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lhilbert / active-microemulsion

Package for the lattice-based simulation of active polymer microemulsions, such as dense DNA suspensions
BSD 2-Clause "Simplified" License
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Changes in simulation parameters lead to incomplete runs #27

Closed lhilbert closed 5 years ago

lhilbert commented 5 years ago

It seems that specific values of the input parameters, most likely the swapping rate s, lead to premature termination/return of the simulation.

For example: staticOpts="-w 0.32 -s 6500 --kRnaPlus 1e-1 --kRnaMinusRbp 5.5555e-4 --kChromPlus 1.000e-3 --kChromMinus 1.6666e-3 --kOn 1.852e-4 --kOff 1.6666e-3 --kRnaTransfer 5.5e-1 -m -t 1",

these options lead to to return of all simulations with ai single time point saved. With nothing except the parameter values changed, the simulation then runs fine and gives complete time courses.

lhilbert commented 5 years ago

Same with -s 7000, next trying to go back to "standard" 4500.

lhilbert commented 5 years ago

And kRnaTransfer back to 1.1e-1

lhilbert commented 5 years ago

Now it is running without immediately returning. Checking again with 5.5e-1 for kRnaTransfer: yes, reproducible behavior. Changing to 5.5e-1 leads to immediate completion without returning more than the very first time point.

lhilbert commented 5 years ago

OK, with the following options seems to be running OK, will stick with that for now...

staticOpts="-w 0.32 -s 6500 --kRnaPlus 1e-1 --kRnaMinusRbp 5.5555e-4 --kChromPlus 1.000e-3 --kChromMinus 1.6666e-3 --kOn 1.852e-4 --kOff 1.6666e-3 --kRnaTransfer 4.0e-1 -m -t 1"

lhilbert commented 5 years ago

Also, changes in swapping rate lead to early termination, 8500 gave early termination, 9000 seems stable.