[SciPy-User] weired results with ode solver

Oz Nahum nahumoz@gmail....
Sat Feb 6 12:33:33 CST 2010


Hi Warren,
Thanks for your answer,

here is my updated code:
#% This file is a matlab script to simulate a batch problem as described
#% in problem 1a.

from scipy.integrate import odeint
from numpy import *
#%clear all;
#clc;

#%Define variables
Coi=3              # initial concentration of oxigen [mg/l]
Csi=10             # initial concentration of substrat [mg/l]
Cbi=0.2            # initial concentration of biomass [mg/l]

#define vector of concentrations
#c1 = array((Coi,Csi,Cbi))
c1=(Coi,Csi,Cbi)
y0=c1
ko=0.1             #% Monod coefficients Oxigen [mg/l]
ks=0.1             #% Monod coefficients Substract [mg/l]

umax=0.125/86400 #  % Maximun growth rate [1/d]

Yo=0.125#;           % Oxigen Yield [mg X / mg O]
Ys=0.25#;            % Substract Yield [mg X / mg S]

Kdec=0.01/86400#;    % Decay rate
kb=1#;              % Biomass Inhibition constant [mg/L]

def rate_func(c,time,ko,ks,umax,Kdec,Yo,Ys,kb):
	co=c[0]#; %concentration of Oxygen
	cs=c[1]#; %concentration of Substrate
	X=c[2]#; %concentration of bacteria
	kgr=umax*(co/(ko+co))*(cs/(ks+cs))#; % specific uptake rate [mol/m3/s]
	Ib=1+X/kb#;  				 		% inhibiton caused by biomass
	foxi=((-kgr/Yo/Ib)*X)#;  %dc/dt of Oxygen
	fsub=((-kgr/Ys/Ib)*X)#;  %dc/dt of Substrate
	fbio=((kgr/Ib-Kdec)*X)#; %inhibition for growth only
	f=array((foxi,fsub,fbio))
	return  f

#Solve ODE
timerange=arange(1,43*86400,3600)
c=odeint(rate_func,c1,timerange,args=(ko,ks,umax,Kdec,Yo,Ys,kb))

from pylab import *
plot(timerange/86400, c[:,0], 'bo')
plot(timerange/86400, c[:,1], 'go')
plot(timerange/86400, c[:,2], 'ko')
show()


I seems that it runs much faster than matlab (though I have not really
checked). It's syntacticly clearer to read. Much more fun.
There is one issue that bothers me still. I don't want to show the
concentrations every second. So I divide by 86400 sec perday. However,
this results in smeared concentrations, where every day has  a few of
them. Why is that ? how can I remove it ?
A line plot would be nice.

Thanks again,

-- 
Oz Nahum
Graduate Student
Zentrum für Angewandte Geologie
Universität Tübingen

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