# Run\_regularly doesn't run if the variable its manipulating is refractory

**URL:** <https://brian.discourse.group/t/run-regularly-doesnt-run-if-the-variable-its-manipulating-is-refractory/1441>\
**Category:** Support\
**Tags:** refractoriness\
**Created:** [28 April 2025 13:11 UTC](https://brian.discourse.group/t/run-regularly-doesnt-run-if-the-variable-its-manipulating-is-refractory/1441 "2025-04-28T13:11:04Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![smestern](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/smestern/32/452_2.png) [@smestern](https://brian.discourse.group/u/smestern)\
**Post date:** [28 April 2025 13:11 UTC](https://brian.discourse.group/t/run-regularly-doesnt-run-if-the-variable-its-manipulating-is-refractory/1441/1 "2025-04-28T13:11:04Z")

</div>

# Description of problem

Howdy Y’all,  
I have a very specific use case. I have been dynamic clamping with brian2 with somewhat decent results.  
However, I was testing a configuration where I would brute force build a hybrid network by overwriting the membrane potential of an in slico neuron with the membrane potential of my clamped in vitro neuron. I accomplished this by running a run\_regularly call every timestep to write to the membrane potential variable.  
However, I’ve encountered an issue: when the neuron spikes, the run\_regularly function stops executing for a few time steps. This behavior only occurs when the variable being overwritten (the membrane potential) has the unless refractory flag set.

# Minimal code to reproduce problem

```auto
from brian2 import *

#run standalone

device = get_device()

set_device('cpp_standalone', build_on_run=True)

#ramp volt

voltage = np.arange(-70, 0, 0.01)

input_volt = TimedArray(voltage*mV, dt=0.01*second)

Eqs = Equations('''

dv/dt = 0*mV/ms: volt (unless refractory)

Vcut : volt

''')

P = NeuronGroup(1, model=Eqs, threshold='v>Vcut', refractory='v>Vcut', method='euler')

P.run_regularly("v = input_volt(t)", dt=0.1*ms)

M = SpikeMonitor(P)

M2 = StateMonitor(P, ['v'], record=True)

P.Vcut = -30*mV

run(60*second, report='text')

```

# What you have aready tried

-Removing the unless refractory flag does fix it.

# Expected output (if relevant)

Neuron membrane potential climbs from -70 to 0

# Actual output (if relevant)

Neuron membrane potential climbs from -70 to -30, where it gets stuck

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<div class="post-metadata">

**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\
**Post date:** [28 April 2025 14:04 UTC](https://brian.discourse.group/t/run-regularly-doesnt-run-if-the-variable-its-manipulating-is-refractory/1441/2 "2025-04-28T14:04:47Z")

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Hi @smestern. I agree that this is not necessarily intuitive, but this is actually working as intended. The `(unless refractory)` flag marks a variable as read-only during the refractoriness period:

> In addition, a variable of a neuron that is in its refractory period is _read-only_: incoming synapses or other code will have no effect on the value of `v` until it leaves its refractory period.  
> [Refractoriness — Brian 2 2.8.0.4 documentation](https://brian2.readthedocs.io/en/stable/user/refractoriness.html#defining-model-behaviour-during-refractoriness)

The way to implement this is to use the underlying mechanism directly as described in [Refractoriness — Brian 2 2.8.0.4 documentation](https://brian2.readthedocs.io/en/stable/user/refractoriness.html#arbitrary-refractoriness). In your example, you’d remove the `unless refracory` and instead write:

```python
'''
dv/dt = int(not_refractory)*0*mV/ms: volt
Vcut : volt
'''

```

Of course, in the example with `dv/dt = 0*mV/ms` the refractoriness does not really matter, but I think you get the idea 😏

Let us know whether this works for you!

PS: Your title somewhat implies that there is a difference between standalone and runtime mode here, but this should work the same in both, otherwise this would be bug…

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<div class="post-metadata">

**Author:** ![smestern](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/smestern/32/452_2.png) [@smestern](https://brian.discourse.group/u/smestern)\
**Post date:** [29 April 2025 15:14 UTC](https://brian.discourse.group/t/run-regularly-doesnt-run-if-the-variable-its-manipulating-is-refractory/1441/3 "2025-04-29T15:14:14Z")

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I see! That makes sense! the `* int(not_refractory)` works great thanks - it reproduces the exact behaviour as the (unless refractory) flag! I will edit the title accordingly for anyone that that may need to reference this thread in future.