Search found 29 matches
- Mon Aug 19, 2024 1:53 pm
- Forum: NEURON + Python
- Topic: h.frecord_init() and Python Multiprocessing
- Replies: 7
- Views: 2596
Re: h.frecord_init() and Python Multiprocessing
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, ...
- Sat Aug 17, 2024 3:30 pm
- Forum: NEURON + Python
- Topic: h.frecord_init() and Python Multiprocessing
- Replies: 7
- Views: 2596
Re: h.frecord_init() and Python Multiprocessing
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...
- Fri Aug 16, 2024 8:53 am
- Forum: NEURON + Python
- Topic: h.frecord_init() and Python Multiprocessing
- Replies: 7
- Views: 2596
Re: h.frecord_init() and Python Multiprocessing
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...
- Mon Aug 05, 2024 11:07 am
- Forum: NEURON + Python
- Topic: h.frecord_init() and Python Multiprocessing
- Replies: 7
- Views: 2596
h.frecord_init() and Python Multiprocessing
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 ...
- Tue Apr 23, 2024 11:47 am
- Forum: Reaction-diffusion in NEURON
- Topic: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
- Replies: 1
- Views: 7500
Re: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
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...
- Sun Apr 14, 2024 1:50 pm
- Forum: Reaction-diffusion in NEURON
- Topic: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
- Replies: 1
- Views: 7500
Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
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...
- Wed Feb 21, 2024 7:06 am
- Forum: NEURON + Python
- Topic: Saving fixed timestep data using cvode variable timestep integration
- Replies: 2
- Views: 8659
Re: Saving fixed timestep data using cvode variable timestep integration
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...
- Tue Feb 20, 2024 1:53 pm
- Forum: NEURON + Python
- Topic: Saving fixed timestep data using cvode variable timestep integration
- Replies: 2
- Views: 8659
Saving fixed timestep data using cvode variable timestep integration
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...
- Thu Jan 18, 2024 11:23 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 22238
Re: Units in NMODL
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...
- Wed Jan 17, 2024 1:16 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 22238
Re: Units in NMODL
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...
- Mon Jan 15, 2024 3:20 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 22238
Re: Units in NMODL
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...
- Mon Jan 15, 2024 11:05 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 22238
Re: Units in NMODL
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 ...
- Sat Jan 13, 2024 2:42 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 22238
Units in NMODL
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 ...
- Tue Dec 19, 2023 2:27 pm
- Forum: NEURON + Python
- Topic: User defined function to set play vectors
- Replies: 2
- Views: 44767
Re: User defined function to set play vectors
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...
- Wed Nov 22, 2023 3:39 pm
- Forum: NEURON + Python
- Topic: User defined function to set play vectors
- Replies: 2
- Views: 44767
User defined function to set play vectors
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...