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Copy pathAll_In_sim_SED_Balance.R
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All_In_sim_SED_Balance.R
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setwd("C:/Users/gi/Desktop/ULTIME_hgII___/In2")
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")
hg<-hg[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
Phgs<-read.csv("Total_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Phgs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Phgs <-Phgs[3:2414,1:12] #ng/L o g/m3
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
SEDhg<-read.csv("Total_Sorbed_Divalent_Hg_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(SEDhg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
SEDhg<-SEDhg[3:2414,1:12] #ng/g
tail(SEDhg)
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[3:2414,1:12]
# unisco matrici del diss Hg
diss_hg<-hg+DOChg+DOCmehg+mehg+hg0; str(diss_hg);tail(diss_hg)
# BILANCIO BURIAL g/m3 * ng/g --> ng/m3
Model_area <-2.961E+11
solids_sed1 <-TOTs$Sed1; solids_sed2 <-TOTs$Sed2
SEDhg_sed1 <-SEDhg$Sed1; SEDhg_sed2 <-SEDhg$Sed2 #ng/g-> SEDhg*solid_sed --> PHg ug/m3
Phg_sed1 <-Phgs$Sed1; Phg_sed2 <-Phgs$Sed2 #ug/m3
burial_sed1 <-burial$Sed1; burial_sed2 <-burial$Sed2 #cm/y
solids_w <-TOTs$Anoxic3
HgT_sed1_ngm3 <- solids_sed1 *SEDhg_sed1 # ng/g*g/m3 -> ng/m3
HgT_sed2_ngm3 <- solids_sed2 *SEDhg_sed2
HgT_sed1_gm3 <-HgT_sed1_ngm3/10^9 # mg/m3->g/m3 hgP
HgT_sed2_gm3 <-HgT_sed2_ngm3/10^9
burial_sed1_m_y<-burial_sed1 /10^2 ; str(burial_sed1_m_y)#cm/y-->m/y
burial_sed2_m_y<-burial_sed2 /10^2 #cm/y-->m/y
burial_sed1_mm_y<-burial_sed1 *10 ; str(burial_sed1_mm_y)#cm/y-->mm/y
burial_sed2_mm_y<-burial_sed2 *10 ; str(burial_sed2_mm_y)#cm/y-->mm/y
HgT_burial_sed1_g_m2_y<-HgT_sed1_gm3*burial_sed1_m_y #g/m3*m/y<-g/m2y
HgT_burial_sed2_g_m2_y<-HgT_sed2_gm3*burial_sed2_m_y
burial1_g_y<-HgT_burial_sed1_g_m2_y*Model_area #g/M2y*m2 -> g/y
burial2_g_y<-HgT_burial_sed2_g_m2_y*Model_area
burial1_mol_y<-burial1_g_y/200.59;burial1_kmol_y<-burial1_mol_y/1000
burial2_kmol_y<-burial2_g_y/(200.59*1000)
burial1_media<-tapply(burial1_kmol_y,rep(1:(length(burial1_kmol_y)/12),each = 12), mean)
burial2_media<-tapply(burial2_kmol_y,rep(1:(length(burial2_kmol_y)/12),each = 12), mean)
burial1_cumul<-cumsum(burial1_media)
burial2_cumul<-cumsum(burial2_media)
summary(burial1_cumul);summary(burial2_cumul)
bb<-cbind(burial1_cumul,burial2_cumul)
#DEPOSIZIONE Phg
#depo m/day * g/m3 --> g/m2d
Vol_anox3<-1E+14
POM_depo_1_day<-POM_depos$Anoxic3/350 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_depo_1_day<-silt_depos$Anoxic3/350 # depo silt m/day (0.014 /d)
fPOM<-mean(POMs$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
fsilt<-mean(silts$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
depo_media1<-POM_depo_1_day #1/day
mean(depo_media1) # 0.005 /d
depo_Phg_ug_m3_d<-depo_media1*Phgs$Anoxic3 #1/day *ug/m3
depo_Phg_g_d <-(depo_Phg_ug_m3_d*Vol_anox3)/10^6
depo_Phg_mol_d <-depo_Phg_g_d/200.59
depo_Phg_kmol_y <-(depo_Phg_mol_d/1000)*365
plot(depo_Phg_kmol_y)
media1_depo_kmol_y <-tapply(depo_Phg_kmol_y,rep(1:(length(depo_Phg_kmol_y)/12),each = 12), mean)
plot(media1_depo_kmol_y)
cum_depo<-cumsum(media1_depo_kmol_y)
plot(cum_depo)
summary(cum_depo)
#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); plot(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
hg_kg_s1<-tail(HgT_sed1_ngm3*m3_sed1/10^12)
hg_kg_s2<-tail(HgT_sed2_ngm3*m3_sed2/10^12)
hg_kmol_s1<-hg_kg_s1/200.59
hg_kmol_s2<-hg_kg_s2/200.59;hg_kmol_s2
hg_kmol_s2+hg_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_hg<- diss_hg$Anoxic3 # ngL diss hg Bottom water
deep_w_hg_gm3<-deep_w_hg/10^6
PWhg1_ngL<-diss_hg$Sed1; PWhg2_ngL<-diss_hg$Sed2 #diss hg ngL SED
PWhg1_ngm3<-PWhg1_ngL*PW1_L/Vol_Sed1_m3
PWhg2_ngm3<-PWhg2_ngL*PW2_L/Vol_Sed2_m3
PWhg1_gm3<-PWhg1_ngm3/10^9; PWhg2_gm3<-PWhg2_ngm3/10^9
par(mfrow=c(1,1))
plot(deep_w_hg, col="darkblue",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg1_ngL, col="orange",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg2_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"))
PWhg1_ng<-PWhg1_ngL*PW1_L; PWhg1_g<-PWhg1_ng/10^9; PWhg1_kmol<-PWhg1_g/(200.59*1000)
PWhg2_ng<-PWhg2_ngL*PW2_L; PWhg2_g<-PWhg2_ng/10^9; PWhg2_kmol<-PWhg2_g/(200.59*1000)
tail (PWhg1_kmol)
tail (PWhg2_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)/(0.05/porosity1) # m2/day*m2/m -->m3/day
term2<-(PWhg1_gm3/porosity1)-(deep_w_hg_gm3) # g/m3
diffusion_g_day<-term1*term2; # m3/day*g/m3--> g/day
diffusion_g_m2_day<-diffusion_g_day/Model_area
diffusion_mol_m2_day<-diffusion_g_m2_day/200.49
diffusion_umol_m2_y<-diffusion_mol_m2_day*10^6*365; summary(diffusion_umol_m2_y); diffusion_kmol_day<-diffusion_g_day/(200.49*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)
plot(diffusion_kmol_cumul)
plot(diffusion_kmol_y_media); tail(diffusion_kmol_y_media,3)
term1b<-(DF*Model_area*porosity2)/(0.05/porosity2)
term2b<-(PWhg2_gm3/porosity2)-(PWhg1_gm3/porosity1) #sempre < 0 (giu - da sed1 a sed2)
diffusion_sed_to_sed_g_day<-term1b*term2b #g/day
plot(porosity2)
diffusion_sed_to_sed_kmol_day<-diffusion_sed_to_sed_g_day/(200.49*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_Phg_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_medie1_2050.csv")
write.csv(sed_balance_long , file="aasediment_input_output1_2050.csv")
sed_balance[164,]
kmol_sepolte<-tail(burial2_cumul,1) # in 164 anni
vi<-Model_area*0.01 #volume ipotetico
a<-kmol_sepolte/vi # kmol/m3 assumendo z = 2 cm
a*10^9 #umol/m3
a*10^12 #nmol/m3
hg_ng_m3<-(a*200.59)*10^12 #ng/m3
hg_ng_g<-hg_ng_m3/218147.0 #sed ng/m3 *m3/g
hg_ng_g
tail(SEDhg) #ng/g
setwd("C:/Users/gi/Desktop/ULTIME_hgII___/IIe_IIIe_IVe/IIe/In2b")
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")
hg<-hg[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
Phgs<-read.csv("Total_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Phgs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Phgs <-Phgs[3:2414,1:12] #ng/L o g/m3
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
SEDhg<-read.csv("Total_Sorbed_Divalent_Hg_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(SEDhg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
SEDhg<-SEDhg[3:2414,1:12] #ng/g
tail(SEDhg)
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[3:2414,1:12]
# unisco matrici del diss Hg
diss_hg<-hg+DOChg+DOCmehg+mehg+hg0; str(diss_hg);tail(diss_hg)
# BILANCIO BURIAL g/m3 * ng/g --> ng/m3
Model_area <-2.961E+11
solids_sed1 <-TOTs$Sed1; solids_sed2 <-TOTs$Sed2
SEDhg_sed1 <-SEDhg$Sed1; SEDhg_sed2 <-SEDhg$Sed2 #ng/g-> SEDhg*solid_sed --> PHg ug/m3
Phg_sed1 <-Phgs$Sed1; Phg_sed2 <-Phgs$Sed2 #ug/m3
burial_sed1 <-burial$Sed1; burial_sed2 <-burial$Sed2 #cm/y
solids_w <-TOTs$Anoxic3
HgT_sed1_ngm3 <- solids_sed1 *SEDhg_sed1 # ng/g*g/m3 -> ng/m3
HgT_sed2_ngm3 <- solids_sed2 *SEDhg_sed2
HgT_sed1_gm3 <-HgT_sed1_ngm3/10^9 # mg/m3->g/m3 hgP
HgT_sed2_gm3 <-HgT_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
HgT_burial_sed1_g_m2_y<-HgT_sed1_gm3*burial_sed1_m_y #g/m3*m/y<-g/m2y
HgT_burial_sed2_g_m2_y<-HgT_sed2_gm3*burial_sed2_m_y
burial1_g_y<-HgT_burial_sed1_g_m2_y*Model_area #g/M2y*m2 -> g/y
burial2_g_y<-HgT_burial_sed2_g_m2_y*Model_area
burial1_mol_y<-burial1_g_y/200.59;burial1_kmol_y<-burial1_mol_y/1000
burial2_kmol_y<-burial2_g_y/(200.59*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 * g/m3 --> g/m2d
Vol_anox3<-1E+14
POM_depo_1_day<-POM_depos$Anoxic3/350 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_depo_1_day<-silt_depos$Anoxic3/350 # depo silt m/day (0.014 /d)
fPOM<-mean(POMs$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
fsilt<-mean(silts$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
depo_media1<-POM_depo_1_day #1/day
mean(depo_media1) # 0.005 /d
depo_Phg_ug_m3_d<-depo_media1*Phgs$Anoxic3 #1/day *ug/m3
depo_Phg_g_d <-(depo_Phg_ug_m3_d*Vol_anox3)/10^6
depo_Phg_mol_d <-depo_Phg_g_d/200.59
depo_Phg_kmol_y <-(depo_Phg_mol_d/1000)*365
plot(depo_Phg_kmol_y)
media1_depo_kmol_y <-tapply(depo_Phg_kmol_y,rep(1:(length(depo_Phg_kmol_y)/12),each = 12), mean)
plot(media1_depo_kmol_y)
cum_depo<-cumsum(media1_depo_kmol_y)
plot(cum_depo)
summary(cum_depo)
#DIFFUSIONE
Oxic1_vol_m3<- 5.9E+12
Oxic1_vol_L <-Oxic1_vol_m3*1000
Vol_Sed1_m3<-volumes$Sed1*10^6; str(Vol_Sed1_m3)
Vol_Sed2_m3<-volumes$Sed2*10^6; str(Vol_Sed2_m3); plot(Vol_Sed2_m3)
Sed1_g_m3 <- TOTs$Sed1; Sed2_g_m3 <- TOTs$Sed2
Sed1_g <-Sed1_g_m3*Vol_Sed1_m3; Sed2_g<-Sed2_g_m3*Vol_Sed2_m3
cm3_sed1 <-Sed1_g/2.43; cm3_sed2<-Sed2_g/2.43
m3_sed1 <-cm3_sed1/10^6; m3_sed2<-cm3_sed2/10^6
m3_PW1 <-Vol_Sed1_m3-m3_sed1; m3_PW2<-Vol_Sed2_m3-m3_sed2
PW1_L <- m3_PW1*1000; PW2_L<- m3_PW2*1000
hg_kg_s1<-tail(HgT_sed1_ngm3*m3_sed1/10^12)
hg_kg_s2<-tail(HgT_sed2_ngm3*m3_sed2/10^12)
hg_kmol_s1<-hg_kg_s1/200.59
hg_kmol_s2<-hg_kg_s2/200.59;hg_kmol_s2
hg_kmol_s2+hg_kmol_s1
bulk1<-bulkD$Sed1;bulk2<-bulkD$Sed2
dryd1<-0.097;dryd2<-0.2425
porosity1<-bulk1-dryd1;
porosity2<-bulk2-dryd2;
Diffusion_coeff<-10^-9 #m2/s
DF<-Diffusion_coeff*60*60*24 #m2/day
# ng/L to g/m3
deep_w_hg<- diss_hg$Anoxic3 # ngL diss hg Bottom water
deep_w_hg_gm3<-deep_w_hg/10^6
PWhg1_ngL<-diss_hg$Sed1; PWhg2_ngL<-diss_hg$Sed2 #diss hg ngL SED
PWhg1_ngm3<-PWhg1_ngL*PW1_L/Vol_Sed1_m3
PWhg2_ngm3<-PWhg2_ngL*PW2_L/Vol_Sed2_m3
PWhg1_gm3<-PWhg1_ngm3/10^9; PWhg2_gm3<-PWhg2_ngm3/10^9
par(mfrow=c(1,1))
plot(deep_w_hg, col="darkblue",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg1_ngL, col="orange",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg2_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"))
PWhg1_ng<-PWhg1_ngL*PW1_L; PWhg1_g<-PWhg1_ng/10^9; PWhg1_kmol<-PWhg1_g/(200.59*1000)
PWhg2_ng<-PWhg2_ngL*PW2_L; PWhg2_g<-PWhg2_ng/10^9; PWhg2_kmol<-PWhg2_g/(200.59*1000)
tail (PWhg1_kmol)
tail (PWhg2_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)/(0.05/porosity1) # m2/day*m2/m -->m3/day
term2<-(PWhg1_gm3/porosity1)-(deep_w_hg_gm3) # g/m3
diffusion_g_day<-term1*term2; # m3/day*g/m3--> g/day
diffusion_g_m2_day<-diffusion_g_day/Model_area
diffusion_mol_m2_day<-diffusion_g_m2_day/200.49
diffusion_umol_m2_y<-diffusion_mol_m2_day*10^6*365; summary(diffusion_umol_m2_y); diffusion_kmol_day<-diffusion_g_day/(200.49*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)
plot(diffusion_kmol_cumul)
plot(diffusion_kmol_y_media); tail(diffusion_kmol_y_media,3)
term1b<-(DF*Model_area*porosity2)/(0.05/porosity2)
term2b<-(PWhg2_gm3/porosity2)-(PWhg1_gm3/porosity1) #sempre < 0 (giu - da sed1 a sed2)
diffusion_sed_to_sed_g_day<-term1b*term2b #g/day
plot(porosity2)
diffusion_sed_to_sed_kmol_day<-diffusion_sed_to_sed_g_day/(200.49*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_Phg_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_medie1_2050.csv")
write.csv(sed_balance_long , file="aasediment_input_output1_2050.csv")
sed_balance[164,]
kmol_sepolte<-tail(burial2_cumul,1) # in 164 anni
vi<-Model_area*0.01 #volume ipotetico
a<-kmol_sepolte/vi # kmol/m3 assumendo z = 2 cm
a*10^9 #umol/m3
a*10^12 #nmol/m3
hg_ng_m3<-(a*200.59)*10^12 #ng/m3
hg_ng_g<-hg_ng_m3/218147.0 #sed ng/m3 *m3/g
hg_ng_g
tail(SEDhg) #ng/g
setwd("C:/Users/gi/Desktop/ULTIME_hgII___/IIe_IIIe_IVe/IIe/In1b")
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")
hg<-hg[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
Phgs<-read.csv("Total_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Phgs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Phgs <-Phgs[3:2414,1:12] #ng/L o g/m3
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
SEDhg<-read.csv("Total_Sorbed_Divalent_Hg_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(SEDhg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
SEDhg<-SEDhg[3:2414,1:12] #ng/g
tail(SEDhg)
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[3:2414,1:12]
# unisco matrici del diss Hg
diss_hg<-hg+DOChg+DOCmehg+mehg+hg0; str(diss_hg);tail(diss_hg)
# BILANCIO BURIAL g/m3 * ng/g --> ng/m3
Model_area <-2.961E+11
solids_sed1 <-TOTs$Sed1; solids_sed2 <-TOTs$Sed2
SEDhg_sed1 <-SEDhg$Sed1; SEDhg_sed2 <-SEDhg$Sed2 #ng/g-> SEDhg*solid_sed --> PHg ug/m3
Phg_sed1 <-Phgs$Sed1; Phg_sed2 <-Phgs$Sed2 #ug/m3
burial_sed1 <-burial$Sed1; burial_sed2 <-burial$Sed2 #cm/y
solids_w <-TOTs$Anoxic3
HgT_sed1_ngm3 <- solids_sed1 *SEDhg_sed1 # ng/g*g/m3 -> ng/m3
HgT_sed2_ngm3 <- solids_sed2 *SEDhg_sed2
HgT_sed1_gm3 <-HgT_sed1_ngm3/10^9 # mg/m3->g/m3 hgP
HgT_sed2_gm3 <-HgT_sed2_ngm3/10^9
burial_sed1_m_y<-burial_sed1 /10^2 ; str(burial_sed1_m_y)#cm/y-->m/y
burial_sed2_m_y<-burial_sed2 /10^2 #cm/y-->m/y
burial_sed1_mm_y<-burial_sed1 *10 ; str(burial_sed1_mm_y)#cm/y-->mm/y
burial_sed2_mm_y<-burial_sed2 *10 ; str(burial_sed2_mm_y)#cm/y-->mm/y
HgT_burial_sed1_g_m2_y<-HgT_sed1_gm3*burial_sed1_m_y #g/m3*m/y<-g/m2y
HgT_burial_sed2_g_m2_y<-HgT_sed2_gm3*burial_sed2_m_y
burial1_g_y<-HgT_burial_sed1_g_m2_y*Model_area #g/M2y*m2 -> g/y
burial2_g_y<-HgT_burial_sed2_g_m2_y*Model_area
burial1_mol_y<-burial1_g_y/200.59;burial1_kmol_y<-burial1_mol_y/1000
burial2_kmol_y<-burial2_g_y/(200.59*1000)
burial1_media<-tapply(burial1_kmol_y,rep(1:(length(burial1_kmol_y)/12),each = 12), mean)
burial2_media<-tapply(burial2_kmol_y,rep(1:(length(burial2_kmol_y)/12),each = 12), mean)
burial1_cumul<-cumsum(burial1_media)
burial2_cumul<-cumsum(burial2_media)
summary(burial1_cumul);summary(burial2_cumul)
bb<-cbind(burial1_cumul,burial2_cumul)
#DEPOSIZIONE Phg
#depo m/day * g/m3 --> g/m2d
Vol_anox3<-1E+14
POM_depo_1_day<-POM_depos$Anoxic3/350 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_depo_1_day<-silt_depos$Anoxic3/350 # depo silt m/day (0.014 /d)
fPOM<-mean(POMs$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
fsilt<-mean(silts$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
depo_media1<-POM_depo_1_day #1/day
mean(depo_media1) # 0.005 /d
depo_Phg_ug_m3_d<-depo_media1*Phgs$Anoxic3 #1/day *ug/m3
depo_Phg_g_d <-(depo_Phg_ug_m3_d*Vol_anox3)/10^6
depo_Phg_mol_d <-depo_Phg_g_d/200.59
depo_Phg_kmol_y <-(depo_Phg_mol_d/1000)*365
plot(depo_Phg_kmol_y)
media1_depo_kmol_y <-tapply(depo_Phg_kmol_y,rep(1:(length(depo_Phg_kmol_y)/12),each = 12), mean)
plot(media1_depo_kmol_y)
cum_depo<-cumsum(media1_depo_kmol_y)
plot(cum_depo)
summary(cum_depo)
#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); plot(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
hg_kg_s1<-tail(HgT_sed1_ngm3*m3_sed1/10^12)
hg_kg_s2<-tail(HgT_sed2_ngm3*m3_sed2/10^12)
hg_kmol_s1<-hg_kg_s1/200.59
hg_kmol_s2<-hg_kg_s2/200.59;hg_kmol_s2
hg_kmol_s2+hg_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_hg<- diss_hg$Anoxic3 # ngL diss hg Bottom water
deep_w_hg_gm3<-deep_w_hg/10^6
PWhg1_ngL<-diss_hg$Sed1; PWhg2_ngL<-diss_hg$Sed2 #diss hg ngL SED
PWhg1_ngm3<-PWhg1_ngL*PW1_L/Vol_Sed1_m3
PWhg2_ngm3<-PWhg2_ngL*PW2_L/Vol_Sed2_m3
PWhg1_gm3<-PWhg1_ngm3/10^9; PWhg2_gm3<-PWhg2_ngm3/10^9
par(mfrow=c(1,1))
plot(deep_w_hg, col="darkblue",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg1_ngL, col="orange",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg2_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"))
PWhg1_ng<-PWhg1_ngL*PW1_L; PWhg1_g<-PWhg1_ng/10^9; PWhg1_kmol<-PWhg1_g/(200.59*1000)
PWhg2_ng<-PWhg2_ngL*PW2_L; PWhg2_g<-PWhg2_ng/10^9; PWhg2_kmol<-PWhg2_g/(200.59*1000)
tail (PWhg1_kmol)
tail (PWhg2_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)/(0.05/porosity1) # m2/day*m2/m -->m3/day
term2<-(PWhg1_gm3/porosity1)-(deep_w_hg_gm3) # g/m3
diffusion_g_day<-term1*term2; # m3/day*g/m3--> g/day
diffusion_g_m2_day<-diffusion_g_day/Model_area
diffusion_mol_m2_day<-diffusion_g_m2_day/200.49
diffusion_umol_m2_y<-diffusion_mol_m2_day*10^6*365; summary(diffusion_umol_m2_y); diffusion_kmol_day<-diffusion_g_day/(200.49*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)
plot(diffusion_kmol_cumul)
plot(diffusion_kmol_y_media); tail(diffusion_kmol_y_media,3)
term1b<-(DF*Model_area*porosity2)/(0.05/porosity2)
term2b<-(PWhg2_gm3/porosity2)-(PWhg1_gm3/porosity1) #sempre < 0 (giu - da sed1 a sed2)
diffusion_sed_to_sed_g_day<-term1b*term2b #g/day
plot(porosity2)
diffusion_sed_to_sed_kmol_day<-diffusion_sed_to_sed_g_day/(200.49*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_Phg_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_medie1_2050.csv")
write.csv(sed_balance_long , file="aasediment_input_output1_2050.csv")
sed_balance[164,]
kmol_sepolte<-tail(burial2_cumul,1) # in 164 anni
vi<-Model_area*0.01 #volume ipotetico
a<-kmol_sepolte/vi # kmol/m3 assumendo z = 2 cm
a*10^9 #umol/m3
a*10^12 #nmol/m3
hg_ng_m3<-(a*200.59)*10^12 #ng/m3
hg_ng_g<-hg_ng_m3/218147.0 #sed ng/m3 *m3/g
hg_ng_g
tail(SEDhg) #ng/g
setwd("C:/Users/gi/Desktop/ULTIME_hgII___/Centrale_NOme")
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")
hg<-hg[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
Phgs<-read.csv("Total_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Phgs)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Phgs <-Phgs[3:2414,1:12] #ng/L o g/m3
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[3:2414,1:12]
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[3:2414,1:12]
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[3:2414,1:12]
SEDhg<-read.csv("Total_Sorbed_Divalent_Hg_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(SEDhg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
SEDhg<-SEDhg[3:2414,1:12] #ng/g
tail(SEDhg)
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[3:2414,1:12]
# unisco matrici del diss Hg
diss_hg<-hg+DOChg+DOCmehg+mehg+hg0; str(diss_hg);tail(diss_hg)
# BILANCIO BURIAL g/m3 * ng/g --> ng/m3
Model_area <-2.961E+11
solids_sed1 <-TOTs$Sed1; solids_sed2 <-TOTs$Sed2
SEDhg_sed1 <-SEDhg$Sed1; SEDhg_sed2 <-SEDhg$Sed2 #ng/g-> SEDhg*solid_sed --> PHg ug/m3
Phg_sed1 <-Phgs$Sed1; Phg_sed2 <-Phgs$Sed2 #ug/m3
burial_sed1 <-burial$Sed1; burial_sed2 <-burial$Sed2 #cm/y
solids_w <-TOTs$Anoxic3
HgT_sed1_ngm3 <- solids_sed1 *SEDhg_sed1 # ng/g*g/m3 -> ng/m3
HgT_sed2_ngm3 <- solids_sed2 *SEDhg_sed2
HgT_sed1_gm3 <-HgT_sed1_ngm3/10^9 # mg/m3->g/m3 hgP
HgT_sed2_gm3 <-HgT_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
HgT_burial_sed1_g_m2_y<-HgT_sed1_gm3*burial_sed1_m_y #g/m3*m/y<-g/m2y
HgT_burial_sed2_g_m2_y<-HgT_sed2_gm3*burial_sed2_m_y
burial1_g_y<-HgT_burial_sed1_g_m2_y*Model_area #g/M2y*m2 -> g/y
burial2_g_y<-HgT_burial_sed2_g_m2_y*Model_area
burial1_mol_y<-burial1_g_y/200.59;burial1_kmol_y<-burial1_mol_y/1000
burial2_kmol_y<-burial2_g_y/(200.59*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 * g/m3 --> g/m2d
Vol_anox3<-1E+14
POM_depo_1_day<-POM_depos$Anoxic3/350 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_depo_1_day<-silt_depos$Anoxic3/350 # depo silt m/day (0.014 /d)
fPOM<-mean(POMs$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
fsilt<-mean(silts$Anoxic3/TOTs$Anoxic3, na.rm=TRUE)
depo_media1<-POM_depo_1_day #1/day
mean(depo_media1) # 0.005 /d
depo_Phg_ug_m3_d<-depo_media1*Phgs$Anoxic3 #1/day *ug/m3
depo_Phg_g_d <-(depo_Phg_ug_m3_d*Vol_anox3)/10^6
depo_Phg_mol_d <-depo_Phg_g_d/200.59
depo_Phg_kmol_y <-(depo_Phg_mol_d/1000)*365
plot(depo_Phg_kmol_y)
media1_depo_kmol_y <-tapply(depo_Phg_kmol_y,rep(1:(length(depo_Phg_kmol_y)/12),each = 12), mean)
plot(media1_depo_kmol_y)
cum_depo<-cumsum(media1_depo_kmol_y)
plot(cum_depo)
summary(cum_depo)
#DIFFUSIONE
Oxic1_vol_m3<- 5.9E+12
Oxic1_vol_L <-Oxic1_vol_m3*1000
Vol_Sed1_m3<-volumes$Sed1*10^6; str(Vol_Sed1_m3)
Vol_Sed2_m3<-volumes$Sed2*10^6; str(Vol_Sed2_m3); plot(Vol_Sed2_m3)
Sed1_g_m3 <- TOTs$Sed1; Sed2_g_m3 <- TOTs$Sed2
Sed1_g <-Sed1_g_m3*Vol_Sed1_m3; Sed2_g<-Sed2_g_m3*Vol_Sed2_m3
cm3_sed1 <-Sed1_g/2.43; cm3_sed2<-Sed2_g/2.43
m3_sed1 <-cm3_sed1/10^6; m3_sed2<-cm3_sed2/10^6
m3_PW1 <-Vol_Sed1_m3-m3_sed1; m3_PW2<-Vol_Sed2_m3-m3_sed2
PW1_L <- m3_PW1*1000; PW2_L<- m3_PW2*1000
hg_kg_s1<-tail(HgT_sed1_ngm3*m3_sed1/10^12)
hg_kg_s2<-tail(HgT_sed2_ngm3*m3_sed2/10^12)
hg_kmol_s1<-hg_kg_s1/200.59
hg_kmol_s2<-hg_kg_s2/200.59;hg_kmol_s2
hg_kmol_s2+hg_kmol_s1
bulk1<-bulkD$Sed1;bulk2<-bulkD$Sed2
dryd1<-0.097;dryd2<-0.2425
porosity1<-bulk1-dryd1;
porosity2<-bulk2-dryd2;
Diffusion_coeff<-10^-9 #m2/s
DF<-Diffusion_coeff*60*60*24 #m2/day
# ng/L to g/m3
deep_w_hg<- diss_hg$Anoxic3 # ngL diss hg Bottom water
deep_w_hg_gm3<-deep_w_hg/10^6
PWhg1_ngL<-diss_hg$Sed1; PWhg2_ngL<-diss_hg$Sed2 #diss hg ngL SED
PWhg1_ngm3<-PWhg1_ngL*PW1_L/Vol_Sed1_m3
PWhg2_ngm3<-PWhg2_ngL*PW2_L/Vol_Sed2_m3
PWhg1_gm3<-PWhg1_ngm3/10^9; PWhg2_gm3<-PWhg2_ngm3/10^9
par(mfrow=c(1,1))
plot(deep_w_hg, col="darkblue",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg1_ngL, col="orange",type="l", ylim=c(0,1.3), ylab="ng/L")
par(new=TRUE)
plot(PWhg2_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"))
PWhg1_ng<-PWhg1_ngL*PW1_L; PWhg1_g<-PWhg1_ng/10^9; PWhg1_kmol<-PWhg1_g/(200.59*1000)
PWhg2_ng<-PWhg2_ngL*PW2_L; PWhg2_g<-PWhg2_ng/10^9; PWhg2_kmol<-PWhg2_g/(200.59*1000)
tail (PWhg1_kmol)
tail (PWhg2_kmol)
# per mol di diffusione importante Length of exchange (=depth sediment..) #diffusione >0 --> verso h20 (su)