directories.doxy File Reference

Documentation on directory structure. More...

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Detailed Description

Documentation on directory structure.

Everything used to generate project artefacts is placed in directory src.

• src/doc : Everything used to generate documentation.
• src/main : Code related files (sources, third party libraries and headers, ...).
  • cpp_execs : Main programs to build executables.
  • cpp_parex : Parameter exploration tool.
    • parex_client : Client side of the parex tool.
    • parex_node : Compute node for the parex tool.
    • parex_protocol : Client-server protocol used with parex.
    • parex_server : Server for parex.
  • cpp_sim : Core simulator: biological concepts, algorithms, time evolution.
    • algo : Algorithms for expansion, division, node insertion, ...
    • bio : Biological concepts: mesh, cell, wall, edge, node, ...
    • coupler : Coupled simulations code.
    • fileformats
    • math : Miscellaneous mathematical constructs.
    • model : Interface for models and extension points for core algorithms.
    • sim : Simulator proper i.e. the simulation driver.
    • util : Miscellaneous utilities( conatiner, timekeeper, ...).
  • cpp_simptshell : SimPT specific classes for the work shell (workspace, project, session, ...)
    • cli : Command line interface.
    • exporters : file export to various formats
    • gui : graphical user interface
    • mesh_drawer
    • session
    • viewer
    • viewers : The viewers that are available.
    • workspace : Deals with workspace construction and management.
  • cpp_simshell: generic classes for the work shell (workspace, project, session, ...)
    • common
    • gui
    • ptree
    • session
    • viewer
    • workspace : Deals with workspace construction and management.
  • cpp_tissue_edit : gui tissue editor.
    • editor : Core editor components.
    • generator : Generator for meshes (regular, Voronoi).
    • slicer : Component with slicing capability.
  • models: model dependent extension points for the algorithms
    • <model name>=""> : items for the named group of models
      • components: component factory to produce component component instances
        • cell_chemistry: model components for cell chemistry
        • cell_daughters: model components for cell daughters
        • cell_split: model components for cell splitting
        • cell2cell_transport: model components for raction and active transport
        • delta_hamiltonian
        • hamiltonian : Hamiltonians for the Metropolis algorithm
        • move_generator: genrate displacements for Monte Carlo algorithm
        • time_evolver : Time evolution schemes.
        • wall_chemistry: model components for wall chemistry
      • resources: mainly the workspace template with its files
      • tests that can be run for this model group
  • resources : Resources i.e. non source code artefacts used in build.
    • cmake : CMake modules used in the build
    • data : third party icons.
    • icons : Icons for desktop use.
    • lib : External software included at source level in build.
    • make : Makefile template.
    • Paraview: the VLeafReader
    • txt
  • swig_sim : Java and Python wrapper sources.
• src/test

Definition in file directories.doxy.