[scilab-Users] No reaction
Adrien Vogt-Schilb
vogt at centre-cired.fr
Thu Oct 6 14:07:52 CEST 2011
Hi
Maybe you should look at x (the output of ode) without ploting it. That
way you'll make sure if the problem comes from the plot or not
Can you attach a file with the new code?
On 06/10/2011 10:00, Jaundre Venter wrote:
> Hi
>
> okay i have made the changes and the reaction curves are looking
> better but for some reason i still get no reaction on the last three
> curves. It is just showing a straight line. can it be that i have
> choosen to plot the wrong type of graph? Maybe because of a time value
> or to much ODE"s?
>
> On Wed, Oct 5, 2011 at 10:24 PM, Jaundre Venter
> <jaundreventer at gmail.com <mailto:jaundreventer at gmail.com>> wrote:
>
> Thank you very much Adrien.
>
> always nice if someone can explain to you where your problems are
> and why. Thanks
>
> Was there any other problems you saw that i have to be aware of?
>
>
> On Wed, Oct 5, 2011 at 5:38 PM, Adrien Vogt-Schilb
> <vogt at centre-cired.fr <mailto:vogt at centre-cired.fr>> wrote:
>
> Hi
>
> When you use ode, it's ok, if say, dx(1) depends on dx(4).
> but you still have say that to scilab properly, something like:
>
> function dx = f(t,x)
> dx(6)=((F+Fab+Floss)*(x(2))), // culture Volume V
> dx(1)=(((mu)*(x(1)))-(((x(1))/(x(6)))*((dx(6))))*(CO)*(x(2)))), //biomass
> concentration X
> and so one
>
> note that because i had to know dx(6) to compute dx(1) i just
> computed dx(6) before dx(1): no problem. and note that i used
> x(2). The idea of the ode is to compute dx from x!
>
> make sure you understand that using dx_6 instead of dx(6),
> your ODE solver is not updating dx_6 at each time step, it is
> using the initial and only dx_6 forever. That's why your last
> varaibles do not move, somehow their speeds are never updated.
> for instance, dx(6)=((F+Fab+Floss)*(HION)), // culture Volume
> V is constance in time (i guess)
>
>
>
> On 05/10/2011 15:00, Jaundre Venter wrote:
>> Hi Adrien
>>
>> i am new to SCILAB! I just want to say that.
>>
>> Yes dx_1 is equal to dx1 but the only reason why i have
>> programmed it like that is becasue the ODE's looks as follows
>> - (see word file attached that can explain the ODE"s better.
>> with regards to the HION and CO it actually refers to [H+]
>> and CO2 as you said. the only reason why n multiplied HION
>> and CO wit hsome ODE's is because some does have a influence
>> on some ODE's.
>>
>> This is the first time i am working with SCILAB thus i am
>> struggling to understand how SCILAB wants the code so that
>> all 9 ODE's are shown and so that the ODE's that is having a
>> effect on other does happen. I though if you refer to dx(1)
>> for example in a other ODE it means that SCILAb will know the
>> dx(1) has a influence on the other ODE.
>>
>> The main goal of my assesment is to deliver similar results
>> obtained from MATLAB on SCILAB. all i got was how the grpahs
>> should look like and the ODE's.
>>
>> On Wed, Oct 5, 2011 at 2:43 PM, Adrien Vogt-Schilb
>> <vogt at centre-cired.fr <mailto:vogt at centre-cired.fr>> wrote:
>>
>> Hi
>>
>> Try to isalote your problem
>> if i understood well, the following code
>>
>>
>> // initial values
>> x0=[0.1, 1e-5, 0, 15, 1.16, 100,0,297,0.5]';
>> t=0:0.005:400;
>> y=ode(x0, 0, t, f);
>>
>> returns y such that sum(y(6:9,:)>x0) == 0 ?
>> if this is true, we do not need the plots to solve the
>> problem
>> can you check that ?
>>
>> I believe the f function is erroneous.
>> It seems that dx_1 should be equal to dx(1) at each time
>> step, and that HION should be equal to x(2) at each time
>> step, etc.
>>
>> in other terms, some of your phisical variables seem to
>> be represented by to variables (i am guessing HION=[H+]
>> and x(2)=[H+] also) but scilab does not have any chance
>> to know that.
>> if my guess is right, you have to rewrite the f function
>> in a way that eliminates all references to HION, dx_1,
>> dx_6 and so on
>>
>>
>> On 05/10/2011 14:27, Jaundre Venter wrote:
>>> Hi all
>>>
>>> Can someone please explain to me the following:
>>>
>>> I am busy with a project of simulation the production of
>>> penicillin in a bio reactor. Now i have 9 ODE's which i
>>> want to simulate.
>>>
>>> now for some reason the last three graphs i am getting
>>> doesn't show any response what so ever. i am using the
>>> following code.
>>>
>>> dx(1)=(((mu)*(x(1)))-(((x(1))/(x(6)))*((dx_6)))*(CO)*(HION)),
>>> //biomass concentration X
>>> dx(2)=((z*(((mu)*(x(1)))-(((F)*(x(1)))/(x(6)))))+(QQ)),
>>> //hydrogen ion concentration H+
>>> dx(3)=((((mupp)*(x(1)))-((K)*(x(3)))-((x(3))/(x(6)))*(dx_6))*(HION)),
>>> //Penicilin concentration P
>>> dx(4)=((-((mu)/(Yxs))*(x(1)))-(((mupp)/(Yps))*(x(1)))-((mx)*(x(1)))+((Fsf)/(x(6)))-((x(4)/(x(6)))*(dx_6))),
>>> //Substrate concentration S
>>> dx(5)=(-(((mu)/(Yxo))*(x(1)))-(((mupp)/(Ypo))*(x(1)))-(((mo))*(x(1)))+((kla)*(cll-(x(5))))-(((x(5))/(x(6)))*(dx_6))),
>>> //dissolved oxygen
>>> dx(6)=((F+Fab+Floss)*(HION)), // culture Volume V
>>> dx(7)=(((rq1)*(dx_1)*(x(6)))+(rq2)*(x(1))*(x(6))),
>>> //Heat generation Qrxn
>>> dx(8)=((((F)/(sf))*(Tf-(x(8))))+(1/((x(6))*(pcp)))*(QT)),
>>> // Temperature T
>>> dx(9)=(((a1)*(dx_1))+((a2)*(x(1)))+(a3)), // CO2
>>> evolution, CO2
>>> endfunction
>>>
>>> now when i ask for plotting the graphs i am using the
>>> following.:
>>>
>>> // initial values
>>> x0=[0.1, 1e-5, 0, 15, 1.16, 100,0,297,0.5]';
>>> t=0:0.005:400;
>>> y=ode(x0, 0, t, f);
>>>
>>> // the plots of each variable
>>> da.title.text="BIOMASS CONCENTRATION"
>>> da.x_label.text="Time, hours";
>>> da.y_label.text="X,g/l ";
>>> scf(1);clf; //Opens and clears figure 1
>>> plot(t,y(1,:))
>>>
>>> da.title.text="HYDROGEN ION H+ CONCENTRATION"
>>> da.y_label.text="H+,mol/l ";
>>> scf(2);clf; //Opens and clears figure 2
>>> plot(t,y(2,:))
>>>
>>> da.title.text="PENICILLIN CONCENTRATION"
>>> da.y_label.text="P,g/l ";
>>> scf(3);clf; //Opens and clears figure 3
>>> plot(t,y(3,:))
>>>
>>> da.title.text="SUBSTRATE CONCENTRATION"
>>> da.y_label.text="S,g/l ";
>>> scf(4);clf; //Opens and clears figure 4
>>> plot(t,y(4,:))
>>>
>>> da.title.text="DISSOLVED OXYGEN CONCENTRATION"
>>> da.y_label.text="C_l,g/l ";
>>> scf(5);clf; //Opens and clears figure 5
>>> plot(t,y(5,:))
>>>
>>> da.title.text="CULTURE VOLUME"
>>> da.y_label.text="V,l";
>>> scf(6);clf; //Opens and clears figure 6
>>> plot(t,y(6,:))
>>>
>>> da.title.text="HEAT OF REACTION"
>>> da.y_label.text="Qrxn,cal";
>>> scf(7);
>>> clf; //Opens and clears figure 7
>>> plot(t,y(7),:)
>>>
>>> da.title.text="TEMPERATURE"
>>> da.y_label.text="T,Kelvin";
>>> scf(8);
>>> clf; //Opens and clears figure 8
>>> plot(t,y(8),:)
>>>
>>> da.title.text="CO2 EVOLUTION"
>>> da.y_label.text="CO2,mmol/l/";
>>> scf(9);
>>> clf; //Opens and clears figure 9
>>> plot(t,y(9),:)
>>>
>>> Am i doing something wrong? before the ODE's i have just
>>> programmed the initial values and constants :
>>>
>>> funcprot(0);
>>> function dx = f(t,x)
>>> K1=1.0e-10 //mol/l
>>> K2=7.0e-05 //mol/l
>>> Kx=0.15 // Contois saturation constant, g/l
>>> Kox=2e-02 // oxygen limitation constant
>>> mux=0.092 // maitenance coefficient on subsrate
>>> p=3 //constant
>>> Kp=0.0002 // inhibition constant
>>> Kop=2e-02 // oxygen limitation constant
>>> K=0.04 // Penicillin hydrolysis constant, per h
>>> Yxs=0.45 // yield constant,g biomass/g glucose =
>>> dimensionless
>>> Yps=0.90 // yield constant, g pinicillin/ g glucose =
>>> dimensionless
>>> mx= 0.014 // Maintenance coefficient on substrate, per h
>>> Yxo=0.04 // yield constant, g biomass/g oxygen =
>>> dimensionless
>>> Ypo=0.20 // yield constant, g penicillin/g oxygen=
>>> dimensionless
>>> mo= 0.467 // maintenance coefficient of oxygen, per h
>>> mup=0.0005 // specific rate of penicilline production
>>> (per h)
>>> sf=600 // Feed substrate concentration, g/l
>>> kla=23 // function of agitation power input and
>>> oxugen flow rate, dimensional
>>> cll=1.16 // dissolved oxygen concentration, g/l
>>> Cab=3 // concentrations in both solutions
>>> Fa=5 // acid flow rate, l/h !!
>>> Fb=5 // base flow rate, l/h !!
>>> delta_t=0.01 // time step in digital PID controller -
>>> arbitrary value!!!
>>> z=10e-5 // constant
>>> F=0.042 // feed substrate flow rate l/h
>>> T0=273 // temperature at freezing, K
>>> Tv=373 // temperature at boiling
>>> T=298 // feed temp of substrate
>>> h=(2.5e-4) // constant
>>> Floss=(x(6)*(h)*(exp(5)*((T-T0)/(Tv-T0))))
>>> Fab=Fa+Fb // volume increase due to influx of acid Fa
>>> and base Fb
>>> Fsf=((sf)*(F))
>>> kg= 7e-3 // Arrhenius constant for growth
>>> kd=10e33 // Arrhenius constant for cell death
>>> Eg= 5100 // Activation energy for growth, cal/mol
>>> Ed= 50000 // Activation energy for cell death, cal/mol
>>> R= 1.987 // gas constant, cal/mol k
>>> T= 297 // Temperature
>>> RT= R*T
>>> alpa= 70 // constant in Kla
>>> betha= 0.4 // constant in Kla
>>> Pw= 30 // Agitation power input, W
>>> fg= 8.6 // Flow rate of oxygen
>>> V=100 // Volume
>>> QE= ((kg*exp(-(Eg/RT)))-(kd*exp(-(Ed/RT))))
>>> kla= alpa*((sqrt(fg)*(Pw/x(6)))^betha)
>>> mu
>>> =(((mux)/(1+((K1)/(x(2)))+((x(2))/(K2))))*((x(3))/(((Kx)*(x(1)))+(x(3))))*((x(5))/(((Kox)*(x(1)))+(x(5))))*(QE))
>>> // Specific growth rate
>>> mupp =
>>> ((mup)*((x(4))/((Kp)+(x(4))+(x(4)^2)/(K1)))*((x(5)^p)/((Kop)*(x(1)))+(x(5)^p)))
>>> // Specific penicillin production rate
>>> B
>>> =(((1e-14/x(2)-x(2))*x(6)-Cab*(Fa+Fb)*delta_t)/(x(6)+(Fa+Fb)*delta_t))
>>> QQ =((-B+sqrt(B^2+4e-14))/2-(x(2)))*(1/delta_t)
>>> dx_6 = (F+Fab+Floss) //Culture Volume V
>>> dx_1 = (((mu)*(x(1)))-((x(1))/(x(6)))*(dx_6)) //biomass
>>> concentration X
>>> rq1 = 60 // yield of heat generation, cal/g biomass
>>> rq2 = 1.6783e-4 // Constant, cal/g biomass h
>>> Tf = 296 // substrate feed temperature, Kelvin
>>> a = 1000 // heat transfer coefficient of
>>> cooling/heating liquid, cal/h degree C
>>> b = 0.60 // constant
>>> Fc=0.1 // Cooling water flow rate, not sure about
>>> value, l/h
>>> pcCpc = 1/2000 // Density times heat capacity of
>>> cooling liquid, per l degree C
>>> pcp = 1/1500 // density times heat capacity of medium
>>> QT = ((x(7)-(((a)*(Fc^b+1))/((Fc)+((a)*(Fc^b))/2*pcCpc))))
>>> a1=0.143 // constant relating CO2 to growth, mmol
>>> CO2/g biomass
>>> a2=4e-7 // Constant relating CO2 to mainteneance
>>> energy, mmol CO2/g biomass h
>>> a3=1e-4 // Constant relating CO2 to penicillin
>>> production, mmol CO2/l h
>>> CO= (((a1)*(dx_1))+((a2)*(x(1)))+(a3)), // CO2
>>> evolution, CO2
>>> HION=((z*(((mu)*(x(1)))-(((F)*(x(1)))/(x(6)))))+(QQ))
>>>
>>> Thanks.
>>
>>
>> --
>> Adrien Vogt-Schilb (Cired)
>> Tel: (+33) 1 43 94 *73 77*
>>
>>
>
>
> --
> Adrien Vogt-Schilb (Cired)
> Tel: (+33) 1 43 94 *73 77*
>
>
>
--
Adrien Vogt-Schilb (Cired)
Tel: (+33) 1 43 94 *73 77*
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