Fix #512: pegsless error reading media consisting of a single element.

.devcontainer/README.md

@@ -0,0 +1,92 @@
+# EGSnrc Development Container
+
+Development Containers is an open standard that is supported by a number of 
+[development tools](https://containers.dev/supporting). A supporting tool allows
+you to develop from your local IDE, such as VS Code and connect to a "remote" 
+development container that hosts the tools and applications for your code.
+In this case, EGSnrc builds and runs in a Linux container but you can be working on a Windows
+or MacOS Desktop.
+
+## Supported Environments
+
+The following environments are all known to work, but any tool that support the development container
+specification should work.
+
+### GitHub Codespaces
+
+This is a paid feature, but if you have access to it then running EGSnrc is as simple as clicking
+the **Code** button in GitHub and choosing to open your repository in GitHub Codespaces. Codespaces
+runs VS Code right inside your web browser but you also have the option of using Codespaces from
+a desktop installation of VS Code. When you are using Codespaces, the remote development container runs
+in the cloud and is hosted by GitHub.
+
+### VS Code
+
+This requires [VS Code](https://code.visualstudio.com/) on Windows or MacOS with
+[Docker Desktop](https://www.docker.com/products/docker-desktop) installed or VS Code on
+Linux with [Docker CE/EE](https://docs.docker.com/install/#supported-platforms). You also need
+the VS Code [Dev Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)
+installed. When using these options, the development container runs on your local machine using Docker.
+
+To use this option, once the above requirements are installed, you simply clone your Git repository and
+open it in VS Code. It will detect that there is a devcontainer configuration and ask if you want to open
+your folder in the development container. Say yes and this will build and launch a docker container that
+is running the code you have cloned.
+
+### Windows Notes
+
+When running locally on Windows using Docker there is an issue with line-endings in files. When you clone
+the repository by default git will convert the line endings in all files to CRLF which is the windows standard.
+Since we are going to be running the code on Linux inside a container, we need the files to have the Unix
+standard LF line endings. There are a couple of ways to handle this:
+
+1. Run these commands before you clone your repository so that git does not convert line endings and treats
+LF as the default.
+
+```
+git config --global core.eol lf
+git config --global core.autocrlf input
+```
+
+These are global settings and if you work on other Git repositories you may not want to do this. But
+if you only are using git for this one repository then this is the easy way to do it.
+
+2. Enable these settings when you clone the repository:
+
+```
+git clone -c core.autocrlf=false -c core.eol=lf https://github.com/nrc-cnrc/EGSnrc
+```
+
+3. Fix the settings and the line endings in all the files after cloning the repository. Run these from the
+root of the cloned repository. If you have made any changes you will lose them, so save them somewhere before
+running these commands.
+
+```
+git config core.eol lf
+git config core.autocrlf input
+git add --update --renormalize
+git rm -rf --cached .
+git reset --hard HEAD
+```
+
+## Runtime Experience
+
+Regardless of which option you use, when the development container starts for the first time it
+needs to download the base Docker image, install the EGSnrc-specific required packages, and then
+configure and build EGSnrc for the first time. Subsequent starts of the development container will
+skip these steps and start faster. Once the container is running you use and run EGSrnc the same
+as you would on any platform. In other words, just follow the standard documentation.
+
+The development container configuration includes building and running the GUI apps. The container
+configuration installs a lightweight GUI desktop that you can access in your browser. Access to
+this desktop will open in your browser automatically when you first start the container but you can open
+it at any time from the **Ports** tab in VS Code. You can run commands like `egs_view` that launch
+GUI applications from the VS Code terminal and they will appear in the UI in the lightweight desktop
+once you open it. You can also run a terminal inside the GUI desktop if preferred.
+
+The default password to login to the GUI is `vscode`.
+
+## Reference Information
+
+* https://containers.dev/
+* [VSCode: Developing inside a Container](https://code.visualstudio.com/docs/devcontainers/containers)

.devcontainer/build-gui-apps.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# If EGS_HOME is not set then source ~/.bashrc
+if [ -z "$EGS_HOME" ]; then
+    source ~/.bashrc
+fi
+
+# Build the GUI Applications
+echo "::step::Building the EGSnrc GUI applications..."
+
+export QTDIR=/usr/lib/qt5
+export EGS_BASE=$(pwd)
+cd ${EGS_BASE}/HEN_HOUSE/gui/ && make --quiet --print-directory
+cd ${EGS_BASE}/HEN_HOUSE/egs++/view/ && make --quiet --print-directory

.devcontainer/devcontainer.json

@@ -0,0 +1,18 @@
+{
+    "image": "debian:bookworm",
+    "features": {
+      "ghcr.io/devcontainers/features/common-utils:2": {
+        "username": "devcontainer"
+      },
+      "ghcr.io/devcontainers/features/desktop-lite:1": {}
+    },
+    "onCreateCommand": ".devcontainer/setup.sh",
+    "postCreateCommand": ".devcontainer/build-gui-apps.sh",
+    "forwardPorts": [6080],
+    "portsAttributes": {
+      "6080": {
+        "label": "desktop",
+        "onAutoForward": "openBrowser"
+      }
+    }
+  }

.devcontainer/setup.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# This runs when the devcontainer is being created
+
+# Install required packages
+echo "::step::Installing required packages for EGSnrc ..."
+sudo apt update
+sudo apt install -y git gcc g++ gfortran make tk wish grace libmotif-dev expect qtbase5-dev
+
+# Build the application
+echo "::step::Building EGSnrc ..."
+export USER=devcontainer
+export EGS_BASE=$(pwd)
+./HEN_HOUSE/scripts/configure.expect devcontainer.conf 3 || true
+
+# Configure .bashrc
+echo "export EGS_HOME=${EGS_BASE}/egs_home/" >> ~/.bashrc
+echo "export EGS_CONFIG=${EGS_BASE}/HEN_HOUSE/specs/devcontainer.conf" >> ~/.bashrc
+echo "source ${EGS_BASE}/HEN_HOUSE/scripts/egsnrc_bashrc_additions" >> ~/.bashrc

.gitignore

@@ -42,6 +42,7 @@ html
 .obj/
 .moc/
 .ui/
+.qmake.stash
 
 ### ignore OS generated files
 *~
@@ -53,3 +54,7 @@ html
 .Trashes
 ehthumbs.db
 Thumbs.db
+
+### ignore devcontainer files
+*devcontainer*
+

HEN_HOUSE/cutils/egs_c_utils.c

@@ -23,7 +23,7 @@
 #
 #  Author:          Iwan Kawrakow, 2004
 #
-#  Contributors:
+#  Contributors:    Cody Crewson
 #
 ###############################################################################
 #
@@ -86,7 +86,11 @@ void  egsOpenControlFile(const char *fname, int *status, int len) {
         if (__my_fd > 0) {
             break;
         }
-        _sleep(1000);
+        #ifdef WIN32
+            Sleep(1000);
+        #else
+            _sleep(1000);
+        #endif
     }
     if (__my_fd < 0) {
         *status = __my_fd;
@@ -208,7 +212,12 @@ void egsReadControlFile(char *buf, const int *n, int *status, int len) {
 
 void egsSleep(const int *secs) {
     unsigned int msecs = *secs * 1000;
-    _sleep(msecs);
+
+    #ifdef WIN32
+        Sleep(msecs);
+    #else
+        _sleep(msecs);
+    #endif
 }
 void egsPerror(const char *str, int len) {
     perror(str);

HEN_HOUSE/doc/src/Makefile

@@ -23,7 +23,7 @@
 #
 #  Author:          Frederic Tessier, 2015
 #
-#  Contributors:
+#  Contributors:    Reid Townson
 #
 ###############################################################################
 

HEN_HOUSE/doc/src/getting-started/getting-started.tex

@@ -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.
 

HEN_HOUSE/doc/src/makedoc.sh

@@ -23,7 +23,7 @@
 #
 #  Author:          Frederic Tessier, 2015
 #
-#  Contributors:
+#  Contributors:    Ernesto Mainegra-Hing
 #
 ###############################################################################
 
@@ -130,5 +130,3 @@ else
     fi
     exit
 fi
-
-

HEN_HOUSE/doc/src/pirs3100-g-app/g_template.f

@@ -5832,7 +5832,7 @@ subroutine get_media_inputs(ounit)
             IPLOTE=0
             MEDIUM=i
             XAXIS = 'kinetic energy / MeV'
-            YAXISE = 'dE/drhoX MeV/g/cm\\S2\\N'
+            YAXISE = 'dE/drhoX MeV/g/cm\S2\N'
             YAXISEmfp = 'mean free path / cm'
             YAXISPmfp = 'mean free path / cm'
             write(GRAPHTITLE,'(24a1)')(media(j,i),j=1,24)

HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM28.inp

@@ -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

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

@@ -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.
 

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

@@ -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

HEN_HOUSE/doc/src/pirs624-dosxyzshow/pirs624-dosxyzshow.tex

@@ -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

HEN_HOUSE/doc/src/pirs701-egsnrc/inputs/chapter2_2.tex

@@ -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
-

HEN_HOUSE/doc/src/pirs701-egsnrc/inputs/chapter2_3.tex

@@ -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

HEN_HOUSE/doc/src/pirs701-egsnrc/inputs/egsnrc_system_considerations.tex

@@ -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}