R/ppH.R

In seacarb: Calculates parameters of the seawater carbonate system

# Copyright (C) 2008 Jean-Pierre Gattuso
#
# This file is part of seacarb.
#
# Seacarb is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.
#
# Seacarb is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with seacarb; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
# sys is 0 if the system is closed and 1 if it is open
# co3 and hco3 are the   amount added in mol/kg


# One adds a certain volume (vol) of HCl (vol  is then negative) or NaOH (vol is then positive) to 1 kg of seawater. 
# vol is in liter
# N is the normality of the HCl or NaOH
# HCl or NaOH are, respectively, a strong acid and a strong base which are therefore fully dissociated. The concentration of H+ or OH- is N mole/l
# HCl 1N: 0.1 ml therefore adds 0.1 e-3 mol of H+, decreasing TA
# NaOH 1N: 0.1 ml therefore adds 0.1 e-3 mol of OH-, increasing TA
# DIC is constant in a closed system
"ppH" <-
function(flag, sys, var1, var2, pCO2a, vol, N, S=35, T=20, P=0, Pt=0, Sit=0, pHscale="T", k1k2='l', kf='pf'){
	if (sys==0) {
		ci <- carb(flag=flag, var1=var1, var2=var2, S=S ,T=T, P=P, Pt=Pt, Sit=Sit,  pHscale=pHscale, k1k2=k1k2, kf=kf)
		alkf <- ci$ALK + vol*N  # final alkalinity
		dicf <- ci$DIC	# final dic
		cf <- carb(flag=15, var1=alkf, var2=dicf, S=S, T=T, P=P,  Pt=Pt, Sit=Sit, pHscale=pHscale, k1k2=k1k2, kf=kf)
		co <- as.data.frame(c("ppH-closed-initial", rep("ppH-closed-final", nrow(cf)))) 
	}
	if (sys==1) {
		ci <- carb(flag=flag, var1=var1, var2=var2, S=S ,T=T, P=P, Pt=Pt, Sit=Sit,  pHscale=pHscale, k1k2=k1k2, kf=kf)
		alkf <- ci$ALK + vol*N # final total alkalinity
		dicf <- ci$DIC	# final dic  before requilibration
		#pHf <- ci$pH + ci$PhiH * (-vol) *N	# final pH using a buffer factor (see Frankignoulle, 1994)
		cc <- carb(flag=15, var1=alkf, var2=dicf, S=S, T=T, P=P, Pt=Pt, Sit=Sit,  pHscale=pHscale, k1k2=k1k2, kf=kf) #  before requilibration	
		cf <- carb(flag=24,var1=pCO2a, var2=alkf, S=S, T=T, P=P, Pt=Pt, Sit=Sit,  pHscale=pHscale, k1k2=k1k2, kf=kf)		
		co <- as.data.frame(c("ppH-open-initial", rep("ppH-open-final", nrow(cf))))
	}
	out <- rbind(ci, cf)
	out <- cbind(co, out)
	names(out)[1] <- "comment"
	return(out[,1:15])
}