zulko / ddeint Goto Github PK

Hi, I try to simulate FOPDT using ddeint. However, it doesn't work for me.
May I have your advice on this?

My system is as shown:

dxdt = (-x(t)+Kp*u(t-d))/taup

where Kp = 1.0 ; d = 180 ; taup = 181 
x(0) = 0.0 and u is a step change from 0 to 0.3

model = lambda x,t,d,Kp,taup : (-x(t)+Kp*u(t-d))/taup
g = lambda t : 0

tt=np.linspace(0,1440,1000)
yy=ddeint(model,g,tt,fargs=(180,1.0,181))

plt.plot(tt,yy)

Hi Zulko,

firstly, thank you for writing ddeint!. I want to solve 7 coupled differential equations with different delays (e.g.,
z1 = (Jd1d1 * Y1(t-d1) + Jd1d2 * Y2(t-d2) + Jd1fsi * Y3(t-d3) + Jd1TA * Y4(t-d4) + Jd1TI * Y5(t-d5) + Jd1ctx * (2. * np.sin(q(t-d6)) + 2.5))
z2 = (Jd2d1 * Y1(t-d21) + Jd2d2 * Y2(t-d22) + Jd2fsi * Y3 + Jd2TA * Y4 + Jd2TI * Y5(t-d25) + Jd2ctx * (2. * np.sin(q(t-d26)) + 2.5))
z3 = (Jfsifsi * Y3(t-d33) + JfsiTA * Y4(t-d34) + JfsiTI * Y5 + Jfsictx * (2. * np.sin(q(t-d36)) + 2.5))
, ...
)
and i'm afraid if ddeint can solve equations like what I want.

Thank you so much,
Atefeh

Hi,

I have a problem about the solution given by ddeint when time delay is set to zero. I expect in this case that the solution is the same as that solved by odeint package. However, there are small deviations from the result of odeint when time delay is zero.

For my dynamc system, I expect the evolution converges to stable states without time delay, which is observed using odeint.

Here is my dynamics: dx/dt = 0.1 + x * (1-x(t-\tau)/5) * (x-1) + 4 * x**2 / (5 + x); \tau is time delay. If it is set zero, then x should converge to some constant. But the solution given by ddeint dose not converge to a stable state.

Thanks for any help!

Michael

Hi Zulko,

firstly, thank you for writing ddeint!. I am trying to solve an initial value problem for the case that x''(t) is known and depends on x(t-dt). In scipy without the delay I do this as following:

def function(z, t):
return np.array([x''(z[1]), z[0]])

then odeint returns an np.array of [x',x]

However in ddeint this seems difficult as I cannot index z. Any help would be appreciated.

Cheers!

Hi do you think it reasonable to enable the variable to be indexed?

Not an issue per se, but the only way I can think of contacting you. This package uses scipy's odeint in the background, right? odeint has a self adjusting time step, such that the array of time instants used is only an array to query the integrated function in, not the actual time steps. Does ddeint not do the same? From what I gather from the code, it should, but when integrateing a simple one variable regulatory function I get different results depending on the time array passed to the function, for some parameters. So much so, that in some cases it diverges awfuly due to numerical errors, and in other cases it correctly displays oscilations.

This is the function in question, just in case:

def model(x, t, d, b, x0, h, tau):
    return -d * x(t) + b/(1+(x(t-tau)/x0)**h)

If you use Zenodo or some other repository to deposit ddeint and create a DOI, we could cite it when we use it in our work.

Since numpy 1.19 a deprecation warning is raised at line 145, namely
VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray

The warning can be turned off with np.warnings.filterwarnings('ignore', category=np.VisibleDeprecationWarning), but still, the issue might need adressing. I actualy don't know why the warning is raised, since the lines 144-145

    results = [dde_.integrate(dde_.t + dt) for dt in np.diff(tt)]
    return np.array([g(tt[0])] + results)

shouldn't return a ragged array.

--> python lotka.py
Computing for d=0.00
capi_return is NULL
Call-back cb_f_in_dvode__user__routines failed.
Traceback (most recent call last):
File "lo.py", line 19, in
yy = ddeint(model,g,tt,fargs=(d,))
File "/usr/local/lib/python2.7/site-packages/ddeint/ddeint.py", line 140, in ddeint
results = [dde_.integrate(dde_.t + dt) for dt in np.diff(tt)]
File "/usr/local/lib/python2.7/site-packages/ddeint/ddeint.py", line 62, in integrate
scipy.integrate.ode.integrate(self,t,step,relax)
File "/usr/local/lib/python2.7/site-packages/scipy/integrate/_ode.py", line 408, in integrate
self.f_params, self.jac_params)
File "/usr/local/lib/python2.7/site-packages/scipy/integrate/_ode.py", line 865, in run
y1, t, istate = self.runner(*args)
File "/usr/local/lib/python2.7/site-packages/ddeint/ddeint.py", line 56, in f2
return f(self.Y,t,*args)
File "lo.py", line 8, in model
x,y = Y(t)
File "/usr/local/lib/python2.7/site-packages/ddeint/ddeint.py", line 42, in call
return (self.g(t) if (t<=self.tc) else self.itpr(t))
File "/usr/local/lib/python2.7/site-packages/scipy/interpolate/polyint.py", line 79, in call
y = self._evaluate(x)
File "/usr/local/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 608, in _evaluate
y_new = self._call(self, x_new)
File "/usr/local/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 566, in _call_linear
y_lo = self._y[lo]
IndexError: index 2 is out of bounds for axis 0 with size 2

This seems like a great module! I love clean APIs like you seem to have implemented. Unfortunately pip seems to give me errors when trying to install; any ideas?

josh@schism:~/Research/projects$ pip3 install ddeint
Collecting ddeint
  Using cached ddeint-0.1.02.tar.gz
    Complete output from command python setup.py egg_info:
    Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.14.tar.gz
    Extracting in /var/folders/sf/pl_p088d46304npx9csknxq40000gn/T/tmpesz7da9o
    Traceback (most recent call last):
      File "/opt/anaconda3/lib/python3.5/site-packages/ez_setup.py", line 143, in use_setuptools
        raise ImportError
    ImportError

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/sf/pl_p088d46304npx9csknxq40000gn/T/pip-build-pqh28rf2/ddeint/setup.py", line 2, in <module>
        ez_setup.use_setuptools()
      File "/opt/anaconda3/lib/python3.5/site-packages/ez_setup.py", line 145, in use_setuptools
        return _do_download(version, download_base, to_dir, download_delay)
      File "/opt/anaconda3/lib/python3.5/site-packages/ez_setup.py", line 125, in _do_download
        _build_egg(egg, tarball, to_dir)
      File "/opt/anaconda3/lib/python3.5/site-packages/ez_setup.py", line 99, in _build_egg
        _extractall(tar)
      File "/opt/anaconda3/lib/python3.5/site-packages/ez_setup.py", line 467, in _extractall
        self.chown(tarinfo, dirpath)
    TypeError: chown() missing 1 required positional argument: 'numeric_owner'

Dear Zulko,

Hello Zulko, my name is JunSeokCha. May I contribute your package to conda-forge?

Sincerely,
JunSeokCha

Hi,
The piece of code in the README to illustrate the basic usage of ddeint does not work for me.
Using

from pylab import cos, linspace, subplots
from ddeint import ddeint

# We solve the following system:
# Y(t) = 1 for t < 0
# dY/dt = -Y(t - 3cos(t)**2) for t > 0

def values_before_zero(t):
    return 1

def model(Y, t):
    return -Y(t - 3 * cos(Y(t)) ** 2)

tt = linspace(0, 30, 2000)
yy = ddeint(model, values_before_zero, tt)

I got the error message

  File "/usr/lib/python3.10/site-packages/ddeint/ddeint.py", line 145, in ddeint
    return np.array([g(tt[0])] + results)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2000,) + inhomogeneous part.

I use scipy version 1.10.1
Thanks for the help!