### ============================================================================
### lsodar -- solves ordinary differential equation systems           
### Compared to the other integrators of odepack
### (a) lsodar switches automatically between stiff and nonstiff methods.
### This means that the user does not have to determine whether the
### problem is stiff or not, and the solver will automatically choose the
### appropriate method.  It always starts with the nonstiff method.
### This is similar to lsoda.
### (b) lsodar finds the root of at least one of a set of constraint
### functions g(i) of the independent and dependent variables.
### It finds only those roots for which some g(i), as a function
### of t, changes sign in the interval of integration.
### It then returns the solution at the root, if that occurs
### sooner than the specified stop condition, and otherwise returns
### the solution according the specified stop condition.
### ============================================================================


lsodar <- function(y, times, func, parms, rtol=1e-6, atol=1e-6,
	jacfunc=NULL, jactype = "fullint", rootfunc=NULL, verbose=FALSE,
  nroot = 0, tcrit = NULL, hmin=0, hmax=NULL, hini=0, ynames=TRUE,
  maxordn = 12, maxords = 5, bandup = NULL, banddown = NULL,
  maxsteps = 5000, dllname=NULL,initfunc=dllname, initpar=parms,
  rpar=NULL, ipar=NULL, nout=0, outnames=NULL, forcings=NULL,
  initforc = NULL, fcontrol=NULL, events=NULL, lags = NULL, ...)    {

### check input
   if (is.list(func)) {            ### IF a list
      if (!is.null(jacfunc) & "jacfunc" %in% names(func))
         stop("If 'func' is a list that contains jacfunc, argument 'jacfunc' should be NULL")
      if (!is.null(rootfunc) & "rootfunc" %in% names(func))
         stop("If 'func' is a list that contains rootfunc, argument 'rootfunc' should be NULL")         
      if (!is.null(initfunc) & "initfunc" %in% names(func))
         stop("If 'func' is a list that contains initfunc, argument 'initfunc' should be NULL")
      if (!is.null(dllname) & "dllname" %in% names(func))
         stop("If 'func' is a list that contains dllname, argument 'dllname' should be NULL")
      if (!is.null(initforc) & "initforc" %in% names(func))
         stop("If 'func' is a list that contains initforc, argument 'initforc' should be NULL")
      if (!is.null(events$func) & "eventfunc" %in% names(func))
         stop("If 'func' is a list that contains eventfunc, argument 'events$func' should be NULL")
      if ("eventfunc" %in% names(func)) {
         if (! is.null(events))
           events$func <- func$eventfunc
         else
           events <- list(func = func$eventfunc)  
      }
     if (!is.null(func$jacfunc)) jacfunc <- func$jacfunc
     if (!is.null(func$rootfunc)) rootfunc <- func$rootfunc
     if (!is.null(func$initfunc)) initfunc <- func$initfunc
     if (!is.null(func$dllname)) dllname <- func$dllname
     if (!is.null(func$initforc)) initforc <- func$initforc
     func <- func$func
  }

  hmax <- checkInput (y, times, func, rtol, atol,
    jacfunc, tcrit, hmin, hmax, hini, dllname)

  n <- length(y)

  if (!is.numeric(maxordn))
    stop("`maxordn' must be numeric")
  if(maxordn < 1 || maxordn > 12)
    stop("`maxord' must be >1 and <=12")
  if (!is.numeric(maxords))
    stop("`maxords' must be numeric")
  if(maxords < 1 || maxords > 5)
    stop("`maxords' must be >1 and <=5")

### Jacobian, method flag
       if (jactype == "fullint" ) jt <- 2 # full, calculated internally
  else if (jactype == "fullusr" ) jt <- 1 # full, specified by user function
  else if (jactype == "bandusr" ) jt <- 4 # banded, specified by user function
  else if (jactype == "bandint" ) jt <- 5 # banded, calculated internally
  else stop("'jactype' must be one of 'fullint', 'fullusr', 'bandusr' or 'bandint'")

  ## check other specifications depending on Jacobian
  if (jt %in% c(4,5) && is.null(bandup))
    stop("'bandup' must be specified if banded Jacobian")
  if (jt %in% c(4,5) && is.null(banddown))
    stop("'banddown' must be specified if banded Jacobian")
  if (is.null(banddown)) banddown <-1
  if (is.null(bandup  )) bandup   <-1

  if (jt %in% c(1,4) && is.null(jacfunc))
    stop ("'jacfunc' NOT specified; either specify 'jacfunc' or change 'jactype'")

### model and Jacobian function

  Ynames <- attr(y,"names")
  JacFunc  <- NULL
  RootFunc <- NULL
  flist<-list(fmat=0,tmat=0,imat=0,ModelForc=NULL)
  ModelInit <- NULL
  Eventfunc <- NULL
  events <- checkevents(events, times, Ynames, dllname, TRUE)
  if (! is.null(events$newTimes)) times <- events$newTimes  

  if (jt == 4 && banddown>0)
    erow<-matrix(data=0, ncol=n, nrow=banddown) else erow<-NULL

  if (is.character(func) | inherits(func, "CFunc")) {   # function specified in a DLL or inline compiled
    DLL <- checkDLL(func,jacfunc,dllname,
                    initfunc,verbose,nout, outnames)
    ## Is there a root function?
    if (!is.null(rootfunc)) {
      if (!is.character(rootfunc) & !inherits(rootfunc, "CFunc"))
        stop("If 'func' is dynloaded, so must 'rootfunc' be")
      rootfuncname <- rootfunc
      if (inherits(rootfunc, "CFunc"))
        RootFunc <- body(rootfunc)[[2]]
      
      else if (is.loaded(rootfuncname, PACKAGE = dllname))  {
        RootFunc <- getNativeSymbolInfo(rootfuncname, PACKAGE = dllname)$address
      } else
        stop(paste("root function not loaded in DLL",rootfunc))
      if (nroot == 0)
        stop("if 'rootfunc' is specified in a DLL, then 'nroot' should be > 0")
    }

    ModelInit <- DLL$ModelInit
    Func    <- DLL$Func
    JacFunc <- DLL$JacFunc
    Nglobal <- DLL$Nglobal
    Nmtot   <- DLL$Nmtot

    if (! is.null(forcings))
      flist <- checkforcings(forcings,times,dllname,initforc,verbose,fcontrol)

    if (is.null(ipar)) ipar<-0
    if (is.null(rpar)) rpar<-0
    Eventfunc <- events$func
    if (is.function(Eventfunc))
      rho <- environment(Eventfunc)
    else
      rho <- NULL
    
  } else {
    if(is.null(initfunc))
      initpar <- NULL # parameter initialisation not needed if function is not a DLL

    rho <- environment(func)
    ## func and jac are overruled, either including ynames, or not
    ## This allows to pass the "..." arguments and the parameters

    if (ynames)    {
      Func    <- function(time,state) {
        attr(state,"names") <- Ynames
         unlist(func   (time,state,parms,...))
      }
      Func2   <- function(time,state)  {
        attr(state,"names") <- Ynames
        func   (time,state,parms,...)
      }
      JacFunc <- function(time,state){
        attr(state,"names") <- Ynames
         rbind(jacfunc(time,state,parms,...),erow)
      }
      RootFunc <- function(time,state) {
        attr(state,"names") <- Ynames
        rootfunc(time,state,parms,...)
      }
      if (! is.null(events$Type))
       if (events$Type == 2)
         Eventfunc <- function(time,state) {
           attr(state,"names") <- Ynames
           events$func(time,state,parms,...)
         }
    } else {                            # no ynames...
      Func    <- function(time,state)
         unlist(func   (time,state,parms,...))

      Func2   <- function(time,state)
        func   (time,state,parms,...)

      JacFunc <- function(time,state)
         rbind(jacfunc(time,state,parms,...),erow)

      RootFunc <- function(time,state)
        rootfunc(time,state,parms,...)

      if (! is.null(events$Type))
       if (events$Type == 2)
         Eventfunc <- function(time,state)
           events$func(time,state,parms,...)
    }

    ## Check derivative function and return the number of output variables +name
    FF <- checkFunc(Func2,times,y,rho)
    Nglobal<-FF$Nglobal
    Nmtot <- FF$Nmtot

    ## Check event function
    if (! is.null(events$Type))
      if (events$Type == 2)
        checkEventFunc(Eventfunc,times,y,rho)

    ## and for rootfunc
    if (! is.null(rootfunc))  {
      tmp2 <- eval(rootfunc(times[1],y,parms,...), rho)
      if (!is.vector(tmp2))
        stop("root function 'rootfunc' must return a vector\n")
      nroot <- length(tmp2)
    } else nroot = 0

    if (jt %in% c(1,4)) {
      tmp <- eval(JacFunc(times[1], y), rho)
      if (!is.matrix(tmp))
      stop("Jacobian function, 'jacfunc' must return a matrix\n")
      dd <- dim(tmp)
      if((jt ==4 && any(dd != c(bandup+banddown+1,n))) ||
         (jt ==1 && any(dd != c(n,n))))
           stop("Jacobian dimension not ok")
    }
  }

### work arrays iwork, rwork
## length of rwork and iwork

  if(jt %in% c(1,2)) lmat <- n^2+2 else
  if(jt %in% c(4,5)) lmat <- (2*banddown+bandup+1)*n+2
  lrn = 20+n*(maxordn+1)+ 3*n +3*nroot       # length in case non-stiff method
  lrs = 20+n*(maxords+1)+ 3*n +lmat+3*nroot  # length in case stiff method
  lrw = max(lrn,lrs)                         # actual length: max of both
  liw = 20 + n

## only first 20 elements passed to solver; other will be allocated in C-code
  iwork <- vector("integer",20)
  rwork <- vector("double",20)
  rwork[] <- 0.
  iwork[] <- 0

  iwork[1] <- banddown
  iwork[2] <- bandup
  iwork[6] <- maxsteps
  if (maxordn != 12) iwork[8] <- maxordn
  if (maxords != 5)  iwork[9] <- maxords
  if (verbose)  iwork[5] = 1    # prints method switches to screen

  if(! is.null(tcrit)) rwork[1] <- tcrit
  rwork[5] <- hini
  rwork[6] <- hmax
  rwork[7] <- hmin

##  the task to be performed.
  if (! is.null(times))
      itask <- ifelse (is.null (tcrit), 1,4) else      # times specified
      itask <- ifelse (is.null (tcrit), 2,5)           # only one step
  if(is.null(times)) times<-c(0,1e8)

## print to screen...
  if (verbose)  printtask(itask,func,jacfunc)

### calling solver
  storage.mode(y) <- storage.mode(times) <- "double"
  IN <-4

  lags <- checklags(lags, dllname)

  on.exit(.C("unlock_solver"))
  out <- .Call("call_lsoda",y,times,Func,initpar,
               rtol, atol, rho, tcrit, JacFunc, ModelInit, Eventfunc,
               as.integer(verbose), as.integer(itask), as.double(rwork),
               as.integer(iwork), as.integer(jt),as.integer(Nglobal),
               as.integer(lrw),as.integer(liw),as.integer(IN),RootFunc,
               as.integer(nroot), as.double (rpar), as.integer(ipar),
               0L, flist, events, lags, PACKAGE="deSolve")

### saving results
  iroot  <- attr(out, "iroot")

  out <- saveOut(out, y, n, Nglobal, Nmtot, func, Func2,
                 iin=c(1,12:21), iout=c(1:3,14,5:9,15:16),nr = 5)


  attr(out, "iroot") <- iroot
  attr(out, "type")  <- "lsodar"
  if (verbose) diagnostics(out)
  return(out)
}