kTot optimization started. Works for first cycle. Second cycle is
slightly off.
kTot optimization works for two cycles. Mismatch for three.
knowncase and standard loops succeed. Sequential testing still
crashes. Getting there.
Tests updated to eat the new setup. Still some problems with the
sequential tests involving the concentration wall boundary.
think I might have fixed the whole tmp bug thingie by being strickter on
the separation parameter. Continued working on why concentrationwalls
dont work with new optimizations
fixed some issues with the debugger tracer with the new flag setup and
rate optimizations
tests now pass, but knowncase tests are no longer valid. No assertions
go mental. Need to figure out why deactivating an affected active site
breaks everything. Not comfy with current mindless hack.
since knowncase tests are not valid, I made some needed changes to
concentrationwalls.
Optimized total rate now works without checking if a site is already
affected in concetrationwall.
updates knowncase tests.
Tests for new total rate implemented and passed. Now using optimized
total rate in the solver. All tests pass with new setup. Cosmetic
changes to testrunner.
Tons of initial implementations regarding the optimized way of setting
up the reaction vectors.. however I am starting to doubt myself, perhaps
using fixed sized vectors is much quicker..?
fixed an issue causing negative accumulated rate values.
added thorough testing of the updating of rate and reaction vectors
fixed stability of test. Alot of crashes still need to be adressed.
switched off changes and reverted what had been broken. all tests pass
again. Ready to continue.
switched changed back on. Starting work on testing the shuffle
algorithm.
implemented dummy reaction class and test for the shuffeling function.
Think I have isolated the issue with old active reactions. Need a break.
fixed a bug where swapped reactions did not get their addresses updated.
fixed a bug in the swapper causing addresses of vacant sites to be
messed up