On 11-07-2013, at 13:53, Raphaëlle Carraud <raphaelle.carr...@oc-metalchem.com>
wrote:
> Sorry for the bug, I had eliminated some lines to avoid making the program
> too big. Here is the version that works :
>
> reaction<-function(z, state, dval, parameters) {
> with(as.list(c(state)),{
> # rate of change
>
> Tr <- 273+90
> P <- 0.98*10^5
>
> K2 <- 10^(2993/Tr-9.226)*(10^-3)
> K3 <- 10^(2072/Tr-7.234)*(10^-3)
> K4 <- 10^(-20.83/Tr-0.5012)
> K5 <- 10^(-965.5/Tr-1.481)
> k1 <- (10^(652.1/Tr-0.7356))*(8.314*Tr/P)^2
> kf2 <- 1.4*10^-33*(Tr/300)^(-3.8)*6.022*10^23*10^-6
> kb2 <- kf2/K2*P/(8.314*Tr)
> kf3 <- 3.1*10^-34*(Tr/300)^(-7.7)*10^(-6)*6.022*10^23
> kb3 <- kf3/K3*P/(8.314*Tr)
> kf4 <- 41
> kf5 <- 0.25
>
> r1 <- k1*A^2*H
> r4 <- kf4*D*G - kf4/K4*E^2
> r5 <- kf5*C*G - kf5/K5*E*I
>
> res1 <- -dA + dB + 2*dC - 2*r1 - 2*r5 #
> res2 <- dA + dD + r1 + r4 #
> res3 <- K2 - C/B^2 #
> res4 <- K3 - D/(A*B) #
> res5 <- r5 + 2*r4 - dE #dHNO2/dz
> res6 <- r5 -dI #dHNO3/dz
> res7 <- -r5 - r4 - dG #dH2O/dz
> res8 <- -r1/2 - dH #dO2/dz
>
> list(c(res1, res2, res3, res4, res5, res6, res7, res8))
> }) # end with(as.list ...
> }
>
> xi <- c(0.3, #x_NO
> 0.1, #x_NO2
> 0, #x_N2O4
> 0, #x_N2O3
> 0.05, #x_HNO2
> 0.05, #x_HNO3
> 0.2, #x_H2O
> 0.3) #x_O2
>
>
> state <- c(A = xi[1]*Pt,
> B = xi[2]*Pt,
> C = xi[3]*Pt,
> D = xi[4]*Pt,
> E = xi[5]*Pt,
> I = xi[6]*Pt,
> G = xi[7]*Pt,
> H = xi[8]*Pt)
>
> dval <- c(dA = 1,
> dB = 1,
> dC = 0.5,
> dD = 0.2,
> dE = 0,
> dI = 0,
> dG = 0,
> dH = 0)
>
> parameters <- c(Pt = 0.98*10^5)
>
Doesn't run.
Since variable Pt is not defined when you calculate vector state. So define Pt
<- …. before xi as in the original example.
In the function reaction isn't variable P just Pt from the parameter vector?
If so then either do P <- Pt or just use Pt directly (but see next remark).
> z <- seq(0, 1, by = 0.01) # en seconde
>
> library(deSolve)
> #out <- ode(y = state, times = z, func = reaction, parameters)
>
> out <- daspk(y = state, dy = dval, times = z, res = reaction, parms = 0)
> head(out)
> plot(out)
>
> I obtain the following message:
>
>> library(deSolve)
>> #out <- ode(y = state, times = z, func = reaction, parameters)
>>
>> out <- daspk(y = state, dy = dval, times = z, res = reaction, parms = 0)
> Error in eval(expr, envir, enclos) : object 'dA' not found.
>
Obviously since dA isn't defined outside of dval when the functions was
defined.
And do parms=parameters if you want to use Pt (as I told you in the previous
post).
> I tried adding the dval and parameters as you said:
> with(as.list(c(state,dval,parameters)),{
>
> I get the following message:
>
> Warning messages:
> 1: In daspk(y = state, dy = dval, times = z, res = reaction, parms = 0) :
> matrix of partial derivatives is singular with direct method-some equations
> redundant
> 2: In daspk(y = state, dy = dval, times = z, res = reaction, parms = 0) :
> Returning early. Results are accurate, as far as they go
>
These are warning messages.
You get plots.
So now is the time to start looking at initial values etc.
Since I know next to nothing about DAE's you are on your own here unless
someone else comes up with suggestions.
> For the calling of the daspk function, I followed the documentation, where
> you have the same inversion:
>
> daefun <- function(t, y, dy, parameters) {
> + res1 <- dy[1] + y[1] - y[2]
> + res2 <- y[2] * y[1] - t
> +
> + list(c(res1, res2))
> + }
>> library(deSolve)
>> yini <- c(1, 0)
>> dyini <- c(1, 0)
>> times <- seq(0, 10, 0.1)
>> ## solver
>> system.time(out <- daspk(y = yini, dy = dyini, times = times, res = daefun,
>> parms = 0))
>
> Is it wrong? When I modify the order, I obtain again that object dA is not
> found, so I guessed the doc was right.
>
Of course see above.
Berend
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