randomization of simulation execution
randomization of simulation execution
Hi, I am running a network simulation that makes use of the ranstream.hoc file from "The Randomness in Neuron Models" entry in the Documentation section on the website to connect neurons as in Hines & Carnevale, 2008 J Neurosci Methods. What I would like to now do is randomization of simulation execution. I want to change the seed value so that the connectivity is different when I run the simulation again. I am not sure how to set this seed value for MCellRan4. Thanks in advance.
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ted
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Re: randomization of simulation execution
The RandomStream class defined by the code in ranstream.hoc uses the value of the Ran4 generator's high index to distinguish between individual streams used in a given simulation. What you want is a single action that will change all of the streams used in a simulation. That's what Ran4's low index is for, and you can specify a new low index with the hoc function mcell_ran4_init(); you'll find this documented in the discussion of MCellRan4 and also mcell_ran4_init.
That raises the question of how to manage the "seeds" that you will feed to mcell_ran4_init. You might want to create a "log" file that contains a single number that keeps track of how many simulations have been run. Your program could then read the log file, increment the number by 1 and write it back to the log file, then use the number as the low index.
That raises the question of how to manage the "seeds" that you will feed to mcell_ran4_init. You might want to create a "log" file that contains a single number that keeps track of how many simulations have been run. Your program could then read the log file, increment the number by 1 and write it back to the log file, then use the number as the low index.