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thomie
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in thomie/egfrd
Sep 8, 2012
Added documentation files to track (latex of GFs and pseudocode)
to prevent occasional gory segfault problems
Zero rate issue
- Introducing an adaptive enlargement factor; just using TOLERANCE sometimes caused the steps to be too large in the first iteration and produced rootfinder search intervals with inverted bounds.
The shells have to be constructed at the "real" position of the CoM, i.e. the one with applied boundaries and projections. In contrast, the calculations have all to be performed using the CoM as calculated in one of the two structures (structure1). That was not the case and is fixed by this commit. Yet to be cleaned up after testing.
Does not work yet, but also does not change anything yet.
Mainly fixes some issue with determining rootfinder boundaries in EDGE_HITS_EDGE cylinder collision and TransitionPair shell construction
This caused problems with particles leaking out of the box structure.
This just makes more sense.
Fixes a problem with particles leaking out of a closed box
Does not work yet, but also does not change anything yet.
... and some cleanup in exception messages relevant to this.
This will "waste" 3% of the maximal available space for domains (instead of 1% before), but appears to work better for small systems, in which collisions and overlaps are more frequent.
This only works for single particles for now, no "mixed pairs" (reactions btw. plane-bound and cylinder-bound particles) yet.
This was not implemented correctly--we forgot about the surface_dissociation_vector. (But then again we also never used this transition...)
...incorporating the check for whether there is a daughter disk on the plane or not, and making the interaction behavior dependent on that.
It seems that the current code can be compiled best on different machines and systems with this setting (rather than newer standards).
It did not show eGFRD planes correctly in some situations because VPython uses a slightly different coordinate convention as eGFRD.
(for testing/profiling)
…_range). (#112) * Fix error 'could not convert template argument' for GCC compiler version > 4.8 (tested on 4.9 and 5.4) * Minor but important fixes: correct integral types, verify instead of assert, tab/spaces in py files, div-0 check, index-out-of-range check. * Fix for GCC 6.2 * made make_table compatible with python 3 * Revert "Fixed 'narrowing'-warning." This reverts commit 02963e8. * Removed unused enumeration variables (side_enum_type) * Commented out failing Python UnitTests. * Removed unused variables/types (less warnings). * Added structure ID to CylindericalSurface tests. * Added structure Type to PlanarSurface_test. * Updated unittest to use the most current BDSimulator. * GreensFunction input variables update. * Update to run cpp tests using one file. * Removed empty file. * Added more working CPP unittests. Closes #110, Closes #111
…oading and recording of total simulated time This is to avoid that "BD only" simulations will not be carried out correctly when there are load-save interrupts on the way. Also, we now allow to specify whether the last time of the load file should be used as a starting time or not, and to monitor the total simulated time using the given instance of the simulator.
Conflicts: egfrd.py (resolved)
eGFRD 2 Prototype pre-release
Fix references in README
- a new optional parameter to set the view center point (default = [0,0,0]) - new default resolution (1600 x 900 pixels)
In particular, an internal issue of boost is fixed by including <boost/detail/workaround.hpp> before <boost/type_traits/remove_pointer.hpp>. This caused linking errors on some systems.
Minor, but important tweaks that improve compilation behavior on some systems.
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Major fix in the 2dRadAbs function. Didn't give correct output first, does now. See commits for details. Still some "todo"s, but code functions properly.
MW.