Update

.github/workflows/mdbook.yml

@@ -0,0 +1,59 @@
+name: Deploy mdBook site to Pages
+
+on:
+  push:
+    branches: ["develop"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      MDBOOK_VERSION: 0.4.36
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install mdBook and Plugins
+        run: |
+          curl --proto '=https' --tlsv1.2 https://sh.rustup.rs -sSf | sh -s -- -y
+          source $HOME/.cargo/env
+          rustup update
+          cargo install --version ${MDBOOK_VERSION} mdbook
+          cargo install mdbook-admonish
+          cargo install mdbook-mermaid
+          cargo install mdbook-toc
+          mdbook-admonish install 
+
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+
+      - name: Build mdBook
+        run: |
+          source $HOME/.cargo/env
+          mdbook build .
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./book
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -1,4 +1,5 @@
 .idea/
+.cache/
 cmake-build-debug/
 cmake-build-release/
 .vscode/*

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "submodules/d3df-patients"]
+	path = submodules/d3df-patients
+	url = git@github.com:Dose3D-Future/d3df-patients.git

.vscode/c_cpp_properties.json

@@ -13,35 +13,63 @@
             "cppStandard": "c++17",
             "intelliSenseMode": "gcc-x64",
             "configurationProvider": "ms-vscode.cmake-tools"
+        },
+                {
+            "name": "linux-faculty-jakub",
+            "includePath": [
+                "/usr/local/include/*",
+                "~/miniforge3/envs/g4rt_devel/include/*",
+                "~/miniforge3/envs/g4rt_devel/include/Geant4/*",
+                "~/miniforge3/envs/g4rt_devel/include/python3.12/*",
+                "~/miniforge3/envs/g4rt_devel/include/spdlog/fmt/**",
+                "${workspaceFolder}/**"
+            ],
+            "defines": [],
+            "compilerPath": "~/miniforge3/envs/g4rt_devel/bin/clang++",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "gcc-x64",
+            "configurationProvider": "ms-vscode.cmake-tools",
+            "mergeConfigurations": false,
+            "browse": {
+                "path": [
+                    "${workspaceFolder}/**",
+                    "/usr/local/include/*",
+                    "~/miniforge3/envs/g4rt_devel/include/*",
+                    "~/miniforge3/envs/g4rt_devel/include/Geant4/*",
+                    "~/miniforge3/envs/g4rt_devel/include/python3.12/*",
+                    "~/miniforge3/envs/g4rt_devel/include/spdlog/fmt/*",
+                    "${workspaceFolder}/*"
+                ],
+                "limitSymbolsToIncludedHeaders": true
+            }
         },
         {
             "name": "alma-jakub",
             "includePath": [
                 "~/work/dose3d/g4rt/*",
                 "/usr/local/include/*",
-                "~/miniforge3/envs/G4ImpressU/include/*",
-                "~/miniforge3/envs/G4ImpressU/include/Geant4/*",
-                "~/miniforge3/envs/G4ImpressU/include/python3.11/*",
-                "~/miniforge3/envs/G4ImpressU/include/spdlog/fmt/**",
+                "~/miniforge3/envs/geant4/include/*",
+                "~/miniforge3/envs/geant4/include/Geant4/*",
+                "~/miniforge3/envs/geant4/include/python3.10/*",
+                "~/miniforge3/envs/geant4/include/spdlog/fmt/**",
                 "${workspaceFolder}/**"
             ],
             "defines": [],
-            "compilerPath": "~/miniforge3/envs/G4ImpressU/bin/g++",
+            "compilerPath": "~/miniforge3/envs/geant4/bin/g++",
             "cStandard": "c11",
             "cppStandard": "c++17",
             "intelliSenseMode": "gcc-x64",
             "configurationProvider": "ms-vscode.cmake-tools",
-            "compilerPathInCppPropertiesJson": "~/miniforge3/envs/G4ImpressU/bin/g++",
-            "configurationProviderInCppPropertiesJson": "ms-vscode.cmake-tools",
             "mergeConfigurations": false,
             "browse": {
                 "path": [
                     "~/work/dose3d/g4rt/*",
                     "/usr/local/include/*",
-                    "~/miniforge3/envs/G4ImpressU/include/*",
-                    "~/miniforge3/envs/G4ImpressU/include/Geant4/*",
-                    "~/miniforge3/envs/G4ImpressU/include/python3.11/*",
-                    "~/miniforge3/envs/G4ImpressU/include/spdlog/fmt/*",
+                    "~/miniforge3/envs/geant4/include/*",
+                    "~/miniforge3/envs/geant4/include/Geant4/*",
+                    "~/miniforge3/envs/geant4/include/python3.10/*",
+                    "~/miniforge3/envs/geant4/include/spdlog/fmt/*",
                     "${workspaceFolder}/*"
                 ],
                 "limitSymbolsToIncludedHeaders": true
@@ -52,7 +80,7 @@
             "includePath": [
                 "${workspaceFolder}/**",
                 "/opt/geant4/include/**",
-                "/home/geant4/miniconda3/envs/g4rt/include/**"
+                "/home/geant4/miniconda3/envs/g4rt_devel/include/**"
             ],
             "defines": [],
             "compilerPath": "/home/geant4/miniconda3/envs/dose3d/bin/g++",

CMakeLists.txt

@@ -1,23 +1,27 @@
 #----------------------------------------------------------------------------
 # Setup the project
-cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 project(G4rt)
 
-#----------------------------------------------------------------------------
-# Ustawienia CMake
 set(CMAKE_VERBOSE_MAKEFILE ON)
-set(CMAKE_COLOR_MAKEFILE ON)
+set(CMAKE_COLOR_MAKEFILE   ON)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_DEFAULT 17)
 set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
-add_compile_definitions(LOGURU_USE_FMTLIB=1)
+add_compile_definitions(LOGURU_USE_FMTLIB=1
+                        LOGURU_FILENAME_WIDTH=32
+                        LOGURU_THREADNAME_WIDTH=16
+                        LOGURU_SCOPE_TEXT_SIZE=256)
+set(CMAKE_BUILD_TYPE Debug)
+set(CMAKE_CXX_FLAGS_DEBUG "-g -O0")
+
 #----------------------------------------------------------------------------
-# Zabronienie budowania w katalogu źródłowym
+# prevent for in-source building
 set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
-set(CMAKE_DISABLE_SOURCE_CHANGES ON)
+set(CMAKE_DISABLE_SOURCE_CHANGES  ON)
 if ("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}")
-    message(SEND_ERROR "In-source builds are not allowed.")
-endif()
+  message(SEND_ERROR "In-source builds are not allowed.")
+endif ()
 
 #----------------------------------------------------------------------------
 set(CMAKE_VERBOSE_MAKEFILE ON)
@@ -26,8 +30,8 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON) # This needs to be done universally to a
 
 #----------------------------------------------------------------------------
 if(NOT $ENV{CLHEP_INCLUDE_DIR} STREQUAL "")
-    set(CMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES $ENV{CLHEP_INCLUDE_DIR})
-endif()
+  set(CMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES $ENV{CLHEP_INCLUDE_DIR})
+endif ()
 #----------------------------------------------------------------------------
 SET(PROJECT_DATA_PATH "${PROJECT_SOURCE_DIR}/data")
 SET(PROJECT_INSTALL_DIR "/opt/g4rt")
@@ -40,26 +44,37 @@ add_definitions(-DJOBS_PATH=\"${PROJECT_SOURCE_DIR}/jobs\")
 add_definitions(-DPROJECT_PY_PATH=\"${PROJECT_SOURCE_DIR}/core/utilities/python\")
 add_definitions(-DPROJECT_BINARY_PATH=\"${PROJECT_BINARY_DIR}\")
 
+#----------------------------------------------------------------------------
+option(BUILD_G4RT "Build the g4rt executable" ON)
+option(BUILD_BG4RT "Build the g4rt_bworld executable" OFF)
+option(BUILD_DCM2DAT "Build the g4rt_bworld executable" ON)
+option(BUILD_TLD "Build the tld executable" ON)
+
 #----------------------------------------------------------------------------
 # Testing suite configuration
+#
 find_package(GTest REQUIRED)
 include(GoogleTest)
 include(CTest)
 
 #----------------------------------------------------------------------------
 # Configure the components (subprojects)
 # NOTE: The order matters! The most independent ones should go first.
-#       If A and B really depend on each other, CMake can build such correctly,
-#       if you specify full path to the include directory
+#       If A and B really depend on each other, CMake  can build such correctly,
+#       if you specify full path to the include directlry
 add_subdirectory(externals)
 add_subdirectory(core)
 add_subdirectory(app)
 
 #----------------------------------------------------------------------------
 message(STATUS "Build type: " ${CMAKE_BUILD_TYPE})
 
+
 #----------------------------------------------------------------------------
-# Copy all scripts to the build directory
+# Copy all scripts to the build directory, i.e. the directory in which we
+# build g4af. This is so that we can run the executable directly because it
+# relies on these scripts being in the current working directory.
+#
 set(RUN_SCRIPTS
     scoring_pre.mac
     scoring_post.mac
@@ -68,9 +83,9 @@ set(RUN_SCRIPTS
 )
 
 foreach(_script ${RUN_SCRIPTS})
-    configure_file(
-        ${PROJECT_SOURCE_DIR}/scripts/${_script}
-        ${PROJECT_BINARY_DIR}/${_script}
-        COPYONLY
+  configure_file(
+    ${PROJECT_SOURCE_DIR}/scripts/${_script}
+    ${PROJECT_BINARY_DIR}/${_script}
+    COPYONLY
     )
-endforeach()
+endforeach()

GEANT4_LICENSE.txt

@@ -0,0 +1,73 @@
+Geant4 Software License
+Version 1.0, 28 June 2006
+
+Copyright (c) Copyright Holders of the Geant4 Collaboration, 1994-2006.
+See http://cern.ch/geant4/license for details on the copyright holders.  All
+rights not expressly granted under this license are reserved.
+
+This software includes voluntary contributions made to Geant4.
+See http://cern.ch/geant4 for more information on Geant4.
+
+Installation, use, reproduction, display, modification and redistribution of
+this software, with or without modification, in source and binary forms, are
+permitted on a non-exclusive basis. Any exercise of rights by you under this
+license is subject to the following conditions:
+
+1. Redistributions of this software,  in whole or in part,  with  or without
+   modification, must reproduce the above copyright notice and these license
+   conditions  in  this  software,  the  user  documentation  and  any other
+   materials provided with the redistributed software.
+
+2. The user documentation,if any,included with a redistribution,must include
+   the following notice:"This product includes software developed by Members
+   of the Geant4 Collaboration ( http://cern.ch/geant4 )."
+   If that  is  where  third-party  acknowledgments  normally  appear,  this
+   acknowledgment  must  be  reproduced  in  the  modified  version  of this
+   software itself.
+
+3. The names "Geant4" and "The Geant4 toolkit" may not be used to endorse or
+   promote software,or products derived therefrom, except with prior written
+   permission  by  license@geant4.org.  If this software is redistributed in
+   modified form,  the name  and  reference of  the modified version must be
+   clearly distinguishable from that of this software.
+
+4. You are under no obligation to provide anyone with  any  modifications of
+   this software that you may develop,including but not limited to bug fixes,
+   patches,  upgrades  or  other enhancements or derivatives of the features,
+   functionality or performance of this software. However, if you publish or
+   distribute your modifications without  contemporaneously  requiring users
+   to enter into a separate written license agreement,  then  you are deemed
+   to have granted all  Members  and all  Copyright Holders  of  the  Geant4
+   Collaboration  a license to your  modifications,  including modifications
+   protected by any patent owned by you,under the conditions of this license.
+
+5. You may not include  this  software in  whole or in part in any patent or
+   patent  application  in  respect  of  any  modification  of this software
+   developed by you.
+
+
+6. DISCLAIMER
+
+ THIS SOFTWARE IS PROVIDED BY THE MEMBERS AND COPYRIGHT HOLDERS OF THE GEANT4
+ COLLABORATION AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ INCLUDING,  BUT NOT LIMITED TO,  IMPLIED WARRANTIES OF  MERCHANTABILITY,  OF
+ SATISFACTORY QUALITY,  AND FITNESS  FOR  A  PARTICULAR PURPOSE  OR  USE  ARE
+ DISCLAIMED. THE MEMBERS OF THE GEANT4 COLLABORATION AND CONTRIBUTORS MAKE NO
+ REPRESENTATION THAT THE SOFTWARE AND MODIFICATIONS THEREOF,WILL NOT INFRINGE
+ ANY PATENT, COPYRIGHT, TRADE SECRET OR OTHER PROPRIETARY RIGHT.
+
+7. LIMITATION OF LIABILITY
+
+ THE  MEMBERS  AND  COPYRIGHT   HOLDERS  OF  THE   GEANT4  COLLABORATION  AND
+ CONTRIBUTORS SHALL HAVE NO LIABILITY FOR DIRECT,INDIRECT,SPECIAL, INCIDENTAL,
+ CONSEQUENTIAL,  EXEMPLARY,  OR PUNITIVE DAMAGES  OF  ANY CHARACTER INCLUDING,
+ WITHOUT LIMITATION, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES, LOSS OF USE,
+ DATA OR PROFITS,  OR BUSINESS INTERRUPTION, HOWEVER CAUSED AND ON ANY THEORY
+ OF CONTRACT,  WARRANTY, TORT  (INCLUDING NEGLIGENCE),  PRODUCT LIABILITY  OR
+ OTHERWISE,  ARISING IN  ANY WAY  OUT OF THE USE  OF  THIS SOFTWARE,  EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+8. This license  shall terminate with immediate effect and without notice if
+   you  fail  to  comply with any  of  the terms of this license,  or if you
+   institute litigation against any Member or Copyright Holder of the Geant4
+   Collaboration with regard to this software.

LICENSE

@@ -0,0 +1,31 @@
+MIT License
+
+Copyright (c) \[20??–2025] \[Dose3D-Future]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+---
+
+This project includes the use of the Geant4 simulation toolkit.
+Geant4 is distributed under the Geant4 Software License (G4SL),
+available at: [https://geant4.web.cern.ch/license](https://geant4.web.cern.ch/license)
+
+Use of Geant4 within this project does not imply endorsement by CERN or the Geant4 Collaboration.
+The authors of this project make no warranty with regard to the accuracy or fitness for purpose
+of the simulation results generated through the use of Geant4.