Implement tumor replicated including forces and diffusion modules (#6)

All work I have done untill the midterm in reproducing the nature paper.

Author: salva24

.clang-format

@@ -49,12 +49,12 @@ DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
 ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
 IncludeCategories:
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-  - Regex:           '^<.*'
-    Priority:        2
-  - Regex:           '.*'
-    Priority:        3
+  - Regex:           '^"[^/]+\"'
+    Priority:        10
+  - Regex:           '^"core/'
+    Priority:        20
+  - Regex:           '^<'
+    Priority:        30
 IncludeIsMainRegex: '([-_](test|unittest))?$'
 IndentCaseLabels: true
 IndentWidth:     2

.clang-tidy

@@ -11,7 +11,10 @@ Checks: >
   openmp-*
   performance-*,
   portability-*,
-  readability-*
+  readability-*,
+  -bugprone-easily-swappable-parameters,
+  -modernize-use-trailing-return-type,
+  -readability-identifier-length
 
 CheckOptions:
   - key:             google-readability-braces-around-statements.ShortStatementLines
@@ -93,8 +96,12 @@ CheckOptions:
     value:           'k'
   - key:             readability-identifier-naming.PrivateMemberPrefix
     value:           ''
+  - key:             readability-identifier-naming.PrivateMemberSuffix
+    value:           '_'
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     value:           ''
+  - key:             readability-identifier-naming.ProtectedMemberSuffix
+    value:           '_'
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     value:           lower_case
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.gitignore

@@ -39,3 +39,86 @@
 
 # debug information files
 *.dwo
+
+build/
+output/
+
+**/.DS_Store
+
+#----------------- intellij -----------------
+.idea
+cx3d-cpp.iml
+
+#----------------- eclipse ------------------
+.project
+.cproject
+.settings/
+
+#----------------- VS Code ------------------
+.vscode/*
+
+#----------------- GNU global ------------------
+GPATH
+GRTAGS
+GTAGS
+
+#------------------- C++ --------------------
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+*.jnilib
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+#------------------- CMake --------------------
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Makefile
+cmake_install.cmake
+install_manifest.txt
+
+#------------------- Doxygen files --------------------
+Doxyfile
+doc/html
+doc/latex
+
+#------------------- Paraview --------------------
+*.vtu
+*.vti
+*.pvtu
+*.pvti
+
+
+#Debugging files
+*.csv
+
+# Result files
+*.xyz
+*.dat
+
+# Draft code for comparing models
+draft_code_my_own_analysis/

CMakeLists.txt

@@ -0,0 +1,33 @@
+cmake_minimum_required(VERSION 3.19.3)
+project(cart_tumor)
+
+
+# BioDynaMo curretly uses the C++17 standard.
+set(CMAKE_CXX_STANDARD 17)
+
+# Use BioDynaMo in this project.
+find_package(BioDynaMo REQUIRED)
+
+# See UseBioDynaMo.cmake in your BioDynaMo build folder for details.
+# Note that BioDynaMo provides gtest header/libraries in its include/lib dir.
+include(${BDM_USE_FILE})
+
+# Consider all files in src/ for BioDynaMo simulation.
+include_directories("src")
+file(GLOB_RECURSE PROJECT_HEADERS src/*.h)
+file(GLOB_RECURSE PROJECT_SOURCES src/*.cc)
+
+bdm_add_executable(${CMAKE_PROJECT_NAME}
+                   HEADERS ${PROJECT_HEADERS}
+                   SOURCES ${PROJECT_SOURCES}
+                   LIBRARIES ${BDM_REQUIRED_LIBRARIES})
+
+# Consider all files in test/ for GoogleTests.
+include_directories("test")
+file(GLOB_RECURSE TEST_SOURCES test/*.cc)
+file(GLOB_RECURSE TEST_HEADERS test/*.h)
+
+bdm_add_test(${CMAKE_PROJECT_NAME}-test
+             SOURCES ${TEST_SOURCES}
+             HEADERS ${TEST_HEADERS}
+             LIBRARIES ${BDM_REQUIRED_LIBRARIES} ${CMAKE_PROJECT_NAME})

README.md

@@ -1 +1,130 @@
-# CARTopiaX
+# CARTopiaX
+
+This repository provides an **agent-based simulation** of tumour-derived organoids and their interaction with **CAR T-cell therapy**.
+Developed as part of Google Summer of Code 2025, the project is released under the **Apache License 2.0**.
+
+The simulation integrates computational modeling and biological insights to explore tumour–immune dynamics and assess treatment outcomes under various scenarios.
+
+---
+
+## Table of Contents
+
+1. [Project Overview](#project-overview)
+2. [Dependencies](#dependencies)
+3. [Installation](#installation)
+4. [Building the Simulation](#building-the-simulation)
+5. [Running the Simulation](#running-the-simulation)
+6. [Visualizing Results](#results)
+7. [Acknowledgments](#acknowledgments)
+8. [License](#license)
+
+
+---
+
+## Project Overview
+
+This project implements an **agent-based model** to simulate the behavior of *tumour-derived organoids* (lab-grown tumour models) and their response to **CAR T-cell therapy**.
+
+With this simulation, researchers can:
+- Recreate in vitro conditions for tumour growth.
+- Introduce CAR T-cells and analyze their effectiveness in solid tumor microenvironments.
+- Explore different treatment strategies and parameter variations.
+- Evaluate outcomes such as tumour reduction, elimination, or relapse risk.
+
+By adjusting biological and therapeutic parameters, the model enables **in silico experimentation** to complement laboratory research.
+
+---
+
+## Dependencies
+
+- [BioDynaMo](https://biodynamo.org/) (tested with version 1.05.132)
+- CMake ≥ 3.13
+- GCC or Clang with C++17 support
+- GoogleTest (for unit testing)
+
+**Note:** Ensure BioDynaMo is installed and sourced before running the simulation.
+
+---
+
+## Installation
+
+Clone the repository:
+```bash
+git clone https://github.com/compiler-research/CARTopiaX.git
+cd CARTopiaX
+
+```
+
+---
+
+## Building the Simulation
+
+**Option 1:**
+Use BioDynaMo’s build system:
+```bash
+biodynamo build
+```
+
+**Option 2:**
+Manual build:
+```bash
+mkdir build && cd build
+cmake ..
+make -j <number_of_processes>
+```
+
+---
+
+## Running the Simulation
+
+After building, run the simulation using one of the following methods:
+
+**Option 1:**
+With BioDynaMo:
+```bash
+biodynamo run
+```
+
+**Option 2:**
+Directly from the build directory:
+```bash
+
+./build/CARTopiaX
+```
+
+---
+
+## Results
+
+Data about tumor growth and diffrent types of cell populations is output in ./output/final_data.csv
+
+To visualize the results in paraview use:
+```bash
+paraview ./output/CARTopiaX/CARTopiaX.pvsm
+
+```
+
+---
+
+## Acknowledgments
+
+This project builds upon the BioDynaMo simulation framework.
+
+> Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer.
+> *BioDynaMo: a modular platform for high-performance agent-based simulation*.
+> Bioinformatics, Volume 38, Issue 2, January 2022, Pages 453–460.
+> [https://doi.org/10.1093/bioinformatics/btab649](https://doi.org/10.1093/bioinformatics/btab649)
+
+Some of the mathematical models and solver implementations are based on the research of
+Luciana Melina Luque and collaborators, as described in:
+
+> Luque, L.M., Carlevaro, C.M., Rodriguez-Lomba, E. et al.
+> *In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy*.
+> Scientific Reports 14, 12307 (2024).
+> [https://doi.org/10.1038/s41598-024-63125-5](https://doi.org/10.1038/s41598-024-63125-5)
+
+---
+
+## License
+
+This project is licensed under the Apache License 2.0. See the [LICENSE](LICENSE) file for details.

bdm.toml

@@ -0,0 +1,14 @@
+[visualization]
+export = true
+interval = 7200
+
+[[visualize_agent]]
+name = "TumorCell"
+additional_data_members = [
+	{name = "diameter_", function = "diameter_"},
+	{name = "volume_", function = "volume_"},
+	{name = "cell_type", function = "GetTypeAsInt"}
+]
+
+[[visualize_diffusion]]
+name = "oxygen"