fda: CSTR – R documentation

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CSTR

Continuously Stirred Tank Reactor

Description

Functions for solving the Continuously Stirred Tank Reactor (CSTR) Ordinary Differential Equations (ODEs). A solution for observations where metrology error is assumed to be negligible can be obtained via lsoda(y, Time, CSTR2, parms); CSTR2 calls CSTR2in. When metrology error can not be ignored, use CSTRfn (which calls CSTRfitLS). To estimate parameters in the CSTR differential equation system (kref, EoverR, a, and / or b), pass CSTRres to nls. If nls fails to converge, first use optim or nlminb with CSTRsse, then pass the estimates to nls.

Usage

CSTR2in(Time, condition =
   c('all.cool.step', 'all.hot.step', 'all.hot.ramp', 'all.cool.ramp',
     'Tc.hot.exponential', 'Tc.cool.exponential', 'Tc.hot.ramp',
     'Tc.cool.ramp', 'Tc.hot.step', 'Tc.cool.step'),
   tau=1)
CSTR2(Time, y, parms)

CSTRfitLS(coef, datstruct, fitstruct, lambda, gradwrd=FALSE)
CSTRfn(parvec, datstruct, fitstruct, CSTRbasis, lambda, gradwrd=TRUE)
CSTRres(kref=NULL, EoverR=NULL, a=NULL, b=NULL,
        datstruct, fitstruct, CSTRbasis, lambda, gradwrd=FALSE)
CSTRsse(par, datstruct, fitstruct, CSTRbasis, lambda)

Arguments

`Time`	The time(s) for which computation(s) are desired
`condition`	a character string with the name of one of ten preprogrammed input scenarios.
`tau`	time for exponential decay of exp(-1) under condition = 'Tc.hot.exponential' or 'Tc.cool.exponential'; ignored for other values of 'condition'.
`y`	Either a vector of length 2 or a matrix with 2 columns giving the observation(s) on Concentration and Temperature for which computation(s) are desired
`parms`	a list of CSTR model parameters passed via the lsoda 'parms' argument. This list consists of the following 3 components: fitstruct a list with 12 components describing the structure for fitting. This is the same as the 'fitstruct' argument of 'CSTRfitLS' and 'CSTRfn' without the 'fit' component; see below. condition a character string identifying the inputs to the simulation. Currently, any of the following are accepted: 'all.cool.step', 'all.hot.step', 'all.hot.ramp', 'all.cool.ramp', 'Tc.hot.exponential', 'Tc.cool.exponential', 'Tc.hot.ramp', 'Tc.cool.ramp', 'Tc.hot.step', or 'Tc.cool.step'. Tlim end time for the computations.
`coef`	a matrix with one row for each basis function in fitstruct and columns c("Conc", "Temp") or a vector form of such a matrix.
`datstruct`	a list describing the structure of the data. CSTRfitLS uses the following components: basismat, Dbasismat basis coefficent matrices with one row for each observation and one column for each basis vector. These are typically produced by code something like the following: basismat <- eval.basis(Time, CSTRbasis) Dbasismat <- eval.basis(Time, CSTRbasis, 1) Cwt, Twt scalar variances of 'fd' functional data objects for Concentration and Temperature used to place the two series on comparable scales. y a matrix with 2 columns for the observed 'Conc' and 'Temp'. quadbasismat, Dquadbasismat basis coefficient matrices with one row for each quadrature point and one column for each basis vector. These are typically produced by code something like the following: quadbasismat <- eval.basis(quadpts, CSTRbasis) Dquadbasismat <- eval.basis(quadpts, CSTRbasis, 1) Fc, F., CA0, T0, Tc input series for CSTRfitLS and CSTRfn as the output list produced by CSTR2in. quadpts Quadrature points created by 'quadset' and stored in CSTRbasis[["quadvals"]][, "quadpts"]. quadwts Quadrature weights created by 'quadset' and stored in CSTRbasis[["quadvals"]][, "quadpts"].
`fitstruct`	a list with 14 components: V volume in cubic meters Cp concentration in cal/(g.K) for computing betaTC and betaTT; see details below. rho density in grams per cubic meter delH cal/kmol Cpc concentration in cal/(g.K) used for computing alpha; see details below. Tref reference temperature. kref reference value EoverR E/R in units of K/1e4 a scale factor for Fco in alpha; see details below. b power of Fco in alpha; see details below. Tcin Tc input temperature vector. fit logical vector of length 2 indicating whether Contentration or Temperature or both are considered to be observed and used for parameter estimation. coef0 data.frame(Conc = Cfdsmth[["coef"]], Temp = Tfdsmth[["coef"]]), where Cfdsmth and Tfdsmth are the objects returned by smooth.basis when applied to the observations on Conc and Temp, respectively. estimate logical vector of length 4 indicating which of kref, EoverR, a and b are taken from 'parvec'; all others are taken from 'fitstruct'.
`lambda`	a 2-vector of rate parameters 'lambdaC' and 'lambdaT'.
`gradwrd`	a logical scalar TRUE if the gradient is to be returned as well as the residuals matrix.
`parvec, par`	initial values for the parameters specified by fitstruct[[ "estimate"]] to be estimated.
`CSTRbasis`	Quadrature basis returned by 'quadset'.
`kref, EoverR, a, b`	the kref, EoverR, a, and b coefficients of the CSTR model as individual arguments of CSTRres to support using 'nls' with the CSTR model. Those actually provided by name will be estimated; the others will be taken from '.fitstruct'; see details.

Details

Ramsay et al. (2007) considers the following differential equation system for a continuously stirred tank reactor (CSTR):

dC/dt = (-betaCC(T, F.in)*C + F.in*C.in)

dT/dt = (-betaTT(Fcvec, F.in)*T + betaTC(T, F.in)*C + alpha(Fcvec)*T.co)

where

betaCC(T, F.in) = kref*exp(-1e4*EoverR*(1/T - 1/Tref)) + F.in

betaTT(Fcvec, F.in) = alpha(Fcvec) + F.in

betaTC(T, F.in) = (-delH/(rho*Cp))*betaCC(T, F.in)

alpha(Fcvec) = (a*Fcvec^(b+1) / (K1*(Fcvec + K2*Fcvec^b)))

K1 = V*rho*Cp

K2 = 1/(2*rhoc*Cpc)

The four functions CSTR2in, CSTR2, CSTRfitLS, and CSTRfn compute coefficients of basis vectors for two different solutions to this set of differential equations. Functions CSTR2in and CSTR2 work with 'lsoda' to provide a solution to this system of equations. Functions CSTSRitLS and CSTRfn are used to estimate parameters to fit this differential equation system to noisy data. These solutions are conditioned on specified values for kref, EoverR, a, and b. The other function, CSTRres, support estimation of these parameters using 'nls'.

CSTR2in translates a character string 'condition' into a data.frame containing system inputs for which the reaction of the system is desired. CSTR2 calls CSTR2in and then computes the corresponding predicted first derivatives of CSTR system outputs according to the right hand side of the system equations. CSTR2 can be called by 'lsoda' in the 'deSolve' package to actually solve the system of equations. To solve the CSTR equations for another set of inputs, the easiest modification might be to change CSTR2in to return the desired inputs. Another alternative would be to add an argument 'input.data.frame' that would be used in place of CSTR2in when present.

CSTRfitLS computes standardized residuals for systems outputs Conc, Temp or both as specified by fitstruct[["fit"]], a logical vector of length 2. The standardization is sqrt(datstruct[["Cwt"]]) and / or sqrt(datstruct[["Twt"]]) for Conc and Temp, respectively. CSTRfitLS also returns standardized deviations from the predicted first derivatives for Conc and Temp.

CSTRfn uses a Gauss-Newton optimization to estimates the coefficients of CSTRbasis to minimize the weighted sum of squares of residuals returned by CSTRfitLS.

CSTRres provides an interface between 'nls' and 'CSTRfn'. It gets the parameters to be estimated via the official function arguments, kref, EoverR, a, and / or b. The subset of these parameters to estimate must be specified both directly in the function call to 'nls' and indirectly via fitstruct[["estimate"]]. CSTRres gets the other CSTRfn arguments (datstruct, fitstruct, CSTRbasis, and lambda) via the 'data' argument of 'nls'.

CSTRsse computes sum of squares of residuals for use with optim or nlminb.

Value

`CSTR2in`	a matrix with number of rows = length(Time) and columns for F., CA0, T0, Tcin, and Fc. This gives the inputs to the CSTR simulation for the chosen 'condition'.
`CSTR2`	a list with one component being a matrix with number of rows = length(tobs) and 2 columns giving the first derivatives of Conc and Temp according to the right hand side of the differential equation. CSTR2 calls CSTR2in to get its inputs.
`CSTRfitLS`	a list with one or two components as follows: res a list with two components Sres = a matrix giving the residuals between observed and predicted datstruct[["y"]] divided by sqrt(datstruct[[c("Cwt", "Twt")]]) so the result is dimensionless. dim(Sres) = dim(datstruct[["y"]]). Thus, if datstruct[["y"]] has only one column, 'Sres' has only one column. Lres = a matrix with two columns giving the difference between left and right hand sides of the CSTR differential equation at all the quadrature points. dim(Lres) = c(nquad, 2). Dres If gradwrd=TRUE, a list with two components: DSres = a matrix with one row for each element of res[["Sres"]] and two columns for each basis function. DLres = a matrix with two rows for each quadrature point and two columns for each basis function. If gradwrd=FALSE, this component is not present.
`CSTRfn`	a list with five components: res the 'res' component of the final 'CSTRfitLS' object reformatted with its component Sres first followed by Lres, using with(CSTRfitLS(...)[["res"]], c(Sres, Lres)). Dres one of two very different gradient matrices depending on the value of 'gradwrd'. If gradwrd = TRUE, Dres is a matrix with one row for each observation value to match and one column for each parameter taken from 'parvec' per fitstruct[["estimate"]]. Also, if fitstruct[["fit"]] = c(1,1), CSTRfn tries to match both Concentration and Temperature, and rows corresponding to Concentration come first following by rows corresponding to Temperature. If gradwrd = FALSE, this is the 'Dres' component of the final 'CSTRfitLS' object reformatted as follows: Dres <- with(CSTRfitLS(...)[["Dres"]], rbind(DSres, DLres)) fitstruct a list components matching the 'fitstruct' input, with coefficients estimated replaced by their initial values from parvec and with coef0 replace by its final estimate. df estimated degrees of freedom as the trace of the appropriate matrix. gcv the Generalized cross validation estimate of the mean square error, as discussed in Ramsay and Silverman (2006, sec. 5.4).
`CSTRres`	the 'res' component of CSTRfd(...) as a column vector. This allows us to use 'nls' with the CSTR model. This can be especially useful as 'nls' has several helper functions to facilitate evaluating goodness of fit and and uncertainty in parameter estimates.
`CSTRsse`	sum(res*res) from CSTRfd(...). This allows us to use 'optim' or 'nlminb' with the CSTR model. This can also be used to obtain starting values for 'nls' in cases where 'nls' fails to converge from the initial provided starting values. Apart from 'par', the other arguments 'datstruct', 'fitstruct', 'CSTRbasis', and 'lambda', must be passed via '...' in 'optim' or 'nlminb'.

References

Ramsay, J. O., Hooker, G., Cao, J. and Campbell, D. (2007) Parameter estimation for differential equations: A generalized smoothing approach (with discussion). Journal of the Royal Statistical Society, Series B, 69, 741-796.

Ramsay, J. O., and Silverman, B. W. (2006) Functional Data Analysis, 2nd ed., Springer, New York.

Ramsay, James O., and Silverman, Bernard W. (2002), Applied Functional Data Analysis, Springer, New York.

Examples

###
###
### 1.  lsoda(y, times, func=CSTR2, parms=...)
###
###
#  The system of two nonlinear equations has five forcing or
#  input functions.
#  These equations are taken from
#  Marlin, T. E. (2000) Process Control, 2nd Edition, McGraw Hill,
#  pages 899-902.
##
##  Set up the problem
##
fitstruct <- list(V    = 1.0,#  volume in cubic meters
                  Cp   = 1.0,#  concentration in cal/(g.K)
                  rho  = 1.0,#  density in grams per cubic meter
                  delH = -130.0,# cal/kmol
                  Cpc  = 1.0,#  concentration in cal/(g.K)
                  rhoc = 1.0,#  cal/kmol
                  Tref = 350)#  reference temperature
#  store true values of known parameters
EoverRtru = 0.83301#   E/R in units K/1e4
kreftru   = 0.4610 #   reference value
atru      = 1.678#     a in units (cal/min)/K/1e6
btru      = 0.5#       dimensionless exponent

#% enter these parameter values into fitstruct

fitstruct[["kref"]]   = kreftru#
fitstruct[["EoverR"]] = EoverRtru#  kref = 0.4610
fitstruct[["a"]]      = atru#       a in units (cal/min)/K/1e6
fitstruct[["b"]]      = btru#       dimensionless exponent

Tlim  = 64#    reaction observed over interval [0, Tlim]
delta = 1/12#  observe every five seconds
tspan = seq(0, Tlim, delta)#

coolStepInput <- CSTR2in(tspan, 'all.cool.step')

#  set constants for ODE solver

#  cool condition solution
#  initial conditions

Cinit.cool = 1.5965#  initial concentration in kmol per cubic meter
Tinit.cool = 341.3754# initial temperature in deg K
yinit = c(Conc = Cinit.cool, Temp=Tinit.cool)

#  load cool input into fitstruct

fitstruct[["Tcin"]] = coolStepInput[, "Tcin"];

#  solve  differential equation with true parameter values

if (require(deSolve)) {
coolStepSoln <- lsoda(y=yinit, times=tspan, func=CSTR2,
  parms=list(fitstruct=fitstruct, condition='all.cool.step', Tlim=Tlim) )
}
###
###
### 2.  CSTRfn
###
###

# See the script in '~R\library\fda\scripts\CSTR\CSTR_demo.R'
#  for more examples.

fda

Functional Data Analysis

v5.1.9

GPL (>= 2)

Authors

J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre], Spencer Graves <spencer.graves@effectivedefense.org> [ctb], Giles Hooker <gjh27@cornell.edu> [ctb]

Initial release

2020-12-16