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POUpdate initial condition in ODE solver each time step
 

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  1. POUpdate initial condition in ODE solver each time step
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    <p>I am wanting to solve a system of ODEs where for the first 30,000 seconds, I want one of my state variables to start from the same initial value. After those 30,000 seconds, I want to change the initial value of that state variable to something different and simulate the system for the rest of time. Here is my code: </p> <pre><code>def ode_rhs(y, t): ydot[0] = -p[7]*y[0]*y[1] + p[8]*y[8] + p[9]*y[8] ydot[1] = -p[7]*y[0]*y[1] + p[8]*y[8] ydot[2] = -p[10]*y[2]*y[3] + p[11]*y[9] + p[12]*y[9] ydot[3] = -p[13]*y[3]*y[6] + p[14]*y[10] + p[15]*y[10] - p[10]*y[2]*y[3] + p[11]*y[9] + p[9]*y[8] - p[21]*y[3] ydot[4] = -p[19]*y[4]*y[5] - p[16]*y[4]*y[5] + p[17]*y[11] - p[23]*y[4] + y[7]*p[20] ydot[5] = -p[19]*y[4]*y[5] + p[15]*y[10] - p[16]*y[4]*y[5] + p[17]*y[11] + p[18]*y[11] + p[12]*y[9] - p[22]*y[5] ydot[6] = -p[13]*y[3]*y[6] + p[14]*y[10] - p[22]*y[6] - p[25]*y[6] - p[23]*y[6] ydot[7] = 0 ydot[8] = p[7]*y[0]*y[1] - p[8]*y[8] - p[9]*y[8] ydot[9] = p[10]*y[2]*y[3] - p[11]*y[9] - p[12]*y[9] - p[21]*y[9] ydot[10] = p[13]*y[3]*y[6] - p[14]*y[10] - p[15]*y[10] - p[22]*y[10] - p[21]*y[10] - p[23]*y[10] ydot[11] = p[19]*y[4]*y[5] + p[16]*y[4]*y[5] - p[17]*y[11] - p[18]*y[11] - p[22]*y[11] - p[23]*y[11] ydot[12] = p[22]*y[10] + p[22]*y[11] + p[22]*y[5] + p[22]*y[6] + p[21]*y[10] + p[21]*y[3] + p[21]*y[9] + p[24]*y[13] + p[25]*y[6] + p[23]*y[10] + p[23]*y[11] + p[23]*y[4] + p[23]*y[6] ydot[13] = p[15]*y[10] + p[18]*y[11] - p[24]*y[13] return ydot pysb.bng.generate_equations(model) alias_model_components() p = np.array([k.value for k in model.parameters]) ydot = np.zeros(len(model.odes)) y0 = np.zeros(len(model.odes)) y0[0:7] = p[0:7] t = np.linspace(0.0,1000000.0,100000) r = odeint(ode_rhs,y0,t) </code></pre> <p>So, in other words, I want to set y0[1] to the same value (100) each time <code>odeint</code> is called for the first 30,000 seconds. I'm effectively trying to let the system equilibrate for an amount of time before inputing a signal into the system. I thought about doing something like <code>if t &lt; 30000: y0[1] = 100</code> as the first line of my <code>ode_rhs()</code> function, but I'm not quite sure that works. </p>
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    1. USWarren Weckesser
    1. USZack
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      1. POUpdate initial condition in ODE solver each time step
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    1. COI'm not sure I follow you, but initial conditions are initial, say at t=0. I doesn't make sense to change the initial conditions after the initial time. Besides, you're only calling `odeint` once. What does "each time odeint is called for the first 30,000 seconds" mean?
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      1. POUpdate initial condition in ODE solver each time step
      1. USjorgeca
    2. COWhy does this question have a `matlab` tag? And why not `scipy`?
      singulars
      1. POUpdate initial condition in ODE solver each time step
      1. USWarren Weckesser
    3. COYou're right - it should have been tagged as `scipy` and not `matlab`. Thank you.
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      1. POUpdate initial condition in ODE solver each time step
      1. USZack
 

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