# NaN warnings appeared in the subexpression of SpatialNeuron **URL:** \ **Category:** Support\ **Created:** [24 July 2024 07:54 UTC](https://brian.discourse.group/t/nan-warnings-appeared-in-the-subexpression-of-spatialneuron/1268 "2024-07-24T07:54:29Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![czx](https://avatars.discourse-cdn.com/v4/letter/c/7ba0ec/32.png) [@czx](https://brian.discourse.group/u/czx)\ **Post date:** [24 July 2024 07:54 UTC](https://brian.discourse.group/t/nan-warnings-appeared-in-the-subexpression-of-spatialneuron/1268/1 "2024-07-24T07:54:29Z")
Description of problem Hi everyone. I’m working with Brian2.7 and studying the example `hh_with_spikes` , and trying to change the `Cm` of the neuron from a constant to a subexpression. The subexpression contains a _square root_ operation. However, when running the code, the variables raised NaN warnings just like below. I think it may be the problem with the SQRT operation, since I also tried other simple subexpressions and they successfully worked. I wonder what the reason is and whether this issue can be avoided. Minimal code to reproduce problem ```auto from brian2 import * from scipy import stats defaultclock.dt = 0.01*ms morpho = Cylinder(length=10*cm, diameter=2*238*um, n=1000, type='axon') El = 10.613*mV ENa = 115*mV EK = -12*mV gl = 0.3*msiemens/cm**2 gNa0 = 120*msiemens/cm**2 gK = 36*msiemens/cm**2 # Typical equations eqs = ''' Im = gl * (El-v) + gNa * m**3 * h * (ENa-v) + gK * n**4 * (EK-v) : amp/meter**2 I : amp (point current) # applied current dm/dt = alpham * (1-m) - betam * m : 1 dn/dt = alphan * (1-n) - betan * n : 1 dh/dt = alphah * (1-h) - betah * h : 1 alpham = (0.1/mV) * 10*mV/exprel((-v+25*mV)/(10*mV))/ms : Hz betam = 4 * exp(-v/(18*mV))/ms : Hz alphah = 0.07 * exp(-v/(20*mV))/ms : Hz betah = 1/(exp((-v+30*mV) / (10*mV)) + 1)/ms : Hz alphan = (0.01/mV) * 10*mV/exprel((-v+10*mV)/(10*mV))/ms : Hz betan = 0.125*exp(-v/(80*mV))/ms : Hz gNa : siemens/meter**2 # strain evolution, the membraine capacitance Cm is related to it ema = (ema0-eDa0)*exp(-t/taufu) + eDa0 : 1 ema0 : 1 eDa0 : 1 taufu : second ''' neuron = SpatialNeuron(morphology=morpho, model=eqs, method="exponential_euler", refractory="m > 0.4", threshold="m > 0.5", Cm="1*uF/cm**2*sqrt(1+ema)", Ri=35.4*ohm*cm) #Cm is related to ema neuron.v = 0*mV neuron.h = 1 neuron.m = 0 neuron.n = .5 neuron.I = 0*amp neuron.gNa = gNa0 #initialize strain parameters neuron.taufu = 111.5*second neuron.ema0 = 0.05 neuron.eDa0 = 0 M = StateMonitor(neuron, ['v','ema'], record=True) run(50*ms, report='text') neuron.I[0] = 1*uA # current injection at one end run(3*ms) neuron.I = 0*amp run(50*ms, report='text') subplot(211) for i in range(10): plot(M.t/ms, M.v.T[:, i*100]/mV) ylabel('v') subplot(212) plot(M.t/ms, M.ema[0]) ylabel('ema') xlabel('Time (ms)') show() ``` What you have aready tried Tried other simple subexpressions such as `Cm = 2* 1* uF/cm** 2`, and it worked. Expected output (if relevant) The variables in the eqs should be normally calculated , since the `ema` in the square root is positive. Actual output (if relevant) NaN warnings like below. Electrical variables such as v is not available. ![image](https://global.discourse-cdn.com/free1/uploads/brian/original/1X/13c6f49cc761bd0146d26b97d1e6b9696215699f.png) Full traceback of error (if relevant) ```auto Starting simulation at t=0. s for a duration of 50. ms WARNING spatialneuron's variable 'm' has NaN, very large values, or encountered an error in numerical integration. This is usually a sign that an unstable or invalid integration method was chosen. [brian2.groups.group.invalid_values] WARNING spatialneuron's variable 'h' has NaN, very large values, or encountered an error in numerical integration. This is usually a sign that an unstable or invalid integration method was chosen. [brian2.groups.group.invalid_values] WARNING spatialneuron's variable 'n' has NaN, very large values, or encountered an error in numerical integration. This is usually a sign that an unstable or invalid integration method was chosen. [brian2.groups.group.invalid_values] 50. ms (100%) simulated in < 1s Starting simulation at t=53. ms for a duration of 50. ms 50. ms (100%) simulated in < 1s ``` ---
**Author:** ![czx](https://avatars.discourse-cdn.com/v4/letter/c/7ba0ec/32.png) [@czx](https://brian.discourse.group/u/czx)\ **Post date:** [27 August 2024 03:02 UTC](https://brian.discourse.group/t/nan-warnings-appeared-in-the-subexpression-of-spatialneuron/1268/3 "2024-08-27T03:02:46Z")
Shall I wirte another individual _eqs_ object for Cm? I would really appreciate it if someone could help . And if I asked a bad question, please let me know.😅 ---
**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:** [5 September 2024 15:25 UTC](https://brian.discourse.group/t/nan-warnings-appeared-in-the-subexpression-of-spatialneuron/1268/4 "2024-09-05T15:25:56Z")
Hi @czx. Apologies for the late reply, I completely overlooked this question (I was away for all of August). Unfortunately, Brian does not actually support defining `Cm` by a subexpression! When you provide an expression for `Cm`, this expression will only be used to initialize `Cm`, i.e. as if you’d have written ```python neuron = SpatialNeuron(...) neuron.Cm = "1*uF/cm**2*sqrt(1+ema)" ``` Evaluating `ema` before `taufu` has been set to a non-zero value will lead to NaN, so `Cm` will be set to NaN… You could set it after defining the other parameters to avoid the NaN, but it would not change over time. I don’t see any easy solution to this for now, Brian’s framework is built for a constant `Cm` (potentially varying over compartments) – some terms necessary for updating `v` at each time step are pre-calculated in the very beginning of the simulation, and some of these terms refer to `Cm`… ---
**Author:** ![czx](https://avatars.discourse-cdn.com/v4/letter/c/7ba0ec/32.png) [@czx](https://brian.discourse.group/u/czx)\ **Post date:** [6 September 2024 02:10 UTC](https://brian.discourse.group/t/nan-warnings-appeared-in-the-subexpression-of-spatialneuron/1268/5 "2024-09-06T02:10:25Z")
Hi @mstimberg That’s all right. Thanks for your kind reply. I will check whether it is necessary to provide an expression for **Cm**. Since the simulation time is relatively short, and it may not lead to an obvious change.