# NOT RUN {
## Various ways to solve the same model.
## =======================================================================
## The example from lsodes source code
## A chemical model
## =======================================================================
n <- 12
y <- rep(1, n)
dy <- rep(0, n)
times <- c(0, 0.1*(10^(0:4)))
rtol <- 1.0e-4
atol <- 1.0e-6
parms <- c(rk1 = 0.1, rk2 = 10.0, rk3 = 50.0, rk4 = 2.5, rk5 = 0.1,
rk6 = 10.0, rk7 = 50.0, rk8 = 2.5, rk9 = 50.0, rk10 = 5.0,
rk11 = 50.0, rk12 = 50.0,rk13 = 50.0, rk14 = 30.0,
rk15 = 100.0,rk16 = 2.5, rk17 = 100.0,rk18 = 2.5,
rk19 = 50.0, rk20 = 50.0)
#
chemistry <- function (time, Y, pars) {
with (as.list(pars), {
dy[1] <- -rk1 *Y[1]
dy[2] <- rk1 *Y[1] + rk11*rk14*Y[4] + rk19*rk14*Y[5] -
rk3 *Y[2]*Y[3] - rk15*Y[2]*Y[12] - rk2*Y[2]
dy[3] <- rk2 *Y[2] - rk5 *Y[3] - rk3*Y[2]*Y[3] -
rk7*Y[10]*Y[3] + rk11*rk14*Y[4] + rk12*rk14*Y[6]
dy[4] <- rk3 *Y[2]*Y[3] - rk11*rk14*Y[4] - rk4*Y[4]
dy[5] <- rk15*Y[2]*Y[12] - rk19*rk14*Y[5] - rk16*Y[5]
dy[6] <- rk7 *Y[10]*Y[3] - rk12*rk14*Y[6] - rk8*Y[6]
dy[7] <- rk17*Y[10]*Y[12] - rk20*rk14*Y[7] - rk18*Y[7]
dy[8] <- rk9 *Y[10] - rk13*rk14*Y[8] - rk10*Y[8]
dy[9] <- rk4 *Y[4] + rk16*Y[5] + rk8*Y[6] +
rk18*Y[7]
dy[10] <- rk5 *Y[3] + rk12*rk14*Y[6] + rk20*rk14*Y[7] +
rk13*rk14*Y[8] - rk7 *Y[10]*Y[3] - rk17*Y[10]*Y[12] -
rk6 *Y[10] - rk9*Y[10]
dy[11] <- rk10*Y[8]
dy[12] <- rk6 *Y[10] + rk19*rk14*Y[5] + rk20*rk14*Y[7] -
rk15*Y[2]*Y[12] - rk17*Y[10]*Y[12]
return(list(dy))
})
}
## =======================================================================
## application 1. lsodes estimates the structure of the Jacobian
## and calculates the Jacobian by differences
## =======================================================================
out <- lsodes(func = chemistry, y = y, parms = parms, times = times,
atol = atol, rtol = rtol, verbose = TRUE)
## =======================================================================
## application 2. the structure of the Jacobian is input
## lsodes calculates the Jacobian by differences
## this is not so efficient...
## =======================================================================
## elements of Jacobian that are not zero
nonzero <- matrix(nc = 2, byrow = TRUE, data = c(
1, 1, 2, 1, # influence of sp1 on rate of change of others
2, 2, 3, 2, 4, 2, 5, 2, 12, 2,
2, 3, 3, 3, 4, 3, 6, 3, 10, 3,
2, 4, 3, 4, 4, 4, 9, 4, # d (dyi)/dy4
2, 5, 5, 5, 9, 5, 12, 5,
3, 6, 6, 6, 9, 6, 10, 6,
7, 7, 9, 7, 10, 7, 12, 7,
8, 8, 10, 8, 11, 8,
3,10, 6,10, 7,10, 8,10, 10,10, 12,10,
2,12, 5,12, 7,12, 10,12, 12,12)
)
## when run, the default length of rwork is too small
## lsodes will tell the length actually needed
# out2 <- lsodes(func = chemistry, y = y, parms = parms, times = times,
# inz = nonzero, atol = atol,rtol = rtol) #gives warning
out2 <- lsodes(func = chemistry, y = y, parms = parms, times = times,
sparsetype = "sparseusr", inz = nonzero,
atol = atol, rtol = rtol, verbose = TRUE, lrw = 353)
## =======================================================================
## application 3. lsodes estimates the structure of the Jacobian
## the Jacobian (vector) function is input
## =======================================================================
chemjac <- function (time, Y, j, pars) {
with (as.list(pars), {
PDJ <- rep(0,n)
if (j == 1){
PDJ[1] <- -rk1
PDJ[2] <- rk1
} else if (j == 2) {
PDJ[2] <- -rk3*Y[3] - rk15*Y[12] - rk2
PDJ[3] <- rk2 - rk3*Y[3]
PDJ[4] <- rk3*Y[3]
PDJ[5] <- rk15*Y[12]
PDJ[12] <- -rk15*Y[12]
} else if (j == 3) {
PDJ[2] <- -rk3*Y[2]
PDJ[3] <- -rk5 - rk3*Y[2] - rk7*Y[10]
PDJ[4] <- rk3*Y[2]
PDJ[6] <- rk7*Y[10]
PDJ[10] <- rk5 - rk7*Y[10]
} else if (j == 4) {
PDJ[2] <- rk11*rk14
PDJ[3] <- rk11*rk14
PDJ[4] <- -rk11*rk14 - rk4
PDJ[9] <- rk4
} else if (j == 5) {
PDJ[2] <- rk19*rk14
PDJ[5] <- -rk19*rk14 - rk16
PDJ[9] <- rk16
PDJ[12] <- rk19*rk14
} else if (j == 6) {
PDJ[3] <- rk12*rk14
PDJ[6] <- -rk12*rk14 - rk8
PDJ[9] <- rk8
PDJ[10] <- rk12*rk14
} else if (j == 7) {
PDJ[7] <- -rk20*rk14 - rk18
PDJ[9] <- rk18
PDJ[10] <- rk20*rk14
PDJ[12] <- rk20*rk14
} else if (j == 8) {
PDJ[8] <- -rk13*rk14 - rk10
PDJ[10] <- rk13*rk14
PDJ[11] <- rk10
} else if (j == 10) {
PDJ[3] <- -rk7*Y[3]
PDJ[6] <- rk7*Y[3]
PDJ[7] <- rk17*Y[12]
PDJ[8] <- rk9
PDJ[10] <- -rk7*Y[3] - rk17*Y[12] - rk6 - rk9
PDJ[12] <- rk6 - rk17*Y[12]
} else if (j == 12) {
PDJ[2] <- -rk15*Y[2]
PDJ[5] <- rk15*Y[2]
PDJ[7] <- rk17*Y[10]
PDJ[10] <- -rk17*Y[10]
PDJ[12] <- -rk15*Y[2] - rk17*Y[10]
}
return(PDJ)
})
}
out3 <- lsodes(func = chemistry, y = y, parms = parms, times = times,
jacvec = chemjac, atol = atol, rtol = rtol)
## =======================================================================
## application 4. The structure of the Jacobian (nonzero elements) AND
## the Jacobian (vector) function is input
## =======================================================================
out4 <- lsodes(func = chemistry, y = y, parms = parms, times = times,
lrw = 351, sparsetype = "sparseusr", inz = nonzero,
jacvec = chemjac, atol = atol, rtol = rtol,
verbose = TRUE)
# The sparsejan variant
# note: errors in inz may cause R to break, so this is not without danger...
# out5 <- lsodes(func = chemistry, y = y, parms = parms, times = times,
# jacvec = chemjac, atol = atol, rtol = rtol, sparsetype = "sparsejan",
# inz = c(1,3,8,13,17,21,25,29,32,32,38,38,43, # ian
# 1,2, 2,3,4,5,12, 2,3,4,6,10, 2,3,4,9, 2,5,9,12, 3,6,9,10, # jan
# 7,9,10,12, 8,10,11, 3,6,7,8,10,12, 2,5,7,10,12), lrw = 343)
# }
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