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Another follow-up here as providing a Dt value inside the Vector().record() method has now broken another part of my code base. In a previous post (https://www.neuron.yale.edu/phpBB/viewtopic.php?t=4605) I got some advice on how to ensure that, when using CVode and running my simulations in chunks, ...

I actually created a post about this titled "Saving fixed timestep data using cvode variable timestep integration" which can be found here https://www.neuron.yale.edu/phpBB/viewtopic.php?t=4668 and followed your (Ted) suggested solution to run my simulation using variable timestep integrat...

Thank you both for your responses. Regarding Teds response, I have slowly changing hormone concentrations with periods of about 5 minutes that are dependent upon much faster changing electrical, calcium, and metabolic components that I need to record. Is there a way to specify different sampling fre...

Hello, I ran into an odd issue with my model in NEURON+Python that I think I have fixed but would appreciate further clarity to check that I have addressed it correctly. I am simulating a large network of endocrine cells with lots of variables and need to run long simulations (15-30 minutes) due to ...

Hello, Just following up on this. It is the last thing I need to figure out to set up my simulations. My other approach not using rxd is to use more POINTERs in my mod files and use of rxd in the way I explain above actually gave me a performance boost in some test simulations. Also the structure of...

Hello, I have been using the rxd module to model paracrine signaling between pancreatic islet cells. While creating a simple example I have run into a problem. I have three cell (nrn.Section) types: A cells that secrete rxd.State G, B cells that secrete rxd.State I, and D cells that secrete rxd.Stat...

Thank you Ted for your quick reply! In case anyone wants to just grab some code to do this: NEURON Vectors t_resamp = h.Vector().indgen(start_time, end_time, Dt) v_resamp = h.Vector().interpolate(t_resamp, t_orig, v_orig) Python NumPy Arrays # You have to add Dt to end_time to include ent_time in yo...

Hello, I recently have had to do some filtering and additional processing of my model output that I didn't need to do before and now need to save my recorded data using a fixed timestep. However, I have a dramatic improvement in execution time using cvode compared to using a fixed timestep and I wou...

Nevermind, I realized that you already answered my question regarding UNITSOFF and UNITON. I see now that I needed to use UNITSON and UNITSOFF in my BREAKPOINT block instead of ASSIGNED. I assumed that I would do it in ASSIGNED because that is where I declare the units but it makes sense that they c...

Thanks for your response, I'll look into that chapter of the NEURON book. WRT to the UNITSOFF and UNITSON: I have plenty of variables in my model that don't have units for which I am using the approach foo () Just so it is explicit that I didn't forget to put units, but that the variable is dimensio...

Also I have two follow-up questions regarding the proper way to use UNITSOFF and UNITSON and for best practices for defining custom units. Part of my computational model involves a large equation that has been broken up into several smaller equations for practicality reasons. These smaller equations...

Understood, thank you Ted. As for the conversion factor syntax, I actually got that from the units tutorial from the NEURON documentation I linked in my original post. I found that it was the most readable and the tutorial stated it was the most clear way to define conversion factors. ...conversion ...

Hello, I have used NEURON to successfully replicate a model ran in XPPAUT. This model is the product of models going back to the 1970s and I have finally traced back through all the prior papers and have done a ton of dimensional analysis to get the units for all my model variables. When attempting ...

Sorry, some of my code was incorrect which makes my question seem silly (maybe it still will be when I correct it). The initial chunk of code in my original post above should have been def set_play_vec(cell): data = h.Vector([0,5,17,2,4,38,22,43,1, 1]) time = h.Vector([1,2,3,4,5,6,7,8,9,10]) data.pl...

I wanted to make this post to get some clarification about the behavior I am observing and also in case anyone else runs into a similar issue. I am using the Vector.play method to set the values of a parameter inside one of my mod files. I started with a toy example that I found here in the forums h...