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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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Hard-coded occurrencesof flavopiridol flag? #28

Closed lhilbert closed 5 years ago

lhilbert commented 5 years ago

In the commands used for scheduling on bwUniCluster, it seems there are some occurrences of hard-coded flavopiridol flags. Does this make sense?

https://github.com/lhilbert/active-microemulsion/blob/3a7b37f403af73d8c9b4d81d2f8ea87213f69455/utils/BwUniClusterScripts/schedulingLib.py#L249

churli commented 5 years ago

Yes, this is expected and necessary for executing the simulations in the way we need.

If no event flag is passed, the simulation start by default by using the rates specified from the command line. That is, the simulation starts in an "active" state.

However in our simulations we need the system to initially relax for a certain amount of time (10m) before an activation event is called. The way we implement this initial relaxation is by disabling the rates at time 0 (i.e. by calling --flavopiridol 0) and then calling --activate at the time we want the system to start with trascription.