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Copy pathFluxes_boxes_mehg.R
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Fluxes_boxes_mehg.R
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setwd("C:/Users/Ginevra/Desktop/new_sim_BS/19_luglio/Anne1e_morehg_tris")
setwd("C:/Users/Ginevra/Desktop/new_sim_BS/19_luglio/SIM_finale2/Anne1e_morehg_tris_pristine")
# FLUSSI TRA BOX
#Leggi dati e taglia gli ultimi anni dopo il 2013 hg<-hg[1:1968,]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
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[1:1968,1:13]
solids<-read.csv("Total_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(solids)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2"); solids<-solids[1:1968,1:13]
tail(solids)
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[1:1968,1:12]
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[1:1968,1:12]
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[1:1968,1:12]
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[1:1968,1:12]
OL1_vol_m3 <-5.9E+12; OL1_vol_L <-OL1_vol_m3*1000
CIL_vol_m3 <-4.5E+12; CIL_vol_L <-CIL_vol_m3*1000
oxy_vol_m3 <-5.9E+12; oxy_vol_L <-oxy_vol_m3*1000
SOL_vol_m3 <-7.4E+12; SOL_vol_L <-SOL_vol_m3*1000
UAL1_vol_m3 <-5.3E+13; UAL1_vol_L <-UAL1_vol_m3*1000
DAOL_vol_m3 <-2.9E+14; DAOL_vol_L <-DAOL_vol_m3*1000
BBL_vol_m3 <-1E+14; BBL_vol_L <-BBL_vol_m3*1000
Sed1_vol<-8.8*10^9
Sed2_vol<-2*10^10
diss_hg_inor<-hg+DOChg+hg0
diss_mehg<-DOCmehg+mehg
diss_tot<-diss_hg_inor+diss_hg_inor
diss_mehg_pM<-diss_mehg/215*1000
diss_hgIpM<-diss_hg_inor/200.59*1000
diss_hg_pM<-diss_hgIpM+diss_mehg_pM
### ....diffusion .....
area<-2.961E+11
sed_diff<-10^-9
eddy_d_OL<-9.5*10^-6 #m2/s
eddy_d_SOL<-9.5*10^-6
eddy_d_AOL<-10^-5
eddy_d_BBL<-8.7^-6
lenght_OL_SOL<-10
lenght_AOL_SOL<-10
lenght_AOL_Sed<-0.05
meHgD_OL_g_L<-diss_mehg$Oxycline /10^9 #OL4
meHgD_SOL_g_L<-diss_mehg$Suboxic1/10^9 # SOL
meHgD_AOL_g_L<-diss_mehg$Suboxic2/10^9 # AOL1
meHgD_BBL_g_L<-diss_mehg$Anoxic3 /10^9 #AOL4
meHgD_Sed_g_L<-diss_mehg$Sed1 /10^9 # sEd
meHgD_OL_g_m3<-meHgD_OL_g_L*1000
meHgD_SOL_g_m3<-meHgD_SOL_g_L*1000;mean(tail(meHgD_SOL_g_m3,12))
meHgD_AOL_g_m3<-meHgD_AOL_g_L*1000;mean(tail(meHgD_AOL_g_m3,12))
meHgD_BBL_g_m3<-meHgD_BBL_g_L*1000
meHgD_Sed_g_m3<-meHgD_Sed_g_L*1000
1968/163
2013-1850
A<-(eddy_d_OL *area)
B<-(eddy_d_SOL *area)
C<-(sed_diff*area)
conc_grad1<-(meHgD_SOL_g_m3-meHgD_OL_g_m3) #g/m3
conc_grad2<-(meHgD_AOL_g_m3-meHgD_SOL_g_m3) #g/m3
conc_grad2b<-(meHgD_SOL_g_m3-meHgD_AOL_g_m3) #g/m3
conc_grad3<-(meHgD_BBL_g_m3-(meHgD_Sed_g_m3/0.95)) #g/m3
diff_OL<- (A/lenght_OL_SOL)*conc_grad1;diff_OL #g/s
diff_SOL<-(B/lenght_AOL_SOL)*conc_grad2;diff_SOL
diff_SOL2<-(B/lenght_AOL_SOL)*conc_grad2b;diff_SOL
diff_Sed<-(C/(lenght_AOL_Sed/0.95))*conc_grad3
diff_OL_mol_d<-(diff_OL/215)*60*60*24
diff_OL_mol_y<-diff_OL_mol_d*365
diff_OL_kmol_y<-diff_OL_mol_y/10^3
mean(tail(diff_OL_kmol_y,12)); summary(tail(diff_OL_kmol_y,12))
diff_SOL_mol_d<-(diff_SOL/215)*60*60*24
diff_SOL_mol_y<-diff_SOL_mol_d*365
diff_SOL_kmol_y<-diff_SOL_mol_y/10^3
mean(tail(diff_SOL_kmol_y,12)); summary(tail(diff_SOL_kmol_y,12))
plot(diff_OL_kmol_y)
#just for check
diff_SOL2_mol_d<-(diff_SOL2/215)*60*60*24
diff_SOL2_mol_y<-diff_SOL2_mol_d*365
diff_SOL2_kmol_y<-diff_SOL2_mol_y/10^3
mean(tail(diff_SOL2_kmol_y,12)); summary(tail(diff_SOL2_kmol_y,12))
#---
diff_Sed_mol_d<-(diff_Sed/215)*60*60*24
diff_Sed_mol_y<-diff_Sed_mol_d*365
diff_Sed_kmol_y<-diff_Sed_mol_y/10^3
mean(tail(diff_Sed_kmol_y,12)); summary(tail(diff_Sed_kmol_y,12))
# solidi ai boundaries ta OL-SOL e sOL_AOL e aOL - SED
solids_OL <-solids$Oxycline
solids_SOL <-solids$Suboxic1
solids_AOL <-solids$Anoxic3
solids_sed1 <-solids$Sed1
solids_sed2 <-solids$Sed2
SEDmehg_OL <-SEDmehg$Oxycline # Hg ng/g-> SEDhg*solid_sed --> PHg ug/m3
SEDmehg_SOL <-SEDmehg$Suboxic1
SEDmehg_AOL <-SEDmehg$Anoxic3
SEDmehg_sed1 <-SEDmehg$Sed1
SEDmehg_sed2 <-SEDmehg$Sed2
Pmehg_OL <-Pmehgs$Oxycline # meHg ug/m3
Pmehg_SOL <-Pmehgs$Suboxic1 # meHg ug/m3
Pmehg_AOL <-Pmehgs$Anoxic3 # meHg ug/m3
meHgT_sed1_ngm3 <- solids_sed1 *SEDmehg_sed1 # ng/g*g/m3 -> ng/m3
meHgT_sed2_ngm3 <- solids_sed2 *SEDmehg_sed2
meHgT_sed1_gm3 <-meHgT_sed1_ngm3/10^9 # mg/m3->g/m3 hgP
meHgT_sed2_gm3 <-meHgT_sed2_ngm3/10^9
#DEPOSIZIONE Phg AOL -> Sed
## .... settling OL - SOL.....
POM_OLdepo_1_day<-POM_depos$Oxycline/20 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_OLdepo_1_day<-silt_depos$Oxycline/20 # depo silt m/day (0.014 /d)
fPOM_OL<-mean(POMs$Oxycline/solids_OL, na.rm=TRUE)
fsilt_OL<-mean(silts$Oxycline/solids_OL, na.rm=TRUE)
# Vd OL
depo_OLmedia1<-POM_OLdepo_1_day #*fPOM_OL)+(silt_OLdepo_1_day*fsilt_OL))/2 #1/day
depo_OLmedia1 # 0.0037 /d
depo_OLPmehg_ug_m3_d<-depo_OLmedia1*Pmehg_OL # 1/day *ug/m3 -> ug/m3d
depo_OLPmehg_g_d <-(depo_OLPmehg_ug_m3_d*oxy_vol_m3)/10^6 # g/d
depo_OLPmehg_mol_d <-depo_OLPmehg_g_d/200.59 # mol/d
depo_OLPmehg_kmol_y <-(depo_OLPmehg_mol_d/1000)*365 # kmol/y
media1_depoOL_kmol_y <-tapply(depo_OLPmehg_kmol_y,rep(1:(length(depo_OLPmehg_kmol_y)/12),each = 12), mean)
## .... settling SOL - AOL.....
POM_SOLdepo_1_day<-POM_depos$Suboxic1 /25 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_SOLdepo_1_day<-silt_depos$Suboxic1/25 # depo silt m/day (0.014 /d)
fPOM_SOL<-mean(POMs$Suboxic1/solids_SOL, na.rm=TRUE)
fsilt_SOL<-mean(silts$Suboxic1/solids_SOL, na.rm=TRUE)
# Vd SOL
depo_SOLmedia1<-POM_SOLdepo_1_day # *fPOM_SOL)+(silt_SOLdepo_1_day*fsilt_SOL))/2 #1/day
depo_SOLmedia1 #
depo_SOLPmehg_ug_m3_d<-depo_SOLmedia1*Pmehg_SOL # 1/day *ug/m3 -> ug/m3d
depo_SOLPmehg_g_d <-(depo_SOLPmehg_ug_m3_d*SOL_vol_m3)/10^6 # g/d
depo_SOLPmehg_mol_d <-depo_SOLPmehg_g_d/200.59 # mol/d
depo_SOLPmehg_kmol_y <-(depo_SOLPmehg_mol_d/1000)*365 # kmol/y
media1_depoSOL_kmol_y <-tapply(depo_SOLPmehg_kmol_y,rep(1:(length(depo_SOLPmehg_kmol_y)/12),each = 12), mean)
#DEPOSIZIONE Phg AOL -> Sed
#depo m/day * g/m3 --> g/m2d
Vol_anox3<-1E+14
POM_AOLdepo_1_day<-POM_depos$Anoxic3/350 #depo m/day * depth(m) --> 1/day (0.003 /d)
silt_AOLdepo_1_day<-silt_depos$Anoxic3/350 # depo silt m/day (0.014 /d)
fPOM_AOL<-mean(POMs$Anoxic3/solids_AOL, na.rm=TRUE)
fsilt_AOL<-mean(silts$Anoxic3/solids_AOL, na.rm=TRUE)
# Vd
depo_AOLmedia1<-POM_AOLdepo_1_day #1/day
depo_AOLmedia1 # 0.005 /d
depo_AOLPmehg_ug_m3_d<-depo_AOLmedia1*Pmehg_AOL # 1/day *ug/m3 -> ug/m3d
depo_AOLPmehg_g_d <-(depo_AOLPmehg_ug_m3_d*Vol_anox3)/10^6 # g/d
depo_AOLPmehg_mol_d <-depo_AOLPmehg_g_d/200.59 # mol/d
depo_AOLPmehg_kmol_y <-(depo_AOLPmehg_mol_d/1000)*365 # kmol/y
media1_depoAOL_kmol_y <-tapply(depo_AOLPmehg_kmol_y,rep(1:(length(depo_AOLPmehg_kmol_y)/12),each = 12), mean)
summary(tail(media1_depoOL_kmol_y,12));
plot(media1_depoOL_kmol_y)
summary(tail(media1_depoSOL_kmol_y,12));
plot(media1_depoSOL_kmol_y)
tail(media1_depoSOL_kmol_y,1)
summary(tail(media1_depoAOL_kmol_y,12));
plot(media1_depoAOL_kmol_y)
tail(media1_depoSOL_kmol_y,1)
tail(media1_depoOL_kmol_y,1)
tail(media1_depoAOL_kmol_y,1)