[Do not merge] Adds 2D membrane-bound diffusion and 2D/3D interaction#5
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tjclement wants to merge 96 commits into
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[Do not merge] Adds 2D membrane-bound diffusion and 2D/3D interaction#5tjclement wants to merge 96 commits into
tjclement wants to merge 96 commits into
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…cles to PlanarSurfaces.
…ticle_radius (as mentioned in paper)
…al shell sizes causing immediate escapes
…ger than r0. Such situations caused tremendously small time deltas
…roll wheel on *NIX systems
* feature/ccd: Changes needed to compile on latest Mac OS
… implemented saving simstate for all new domain types
…culation, preventing creation of domains
… bug, modified and added validation models
…lushes to copynumbers and reaction record files so they can be monitored in real-time during a simulation run.
…fixed K_d calculation
…inux machines that installed it through a package manager
…always having whitespace between numerics in the rows
… PairPlanar, to prevent convergence error loops
…plane_edges * commit 'cd567b1ff0c2b20a4c0a9d72d30118cfe7596788': Update for VS2019, minor formatting fixes. # Conflicts: # CMakeSettings.json # src/eGFRD/EGFRDSimulator.hpp # src/eGFRD/Single.hpp
…plane_edges * commit '0f5dded6c93f8f49f696943182603f1f580a6929': Update build-information for libccd requirement. Use libCCD for Cylinder/Cylinder collision testing. Added tests for orientation and scaling (libCCD does not handle small values very well). Visualizer demo 5 shows work. # Conflicts: # samples/equilibrium/equilibrium.gfrd # src/eGFRD/CMakeLists.txt # src/eGFRD/EGFRDSimulator.hpp # src/eGFRD/ShellCreateUtils.hpp # src/gfrdVisualizer/gfrdVisualizer.cpp # test/TestCCD/CMakeLists.txt
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The work of my MSc project has not yet been merged into upstream, and it would be good to do so so others can expand on it.
The code is operational, but contains some simulation irregularities, as described in section 5.1 of the thesis "Simulation of multiplexing in immune cell receptors using eGFRD". Pieter Rein ten Wolde can provide a copy to those who would like to know more.
I would suggest that this work is not yet merged into upstream master, but rather into a separate feature branch, until the irregularities have been studied further.