I'm trying to set the initial Calcium concentration for this model with no luck. I've tried self.model_params = {'tau_m': 10.0, # membrane time constant (ms) ... 'Ca': 0.1 #initial calcium concentration } This method doesn't throw an exception but it also doesn't change the initial calcium concentration.
I've also tried self.nodes_e.set(Ca=0.1) which throws an exception nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function SetStatus_id: Unused dictionary items: Ca
Any suggestions?
Hi,
Thank you for writing in. The neuron model having a calcium concentration is something of a fluke, as it was originally introduced only as a component in simulating structural plasticity. Therefore, I would recommend using this calcium value only if you are not otherwise planning to use structural plasticity mechanisms.
I have created a pull request that makes the calcium concentration available for setting: https://github.com/nest/nest-simulator/pull/2627 as it seems like this should anyway exist as a feature. Please let me know if this works for you.
In the ideal case we would not use the calcium concentration from the structural plasticity part of NEST, but track the concentration as part of the neuron model itself (e.g. in models/iaf_psc....cpp,h). NESTML is a modelling language for NEST that was created to allow you to easily express custom neuron (and synaptic) dynamics, and to generate code for it and build an extension module for NEST. Please see here for writing your neuron model in NESTML: https://nestml.readthedocs.org/
Yours, Charl
On Mon, Mar 6, 2023, at 21:45, Abbey Durell wrote:
I'm trying to set the initial Calcium concentration for this model with no luck. I've tried self.model_params = {'tau_m': 10.0, # membrane time constant (ms) ... 'Ca': 0.1 #initial calcium concentration } This method doesn't throw an exception but it also doesn't change the initial calcium concentration.
I've also tried self.nodes_e.set(Ca=0.1) which throws an exception nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function SetStatus_id: Unused dictionary items: Ca
Any suggestions? _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Thanks for this! This worked perfect.
I'm an undergrad doing some research. I'm not a CS major but I know enough to be dangerous. I was able to compile your code and get it working. I'm curious, do you know how I would change the connection rules as shown here (https://nest-simulator.readthedocs.io/en/v3.4/synapses/connection_management...) or should I open a new thread?
Great to hear!
I'm not sure what exactly you mean by changing the connection rules, could you elaborate? Perhaps a new thread for that would make the most sense.
Cheers, Charl
On Sat, Mar 18, 2023, at 22:40, Abbey Durell wrote:
Thanks for this! This worked perfect.
I'm an undergrad doing some research. I'm not a CS major but I know enough to be dangerous. I was able to compile your code and get it working. I'm curious, do you know how I would change the connection rules as shown here (https://nest-simulator.readthedocs.io/en/v3.4/synapses/connection_management...) or should I open a new thread? _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi Abbey,
This is an open issue (stale). As far as I am aware, the solution hasn't been merged with the latest issue. Check it out here: https://github.com/nest/nest-simulator/issues/2212
In my work, I have been using NEST v2.20.2 as a temporary workaround---where it is quite straight forward. Depending upon how urgently you need to control autapses and multapses you can choose to use Sandra's test branch (https://github.com/nest/nest-simulator/issues/2212#issuecomment-1178877744) or use NEST v2.20.x.
Best, Ady
On 3/28/23 2:46 AM, "Abbey Durell" durell_abbey@wheatoncollege.edu wrote:
Thanks. I really appreciate the help. I just opened a new thread. _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi Ady,
Thanks for this. I was able to get allow_autapses and the other properties to work as expected. I also wanted to change the p and rule settings for the node connections. I've tried using the PR from listed above as a pattern like this:
In conn_builder.cpp I added
if (conn_spec->known(names::make_symmetric)){ updateValue< double >( conn_spec, names::p, p_ ); }
In sp_manager.cpp I added
if ( syn_spec->known( names::p ) ) { def< double >( conn_spec, names::p, getValue< double >( syn_spec, names::p ) ); }
Setting the "p" does not seem to make any changes though. Any suggestions?
Thanks, Abbey
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aadhar.sharma＠saturn.uni-freiburg.de -
Abbey Durell -
Charl Linssen