[scilab-Users] No reaction
Jaundre Venter
jaundreventer at gmail.com
Mon Oct 31 21:10:27 CET 2011
Hi Adrien
Sorry for late response but had some issues on other projects that i had to
attend.
i am still getting no reactions what so ever for the last three curves. see
attached the new code. i don't know it is showing 0 or at the initial
values! i have checked the mass balance if some input values are wrong that
is causing the no reaction but the constant etc is correct.
On Thu, Oct 6, 2011 at 2:07 PM, Adrien Vogt-Schilb <vogt at centre-cired.fr>wrote:
> 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>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>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
>>> > 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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