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segrelab / COMETS_Protocols

COMETS simulations examples and protocols
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Error in Example "Modelling the diurnal cycle" #1

Open bigsuicideparty opened 2 years ago

bigsuicideparty commented 2 years ago

I ran into a few issues with example "Modelling the diurnal cycle"

I was not able to import comets as c, so I changed it to import cometspy as c

After running the script

simulation = c.comets(layout, sim_params) gave me [ValueError: the initial pop of a model is outside of layout.grid. Either increase layout.grid or adjust COBRAModel's initial_pop]()

Any idea what might be the issue?

dukovski commented 2 years ago

Did you install comets? You can get it at runcomets.org.

If you did install comets, this error seems like you are assigning biomass to a nonexisting point in the grid. For example, if the grid was 1x1 points, you assigned biomass to point x=5 y=3 or so. Make sure that your point in a 1x1 grid is (0,0).