Cell

Physics simulation for colliding discs. Idea:

• Define different disc types (mass, radius, color)
• Define reactions:
  • unimolecular: transformation (A -> B), decomposition (A -> B + C)
  • bimolecular: combination (A + B -> C), exchange (A + B -> C + D)
  • with time-based (unimolecular) or collision-based (bimolecular) probabilities
• Define compartments with semi-permeable membranes
  • Define membrane types (radius, disc count)
  • Set permeabilities: Inward, outward, bidirectional or no permeability based on disc type
  • Set distribution: Frequency for each disc type
  • Add membranes at specified positions (currently only manually with a table)
  • If use distribution is disabled in Setup, add discs manually as well
• Set time step, time scale and average velocity in Setup
• Track state of the simulation with plots and a real-time view
• Shortcuts: Press F to toggle fullscreen, Space to toggle simulation start/stop

Uses an sf::RenderWindow for rendering in the OpenGL context of Qt for performance reasons (I haven't tested performance of QtGraphicsView but I don't think it can display thousands of circles with decent FPS so I'm sticking with SFML).

Test code coverage (currently only libcell, didn't write tests for the GUI): cellcoverage.myactivities.net

Build

You can find the necessary build steps for linux/mac in the scripts/unix/setup.sh script and for windows in scripts/windows/setup.ps1. If you run them, they might even compile everything for you, but I wouldn't count on it since there are some dependencies vcpkg won't install (especially on linux/mac, see setup.sh). Binaries are dumped into build_release/Release/ and build_debug/Debug/.

VS Code

There is a CMakePresetsWindows.json located in scripts/ that currently only works on windows that I personally use with vs code. I wanted to use clang-tidy on windows and needed to use ninja for that, but I had trouble convincing ninja to use the msvc compiler over gcc, so I manually set the compiler to cl in the presets. It of course selected the x86 version over the x64 one for whatever reason. So I told cmake where to find cl and all the dependencies by adding "cmake.environment": { "PATH": ..., "LIB": ..., "INCLUDE": "... } to my .vscode/settings.json. I obtained the environmental variables by starting the "x64 Native Tools Command Prompt for VS 2022" and echoed %PATH%, %LIB% and %INCLUDE%. Took me a few days to get this to work.

To not get any include errors you need to add the respective folder to the .vscode/c_cpp_properties.json, here's mine as an example (currently working on windows):

c_cpp_properties.json

{
    "configurations": [
        {
            "includePath": [
                "${workspaceFolder}/contrib/qcustomplot/",
                "${workspaceFolder}/src/lib/",
                "${workspaceFolder}/src/lib/cell/",
                "${workspaceFolder}/src/lib/gui/core",
                "${workspaceFolder}/src/lib/gui/delegates/",
                "${workspaceFolder}/src/lib/gui/dialogs/",
                "${workspaceFolder}/src/lib/gui/models/",
                "${workspaceFolder}/src/lib/gui/widgets/",
                "${workspaceFolder}/build_debug/libcellgui_autogen/include",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtConcurrent",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtCore",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtDBus",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtDeviceDiscoverySupport",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtExampleIcons",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtExamplesAssetDownloader",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtFbSupport",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtGui",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtNetwork",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtOpenGL",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtOpenGLWidgets",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtPrintSupport",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtSql",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtTest",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtWidgets",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/Qt6/QtXml",
                "${workspaceFolder}/build_debug/vcpkg_installed/x64-windows/include/"
            ],
            "defines": [
                "GLOG_USE_GLOG_EXPORT"
            ],
            "cStandard": "c17"
        }
    ],
    "version": 4
}