumulative meterset weight). If multiple SYNC CMs are included, the index is used to synchronize motion. Use a repeated index to simulate motion with the beam off.
+The format of the sequence file is described in section 15.3.8 of the BEAMnrc Users Manual (\href{https://nrc-cnrc.github.io/EGSnrc/doc/pirs509a-beamnrc.pdf}{PIRS509a}). Using this file, it is possible to model motion like jaw tracking, based on the \textit{index} parameter (i.e. fractional MU or cumulative meterset weight). If multiple SYNC CMs are included, the index is used to synchronize motion. Use a repeated index to simulate motion with the beam off.
 
 In the following, we define 2 static fields and 1 dynamic field in 6 steps. The upper y-jaws are at $40 \le z \le 50$ and x-jaws at $51 \le z \le 61$. From index 0.0 to 3.0 (30\% of the simulation), the jaws are statically positioned. Similarly from 0.3 to 0.6. The repeated indices, 0.3 and 0.6, result in simulated collimator shifts while the beam is off. Finally, from index 0.6 to 1.0 (40\%) there is a motion of the x-jaws from a nearly-closed position to a $2 \times 2$ opening.
 

@@ -19,7 +19,7 @@
                          [ pair_nrc ]
         Photoelectron angular sampling= Off or On (Default is On)
                          If Off, photo-electrons get the direction of the
-                         `mother' photon, with On, Sauter's furmula is
+                         `mother' photon, with On, Sauter's formula is
                          used (which is, strictly speaking, valid only for
                          K-shell photo-absorption).
                          If the user has a better approach, replace the macro

@@ -5976,7 +5976,7 @@ \subsection{ {\tt Pair angular sampling} ({\tt IPRDST})}
 by Motz et al\cite{Mo69} is used to determine the positron/electron emission
 angles.  This option is similar to the sampling technique used by
 EGS4/BEAM.  Finally if {\tt Pair angular sampling= Simple} (the default), then only
-the first term in the the Motz et al equation 3D-2003 is used.  The {\tt KM} option
+the first term in the Motz et al equation 3D-2003 is used.  The {\tt KM} option
 becomes less efficient with increasing accelerator energies and, moreover, involves
 assumptions that are questionable at low energy.  For these reasons, the default
 setting is {\tt Simple}.
@@ -6082,7 +6082,7 @@ \subsection{{\tt Photon cross sections} ({\tt photon\_xsections})}
 \& Salvat's renormalized cross sections when simulating photoelectric events,
 with either the XCOM ({\tt mcdf-xcom}) or Evaluated Photon Data Library ({\tt
 mcdf-epdl}) used for all other cross sections.  The more accurate modeling of
-photoelectric events allowed by the the Sabbatucci \& Salvat cross sections does
+photoelectric events allowed by the Sabbatucci \& Salvat cross sections does
 incur a CPU time penalty (up to 6\% for a 30 kV beam) and so this option is only
 of interest for low energy simulations. Use of these renormalized cross sections
 is necessary for agreement with PENELOPE results in ICRU90\cite{ICRU90}.
@@ -7486,7 +7486,7 @@ \subsubsection{SYNCJAWS}
 that used by any other synchronized CMs in the accelerator.  {\tt MU\_RND} is generated by the first (most upstream) synchronized
 CM (which could be SYNCJAWS) and is then passed on to any downstream synchronized CMs.
 Thus, the dynamic motion of the jaws can be coordinated (synchronized) with the dynamic motion of all other synchronized CMs
-in the the accelerator.  Moreover, if an accelerator with synchronized CMs has been compiled as a shared library for use
+in the accelerator.  Moreover, if an accelerator with synchronized CMs has been compiled as a shared library for use
 in DOSXYZnrc source 20
 (synchronized phase space source) or source 21 (synchronized BEAM treatment head simulation), then {\tt MU\_RND} is passed from the
 accelerator simulation to DOSXYZnrc.  This allows the dynamic motion of the source plane in DOSXYZnrc sources 20 and 21 to be synchronized with
@@ -9013,7 +9013,7 @@ \subsection{Creating additional cross section data}
 \index{PEGS4!input file}
 where {\tt inputfile} omits the {\tt .pegs4inp} extention and
 {\tt densityfile} omits the {\tt .density} extension.  The {\tt .pegs4inp}
-file specifies whether the the medium is an element ({\tt ELEM}),
+file specifies whether the medium is an element ({\tt ELEM}),
 compound ({\tt COMP}) or mixture ({\tt MIXT}); the composition of
 the medium (by mass, {\tt RHOZ}, in the case of {\tt MIXT} and
 number of atoms, {\tt PZ}, in the case of {\tt COMP}); the density ({\tt RHO};
@@ -9225,8 +9225,8 @@ \subsection{Pegsless Mode}
 correction to apply to calculated bremsstrahlung cross-sections.
 Options are:
 \begin{itemize}
-\item {\tt KM} $[$IAPRIM=0$]$ (the default): Apply Koch and Motz\cite{KM59} empirical corrections.
-\item {\tt NRC} $[$IAPRIM=1$]$: Apply NRC corrections based on NIST/ICRU\cite{Ro89a}.  These corrections are read from the file
+\item {\tt KM} $[$IAPRIM=0$]$ : Apply Koch and Motz\cite{KM59} empirical corrections.
+\item {\tt NRC} $[$IAPRIM=1$]$: (the default) Apply NRC corrections based on NIST/ICRU\cite{Ro89a}.  These corrections are read from the file
 {\tt \$HEN\_HOUSE/pegs4/aprime.data}.
 \item {\tt None} $[$IAPRIM=2$]$: No corrections applied.
 \end{itemize}
@@ -10428,7 +10428,7 @@ \subsection{Changes from {\tt BEAM00} to {\tt BEAMnrc02}}
 space source incident from multiple, user-selected angles.  This allows
 modelling of arc therapy.
 
-\item Added an option to DOSXYZnrc which allows the the user to output a
+\item Added an option to DOSXYZnrc which allows the user to output a
 {\tt .egsphant} file from non-CT data.  This allows you to display isodose
 contours using {\tt dosxyz\_show} in non-CT phantoms.
 

@@ -413,7 +413,7 @@ \subsection{The fast track}
 accelerator defined in {\em modulename}{\tt .module}.
 
 Alternatively, if the accelerator has already been compiled and the input file exists
-in the the {\tt \$EGS\_HOME/BEAM\_accelname} directory, you can specify the input file
+in the {\tt \$EGS\_HOME/BEAM\_accelname} directory, you can specify the input file
 (and accompanying PEGS4 data) as command line arguments.  Within the
 {\tt \$EGS\_HOME/BEAM\_accelname} directory type:
 \begin{verbatim}
@@ -699,7 +699,7 @@ \subsection{Defining the phantom voxel-by-voxel}
 in the group, for as many groups as is required.
 
 The second step is to define the media used in the phantom.  The number
-of media that you intend to use must be entered first, the the {\sf
+of media that you intend to use must be entered first, the {\sf
 Define media} button selected.  On this new window, an option menu is
 used to select each medium.  The first entry,
 medium 1, is the default medium.  Once these have been specified, click

@@ -212,7 +212,7 @@ \section{\sffamily Compiling and running}
 i_{\rm gray} = {\sqrt{\rho} - \sqrt{\rho_{min}} \over
 \sqrt{\rho_{max}} - \sqrt{\rho_{min}}} N_{\rm gray}
 \end{displaymath}
-where $\rho$ is the the actual voxel density, $\rho_{min}$ and
+where $\rho$ is the actual voxel density, $\rho_{min}$ and
 $\rho_{max}$ the minimum and maximum density of the specified
 displayable density window (see below) and $N_{\rm gray}$ the
 number of gray shades allocated. Note that the

@@ -1122,7 +1122,7 @@ \subsubsection{Incoherent (Compton) scattering}
 time when electron transport is included. Binding effects and
 Doppler broadening for coherent scattering are therefore turned
 on by default in the {\tt block data} sub-program (the switch
-{\tt IBCMP} is set to unity).
+{\tt IBCMP} is set to 3, {\tt norej}).
 \index{IBCMP}
 
 Since the 2009 release of EGSnrc, the user has the option to change
@@ -1268,7 +1268,7 @@ \subsubsection{Photo-electric absorption}
 (in the {\tt COMIN/EDGE} common block-see Section~\ref{common_blocks}). If {\tt IEDGFL} of the
 region is non-zero, a detailed simulation is performed,
 otherwise a simplified treatment of the photo-absorption process
-is undertaken. The default setting of {\tt IEDGFL} is one.
+is undertaken. The default setting of {\tt IEDGFL} is 1.
 \index{IEDGFL}
 
 \paragraph{Detailed simulation of photo-electric absorption}\hfill
@@ -1726,7 +1726,7 @@ \subsubsection{Changing photon cross sections}
 
 In the current version of EGSnrc, the user has the option to use
 photon cross section data other than the default
-Storm \& Israel data.  To do this, the user must
+XCOM data.  To do this, the user must
 set the character variable {\tt photon\_xsections} (part of the
 {\tt COMIN/MEDIA} common block) to the name of the cross section
 data to use.  Cross sections included with the EGSnrc distribution
@@ -2046,4 +2046,3 @@ \subsection{Atomic Relaxations}
 \index{AUSGAB}
 \index{IARG!25,26,27:}
 %\clearpage
-
@@ -606,7 +606,7 @@ \subsubsection{Bremsstrahlung}
 $\tilde{f}_c(E,Z)$ have the same definitions as for the
 pair production process (see section \ref{pair}),
 and $A'(E,Z)$ is an empirical correction factor (see below).
-For compounds and mixture the the cross section can be
+For compounds and mixture the cross section can be
 approximated in the same form with the replacements given
 by Eq. (\ref{pair_replace}) in section \ref{pair} (page~\pageref{pair}).
 
@@ -1326,7 +1326,7 @@ \subsubsection{Two Photon Positron-Electron Annihilation}
 has a maximum
 of $1$ for $\epsilon = 1/(\tau+2)$ and
 thus is a valid rejection function\footnote{Note that our $g(\varepsilon)$ is
-the $g(\varepsilon)$ defined in Eq (2.12.26) of the the EGS4 manual
+the $g(\varepsilon)$ defined in Eq (2.12.26) of the EGS4 manual
 divided by its maximum.}. The sampling algorithm is then as follows:
 \begin{enumerate}
 \item

@@ -526,7 +526,7 @@ \subsection{Execution}
 
 \index{execution in batch}
 If \verb+queue+ is not specified when the batch option ``{\tt b}'' is being
-used, then the default que on your system is used.
+used, then the default queue on your system is used.
 \index{interactive execution}
 
 \index{debug}

@@ -740,8 +740,8 @@ \section{EGS User Guide to MORTRAN3}
  but not
                     Y = DUMPX;
 
-      Normally, the text generated by a macro is itself elegible
- for replacement by other macros, or even by the the same macro
+      Normally, the text generated by a macro is itself eligible
+ for replacement by other macros, or even by the same macro
  that generated the text.
 
  \end{verbatim}

@@ -431,7 +431,7 @@ \subsection{ The COMMON Blocks}
         %       it is never turned off in default EGSnrc.\\
 	&IRAYLR	&Array(\$MXREG) of flags for turning on (=1)
                             coherent (Rayleigh) scattering in
-                            various regions (default=0$\Rightarrow$ off).\\
+                            various regions (default=1$\Rightarrow$ on).\\
 &&\\
 \hline
 \multicolumn{3}{c}{$^*$ NOSCAT is no longer available since there is
@@ -1233,7 +1233,7 @@ \subsubsection{Pre-HATCH Call Initialisation (Step 2)}
 \item[IRAYLR] The elements of this integer array (dimensioned {\tt
 IRAYLR(\$MXREG)} and passed in\\ {\tt COMMON/MISC/)} are to be set to 1
 prior to calling {\tt HATCH} if coherent (Rayleigh) scattering is to be done
-in a particular region. The default values are 0.
+in a particular region. The default values are 1.
 See section~\ref{rayleigh}(page~\pageref{rayleigh}).
 Execution is only terminated if set to 1, user wants to use photon data
 from PEGS4 file, and Rayleigh data are not included.
@@ -1334,7 +1334,7 @@ \subsubsection{Pre-HATCH Call Initialisation (Step 2)}
 The cross section data must be contained in file
 {\tt \$HEN\_HOUSE/data/comp\_xsections\_compton.data}.  If the user does
 not supply a name for {\tt comp\_xsections}, then the default Compton
-data used with {\tt IBCMP}=2 is in {\tt \$HEN\_HOUSE/data/compton\_sigma.data}.
+data used with {\tt IBCMP}=3 is in {\tt \$HEN\_HOUSE/data/compton\_sigma.data}.
 See section~\ref{comp_xsect} (page~\pageref{comp_xsect}).
 
 If using {\tt get\_transport\_parameter}, then {\tt comp\_xsections} can be
@@ -1395,10 +1395,10 @@ \subsubsection{Pre-HATCH Call Initialisation (Step 2)}
 \item[photon\_xsections] A character variable ({\tt character*16}) defined
 in {\tt COMMON/MEDIA} which must be defined prior to calling {\tt HATCH}
 if the user wants to use photon cross section data other than the default
-(Storm \& Israel\cite{SI70}) data.  Current possible settings of
+XCOM data. Current possible settings of
 {\tt photon\_xsections} are: {\tt epdl} (the Evaluated Photon Data
-Library\cite{Cu90}), {\tt xcom} (XCOM from Berger \& Hubbell\cite{BH87}),
-{\tt si} (Storm \& Israel--also the default if not set),
+Library\cite{Cu90}), {\tt xcom} (XCOM from Berger \& Hubbell\cite{BH87}, default),
+{\tt si} (Storm \& Israel),
 and {\tt pegs4} (to use PEGS4 photon data).
 The user can supply their own cross section data.  For a user-supplied data
 set, {\tt photon\_xsections}, the cross section data for photoelectric,
@@ -1422,7 +1422,7 @@ \subsubsection{Pre-HATCH Call Initialisation (Step 2)}
 be set to 1 prior to calling {\tt HATCH} if the user wants to output a summary
 of the photon cross section data.  The default value is 0.  Cross section
 data is written to the file\\ {\tt \$EGS\_HOME/user\_code/inputfile.xsections}.
-Prior to the current EGSnrc release, the default was to print this file and
+Previously, the default was to print this file and
 there was no input for turning it off.
 
 If using {\tt get\_transport\_parameter}, then {\tt xsec\_out} can be set

@@ -117,12 +117,10 @@ \subsubsection{Photon data for EGSnrc}
 grid with {\tt \$MXGE} energy points. However, EGSnrc still needs the
 PEGS4 data file for material information, photon threshold energies
 ({\tt AP, UP}), and a fraction of the electron data.
-By default data is read from the
-Storm and Israel\cite{SI70} photon cross section compilation
-({\tt si\_pair.data, si\_photo.data, si\_rayleigh.data and
-si\_triplet.data}).
-As alternative, EGSnrc offers such cross section data files
-for the XCOM\cite{HS95} ({\tt xcom\_*.data}) and EPDL97\cite{Cu89}
+By default data is read from the XCOM\cite{HS95} photon cross section
+compilation ({\tt xcom\_pair.data, xcom\_photo.data, xcom\_rayleigh.data and
+xcom\_triplet.data}). As alternatives, EGSnrc offers cross section data files
+for the Storm and Israel\cite{SI70}({\tt si\_*.data}) and EPDL97\cite{Cu89}
 ({\tt epdl\_*.data}) photon cross section compilations.
 New photon cross section compilations can be added following the
 same format as above, \ie, {\tt prefix\_*.data}.
@@ -132,7 +130,7 @@ \subsubsection{Photon data for EGSnrc}
 
   :start MC transport parameter:
       .                             # This entry is case sensitive
-      Photon cross sections = xcom  # xcom, epdl, si(default) or any_prefix
+      Photon cross sections = xcom  # xcom (default), epdl, si or any_prefix
       .
   :stop MC transport parameter:
 

@@ -23,7 +23,7 @@
 %
 %  Author:          Blake Walters, 2013
 %
-%  Contributors:
+%  Contributors:    Frederic Tessier
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -135,8 +135,8 @@ \subsection{User Code Inputs for Pegsless Mode}
 correction to apply to calculated bremsstrahlung cross-sections.
 Options are:
 \begin{itemize}
-\item {\tt KM} $[$IAPRIM=0$]$ (the default): Apply Koch and Motz\cite{KM59} empirical corrections.
-\item {\tt NRC} $[$IAPRIM=1$]$: Apply NRC corrections based on NIST/ICRU\cite{Ro89a}.  These corrections are read from the file
+\item {\tt KM} $[$IAPRIM=0$]$: Apply Koch and Motz\cite{KM59} empirical corrections.
+\item {\tt NRC} $[$IAPRIM=1$]$: (the default) Apply NRC corrections based on NIST/ICRU\cite{Ro89a}.  These corrections are read from the file
 {\tt \$HEN\_HOUSE/pegs4/aprime.data}.
 \item {\tt None} $[$IAPRIM=2$]$: No corrections applied.
 \end{itemize}