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### ============================================================================
###
### ode.1D, ode.2D ode.band: special-purpose integration routines
### ode.1D is designed for solving multi-component 1-D reaction-transport models
### ode.2D is designed for solving multi-component 2-D reaction-transport models
### ode.band is designed for solving single-component 1-D reaction-transport models
### ode.1D,ode.band offer the choice between the integrators vode,
### lsode, lsoda, lsodar and lsodes.
### ode.2D uses lsodes.
###
### KS: added **bandwidth** to ode.1D
### to do: make it work with lsodes + with ode.2D, ode.3D!!
### ============================================================================
ode <- function (y, times, func, parms,
method = c("lsoda","lsode","lsodes","lsodar","vode","daspk",
"euler", "rk4", "ode23", "ode45", "radau",
"bdf", "bdf_d", "adams", "impAdams", "impAdams_d",
"iteration"),
...) {
if (is.null(method)) method <- "lsoda"
if (is.list(method)) {
# is() should work from R 2.7 on ...
# if (!is(method, "rkMethod"))
if (!inherits(method, "rkMethod" ))
stop("'method' should be given as string or as a list of class 'rkMethod'")
out <- rk(y, times, func, parms, method = method, ...)
} else if (is.function(method))
out <- method(y, times, func, parms,...)
else if (is.complex(y))
out <- switch(match.arg(method),
vode = zvode(y, times, func, parms, ...),
bdf = zvode(y, times, func, parms, mf = 22, ...),
bdf_d = zvode(y, times, func, parms, mf = 23, ...),
adams = zvode(y, times, func, parms, mf = 10, ...),
impAdams = zvode(y, times, func, parms, mf = 12, ...),
impAdams_d = zvode(y, times, func, parms, mf = 13, ...)
)
else
out <- switch(match.arg(method),
lsoda = lsoda(y, times, func, parms, ...),
vode = vode(y, times, func, parms, ...),
lsode = lsode(y, times, func, parms, ...),
lsodes= lsodes(y, times, func, parms, ...),
lsodar= lsodar(y, times, func, parms, ...),
daspk = daspk(y, times, func, parms, ...),
euler = rk(y, times, func, parms, method = "euler", ...),
rk4 = rk(y, times, func, parms, method = "rk4", ...),
ode23 = rk(y, times, func, parms, method = "ode23", ...),
ode45 = rk(y, times, func, parms, method = "ode45", ...),
radau = radau(y, times, func, parms, ...),
bdf = lsode(y, times, func, parms, mf = 22, ...),
bdf_d = lsode(y, times, func, parms, mf = 23, ...),
adams = lsode(y, times, func, parms, mf = 10, ...),
impAdams = lsode(y, times, func, parms, mf = 12, ...),
impAdams_d = lsode(y, times, func, parms, mf = 13, ...),
iteration = iteration(y, times, func, parms, ...)
)
return(out)
}
### ============================================================================
ode.1D <- function (y, times, func, parms, nspec = NULL,
dimens = NULL, method = c("lsoda","lsode",
"lsodes","lsodar","vode","daspk",
"euler", "rk4", "ode23", "ode45","radau",
"bdf", "adams", "impAdams", "iteration"),
names = NULL, bandwidth = 1,
restructure = FALSE, ...) {
# check input
if (is.character(method)) method <- match.arg(method)
islsodes <- FALSE
if (is.character(method))
if (method=="lsodes") islsodes <- TRUE
if (is.null(method)) method <- "lsoda"
if (any(!is.na(pmatch(names(list(...)), "jacfunc"))))
stop ("cannot run ode.1D with jacfunc specified - remove jacfunc from call list")
if (is.null(nspec) && is.null(dimens))
stop ("cannot run ode.1D: nspec OR dimens should be specified")
# if (islsodes && bandwidth != 1)
# stop ("cannot combine 'method = lsodes' with 'bandwidth' not = 1")
iscomplex <- is.complex(y)
N <- length(y)
if (is.null(nspec) )
nspec <- N/dimens
if (N %% nspec != 0 )
stop ("cannot run ode.1D: nspec is not an integer fraction of number of state variables")
if (! is.null(names) && length(names) != nspec)
stop("length of 'names' should equal 'nspec'")
# Use ode.band if implicit method with nspec=1
if (is.character(method))
if( nspec == 1 & method %in% c("lsoda","lsode","lsodar","vode","daspk","radau")) {
out <- ode.band(y, times, func, parms, nspec = nspec,
method = method, bandup = nspec * bandwidth,
banddown = nspec * bandwidth, ...)
attr(out,"ynames") <- names
if (is.null(dimens)) dimens <- N/nspec
attr (out, "dimens") <- dimens
attr (out, "nspec") <- nspec
return(out)
}
# Use lsodes
explicit <- FALSE
adams_expl <- FALSE
if (is.character(method)){
if (method %in% c("euler", "rk4", "ode23", "ode45", "iteration"))
explicit <- TRUE
adams_expl <- explicit | method == "adams"
}
if (is.character(func) & !explicit || islsodes) {
if (is.character(method))
if (! method %in% c("lsodes", "euler", "rk4", "ode23", "ode45", "iteration"))
warning("ode.1D: R-function specified in a DLL-> integrating with lsodes")
if (is.null(dimens) ) dimens <- N/nspec
if (bandwidth != 1) # try to remove this....
out <- lsodes(y=y,times=times,func=func,parms,...)
else
out <- lsodes(y=y,times=times,func=func,parms,sparsetype="1D",
nnz=c(nspec,dimens,bandwidth),...)
# a Runge-Kutta or Euler
} else if (is.list(method)) {
# is() should work from R 2.7 on ...
# if (!is(method, "rkMethod"))
if (!inherits(method, "rkMethod" ))
stop("'method' should be given as string or as a list of class 'rkMethod'")
out <- rk(y, times, func, parms, method = method, ...)
# a function that does not need restructuring
} else if (is.function(method) && !restructure)
out <- method(y, times, func, parms,...)
else if (is.function(method) && restructure) {
NL <- names(y)
# internal function #
bmodel <- function (time,state,pars,model,...) {
Modconc <- model(time,state[ij],pars,...) # ij: reorder state variables
c(list(Modconc[[1]][ii]), Modconc[-1]) # ii: reorder rate of change
}
if (is.character(func))
stop ("cannot run ode.1D with R-function specified in a DLL")
ii <- as.vector(t(matrix(data=1:N,ncol=nspec))) # from ordering per slice -> per spec
ij <- as.vector(t(matrix(data=1:N,nrow=nspec))) # from ordering per spec -> per slice
bmod <- function(time,state,pars,...)
bmodel(time,state,pars,func,...)
out <- method(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
out[,(ii+1)] <- out[,2:(N+1)]
if (! is.null(NL)) colnames(out)[2:(N+1)]<- NL
}
# an explicit method... as a string
else if (adams_expl) {
if (method == "euler")
out <- rk(y, times, func, parms, method = "euler", ...)
else if (method == "rk4")
out <- rk(y, times, func, parms, method = "rk4", ...)
else if (method == "ode23")
out <- rk(y, times, func, parms, method = "ode23", ...)
else if (method == "ode45")
out <- rk(y, times, func, parms, method = "ode45", ...)
else if (method == "adams" && ! iscomplex)
out <- lsode(y, times, func, parms, mf = 10, ...)
else if (method == "adams" && iscomplex)
out <- zvode(y, times, func, parms, mf = 10, ...)
else if (method == "iteration")
out <- iteration(y, times, func, parms, ...)
# an implicit method that needs restructuring...
} else {
NL <- names(y)
# internal function #
bmodel <- function (time,state,pars,model,...) {
Modconc <- model(time,state[ij],pars,...) # ij: reorder state variables
c(list(Modconc[[1]][ii]), Modconc[-1]) # ii: reorder rate of change
}
if (is.character(func))
stop ("cannot run ode.1D with R-function specified in a DLL")
ii <- as.vector(t(matrix(data=1:N,ncol=nspec))) # from ordering per slice -> per spec
ij <- as.vector(t(matrix(data=1:N,nrow=nspec))) # from ordering per spec -> per slice
bmod <- function(time,state,pars,...)
bmodel(time,state,pars,func,...)
if (is.null(method))
method <- "lsode"
if (iscomplex) {
if (method == "vode")
out <- zvode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "bdf")
out <- zvode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "impAdams")
out <- zvode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
mf = 15, ...)
}
else if (method == "vode")
out <- vode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "lsode" || method == "bdf")
out <- lsode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "impAdams")
out <- lsode(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
mf = 15, ...)
else if (method == "lsoda")
out <- lsoda(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "lsodar")
out <- lsodar(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "daspk")
out <- daspk(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else if (method == "radau")
out <- radau(y[ii], times, func=bmod, parms=parms,
bandup=nspec*bandwidth, banddown=nspec*bandwidth,
jactype="bandint", ...)
else
stop ("cannot run ode.1D: not a valid 'method'")
out[,(ii+1)] <- out[,2:(N+1)]
if (! is.null(NL)) colnames(out)[2:(N+1)]<- NL
}
if (is.null(dimens)) dimens <- N/nspec
attr (out, "dimens") <- dimens
attr (out, "nspec") <- nspec
attr(out, "ynames") <- names
return(out)
}
### ============================================================================
ode.2D <- function (y, times, func, parms, nspec=NULL, dimens,
method= c("lsodes","euler", "rk4", "ode23", "ode45", "adams","iteration"),
names = NULL, cyclicBnd = NULL, ...) {
# check input
if (is.character(method)) method <- match.arg(method)
if (is.null(method)) method <- "lsodes"
islsodes <- FALSE
if (is.character(method))
if (method=="lsodes") islsodes <- TRUE
if (any(!is.na(pmatch(names(list(...)), "jacfunc"))))
stop ("cannot run ode.2D with jacfunc specified - remove jacfunc from call list")
if (is.null(dimens))
stop ("cannot run ode.2D: dimens should be specified")
if (length(dimens)!=2)
stop ("cannot run ode.2D: dimens should contain 2 values")
N <- length(y)
if (N%%prod(dimens) !=0 )
stop ("cannot run ode.2D: dimensions are not an integer fraction of number of state variables")
if (is.null (nspec))
nspec <- N/prod(dimens) else
if (nspec*prod(dimens) != N)
stop ("cannot run ode.2D: dimens[1]*dimens[2]*nspec is not equal to number of state variables")
if (! is.null(names) && length(names) != nspec)
stop("length of 'names' should equal 'nspec'")
Bnd <- c(0,0)
if (! is.null(cyclicBnd)) {
if (max(cyclicBnd) > 2 )
stop ("cannot run ode.2D: cyclicBnd should be a vector or number not exceeding 2")
Bnd[cyclicBnd[cyclicBnd>0]]<-1
}
# use lsodes - note:expects rev(dimens)...
if (is.character(func) || islsodes) {
if (is.character(method))
if ( method != "lsodes")
warning("ode.2D: R-function specified in a DLL-> integrating with lsodes")
# if (bandwidth != 1) # try to use sparsetype also for bandwidth != 1
# out <- lsodes(y=y,times=times,func=func,parms,...)
# else
bandwidth<-1
out <- lsodes(y=y, times=times, func=func, parms, sparsetype="2D",
nnz=c(nspec, rev(dimens), rev(Bnd), bandwidth), ...)
# a runge kutta
} else if (is.list(method)) {
if (!inherits(method, "rkMethod" ))
stop("'method' should be given as string or as a list of class 'rkMethod'")
out <- rk(y, times, func, parms, method = method, ...)
# a function
} else if (is.function(method))
out <- method(y, times, func, parms,...)
# an explicit method
else if (method %in% c("euler", "rk4", "ode23", "ode45", "adams","iteration")) {
if (method == "euler")
out <- rk(y, times, func, parms, method = "euler", ...)
else if (method == "rk4")
out <- rk(y, times, func, parms, method = "rk4", ...)
else if (method == "ode23")
out <- rk(y, times, func, parms, method = "ode23", ...)
else if (method == "ode45")
out <- rk(y, times, func, parms, method = "ode45", ...)
else if (method == "adams")
out <- lsode(y, times, func, parms, mf = 10, ...)
else if (method == "iteration")
out <- iteration(y, times, func, parms, ...)
} else {
stop ("cannot run ode.2D: not a valid 'method'")
}
attr (out,"dimens") <- dimens
attr (out,"nspec") <- nspec
attr (out,"ynames") <- names
return(out)
}
### ============================================================================
ode.3D <- function (y, times, func, parms, nspec=NULL, dimens,
method= c("lsodes","euler", "rk4", "ode23", "ode45", "adams","iteration"),
names = NULL, cyclicBnd = NULL, ...){
# check input
if (is.character(method)) method <- match.arg(method)
if (is.null(method)) method <- "lsodes"
if (any(!is.na(pmatch(names(list(...)), "jacfunc"))))
stop ("cannot run ode.3D with jacfunc specified - remove jacfunc from call list")
if (is.null(dimens))
stop ("cannot run ode.3D: dimens should be specified")
if (length(dimens)!=3)
stop ("cannot run ode.3D: dimens should contain 3 values")
N <- length(y)
if (N%%prod(dimens) !=0 )
stop ("cannot run ode.3D: dimensions are not an integer fraction of number of state variables")
if (is.null (nspec))
nspec <- N/prod(dimens) else
if (nspec*prod(dimens) != N)
stop ("cannot run ode.3D: dimens[1]*dimens[2]*dimens[3]*nspec is not equal to number of state variables")
if (! is.null(names) && length(names) != nspec)
stop("length of 'names' should equal 'nspec'")
Bnd <- c(0,0,0) # cyclicBnd not included
if (! is.null(cyclicBnd)) {
if (max(cyclicBnd) > 3 )
stop ("cannot run ode.3D: cyclicBnd should be a vector or number not exceeding 3")
Bnd[cyclicBnd[cyclicBnd>0]]<-1
}
# use lsodes - note:expects rev(dimens)...
if (is.character(func) || method=="lsodes") {
if ( method != "lsodes")
warning("ode.3D: R-function specified in a DLL-> integrating with lsodes")
# if (bandwidth != 1) # try to use sparsetype also for bandwidth != 1
# out <- lsodes(y=y,times=times,func=func,parms,...)
# else
bandwidth<-1
out <- lsodes(y=y, times=times, func=func, parms, sparsetype="3D",
nnz=c(nspec,rev(dimens), rev(Bnd), bandwidth), ...)
# a runge-kutta
} else if (is.list(method)) {
if (!inherits(method, "rkMethod"))
stop("'method' should be given as string or as a list of class 'rkMethod'")
out <- rk(y, times, func, parms, method = method, ...)
# another function
} else if (is.function(method))
out <- method(y, times, func, parms,...)
# an explicit method
else if (method %in% c("euler", "rk4", "ode23", "ode45", "adams","iteration")) {
if (method == "euler")
out <- rk(y, times, func, parms, method="euler", ...)
else if (method == "rk4")
out <- rk(y, times, func, parms, method = "rk4", ...)
else if (method == "ode23")
out <- rk(y, times, func, parms, method = "ode23", ...)
else if (method == "ode45")
out <- rk(y, times, func, parms, method = "ode45", ...)
else if (method == "adams")
out <- lsode(y, times, func, parms, mf = 10, ...)
else if (method == "iteration")
out <- iteration(y, times, func, parms, ...)
} else {
stop ("cannot run ode.3D: not a valid 'method'")
}
attr (out,"dimens") <- dimens
attr (out,"nspec") <- nspec
attr (out,"ynames") <- names
return(out)
}
### ============================================================================
ode.band <- function (y, times, func, parms, nspec = NULL, dimens = NULL,
bandup = nspec, banddown = nspec,
method = "lsode", names = NULL, ...) {
if (is.null(bandup) )
stop ("cannot run ode.band: bandup is not specified")
if (is.null(banddown))
stop ("cannot run ode.band: banddown is not specified")
if (is.null(nspec) && is.null(dimens))
stop ("cannot run ode.band: nspec OR dimens should be specified")
N <- length(y)
if (is.null(nspec) )
nspec <- N/dimens
if (N %% nspec != 0 )
stop ("cannot run ode.band: nspec is not an integer fraction of number of state variables")
if (! is.null(names) && length(names) != nspec)
stop("length of 'names' should equal 'nspec'")
if (is.null(method))
method <- "lsode"
if (method == "vode")
out <- vode(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else if (method == "lsode")
out <- lsode(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else if (method == "lsoda")
out <- lsoda(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else if (method == "lsodar")
out <- lsodar(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else if (method == "daspk")
out <- daspk(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else if (method == "radau")
out <- radau(y, times, func, parms=parms, bandup=bandup, banddown=banddown,
jactype="bandint", ...)
else
stop ("cannot run ode.band: method should be one of vode, lsoda, lsodar or lsode")
N <- length(y)
attr (out,"dimens") <- N/nspec
attr (out,"nspec") <- nspec
attr (out, "ynames") <- names
return(out)
}
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