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Copy path6_Sediment_Mass_Balance_mehg_2050.R
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6_Sediment_Mass_Balance_mehg_2050.R
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#setwd("C:/Users/gi/Dropbox/BlackSea2/implementazione/new_sim0/_met/Wh1")
setwd("C:/Users/Ginevra/Desktop/new_sim_BS/19_luglio/Anne1e_morehg_tris")
setwd('C:/Users/gi/Documents/Lavoro/SIM_finale/Anne1e_morehg_tris')
setwd("C:/Users/Ginevra/Desktop/new_sim_BS/19_luglio/SIM_finale2/Anne1e_morehg_tris_pristine2")
hg<-read.csv("Dissolved_Divalent_Hg.csv", skip = 1,header=FALSE, sep = ",", dec=".")
names(hg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
str(hg)
hg<-hg[3:2414,1:13]
hgT<-read.csv("Total_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(hgT)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
hgT<-hgT[3:2414,1:13]
DOChg<-read.csv("DOC_Sorbed_Divalent_Hg.csv", header=FALSE, skip =1, sep = ",", dec=".")
names(DOChg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
DOChg<-DOChg[3:2414,1:13]
mehg<-read.csv("Dissolved_Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(mehg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
mehg<-mehg[3:2414,1:13]
DOCmehg<-read.csv("DOC_Sorbed_Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(DOCmehg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
DOCmehg<-DOCmehg[3:2414,1:13]
hg0<-read.csv("Elemental_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(hg0)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
hg0<-hg0[3:2414,1:13]
mehgT<-read.csv("Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(mehgT)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
mehgT<-mehgT[3:2414,1:13]
POM_depos<-read.csv("POM_Dep_Vel.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(POM_depos)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
POM_depos<-POM_depos[3:2414,1:13]
silt_depos<-read.csv("Silt_Dep_Vel.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(silt_depos)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
silt_depos<-silt_depos[3:2414,1:13]
silts<-read.csv("Silts_Fines.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(silts)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
silts<-silts[3:2414,1:13]
POMs<-read.csv("Organic_Matter.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(POMs)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1", "Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3", "Sed1","Sed2")
POMs <-POMs[3:2414,1:13]
Pmehgs<-read.csv("Total_Sorbed_Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Pmehgs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Pmehgs <-Pmehgs[3:2414,1:13] #ng/L
TOTs<-read.csv("Total_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(TOTs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
TOTs <-TOTs[3:2414,1:13]
burial<-read.csv("Sediment_Burial_Velocity.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(burial)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
burial<-burial[3:2414,1:13]
volumes<-read.csv("Segment_Volume.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(volumes)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
volumes<-volumes[3:2414,1:13]
SEDmehg<-read.csv("Total_Sorbed_Methyl_Hg_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(SEDmehg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
SEDmehg<-SEDmehg[3:2414,1:13] #ng/g
bulkD<-read.csv("Sediment_Bulk_Density.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(bulkD)<-c("Time", "Oxic1", "Oxic2","CIL","Oxycline",
"Suboxic1","Suboxic2", "Anoxic1", "Anoxic2",
"Anoxic3","Sed1","Sed2")
bulkD<-bulkD[3:2414,1:13]
# unisco matrici del diss Hg
diss_mehg <- DOCmehg+mehg
diss_mehg_pM <- diss_mehg/215*1000
# BILANCIO BURIAL g/m3 * ng/g --> ng/m3
Model_area <-2.961E+11
solids_sed1 <-TOTs$Sed1; solids_sed2 <-TOTs$Sed2
SEDmehg_sed1 <-SEDmehg$Sed1; SEDmehg_sed2 <-SEDmehg$Sed2 # SEDmehg (ng/g) * solid_sed (g/m3) --> PMeHg ng/m3
Pmehg_sed1 <-Pmehgs$Sed1; Pmehg_sed2 <-Pmehgs$Sed2 #ng/L or ug/m3
burial_sed1 <-burial$Sed1; burial_sed2 <-burial$Sed2 #cm/y
solids_w <-TOTs$Anoxic3
MeHg_sed1_ngm3 <- solids_sed1 *SEDmehg_sed1 #ng/g*g/m3
MeHg_sed2_ngm3 <- solids_sed2 *SEDmehg_sed2
MeHg_sed1_gm3 <-MeHg_sed1_ngm3/10^9 #mg/m3->g/m3 hgP
MeHg_sed2_gm3 <-MeHg_sed2_ngm3/10^9
burial_sed1_m_y<-burial_sed1/10^2 ; str(burial_sed1_m_y)#cm/y-->m/y
burial_sed2_m_y<-burial_sed2/10^2 #cm/y-->m/y
burial_sed1_mm_y<-burial_sed1 *10 ; str(burial_sed1_mm_y)#cm/y-->mm/y
burial_sed2_mm_y<-burial_sed2 *10 ; str(burial_sed2_mm_y)#cm/y-->mm/y
MeHg_burial_sed1_g_m2_y<-MeHg_sed1_gm3*burial_sed1_m_y #g/m3*m/y<-g/m2y
MeHg_burial_sed2_g_m2_y<-MeHg_sed2_gm3*burial_sed2_m_y
burial1_g_y<-MeHg_burial_sed1_g_m2_y*Model_area #g/M2y*m2 -> g/y
burial2_g_y<-MeHg_burial_sed2_g_m2_y*Model_area
burial1_mol_y<-burial1_g_y/215; burial1_kmol_y<-burial1_mol_y/1000
burial2_kmol_y<-burial2_g_y/(215*1000)
burial1_media<-tapply(burial1_kmol_y,rep(1:(length(burial1_kmol_y)/12),each = 12), mean)
burial2_media<-tapply(burial2_kmol_y,rep(1:(length(burial2_kmol_y)/12),each = 12), mean)
burial1_cumul<-cumsum(burial1_media)
burial2_cumul<-cumsum(burial2_media)
summary(burial1_cumul);summary(burial2_cumul)
bb<-cbind(burial1_cumul,burial2_cumul)
#DEPOSIZIONE Phg
#depo m/day * depth(m) --> 1/day
Vol_anox3<-1E+14
POM_depo_1_day<-POM_depos$Anoxic3/350
silt_depo_1_day<-silt_depos$Anoxic3/350
fPOM<-mean(POMs$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
fsilt<-mean(silts$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
depo_media1<-POM_depo_1_day
mean(depo_media1) # 0.005 /d
depo_Pmehg_ug_m3_d <-depo_media1*Pmehgs$Anoxic3 #1/day *ug/m3 ->ug/m3d
depo_Pmehg_g_d <-(depo_Pmehg_ug_m3_d*Vol_anox3)/10^6 #ug/m3d
depo_Pmehg_mol_d <-depo_Pmehg_g_d/215
depo_Pmehg_kmol_y <-(depo_Pmehg_mol_d/1000)*365;mean(depo_Pmehg_kmol_y[1957:1968])
plot(depo_Pmehg_kmol_y)
media1_depo_kmol_y <-tapply(depo_Pmehg_kmol_y,rep(1:(length(depo_Pmehg_kmol_y)/12),each = 12), mean)
plot(media1_depo_kmol_y)
#DIFFUSIONE
Oxic1_vol_m3 <- 5.9E+12
Oxic1_vol_L <-Oxic1_vol_m3*1000
Vol_Sed1_m3<-volumes$Sed1 *10^6; str(Vol_Sed1_m3)
Vol_Sed2_m3<-volumes$Sed2 *10^6; str(Vol_Sed2_m3);
Sed1_g_m3 <- TOTs$Sed1; Sed2_g_m3 <- TOTs$Sed2
Sed1_g <-Sed1_g_m3*Vol_Sed1_m3; Sed2_g<-Sed2_g_m3*Vol_Sed2_m3
cm3_sed1 <-Sed1_g/2.43; cm3_sed2<-Sed2_g/2.43
m3_sed1 <-cm3_sed1/10^6; m3_sed2<-cm3_sed2/10^6
m3_PW1 <-Vol_Sed1_m3-m3_sed1; m3_PW2<-Vol_Sed2_m3-m3_sed2
PW1_L <- m3_PW1*1000; PW2_L<- m3_PW2*1000
mehg_kg_s1<-tail(MeHg_sed1_ngm3*m3_sed1/10^12)
mehg_kg_s2<-tail(MeHg_sed2_ngm3*m3_sed2/10^12)
mehg_kmol_s1<-mehg_kg_s1/215
mehg_kmol_s2<-hg_kg_s2/215;mehg_kmol_s2
mehg_kmol_s2+mehg_kmol_s1
bulk1<-bulkD$Sed1;bulk2<-bulkD$Sed2
dryd1<-0.097;dryd2<-0.2425
porosity1<-bulk1-dryd1;porosity2<-bulk2-dryd2
Diffusion_coeff<-10^-9 #m2/s
DF<-Diffusion_coeff*60*60*24 #m2/day
# ng/L to g/m3
deep_w_mehg<- diss_mehg$Anoxic3 #diss hg ngL Bottom water
deep_w_mehg_gm3<-deep_w_mehg/10^6
PWmehg1_ngL<-diss_mehg$Sed1; PWmehg2_ngL<-diss_mehg$Sed2 #diss hg ngL SED
PWmehg1_ngm3<-PWmehg1_ngL*PW1_L/Vol_Sed1_m3
PWmehg2_ngm3<-PWmehg2_ngL*PW2_L/Vol_Sed2_m3
PWmehg1_gm3<-PWmehg1_ngm3/10^9; PWmehg2_gm3<-PWmehg2_ngm3/10^9
par(mfrow=c(1,1))
plot(deep_w_mehg, col="darkblue",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWmehg1_ngL, col="orange",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWmehg2_ngL, col="brown",type="l", ylim=c(0,1.3), ylab="ng/L")
legend(0,1.2,pch=19, col=c("darkblue", "orange", "brown"),
legend=c("deep w", "PW1", "PW2"))
PWmehg1_ng<-PWmehg1_ngL*PW1_L
PWmehg2_ng<-PWmehg2_ngL*PW2_L
PWmehg1_g<-PWmehg1_ng/10^9
PWmehg2_g<-PWmehg2_ng/10^9
PWmehg1_kmol<-PWmehg1_g/(215*1000)
PWmehg2_kmol<-PWmehg2_g/(215*1000)
tail (PWmehg1_kmol)
tail (PWmehg2_kmol)
# per mol di diffusione importante Length of exchange (=depth sediment..?)
#diffusione >0 --> verso h20 (su)
# diff <0 --> verso sedimento (giu)
term1<-(DF*Model_area*porosity1)/(0.03/porosity1) # m2/day*m2/m -->m3/day
term2<-(PWmehg1_gm3/porosity1)-(deep_w_mehg_gm3) # g/m3
diffusion_g_day<-term1*term2; plot(diffusion_g_day) # m3/day*g/m3--> g/day
diffusion_g_m2_day<-diffusion_g_day/Model_area
diffusion_mol_m2_day<-diffusion_g_m2_day/215
diffusion_umol_m2_y<-diffusion_mol_m2_day*10^6*365; summary(diffusion_umol_m2_y); diffusion_kmol_day<-diffusion_g_day/(215*1000)
diffusion_kmol_y<-diffusion_kmol_day*365
diffusion_kmol_y_media<-tapply(diffusion_kmol_y,rep(1:(length(diffusion_kmol_y)/12),each = 12), mean)
diffusion_kmol_cumul<-cumsum(diffusion_kmol_y_media)
tail(diffusion_kmol_cumul)
plot(diffusion_kmol_y_media); tail(diffusion_kmol_y_media,3)
term1b<-(DF*Model_area*porosity2)/(0.05/porosity2)
term2b<-(PWmehg2_gm3/porosity2)-(PWmehg1_gm3/porosity1) #sempre < 0 (giu - da sed1 a sed2)
diffusion_sed_to_sed_g_day<-term1b*term2b #g/day
diffusion_sed_to_sed_kmol_day<-diffusion_sed_to_sed_g_day/(215*1000)
diffusion_sed_to_sed_kmol_y<-diffusion_sed_to_sed_kmol_day*365
diffusion_sed_to_sed_kmol_y_media<-tapply(diffusion_sed_to_sed_kmol_y,rep(1:(length(diffusion_sed_to_sed_kmol_y)/12),each = 12), mean)
diffusion_sed_to_sed_kmol_cumul<-cumsum(diffusion_sed_to_sed_kmol_y_media)
tail(diffusion_sed_to_sed_kmol_cumul)
sed_balance<-cbind(media1_depo_kmol_y,burial1_media,
burial2_media,diffusion_kmol_y_media,diffusion_sed_to_sed_kmol_y_media)
sed_balance_long<-cbind(depo_Pmehg_kmol_y, burial1_kmol_y, burial2_kmol_y,
diffusion_kmol_y, diffusion_sed_to_sed_kmol_y)
getwd()
write.csv(sed_balance, file="aasediment_input_output_medie_mehg_2050.csv")
write.csv(sed_balance_long , file="aasediment_input_output_mehg_2050.csv")