pyrates-neuroscience/pycobi

Python package for automated bifurcation analysis and parameter continuations, based on Auto-07p.

pycobi's Issues

Error: `invalid literal for int() with base 10`

Hello,

I am currently trying to use PyCoBi to simulate non-linear effects in microring resonators for photonic neuromorphic computing and I am exploring continuation analysis of some of our (potential) neuron structures. I have rate equations obtained from the literature but I encounter the following errors in various scenarios:

• If I simply copy the Van der Pol operator from PyRates, I get the following error: invalid literal for int() with base 10
• If I use my actual equations, I get the following error: TypeError: _lambdifygenerated() missing 1 required positional argument: 'Pin'

My operator for my use case is the following:

# A simple MRR without graphene.
mrr_si_no_gr:
  base: OperatorTemplate
  equations:
    - "d/dt * a = Pin^0.5"
    - "d/dt * n = - n / tau + abs(a)^4."
  variables:
    a: output(0.0 + 0.0j)
    n: variable(1000000000000.0)
    Pin: input(0.0)
    tau: 0.0
    n_kerr: 0.0
    theta_fcd: 0.0
    gamma_fca: 0.0
    alpha_tpa: 0.0
    i: 0.0+1.0j

# A simple node with a single MRR.
MRRNODE:
  base: NodeTemplate
  operators:
    - mrr_si_no_gr

# Example circuit for Aashu's paper.
AASHU:
  base: CircuitTemplate
  nodes:
    mrr: MRRNODE
  edges:

And my current Python code is the following:

from pycobi import ODESystem
import numpy as np
import matplotlib.pyplot as plt

ode = ODESystem.from_yaml(
    "aashu/AASHU",
    working_dir="target/",
    auto_dir="~/auto-07p",
    node_vars={
        "mrr/mrr_si_no_gr/Pin": 19.54,
    }
)

Note that Aashu is a reference to the file name I gave to my YAML file since I am trying to recreate a paper from Aashu Jha, et al. I should also mention that this is a somewhat minimal reproduction example because the actual rate equations are much longer and more complicated.

As far as I know, I am using the latest version of the library, of auto-07b, and Python 3.10.14.