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Hi



The file will run if you fix it as follows, but the plotted results are not
convincing at first glance, nevertheless, this is what is needed to make it
run:



Change all occurrences of lowercase "voi" (variable of integration) to
uppercase "VOI".



Change the calls to from log(x,10) to log10(x). This needs to be done 4
times, twice each for each of the two algebraic: algebraic[46] and
algebraic[47].



I've attached a fixed file.



I've also logged a bug for the code generator for Python.
https://tracker.physiomeproject.org/show_bug.cgi?id=2850. We'd appreciate
it if you would create a login for yourself on our tracker and add yourself
as a CC to this tracker item.



Regards,

Randall

From: cellml-discussion-bounces at cellml.org
[mailto:cellml-discussion-bounces at cellml.org] On Behalf Of Kamran
Sent: Saturday, 5 March 2011 12:33 p.m.
To: cellml-discussion at cellml.org
Subject: [cellml-discussion] Python CellML's code doesn't work - python
2.6.6



Hi there

I've downloaded several python codes from CellML. None of them works when I
run them by python 2.6.6. I have installed numpy and scipy and they work
properly. I guess the problem is related to the generic ode solver. Here is
the errors:




darwin at darwinComputer:~/Projects/simple CICR/temp$ python rawshan.py
capi_return is NULL
Call-back cb_f_in_dvode__user__routines failed.
Traceback (most recent call last):
File "rawshan.py", line 838, in <module>
(voi, states, algebraic) = solve_model()
File "rawshan.py", line 818, in solve_model
r.integrate(t)
File "/usr/lib/python2.6/dist-packages/scipy/integrate/ode.py", line 260,
in integrate
self.f_params,self.jac_params)
File "/usr/lib/python2.6/dist-packages/scipy/integrate/ode.py", line 435,
in run
y1,t,istate = self.runner(*(args[:5]+tuple(self.call_args)+args[5:]))
File "rawshan.py", line 605, in computeRates
algebraic[46] = -(log((states[5]/1.00000), 10))+3.00000
TypeError: return arrays must be of ArrayType


rawshan.py is the python code downloaded from here
<http://models.cellml.org/exposure/d72a36fe0b7e121068c96bcb1ff6044a/shannon_
wang_puglisi_weber_bers_2004_a.cellml/@@cellml_codegen/Python/raw> .

Thank you
Kamran Bigdely-Shamloo
University of Calgary, AB, Canada

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• [cellml-discussion] Python CellML's code doesn't work - python 2.6.6, Kamran, 03/05/2011
  • [cellml-discussion] Python CellML's code doesn't work - python 2.6.6, Randall Britten, 03/07/2011

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