version 1.0

DESCRIPTION

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+Package: HomoPolymer
+Type: Package
+Title: Theoretical Model to Simulate Radical Polymerization
+Version: 1.0
+Date: 2014-12-23
+Author: Gianmarco Polotti
+Maintainer: Gianmarco Polotti <gianmarco.polotti@gmail.com>
+Description: A theoretical model to simulate  radical polymerization. Material, energy and population balances are integrated for batch, semi batch and continuous process in a ideally mixed reactor. Limitations: single monomer (i.e.homo polymer), one phase (organic, aqueous). Datasets with chemical-physical data for the most common monomers is included. Some background in polymer science is suggested for its use. Graphical interface for a quick and friendly use is available.
+Depends: R (>= 3.0.0), RGtk2, MenuCollection
+Imports: deSolve
+LazyData: true
+LazyLoad: true
+License: GPL-2
+Packaged: 2015-01-11 19:21:42 UTC; PolGia0
+NeedsCompilation: no
+Repository: CRAN
+Date/Publication: 2015-01-12 10:27:23

MD5

@@ -0,0 +1,56 @@
+e6d285fe519b02823fd5c5f318e269a7 *DESCRIPTION
+92ebad46ec23b191b25255c90e3d3144 *NAMESPACE
+c1f9a4f720a0d90331ce550151f49c63 *R/PlotBasic.R
+b8fb117ecce67b5eed9018ea748b38b4 *R/PlotChoice.r
+88b2ce113a8c17b34f0dcfc72ec4a17b *R/StopConditions.R
+01363e3fa086be4df2411f7c96258ad1 *R/func_homo.R
+3849e33a02ee68d8a96f0ff4435961f8 *R/gel.R
+62e125e291fde88ce56e522afae96648 *R/inpbox_computational_options.R
+2570e2ccaf9fef2d1eb6eb4db02f2841 *R/inpbox_flow_options.R
+0c2c727f147fbc8c084460d13b71c2c3 *R/inpbox_reaction_formulation.R
+1b459145f1f5e4c864ec2efd414266ac *R/integral.R
+a8d8256ad9de7c26539dfada4538eabf *R/polymer_toolbar.r
+606f5028a713d31fc5e46e88dab96432 *R/prepare.R
+043fce87272549b9e83e81db1585cab6 *build/vignette.rds
+326fb3abe08f21af0afd36533c56ac9b *data/DBk.rda
+d3150d004dfb47e2198e6d2b69df69c5 *data/DBpp.rda
+b71ab0cbae065ccab0ec0eeba0cd22b9 *inst/doc/Data_and_model_equations.Rnw
+47e1aae01299a26524f5d476e672f261 *inst/doc/Data_and_model_equations.pdf
+f71ac6bf27f738ff993984af5eecd58b *inst/doc/User_manual.Rnw
+a5ec67fdd3045cbf3efea8e1420c1721 *inst/doc/User_manual.pdf
+614e2627ba3a278927b45343e71da2fb *man/DBk.Rd
+ad3de7a4a3ade104ae0036671bf463ed *man/DBpp.Rd
+6b48bcb01e7bdebdc2bbe74f5a4c249a *man/PlotBasic.Rd
+efb4e3fb852c51a64c6679c6a778265a *man/PlotChoice.Rd
+1915c6b7578b61fdb4cb52a43dc0969f *man/StopConditions.Rd
+9cde43c3138650a60bdb0b892379de36 *man/figures/flow.png
+9cdaf63788ce5a277a9a512ed4e8fe98 *man/figures/process.png
+4d76ab531454b085f5ba9d42d986b7cb *man/figures/recipe.png
+7100825215483e5547a75540356c2833 *man/func_homo.Rd
+35ae90114220d6b31b4e227e04afce04 *man/gel.Rd
+490f1d5d73f4139b76603e0544b48cd2 *man/homopolymer-package.Rd
+77158e0ac8eed3e248877d844fafd6c8 *man/inpbox_computational_options.Rd
+b0d43d879e58c8cdaab21fb346f9e551 *man/inpbox_flow_options.Rd
+993783d7781d5c514260822dba20dd45 *man/inpbox_reaction_formulation.Rd
+31bd837c1a971b912a24425b1858a425 *man/integral.Rd
+46709e6c1dc20d937bbf96f40f66f95e *man/polymer_toolbar.Rd
+a29ceb63bf5bea4772e867c3ad38ce31 *man/prepare.Rd
+b71ab0cbae065ccab0ec0eeba0cd22b9 *vignettes/Data_and_model_equations.Rnw
+f71ac6bf27f738ff993984af5eecd58b *vignettes/User_manual.Rnw
+f8e59ceb3b83d7b74902b5745de2ce4d *vignettes/images/AA.png
+cf15f53682d14fffbc7deaf4a00c3281 *vignettes/images/AA1.png
+9889a948ffdb26858a7435f96ae28ed5 *vignettes/images/AA1r.png
+f8ea1046aecc0ca0ce6d9ccb86c1643d *vignettes/images/AAr.png
+0f85949842e5f74757d07a2e08b7d95b *vignettes/images/EA.png
+f992842ff4cf9aa967d3b6472ca81a73 *vignettes/images/EAr.png
+54d16c5550db5b11a6df5926141d7529 *vignettes/images/MMA.png
+38b15b2646597f9c1b706997bd1ec66f *vignettes/images/MMAr.png
+1cf386627bf04e0ee6813a5f135fa71c *vignettes/images/fig1.png
+3755c4313d5e0d97fada832a947a339b *vignettes/images/fig2.png
+78626c61a7cc324fa07f6bce947bd062 *vignettes/images/fig3.png
+2a14cca51b38e365422c7b6ccd5df0e5 *vignettes/images/fig4.png
+2e872b9f91bdc6077bc2d256b3daf09a *vignettes/images/fig5.png
+84bb73b12161f799cd561ebe7ee6dc22 *vignettes/images/fig6.png
+9905ffa694b18d7620503674fffffc46 *vignettes/images/fig7.png
+6938d59146f1dadd4a3197df87d32915 *vignettes/images/schema.png
+85db6ff7fe5e58d5b14a8427443e5583 *vignettes/images/toolbar.png

NAMESPACE

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+import(RGtk2)
+import(MenuCollection)
+import(deSolve)
+## Exported functions:
+export(StopConditions)
+export(prepare)
+export(polymer_toolbar)
+export(PlotChoice)
+export(PlotBasic)
+export(integral)
+export(gel)
+export(func_homo)
+export(inpbox_reaction_formulation)
+export(inpbox_flow_options)
+export(inpbox_computational_options)
+

R/PlotBasic.R

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+PlotBasic <-function(out,pars){
+	dev.new()
+	op<-par(mfrow=c(2,2),pty = "s",mar=c(4,3,1,1),cex.axis=0.8,tck=-0.01,cex.lab=0.8,font=2,mgp=c(2,1,0))
+	plot(out$time,out$X*100,type='l',xlab='Time(min)',ylab='X(%)',col='red');grid()
+	plot(out$time,out$M*pars['MWM']/1000*out$Vl,type='l',xlab='Time(min)',ylab='M(Kg)',col='red');grid()
+	plot(out$time,out$T-273.16,type='l',xlab='Time(min)',ylab='Temperature(C)',col='red');grid()
+	lgMn<-log10(out$Mnm)
+	lgMw<-log10(out$Mwm)
+	plot(out$time,lgMn,type='l',xlab='Time(min)',ylab='log Mn(red), log Mw(blue) in (g/mol)',col='red',
+	ylim=c(min(lgMn[-1],lgMw[-1]),max(lgMn[-1],lgMw[-1])));grid()
+	lines(out$time,lgMw,col='blue')
+	par(op)
+}

R/PlotChoice.r

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+PlotChoice<-function(out,otab){
+	plotgraph<-function(out,vx,vy,vz=NULL){
+		par(mar=c(5,4,4,5)+.1)
+		xlim<-c(min(out[,vx]),max(out[,vx]))
+		ylim<-c(min(out[,vy]),max(out[,vy]))
+		plot(out[,vx],out[,vy[1]],xlim=xlim,ylim=ylim,type='n',
+			 xlab=otab$text[ix],ylab=otab$text[iy],col.lab='red')
+		grid()
+		for(i in 1:length(vy))points(out[,vx],out[,vy[i]],col='red')
+		for(i in 1:length(vy))lines(out[,vx],out[,vy[i]],col='red')
+		if(!is.null(vz)){
+			par(new=TRUE)
+			zlim<-c(min(out[,vz]),max(out[,vz]))
+			plot(out[,vx],out[,vz[1]],type='n',xaxt="n",yaxt="n",xlab=otab$text[ix],
+			ylab=otab$text[iy],,col.lab='red',xlim=xlim,ylim=zlim)
+			for(i in 1:length(vz))points(out[,vx],out[,vz[i]],col='blue')
+			for(i in 1:length(vz))lines(out[,vx],out[,vz[i]],col='blue')
+			axis(4)
+			zlab<-otab$text[iz]
+			mtext(zlab,side=4,line=3,col='blue')
+		}
+	}
+	var.list<-otab$text
+	ans<-inpboxck(c('Variable on x-axis','Secondary y-axis'),var.list,c('-1','FALSE'))
+	ix<-as.numeric(ans[[1]])
+	vx<-which(names(out)==otab$symbol[ix])
+	vz<-ans[[2]]
+	ans<-inpboxlist(var.list,'Variables on y main axis')
+	iy<-as.numeric(ans[[1]])
+	vy<-which(names(out)==otab$symbol[iy])
+	if(as.logical(vz)){
+	   ans<-inpboxlist(var.list,'Variables on y secondary axis')
+	   iz<-as.numeric(ans[[1]])
+	   vz<-which(names(out)==otab$symbol[iz])
+	   plotgraph(out,vx,vy,vz)
+	}else{
+	   plotgraph(out,vx,vy)
+	}
+}
+

R/StopConditions.R

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+StopConditions<-function(t,y,pars,...){
+	yroot<-rep(1,6)
+	yroot[1]<- y['M']
+	yroot[2]<-y['X']-pars['Xlim']
+	yroot[3]<- y['I']
+	if(pars['pH0']!=0){
+		yroot[4]<-y['HA']-1e-8
+#		yroot[5]<-y['M']-y['HA']
+	}
+	return(yroot)
+}

R/func_homo.R

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+func_homo <-function(t,y,pars,Kpf,Kdf,Kfz,Kfm,Kfs,Kfp,Kps,Kpss,KfCTA,KfCCTA,Ktf,Ktd,Ktc,roM,roS,roP){
+	with(as.list(c(y,pars)),{
+	#browser()
+		Kd1<-function(T){return(1.178855e16*exp(-28925.227/1.987/T))}
+		Kd2<-function(T){return(1.3e15*exp(-27756.9/1.987/T))}
+		Kc<-function(X){return(3*X^2-3.17*X+2.9)}
+		FWin<-FinM+FinI+FinZ+FinS+FinCTA+FinCCTA+FinNa
+		Fin<-FinM+FinI+FinZ															#mol/min
+		#composition of in flow
+		if(FinS!=0)Fin<-Fin+FinS
+		if(FinCTA!=0)Fin<-Fin+FinCTA
+		if(FinCCTA!=0)Fin<-Fin+FinCCTA
+		if(FinNa!=0)Fin<-Fin+FinNa
+		uM<-0
+		uI<-0 
+		uZ<-0
+		uS<-0
+		uCTA<-0
+		uCCTA<-0
+		uNa<-0
+		Cpin<-0
+		roin<-0
+		if(Fin!=0){
+			uM<-FinM/Fin															#molar fraction
+			uI<-FinI/Fin															#molar fraction
+			uZ<-FinZ/Fin															#molar fraction
+			if(FinS!=0)uS<-FinS/Fin													#molar fraction
+			if(FinCTA!=0)uCTA<-FinCTA/Fin											#molar fraction
+			if(FinCCTA!=0)uCCTA<-FinCCTA/Fin										#molar fraction
+			if(FinNa!=0)uNa<-FinNa/Fin												#molar fraction
+			Cpin<-FinM/FWin*MWM/1000*CpM+FinS/FWin*MWS/1000*CpS  					#cal/mol/k
+			roin<-uM*roM(Tin)*1000/MWM 												#mol/L
+			if(uS!=0)roin<-roin+uS*roS(Tin)*1000/MWS 								#mol/L
+		}
+		Hin<-H0+Cpin*(Tin-T0) 														#cal/mol              
+		#composition of out flow
+		Mtm<-M+I+S+Z+P+Na+CTA+CCTA													#mol/L
+		zM<-M/Mtm																	#molar fraction
+		zI<-I/Mtm																	#molar fraction
+		zS<-S/Mtm																	#molar fraction
+		zZ<-Z/Mtm																	#molar fraction
+		zP<-P/Mtm																	#molar fraction
+		zNa<-Na/Mtm																	#molar fraction
+		zCTA<-CTA/Mtm																#molar fraction
+		zCCTA<-CCTA/Mtm																#molar fraction
+		MWm<-(zM+zP)*MWM+zI*MWI+zS*MWS+zZ*MWZ+zNa*MWNa+zCTA*MWCTA+zCCTA*MWCCTA		#g/mol
+		Fout<-FWout*1000/MWm														#mol/min
+		#gel effect parameter determination
+		Cgel<-gel(y,pars,roM,roS,roP)
+		Ktb<-Ktf(T)
+		Ktt<-Ktb
+		Ktr<-0
+		Kts<-0
+		if(DCT)Ktt<-Ktb*Cgel$Ft
+		if(ST)Kts<-Ktb*Cgel$Fs
+		if(RT){
+			Ktrmin<-Kpf(T)*M*Cgel$Ktrmin
+			Ktrmax<-Kpf(T)*M*Cgel$Ktrmax
+			Ktr<-Ktrmin+(Ktrmax-Ktrmin)*X
+		}
+		if((Ktr!=0)&(Kts!=0))Ktb<-1/(1/Ktt+1/Kts+1/Ktr)
+		if((Ktr==0)&(Kts!=0))Ktb<-1/(1/Ktt+1/Kts)
+		if((Ktr!=0)&(Kts==0))Ktb<-1/(1/Ktt+1/Ktr)
+		if((Ktr==0)&(Kts==0))Ktb<-Ktt
+		Ktd<-Ktd(T)/Ktf(T)*Ktb
+		Ktc<-Ktc(T)/Ktf(T)*Ktb
+		Kp<-Kpf(T)
+		if(DCP)Kp<-Kp*Cgel$Fp
+		Kd<-Kdf(T)
+		if(DCI)Kd<-Kd*Cgel$Fd
+		Kd1<-Kd1(T)
+		if(DCI)Kd1<-Kd1*Cgel$Fd
+		Kd2<-Kd2(T)
+		if(DCI)Kd2<-Kd2*Cgel$Fd
+		Cp<-zM*CpM*MWM/1000+zS*MWS/1000*CpS+zP*CpP*MWM/1000  						#cal/mol/k
+		roout<-zM*roM(T)*1000/MWM+zP*roP(T)*1000/MWM 								#mol/L
+		if(MWS!=0)roout<-roout+zS*roS(T)*1000/MWS    								#mol/L
+		#(A3.14)
+		if(pH0!=0){
+			# case of water soluble monomers
+			AM<-M-HA
+			if(DPH){
+				pH<--log10(HA/AM)+pH0+log10(HA0/(M0-HA0))
+				if(pH>14)pH<-14
+			}else{
+				pH<-pH0
+			}
+			#(A3.8)
+			RI<-2*Kd*I+2*Kd1*HA+2*Kd2*AM  											#mol/L/min
+			#(A1.25) Radical Balance under SSA
+			R<-0.5*(sqrt((Kfz(T)*Z/Ktb)^2+4*RI/Ktb)-Kfz(T)*Z/Ktb) 					#mol/L
+			#(12.4)
+			alfa2<-1/(1+10^(KdisP-pH))
+			alfa3<-1/(1+10^(KdisP-pH))
+			HP<-P/(1+alfa2)
+			PM<-alfa2*P/(1+alfa2)
+			HR<-R/(1+alfa3)
+			RM<-alfa3*R/(1+alfa3)
+			#(A3.22)
+			B<-Kc(X)*(HP-Na-P)-1
+			C<-Kc(X)*Na*(P-HP)
+			Pc<-(-B-sqrt(B^2-4*Kc(X)*C))/(2*Kc(X))
+			#(A3.23)
+			Rc<-Kc(X)*(Na-Pc)*RM
+			#(A3.16)
+			Kpp<-Kp*(HA/M+Kratio*HR*AM/(R*M)+Kratio*Rc*AM/(R*M))
+		}else{
+			# case of oil soluble monomers
+			AM<-0
+			HA<-M
+			pH<-0
+			KdisM<-0
+			KdisP<-0
+			RI<-2*Kd*I					 												#mol/L/min
+			R<-0.5*(sqrt((Kfz(T)*Z/Ktb)^2+4*RI/Ktb)-Kfz(T)*Z/Ktb) 						#mol/L
+			alfa2<-1
+			alfa3<-1
+			HP<-P
+			PM<-0
+			HR<-R
+			RM<-0
+			Pc<-0
+			Rc<-0
+			Kpp<-Kp
+		}
+		#(A1.29) Enthalpy
+		H<-H0+Cp*(T-T0)  											 				#cal/mol 
+		#(A1.32)
+		Tau<-Ktd*(Kpp*M*R)/(Kpp*M)^2+Kfm(T)/Kpp+Kfs(T)*S/(Kpp*M)+KfCTA(T)*CTA/(Kpp*M)+KfCCTA(T)*CCTA/(Kpp*M)+Kfz(T)*Z/(Kpp*M)
+		#(A1.33)
+		Beta<-Ktc*(Kpp*M*R)/(Kpp*M)^2
+		#(A1.42)
+		Gam<-1+RI/(Kpp*M*R)+Kfm(T)/Kpp+Kfs(T)*S/(Kpp*M)+KfCTA(T)*CTA/(Kpp*M)+KfCCTA(T)*CCTA/(Kpp*M)+Kfz(T)*Z/(Kpp*M)
+		#(A1.43)
+		Lam<-Ktb*R/(Kpp*M)+Kfm(T)/Kpp+Kfs(T)*S/(Kpp*M)+KfCTA(T)*CTA/(Kpp*M)+KfCCTA(T)*CCTA/(Kpp*M)+Kfz(T)*Z/(Kpp*M)+Kfp(T)*Mu1/(Kpp*M)
+		#(A1.44)
+		Eta<-1+Kfm(T)/Kpp+Kfs(T)*S/(Kpp*M)+KfCTA(T)*CTA/(Kpp*M)+KfCCTA(T)*CCTA/(Kpp*M)+Kfz(T)*Z/(Kpp*M)+Kps(T)*Mu1/(Kpp*M)+RI/(Kpp*M*R)
+		+(Kfp(T)/Kpp+Kpss(T)/Kpp)*Mu2/M
+		if(LIN){
+			#(A1.30)
+			Mn<-MWM/(Tau+Beta/2)
+			#(A1.31)
+			Mw<-MWM*(2*Tau+3*Beta)/(Tau+Beta)^2
+		}else{
+			#(A1.45)
+			Mn<-MWM*Mu1/Mu0
+			if(is.na(Mn))Mn<-MWM
+			#(A1.46)
+			Mw<-MWM*Mu2/Mu1
+			if(is.na(Mw))Mw<-MWM
+		}
+		if(Mn<MWM)Mn<-MWM
+		if(Mw<MWM)Mw<-MWM
+		#Derivative output vector
+		yp<-rep(0,19)
+		#(A1.18) Monomer
+		dM<-Kpp*M*R 																#mol/L/min
+		yp[1]<-Fin*uM-dM*Vl-Fout*zM 												#mol/min
+		#molar conversion
+		yp[2]<--yp[1]/M0															#1/min
+		#(A3.12) undissociated monomer
+		if(pH0!=0){
+			yp[4]<--Kp*R*HA*Vl 														#mol/min
+		}else{
+			yp[4]<-yp[1]
+		}
+		#(A1.19) Initiator
+		yp[5]<-Fin*uI-2*Kd*I*Vl-Fout*zI												#mol/min
+		#(A1.20) Solvent
+		if(S0!=0)yp[6]<-Fin*uS-Kfs(T)*S*R*Vl-Fout*zS								#mol/min
+		#(A1.21) Polymer
+		yp[7]<-dM*Vl-Fout*zP														#mol/min
+		#(A1.22) Inhibitor
+		if(Z0!=0)yp[8]<-Fin*uZ-Kfz(T)*Z*R*Vl-Fout*zZ								#mol/min
+		#(A1.23) CTA
+		if(CTA0!=0)yp[9]<-Fin*uCTA-KfCTA(T)*CTA*R*Vl-Fout*zCTA						#mol/min
+		#(A1.24) CCTA
+		if(CCTA0!=0)yp[10]<-Fin*uCCTA-KfCCTA(T)*CCTA*R*Vl-Fout*zCCTA				#mol/min
+		# Counter ions balance
+		if(Na0!=0)y[11]<-Fin*uNa-Fout*zNa											#mol/min
+		#(A1.27) Energy balance
+		if(!ISOT){
+			yp[12]<-Fin*Hin+dM*Vl*DHp-UA*(T-Tj)-Fout*H
+			yp[12]<-yp[12]/(Vl*roout*Cp)												#k/min
+		}else{
+			yp[12]<-0
+		}
+		#total volume
+		if(Fin!=0)yp[3]<-yp[3]+Fin/roin
+		if(Fout!=0)yp[3]<-yp[3]-Fout/roout
+		yp[3]<-yp[3]+MWM/1000*(1/roM(T)-1/roP(T))*yp[1]
+		yp[3]<-yp[3]+MWM/1000*M*(roP2/roP(T)^2-roM2/roM(T)^2)*yp[12]				#L/min
+		#(A1.45)
+		yp[13]<-dM*Vl/Mn															#mol^2/min/g
+		#(A1.46)
+		yp[14]<-dM*Vl*Mw 															#g/min
+		if(LIN){
+		yp[15]<-0
+		yp[16]<-0
+		yp[17]<-0
+		yp[18]<-0
+		yp[19]<-0		
+		}else{
+		#(A1.39) 0th moment 
+		yp[15]<-(Tau+Beta/2-Kpss(T)*Mu1/(Kpp*M)-Kps(T)*Mu0/(Kpp*M))*Kpp*M*R*Vl-Mu0*Fout*Vl
+		#(A1.40) 1st moment
+		yp[16]<-(Tau-Ktd*R/(Kpp*M))*Kpp*M*R*Vl-Mu1*Fout*Vl
+		#(A1.41) 2nd moment
+		yp[17]<-(Gam+2*(1+(Kps(T)*Mu1+Kpss(T)*Mu2)/(Kpp*M))*Eta/Gam+Ktc*R/(Kpp*M)*(Eta/Lam)^2)*Kpp*M*R*Vl-Mu2*Fout*Vl
+		#(A1.47)
+		yp[18]<-(Kfp(T)*Mu1*R+Kps(T)*R*Mu0-Mu0*BN3*Fout)*Vl
+		#(A1.48)
+		yp[19]<-(Kpss(T)*Mu2*R-Mu0*BN4*Fout)*Vl
+		}
+		der<-c(AM,R,Kp,Ktb,Kd,Mn,Mw,Cp,roin,roout,pH,Kpp)
+		attributes(der)<-NULL
+		names(der)<-c("AM","R","Kp","Ktb","Kd","Mn","Mw","Cp","roin","roout","pH","Kpp")
+		return(list(yp,der))
+	})
+}